just updated and cannot add or delete annotations

classic Classic list List threaded Threaded
10 messages Options
Reply | Threaded
Open this post in threaded view
|

just updated and cannot add or delete annotations

Sofia Robb
Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:


 

Packaging Grails application

> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y

| Installed plugin spring-websocket-1.3.1.....

> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y

| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?



Thank you,

Sofia








Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: just updated and cannot add or delete annotations

Sofia Robb
So, the do get added, and they do get deleted. I just need to close the error window and reload the page, and everything is as it should be, but this happens for every new annotation and deletion event.

On Thu, Nov 16, 2017 at 2:35 PM, Sofia Robb <[hidden email]> wrote:
Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:


 

Packaging Grails application

> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y

| Installed plugin spring-websocket-1.3.1.....

> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y

| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?



Thank you,

Sofia








Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: just updated and cannot add or delete annotations

nathandunn
In reply to this post by Sofia Robb

Is there anything in the catalina.out?  

The build part looks fine. 

Nathan

On Nov 16, 2017, at 1:35 PM, Sofia Robb <[hidden email]> wrote:

Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:

 

Packaging Grails application
> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y
| Installed plugin spring-websocket-1.3.1.....
> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y
| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?


Thank you,
Sofia







Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: just updated and cannot add or delete annotations

nathandunn
In reply to this post by Sofia Robb

Have you purged the cache / used an anonymous different browser?    

Is there anything weird in the console at startup?  Mostly wondering if there is a library collision with the web sockets.

Nathan


On Nov 16, 2017, at 1:41 PM, Sofia Robb <[hidden email]> wrote:

So, the do get added, and they do get deleted. I just need to close the error window and reload the page, and everything is as it should be, but this happens for every new annotation and deletion event.

On Thu, Nov 16, 2017 at 2:35 PM, Sofia Robb <[hidden email]> wrote:
Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:

 

Packaging Grails application
> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y
| Installed plugin spring-websocket-1.3.1.....
> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y
| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?


Thank you,
Sofia







Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: just updated and cannot add or delete annotations

Sofia Robb
In reply to this post by nathandunn
There is some SEVERE stuff but it is all before I stopped tomcat and started up the new war. I highlighed in yellow where I restarted and launched the new war file.

Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 1] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 2] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 3] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 4] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 5] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@37e2f15b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@687a09db]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f2a35e4]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@65efc8d2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@638725a1]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@decb920]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@16de5917]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@44d3c564]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@1e235a72]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@76eed52f]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@121c2c04]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@48be23c6]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@4cca0069]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@4c8de372]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f829aeb]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@61b2ece]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1aceaf2c]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@397b4974]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1205d972]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@4db7e8a2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@226f89f7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@41bc4427]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@7d4ecb2b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@fceced8]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@5130dee7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@720e259a]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 347 ms
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:00:01 PM org.apache.catalina.util.SessionIdGenerator createSecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [9,099] milliseconds.
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 53,582 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 214 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 1,285 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 332 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 314 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 499 ms
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 253 ms
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 56841 ms
Nov 16, 2017 2:03:50 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 2:03:50 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 309 ms
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 32,682 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 195 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 302 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 150 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 134 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 215 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 140 ms
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 33883 ms

On Thu, Nov 16, 2017 at 3:07 PM, Nathan Dunn <[hidden email]> wrote:

Is there anything in the catalina.out?  

The build part looks fine. 

Nathan

On Nov 16, 2017, at 1:35 PM, Sofia Robb <[hidden email]> wrote:

Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:

 

Packaging Grails application
> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y
| Installed plugin spring-websocket-1.3.1.....
> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y
| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?


Thank you,
Sofia







Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: just updated and cannot add or delete annotations

nathandunn

Not seeing anything remarkable.  

If you are updating from master directly, it may have also changed the JBrowse version. 

I would do a clean-all in there as well. 

./apollo clean-all && ./apollo deploy 

Hopefully that fixes it. 

Nathan


On Nov 16, 2017, at 2:20 PM, Sofia Robb <[hidden email]> wrote:

There is some SEVERE stuff but it is all before I stopped tomcat and started up the new war. I highlighed in yellow where I restarted and launched the new war file.

Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 1] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 2] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 3] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 4] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 5] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@37e2f15b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@687a09db]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f2a35e4]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@65efc8d2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@638725a1]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@decb920]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@16de5917]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@44d3c564]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@1e235a72]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@76eed52f]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@121c2c04]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@48be23c6]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@4cca0069]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@4c8de372]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f829aeb]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@61b2ece]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1aceaf2c]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@397b4974]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1205d972]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@4db7e8a2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@226f89f7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@41bc4427]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@7d4ecb2b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@fceced8]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@5130dee7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@720e259a]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 347 ms
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:00:01 PM org.apache.catalina.util.SessionIdGenerator createSecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [9,099] milliseconds.
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 53,582 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 214 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 1,285 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 332 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 314 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 499 ms
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 253 ms
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 56841 ms
Nov 16, 2017 2:03:50 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 2:03:50 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 309 ms
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 32,682 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 195 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 302 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 150 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 134 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 215 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 140 ms
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 33883 ms

On Thu, Nov 16, 2017 at 3:07 PM, Nathan Dunn <[hidden email]> wrote:

Is there anything in the catalina.out?  

The build part looks fine. 

Nathan

On Nov 16, 2017, at 1:35 PM, Sofia Robb <[hidden email]> wrote:

Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:

 

Packaging Grails application
> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y
| Installed plugin spring-websocket-1.3.1.....
> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y
| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?


Thank you,
Sofia







Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: just updated and cannot add or delete annotations

Sofia Robb
In reply to this post by Sofia Robb
I cleaned and deployed, same messages. But I had another user try it out and he says it works just fine for him. Whats up with that?

On Thu, Nov 16, 2017 at 3:32 PM, Nathan Dunn <[hidden email]> wrote:

Not seeing anything remarkable.  

If you are updating from master directly, it may have also changed the JBrowse version. 

I would do a clean-all in there as well. 

./apollo clean-all && ./apollo deploy 

Hopefully that fixes it. 

Nathan


On Nov 16, 2017, at 2:20 PM, Sofia Robb <[hidden email]> wrote:

There is some SEVERE stuff but it is all before I stopped tomcat and started up the new war. I highlighed in yellow where I restarted and launched the new war file.

Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 1] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 2] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 3] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 4] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 5] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@37e2f15b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@687a09db]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f2a35e4]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@65efc8d2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@638725a1]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@decb920]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@16de5917]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@44d3c564]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@1e235a72]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@76eed52f]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@121c2c04]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@48be23c6]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@4cca0069]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@4c8de372]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f829aeb]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@61b2ece]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1aceaf2c]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@397b4974]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1205d972]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@4db7e8a2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@226f89f7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@41bc4427]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@7d4ecb2b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@fceced8]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@5130dee7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@720e259a]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 347 ms
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:00:01 PM org.apache.catalina.util.SessionIdGenerator createSecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [9,099] milliseconds.
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 53,582 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 214 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 1,285 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 332 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 314 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 499 ms
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 253 ms
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 56841 ms
Nov 16, 2017 2:03:50 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 2:03:50 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 309 ms
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 32,682 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 195 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 302 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 150 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 134 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 215 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 140 ms
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 33883 ms

On Thu, Nov 16, 2017 at 3:07 PM, Nathan Dunn <[hidden email]> wrote:

Is there anything in the catalina.out?  

The build part looks fine. 

Nathan

On Nov 16, 2017, at 1:35 PM, Sofia Robb <[hidden email]> wrote:

Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:

 

Packaging Grails application
> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y
| Installed plugin spring-websocket-1.3.1.....
> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y
| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?


Thank you,
Sofia







Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: just updated and cannot add or delete annotations

nathandunn

It is probably that your browser cache has the older spring web-socket library.   If you wipe cache and/or try another browser / computer I’m wondering if it might work.

Nathan

On Nov 16, 2017, at 2:54 PM, Sofia Robb <[hidden email]> wrote:

I cleaned and deployed, same messages. But I had another user try it out and he says it works just fine for him. Whats up with that?

On Thu, Nov 16, 2017 at 3:32 PM, Nathan Dunn <[hidden email]> wrote:

Not seeing anything remarkable.  

If you are updating from master directly, it may have also changed the JBrowse version. 

I would do a clean-all in there as well. 

./apollo clean-all && ./apollo deploy 

Hopefully that fixes it. 

Nathan


On Nov 16, 2017, at 2:20 PM, Sofia Robb <[hidden email]> wrote:

There is some SEVERE stuff but it is all before I stopped tomcat and started up the new war. I highlighed in yellow where I restarted and launched the new war file.

Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 1] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 2] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 3] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 4] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 5] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@37e2f15b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@687a09db]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f2a35e4]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@65efc8d2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@638725a1]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@decb920]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@16de5917]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@44d3c564]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@1e235a72]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@76eed52f]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@121c2c04]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@48be23c6]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@4cca0069]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@4c8de372]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f829aeb]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@61b2ece]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1aceaf2c]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@397b4974]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1205d972]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@4db7e8a2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@226f89f7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@41bc4427]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@7d4ecb2b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@fceced8]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@5130dee7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@720e259a]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 347 ms
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:00:01 PM org.apache.catalina.util.SessionIdGenerator createSecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [9,099] milliseconds.
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 53,582 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 214 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 1,285 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 332 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 314 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 499 ms
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 253 ms
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 56841 ms
Nov 16, 2017 2:03:50 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 2:03:50 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 309 ms
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 32,682 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 195 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 302 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 150 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 134 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 215 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 140 ms
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 33883 ms

On Thu, Nov 16, 2017 at 3:07 PM, Nathan Dunn <[hidden email]> wrote:

Is there anything in the catalina.out?  

The build part looks fine. 

Nathan

On Nov 16, 2017, at 1:35 PM, Sofia Robb <[hidden email]> wrote:

Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:

 

Packaging Grails application
> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y
| Installed plugin spring-websocket-1.3.1.....
> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y
| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?


Thank you,
Sofia







Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: just updated and cannot add or delete annotations

Sofia Robb
In reply to this post by Sofia Robb
Yeah, that is what is was. I tried in safari and it worked, i opened a new chrome window and it worked. Thank you for your hand holding :)

Fixed!!!

On Thu, Nov 16, 2017 at 3:56 PM, Nathan Dunn <[hidden email]> wrote:

It is probably that your browser cache has the older spring web-socket library.   If you wipe cache and/or try another browser / computer I’m wondering if it might work.

Nathan


On Nov 16, 2017, at 2:54 PM, Sofia Robb <[hidden email]> wrote:

I cleaned and deployed, same messages. But I had another user try it out and he says it works just fine for him. Whats up with that?

On Thu, Nov 16, 2017 at 3:32 PM, Nathan Dunn <[hidden email]> wrote:

Not seeing anything remarkable.  

If you are updating from master directly, it may have also changed the JBrowse version. 

I would do a clean-all in there as well. 

./apollo clean-all && ./apollo deploy 

Hopefully that fixes it. 

Nathan


On Nov 16, 2017, at 2:20 PM, Sofia Robb <[hidden email]> wrote:

There is some SEVERE stuff but it is all before I stopped tomcat and started up the new war. I highlighed in yellow where I restarted and launched the new war file.

Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 1] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 2] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 3] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 4] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 5] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@37e2f15b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@687a09db]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f2a35e4]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@65efc8d2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@638725a1]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@decb920]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@16de5917]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@44d3c564]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@1e235a72]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@76eed52f]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@121c2c04]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@48be23c6]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@4cca0069]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@4c8de372]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f829aeb]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@61b2ece]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1aceaf2c]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@397b4974]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1205d972]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@4db7e8a2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@226f89f7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@41bc4427]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@7d4ecb2b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@fceced8]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@5130dee7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@720e259a]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 347 ms
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:00:01 PM org.apache.catalina.util.SessionIdGenerator createSecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [9,099] milliseconds.
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 53,582 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 214 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 1,285 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 332 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 314 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 499 ms
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 253 ms
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 56841 ms
Nov 16, 2017 2:03:50 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 2:03:50 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 309 ms
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 32,682 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 195 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 302 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 150 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 134 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 215 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 140 ms
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 33883 ms

On Thu, Nov 16, 2017 at 3:07 PM, Nathan Dunn <[hidden email]> wrote:

Is there anything in the catalina.out?  

The build part looks fine. 

Nathan

On Nov 16, 2017, at 1:35 PM, Sofia Robb <[hidden email]> wrote:

Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:

 

Packaging Grails application
> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y
| Installed plugin spring-websocket-1.3.1.....
> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y
| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?


Thank you,
Sofia







Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: just updated and cannot add or delete annotations

nathandunn

NP.  I’m glad I didn’t have to patch anything.


On Nov 16, 2017, at 3:05 PM, Sofia Robb <[hidden email]> wrote:

Yeah, that is what is was. I tried in safari and it worked, i opened a new chrome window and it worked. Thank you for your hand holding :)

Fixed!!!

On Thu, Nov 16, 2017 at 3:56 PM, Nathan Dunn <[hidden email]> wrote:

It is probably that your browser cache has the older spring web-socket library.   If you wipe cache and/or try another browser / computer I’m wondering if it might work.

Nathan


On Nov 16, 2017, at 2:54 PM, Sofia Robb <[hidden email]> wrote:

I cleaned and deployed, same messages. But I had another user try it out and he says it works just fine for him. Whats up with that?

On Thu, Nov 16, 2017 at 3:32 PM, Nathan Dunn <[hidden email]> wrote:

Not seeing anything remarkable.  

If you are updating from master directly, it may have also changed the JBrowse version. 

I would do a clean-all in there as well. 

./apollo clean-all && ./apollo deploy 

Hopefully that fixes it. 

Nathan


On Nov 16, 2017, at 2:20 PM, Sofia Robb <[hidden email]> wrote:

There is some SEVERE stuff but it is all before I stopped tomcat and started up the new war. I highlighed in yellow where I restarted and launched the new war file.

Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 1] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 2] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 3] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 4] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 5] but has failed to stop it. This is very likely to create a memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@37e2f15b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@687a09db]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f2a35e4]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@65efc8d2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@638725a1]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@decb920]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@16de5917]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@44d3c564]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@1e235a72]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@76eed52f]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@121c2c04]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@48be23c6]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@4cca0069]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@4c8de372]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f829aeb]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@61b2ece]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1aceaf2c]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@397b4974]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1205d972]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@4db7e8a2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@226f89f7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@41bc4427]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@7d4ecb2b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@fceced8]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@5130dee7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@720e259a]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 347 ms
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:00:01 PM org.apache.catalina.util.SessionIdGenerator createSecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [9,099] milliseconds.
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 53,582 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 214 ms
Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 1,285 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 332 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 314 ms
Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 499 ms
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 253 ms
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 56841 ms
Nov 16, 2017 2:03:50 PM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Nov 16, 2017 2:03:50 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 309 ms
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 32,682 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 195 ms
Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/examples
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 302 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/sample
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 150 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/docs
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 134 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 215 ms
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat/webapps/manager
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 140 ms
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 33883 ms

On Thu, Nov 16, 2017 at 3:07 PM, Nathan Dunn <[hidden email]> wrote:

Is there anything in the catalina.out?  

The build part looks fine. 

Nathan

On Nov 16, 2017, at 1:35 PM, Sofia Robb <[hidden email]> wrote:

Hello All,

I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error.

When I was creating a new war file with my updates, I said Y to these two questions:

 

Packaging Grails application
> You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y
| Installed plugin spring-websocket-1.3.1.....
> You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y
| Compiling 225 source files

 

but when I go to my_server:8080 I see the tomcat/7.0.54 page. 

 

I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version?


Thank you,
Sofia







Add Error"
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"6a64196b-3db4-47aa-8587-26677b5640dc","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510867307160,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00001","uniquename":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307126,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"4a49378d-4cf5-4dc7-b16e-dce934329b9f","location":{"strand":1,"id":96631,"fmin":14217568,"fmax":14217584},"id":96630,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"38058928-023b-4e00-a160-9e984318a197","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307153,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"38058928-023b-4e00-a160-9e984318a197","location":{"strand":1,"id":96649,"fmin":14252990,"fmax":14252996},"id":96648,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"41161688-4bbc-4a73-a120-f5654ecf9468","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307131,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"41161688-4bbc-4a73-a120-f5654ecf9468","location":{"strand":1,"id":96634,"fmin":14224204,"fmax":14224328},"id":96633,"properties":[],"date_last_modified":1510867307194},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"24eec342-d373-4489-a433-693486654be1","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307158,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"24eec342-d373-4489-a433-693486654be1","location":{"strand":1,"id":96652,"fmin":14217568,"fmax":14252996},"id":96651,"properties":[],"date_last_modified":1510867307197},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"013ecdab-3ea6-434e-bf8e-3e804804ab65","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307149,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"013ecdab-3ea6-434e-bf8e-3e804804ab65","location":{"strand":1,"id":96646,"fmin":14251072,"fmax":14251271},"id":96645,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3281840f-840f-42b2-9276-46ab915a930c","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307140,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3281840f-840f-42b2-9276-46ab915a930c","location":{"strand":1,"id":96640,"fmin":14238251,"fmax":14238430},"id":96639,"properties":[],"date_last_modified":1510867307195},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"3894f50f-7398-4d2f-bb56-6f049e959f25","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307144,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"3894f50f-7398-4d2f-bb56-6f049e959f25","location":{"strand":1,"id":96643,"fmin":14246833,"fmax":14246964},"id":96642,"properties":[],"date_last_modified":1510867307196},{"owner":"None","parent_name":"Gpc6-00001","uniquename":"1d193c70-61ec-4181-b755-262f89fd8f7a","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510867307136,"sequence":"scaf_00001","parent_id":"6a64196b-3db4-47aa-8587-26677b5640dc","name":"1d193c70-61ec-4181-b755-262f89fd8f7a","location":{"strand":1,"id":96637,"fmin":14224818,"fmax":14224958},"id":96636,"properties":[],"date_last_modified":1510867307195}],"parent_id":"051b9113-9cd6-46d3-aaf8-8c36907b1dd7","name":"Gpc6-00001","location":{"strand":1,"id":96629,"fmin":14217568,"fmax":14252996},"id":96628,"properties":[],"date_last_modified":1510867307223}],"sequenceAlterationEvent":false,"operation":"ADD"}




Delete Error:
Error Performing Operation
{"features":[{"owner":"[hidden email]","parent_name":"Gpc6","uniquename":"5018a3ba-aeb3-4743-bf4b-192d1985157b","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1510866938833,"sequence":"scaf_00001","children":[{"owner":"None","parent_name":"Gpc6-00002","uniquename":"0023f447-2222-4fc6-8022-1ead2c7e0b85","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938814,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"0023f447-2222-4fc6-8022-1ead2c7e0b85","location":{"strand":1,"id":96612,"fmin":14246833,"fmax":14246964},"id":96611,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"48ca51b2-53a3-44b8-be95-552196d46cc0","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938818,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"48ca51b2-53a3-44b8-be95-552196d46cc0","location":{"strand":1,"id":96615,"fmin":14251072,"fmax":14251271},"id":96614,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938794,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"8c13634b-cc03-4dc0-a7e7-057f9fedb4ae","location":{"strand":1,"id":96600,"fmin":14217568,"fmax":14217584},"id":96599,"properties":[],"date_last_modified":1510866938947},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"3fecc4fa-1ebf-4331-99ce-128084eacc72","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938799,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"3fecc4fa-1ebf-4331-99ce-128084eacc72","location":{"strand":1,"id":96603,"fmin":14224204,"fmax":14224328},"id":96602,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"7261a375-364c-4dd1-8f1d-186477d86313","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938824,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"7261a375-364c-4dd1-8f1d-186477d86313","location":{"strand":1,"id":96618,"fmin":14252990,"fmax":14252996},"id":96617,"properties":[],"date_last_modified":1510866938950},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"805b901f-7f3c-4c8d-8028-44f457e921e5","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938809,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"805b901f-7f3c-4c8d-8028-44f457e921e5","location":{"strand":1,"id":96609,"fmin":14238251,"fmax":14238430},"id":96608,"properties":[],"date_last_modified":1510866938949},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"f4fc278a-9385-472d-a12d-bda4e2071d36","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938804,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"f4fc278a-9385-472d-a12d-bda4e2071d36","location":{"strand":1,"id":96606,"fmin":14224818,"fmax":14224958},"id":96605,"properties":[],"date_last_modified":1510866938948},{"owner":"None","parent_name":"Gpc6-00002","uniquename":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1510866938831,"sequence":"scaf_00001","parent_id":"5018a3ba-aeb3-4743-bf4b-192d1985157b","name":"ceaeaa77-6e6f-4129-b767-d5c462eb87df","location":{"strand":1,"id":96621,"fmin":14217568,"fmax":14252996},"id":96620,"properties":[],"date_last_modified":1510866938950}],"parent_id":"c5e5935b-6002-46ba-85f7-df1ec9853420","name":"Gpc6-00002","location":{"strand":1,"id":96598,"fmin":14217568,"fmax":14252996},"id":96597,"properties":[],"date_last_modified":1510866938947}],"sequenceAlterationEvent":false,"operation":"DELETE"}



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.