how to add users and ref genome/organism in Apollo v2.0.6

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how to add users and ref genome/organism in Apollo v2.0.6

Isabel Marcelino-2

Dear All,

 

I’m having some problems to add both users(and/or groups) and organisms either from the Apollo annotator (webpage) or using command lines.

 

For instance, when I try to add an organism or a group in the webpage, the following message appears on the terminal:

2017-08-30 16:20:45,421 [http-bio-8010-exec-12] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]

2017-08-30 16:21:10,939 [http-bio-8010-exec-12] DEBUG apollo.GroupController  - loadGroups

| Error 2017-08-30 16:21:10,981 [http-bio-8010-exec-12] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}

2017-08-30 16:21:25,891 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:21:25,892 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:22:25,887 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:22:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:23:25,901 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:23:25,903 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:24:25,897 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:24:25,898 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:25:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:25:25,889 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:26:14,680 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - dataObject does not contain organism (may not be needed)

2017-08-30 16:26:14,694 [http-bio-8010-exec-3] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]

2017-08-30 16:26:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:26:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

 

I tried to use some scripts available in Apollo-2.0.6/docs/webservices/examples/groovy, but I think I have some problems with the syntax and I’m not getting good results neither.

 

To load the reference genomes, I followed the instructions  given here:

http://genomearchitect.readthedocs.io/en/latest/Data_loading.html

 

I would really appreciate if you could help me on that.

Thanks,

Isabel

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé

Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex

Guadeloupe, FWI

 

 




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L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
www.avast.com






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Re: how to add users and ref genome/organism in Apollo v2.0.6

nathandunn

What command are you running to add users? 

Also, have you added the first admin user?  This should show up automatically if no users are on the site. (http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#login-to-the-web-interface)

It might be easier to add users through the interface via the user tab if there aren’t that many.  

Not sure if this guide will be helpful:  http://genomearchitect.github.io/users-guide/

Nathan

On Aug 31, 2017, at 6:35 AM, Isabel Marcelino <[hidden email]> wrote:

Dear All,
 
I’m having some problems to add both users(and/or groups) and organisms either from the Apollo annotator (webpage) or using command lines. 
 
For instance, when I try to add an organism or a group in the webpage, the following message appears on the terminal: 
2017-08-30 16:20:45,421 [http-bio-8010-exec-12] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]
2017-08-30 16:21:10,939 [http-bio-8010-exec-12] DEBUG apollo.GroupController  - loadGroups
| Error 2017-08-30 16:21:10,981 [http-bio-8010-exec-12] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
2017-08-30 16:21:25,891 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:21:25,892 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:22:25,887 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:22:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:23:25,901 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:23:25,903 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:24:25,897 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:24:25,898 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:25:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:25:25,889 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:26:14,680 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - dataObject does not contain organism (may not be needed)
2017-08-30 16:26:14,694 [http-bio-8010-exec-3] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]
2017-08-30 16:26:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:26:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
 
I tried to use some scripts available in Apollo-2.0.6/docs/webservices/examples/groovy, but I think I have some problems with the syntax and I’m not getting good results neither.
 
To load the reference genomes, I followed the instructions  given here:
 
I would really appreciate if you could help me on that.
Thanks,
Isabel
*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé
Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex
Guadeloupe, FWI
 
 



Avast logo

L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. 
www.avast.com


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RE: how to add users and ref genome/organism in Apollo v2.0.6

Isabel Marcelino-2

Hi Nathan,

Regarding the commands, I tried to use the ones in Apollo Documentation Release 2.0.7 (Jun28, 2017) –Chapter 13 (add_users.groovy and add organism.groovy).

Yesterday, I added the first admin user. Because an email was requested, I used my professional email as username and not the user that I added to the apollo-config.groovy file (web_apollo_users_admin). Maybe this is the problem….but I don’t know how to fix that.

Thanks for the help,

Isabel

 

 

De : [hidden email] [mailto:[hidden email]] De la part de Nathan Dunn
Envoyé : 31 August, 2017 11:04 AM
À : [hidden email]
Objet : Re: [apollo] how to add users and ref genome/organism in Apollo v2.0.6

 

 

What command are you running to add users? 

 

Also, have you added the first admin user?  This should show up automatically if no users are on the site. (http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#login-to-the-web-interface)

 

It might be easier to add users through the interface via the user tab if there aren’t that many.  

 

Not sure if this guide will be helpful:  http://genomearchitect.github.io/users-guide/

 

Nathan

 

On Aug 31, 2017, at 6:35 AM, Isabel Marcelino <[hidden email]> wrote:

 

Dear All,

 

I’m having some problems to add both users(and/or groups) and organisms either from the Apollo annotator (webpage) or using command lines. 

 

For instance, when I try to add an organism or a group in the webpage, the following message appears on the terminal: 

2017-08-30 16:20:45,421 [http-bio-8010-exec-12] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]

2017-08-30 16:21:10,939 [http-bio-8010-exec-12] DEBUG apollo.GroupController  - loadGroups

| Error 2017-08-30 16:21:10,981 [http-bio-8010-exec-12] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}

2017-08-30 16:21:25,891 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:21:25,892 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:22:25,887 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:22:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:23:25,901 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:23:25,903 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:24:25,897 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:24:25,898 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:25:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:25:25,889 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:26:14,680 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - dataObject does not contain organism (may not be needed)

2017-08-30 16:26:14,694 [http-bio-8010-exec-3] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]

2017-08-30 16:26:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:26:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

 

I tried to use some scripts available in Apollo-2.0.6/docs/webservices/examples/groovy, but I think I have some problems with the syntax and I’m not getting good results neither.

 

To load the reference genomes, I followed the instructions  given here:

 

I would really appreciate if you could help me on that.

Thanks,

Isabel

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé

Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex

Guadeloupe, FWI

 

 

 

Avast logo

L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. 
www.avast.com






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.

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Re: how to add users and ref genome/organism in Apollo v2.0.6

nathandunn

That all sounds correct.  I use my professional email as the username. 

I think this is what you are referring to? 

add_users.groovy -username [hidden email] -password admin_password \
    -newuser [hidden email] -newpassword newuserpass \
    -destinationurl http://localhost:8080/apollo
add_organism.groovy -name yeast -url http://localhost:8080/apollo/ \
    -directory /opt/apollo/yeast -username [hidden email] -password admin_password
If you have a lot of users / organisms (or are doing an integration) this should work, otherwise I would use the user interface. 

If you don’t include the username and password it should prompt you. 

Can you:

1 - Confirm that you can login with the “admin” user that is your professional email.
2 - Confirm that you see an “admin” tab (6 total tabs) when logged in with that user.

  

3 - What do you see when attempt to add an additional user from the command-line as well as the server logs (catalina.out)? 


Nathan

On Aug 31, 2017, at 11:15 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan, 
Regarding the commands, I tried to use the ones in Apollo Documentation Release 2.0.7 (Jun28, 2017) –Chapter 13 (add_users.groovy and add organism.groovy).
Yesterday, I added the first admin user. Because an email was requested, I used my professional email as username and not the user that I added to the apollo-config.groovy file (web_apollo_users_admin). Maybe this is the problem….but I don’t know how to fix that.
Thanks for the help,
Isabel
 
 
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 31 August, 2017 11:04 AM
À : [hidden email]
Objet : Re: [apollo] how to add users and ref genome/organism in Apollo v2.0.6
 
 
What command are you running to add users? 
 
Also, have you added the first admin user?  This should show up automatically if no users are on the site. (http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#login-to-the-web-interface)
 
It might be easier to add users through the interface via the user tab if there aren’t that many.  
 
Not sure if this guide will be helpful:  http://genomearchitect.github.io/users-guide/
 
Nathan
 
On Aug 31, 2017, at 6:35 AM, Isabel Marcelino <[hidden email]> wrote:
 
Dear All,
 
I’m having some problems to add both users(and/or groups) and organisms either from the Apollo annotator (webpage) or using command lines. 
 
For instance, when I try to add an organism or a group in the webpage, the following message appears on the terminal: 
2017-08-30 16:20:45,421 [http-bio-8010-exec-12] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]
2017-08-30 16:21:10,939 [http-bio-8010-exec-12] DEBUG apollo.GroupController  - loadGroups
| Error 2017-08-30 16:21:10,981 [http-bio-8010-exec-12] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
2017-08-30 16:21:25,891 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:21:25,892 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:22:25,887 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:22:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:23:25,901 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:23:25,903 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:24:25,897 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:24:25,898 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:25:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:25:25,889 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:26:14,680 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - dataObject does not contain organism (may not be needed)
2017-08-30 16:26:14,694 [http-bio-8010-exec-3] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]
2017-08-30 16:26:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:26:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
 
I tried to use some scripts available in Apollo-2.0.6/docs/webservices/examples/groovy, but I think I have some problems with the syntax and I’m not getting good results neither.
 
To load the reference genomes, I followed the instructions  given here:
 
I would really appreciate if you could help me on that.
Thanks,
Isabel
*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé
Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex
Guadeloupe, FWI
 
 

 


Avast logo
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. 
www.avast.com





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.

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RE: how to add users and ref genome/organism in Apollo v2.0.6

Isabel Marcelino-2

Hi Nathan,

I finally managed to add new users and even organisms (the yeast and volvox examples that are under /var/www/jbrowse/JBrowse-1.12.3/sample_data/json/volvox) using the user interface. Still, I cannot see the sequences… Do you have any suggestion, please?

Thank you.

Isabel

 

 

De : [hidden email] [mailto:[hidden email]] De la part de Nathan Dunn
Envoyé : 31 August, 2017 2
:59 PM
À : [hidden email]
Objet : Re: [apollo] how to add users and ref genome/organism in Apollo v2.0.6

 

 

That all sounds correct.  I use my professional email as the username. 

 

I think this is what you are referring to? 

 

add_users.groovy -username [hidden email] -password admin_password \
    -newuser [hidden email] -newpassword newuserpass \
    -destinationurl http://localhost:8080/apollo
add_organism.groovy -name yeast -url http://localhost:8080/apollo/ \
    -directory /opt/apollo/yeast -username [hidden email] -password admin_password

If you have a lot of users / organisms (or are doing an integration) this should work, otherwise I would use the user interface. 

 

If you don’t include the username and password it should prompt you. 

 

Can you:

 

1 - Confirm that you can login with the “admin” user that is your professional email.

2 - Confirm that you see an “admin” tab (6 total tabs) when logged in with that user.

 

  

 

3 - What do you see when attempt to add an additional user from the command-line as well as the server logs (catalina.out)? 

 

 

Nathan

 

On Aug 31, 2017, at 11:15 AM, Isabel Marcelino <[hidden email]> wrote:

 

Hi Nathan, 

Regarding the commands, I tried to use the ones in Apollo Documentation Release 2.0.7 (Jun28, 2017) –Chapter 13 (add_users.groovy and add organism.groovy).

Yesterday, I added the first admin user. Because an email was requested, I used my professional email as username and not the user that I added to the apollo-config.groovy file (web_apollo_users_admin). Maybe this is the problem….but I don’t know how to fix that.

Thanks for the help,

Isabel

 

 

De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 31 August, 2017 11:04 AM
À : [hidden email]
Objet : Re: [apollo] how to add users and ref genome/organism in Apollo v2.0.6

 

 

What command are you running to add users? 

 

Also, have you added the first admin user?  This should show up automatically if no users are on the site. (http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#login-to-the-web-interface)

 

It might be easier to add users through the interface via the user tab if there aren’t that many.  

 

Not sure if this guide will be helpful:  http://genomearchitect.github.io/users-guide/

 

Nathan

 

On Aug 31, 2017, at 6:35 AM, Isabel Marcelino <[hidden email]> wrote:

 

Dear All,

 

I’m having some problems to add both users(and/or groups) and organisms either from the Apollo annotator (webpage) or using command lines. 

 

For instance, when I try to add an organism or a group in the webpage, the following message appears on the terminal: 

2017-08-30 16:20:45,421 [http-bio-8010-exec-12] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]

2017-08-30 16:21:10,939 [http-bio-8010-exec-12] DEBUG apollo.GroupController  - loadGroups

| Error 2017-08-30 16:21:10,981 [http-bio-8010-exec-12] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}

2017-08-30 16:21:25,891 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:21:25,892 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:22:25,887 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:22:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:23:25,901 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:23:25,903 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:24:25,897 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:24:25,898 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:25:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:25:25,889 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

2017-08-30 16:26:14,680 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - dataObject does not contain organism (may not be needed)

2017-08-30 16:26:14,694 [http-bio-8010-exec-3] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]

2017-08-30 16:26:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session

| Error 2017-08-30 16:26:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site

 

I tried to use some scripts available in Apollo-2.0.6/docs/webservices/examples/groovy, but I think I have some problems with the syntax and I’m not getting good results neither.

 

To load the reference genomes, I followed the instructions  given here:

 

I would really appreciate if you could help me on that.

Thanks,

Isabel

*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé

Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex

Guadeloupe, FWI

 

 

 

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Re: how to add users and ref genome/organism in Apollo v2.0.6

nathandunn

In Apollo you have to zoom in all the way for the sequence track to show up.   If you have an annotation created you can also right-click and choose “Zoom to Base Level”.

Nathan

On Sep 5, 2017, at 6:20 AM, Isabel Marcelino <[hidden email]> wrote:

Hi Nathan, 
I finally managed to add new users and even organisms (the yeast and volvox examples that are under /var/www/jbrowse/JBrowse-1.12.3/sample_data/json/volvox) using the user interface. Still, I cannot see the sequences… Do you have any suggestion, please? 
Thank you.
Isabel
 
 
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 31 August, 2017 2
:59 PM
À : [hidden email]
Objet : Re: [apollo] how to add users and ref genome/organism in Apollo v2.0.6
 
 
That all sounds correct.  I use my professional email as the username. 
 
I think this is what you are referring to? 
 
add_users.groovy -username [hidden email] -password admin_password \
    -newuser [hidden email] -newpassword newuserpass \
    -destinationurl http://localhost:8080/apollo
add_organism.groovy -name yeast -url http://localhost:8080/apollo/ \
    -directory /opt/apollo/yeast -username [hidden email] -password admin_password
If you have a lot of users / organisms (or are doing an integration) this should work, otherwise I would use the user interface. 
 
If you don’t include the username and password it should prompt you. 
 
Can you:
 
1 - Confirm that you can login with the “admin” user that is your professional email.
2 - Confirm that you see an “admin” tab (6 total tabs) when logged in with that user.
 
  <image002.png>
 
3 - What do you see when attempt to add an additional user from the command-line as well as the server logs (catalina.out)? 
 
 
Nathan
 
On Aug 31, 2017, at 11:15 AM, Isabel Marcelino <[hidden email]> wrote:
 
Hi Nathan, 
Regarding the commands, I tried to use the ones in Apollo Documentation Release 2.0.7 (Jun28, 2017) –Chapter 13 (add_users.groovy and add organism.groovy).
Yesterday, I added the first admin user. Because an email was requested, I used my professional email as username and not the user that I added to the apollo-config.groovy file (web_apollo_users_admin). Maybe this is the problem….but I don’t know how to fix that.
Thanks for the help,
Isabel
 
 
De : [hidden email] [[hidden email]] De la part de Nathan Dunn
Envoyé : 31 August, 2017 11:04 AM
À : [hidden email]
Objet : Re: [apollo] how to add users and ref genome/organism in Apollo v2.0.6
 
 
What command are you running to add users? 
 
Also, have you added the first admin user?  This should show up automatically if no users are on the site. (http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#login-to-the-web-interface)
 
It might be easier to add users through the interface via the user tab if there aren’t that many.  
 
Not sure if this guide will be helpful:  http://genomearchitect.github.io/users-guide/
 
Nathan
 
On Aug 31, 2017, at 6:35 AM, Isabel Marcelino <[hidden email]> wrote:
 
Dear All,
 
I’m having some problems to add both users(and/or groups) and organisms either from the Apollo annotator (webpage) or using command lines. 
 
For instance, when I try to add an organism or a group in the webpage, the following message appears on the terminal: 
2017-08-30 16:20:45,421 [http-bio-8010-exec-12] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]
2017-08-30 16:21:10,939 [http-bio-8010-exec-12] DEBUG apollo.GroupController  - loadGroups
| Error 2017-08-30 16:21:10,981 [http-bio-8010-exec-12] ERROR apollo.GroupController  - {error=User does not have permission for any organisms.}
2017-08-30 16:21:25,891 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:21:25,892 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:22:25,887 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:22:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:23:25,901 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:23:25,903 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:24:25,897 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:24:25,898 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:25:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:25:25,889 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
2017-08-30 16:26:14,680 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - dataObject does not contain organism (may not be needed)
2017-08-30 16:26:14,694 [http-bio-8010-exec-3] DEBUG apollo.UserController  - number of groups for user: null for [hidden email]
2017-08-30 16:26:25,888 [http-bio-8010-exec-3] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2017-08-30 16:26:25,888 [http-bio-8010-exec-3] ERROR apollo.AnnotatorController  - User does not have permissions for the site
 
I tried to use some scripts available in Apollo-2.0.6/docs/webservices/examples/groovy, but I think I have some problems with the syntax and I’m not getting good results neither.
 
To load the reference genomes, I followed the instructions  given here:
 
I would really appreciate if you could help me on that.
Thanks,
Isabel
*************************************************
Isabel MARCELINO, PhD
Unité Environnement Santé
Institut Pasteur de Guadeloupe
Morne Jolivière - B.P. 484
97183 LES ABYMES Cedex
Guadeloupe, FWI
 
 

 


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