Re: Questions regarding JCVI MedicMine upgrade to 2.x

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

Re: Questions regarding JCVI MedicMine upgrade to 2.x

Julie Sullivan-2
Hi Yongwook!

1. Which version of tomcat are you using? We use Tomcat 8.5.

Could be a config issue:

https://intermine.readthedocs.io/en/latest/system-requirements/software/tomcat/#after-installation

2. We didn't change that part of the model AFAIK. Looking here (and in
core.xml), I don't think mRNA is in the core model anyway:

https://github.com/intermine/intermine/blob/dev/bio/model/genomic_additions.xml

Maybe a local change? What model was your code expecting?

(I've CCed the intermine dev list because I think your issues will be
useful for everyone!)

Cheers
Julie

On 31/01/2019 23:02, Choi, Yongwook wrote:

> Hi Julie,
>
> Thank you for your very helpful answers. I have resolved the problems, and completed data loading, post processing, and deploying it on my VM. But I still have some problem and questions.
>
> 1. The site is not working for report pages. Below are the URL and the error message saying “showInHeader” property is not found. Have you seen this type of errors? Do you have any suggestions on how to investigate this?
>
> "GET /medicmine2/report.do?id=1000004&trail=%7c1000004 HTTP/1.1" 500 16592
>
> SEVERE [http-nio-8080-exec-52] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [action] in context with path [/medicmine2] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: ServletException in '/report.jsp': Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]] with root cause
>   javax.el.PropertyNotFoundException: Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]
>
> 2. For the problem regarding protein FASTA (#3 in previous email), I just commented out the assignment of mRNA for protein and keep Transcript assignment (code below). I just wonder if this is related to some model change in Intermine.
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Questions regarding JCVI MedicMine upgrade to 2.x

Choi, Yongwook
Hi Julie,

1. I am also using Tomcat 8.5. Other pages (such as begin, dataCategories, keywordSearchResults, results, templates, etc.) are working fine.

2. I didn’t make any updates but will look into it.

Thank you!
Yongwook

On 2/1/19, 3:24 AM, "Julie Sullivan" <[hidden email]> wrote:

    Hi Yongwook!
   
    1. Which version of tomcat are you using? We use Tomcat 8.5.
   
    Could be a config issue:
   
    https://intermine.readthedocs.io/en/latest/system-requirements/software/tomcat/#after-installation
   
    2. We didn't change that part of the model AFAIK. Looking here (and in
    core.xml), I don't think mRNA is in the core model anyway:
   
    https://github.com/intermine/intermine/blob/dev/bio/model/genomic_additions.xml
   
    Maybe a local change? What model was your code expecting?
   
    (I've CCed the intermine dev list because I think your issues will be
    useful for everyone!)
   
    Cheers
    Julie
   
    On 31/01/2019 23:02, Choi, Yongwook wrote:
    > Hi Julie,
    >
    > Thank you for your very helpful answers. I have resolved the problems, and completed data loading, post processing, and deploying it on my VM. But I still have some problem and questions.
    >
    > 1. The site is not working for report pages. Below are the URL and the error message saying “showInHeader” property is not found. Have you seen this type of errors? Do you have any suggestions on how to investigate this?
    >
    > "GET /medicmine2/report.do?id=1000004&trail=%7c1000004 HTTP/1.1" 500 16592
    >
    > SEVERE [http-nio-8080-exec-52] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [action] in context with path [/medicmine2] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: ServletException in '/report.jsp': Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]] with root cause
    >   javax.el.PropertyNotFoundException: Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]
    >
    > 2. For the problem regarding protein FASTA (#3 in previous email), I just commented out the assignment of mRNA for protein and keep Transcript assignment (code below). I just wonder if this is related to some model change in Intermine.
   
   

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Questions regarding JCVI MedicMine upgrade to 2.x

HongKee Moon
In reply to this post by Julie Sullivan-2
Hi Yongwook,

Based on the error, I might be able to guess the wrong format of webconfig-model.xml located in webapp/resource/webapp/WEB-INF.
Usually, showInHeader attribute is used in table entity, not in the fieldconfig entity.

Please, refer the below pages.

Cheers,
HongKee


On Feb 1, 2019, at 9:24 AM, Julie Sullivan <[hidden email]> wrote:

1. The site is not working for report pages. Below are the URL and the error message saying “showInHeader” property is not found. Have you seen this type of errors? Do you have any suggestions on how to investigate this?
"GET /medicmine2/report.do?id=1000004&trail=%7c1000004 HTTP/1.1" 500 16592
SEVERE [http-nio-8080-exec-52] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [action] in context with path [/medicmine2] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: ServletException in '/report.jsp': Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]] with root cause
 javax.el.PropertyNotFoundException: Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]


--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany

Office: CSBD 008

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Questions regarding JCVI MedicMine upgrade to 2.x

Choi, Yongwook

Thank you for sharing your experience, HongKee.

 

I have checked our webconfig-model.xml file (https://github.com/ywchoi/medicmine/blob/upgrade-3.1/webapp/src/main/webapp/WEB-INF/webconfig-model.xml ). Indeed, all the showInHeader attributes were used in table entity, not in fieldconfig entity.

 

According to the Intermine document, showInHeader is an optional parameter, but from the following error message, it seems the parameter is expected:

“Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]”

 

The webconfig-model.xml file is the same one used with Intermine 1.x version. So I wonder if we need any updates in this file for upgrading to 2.x versions.

 

Thanks!

Yongwook

 

From: HongKee Moon <[hidden email]>
Date: Monday, February 4, 2019 at 4:28 AM
To: "Choi, Yongwook" <[hidden email]>
Cc: InterMine Devs <[hidden email]>, Julie Sullivan <[hidden email]>
Subject: Re: [InterMine Dev] Questions regarding JCVI MedicMine upgrade to 2.x

 

Hi Yongwook,

 

Based on the error, I might be able to guess the wrong format of webconfig-model.xml located in webapp/resource/webapp/WEB-INF.

Usually, showInHeader attribute is used in table entity, not in the fieldconfig entity.

 

Please, refer the below pages.

 

Cheers,

HongKee

 

 

On Feb 1, 2019, at 9:24 AM, Julie Sullivan <[hidden email]> wrote:

 

1. The site is not working for report pages. Below are the URL and the error message saying “showInHeader” property is not found. Have you seen this type of errors? Do you have any suggestions on how to investigate this?
"GET /medicmine2/report.do?id=1000004&trail=%7c1000004 HTTP/1.1" 500 16592
SEVERE [http-nio-8080-exec-52] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [action] in context with path [/medicmine2] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: ServletException in '/report.jsp': Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]] with root cause
 javax.el.PropertyNotFoundException: Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]

 


--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany

 

Office: CSBD 008

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de

 


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Questions regarding JCVI MedicMine upgrade to 2.x

HongKee Moon
Dear Yongwook,

I do not think your webconfig-model.xml has a problem.
When I briefly checked your codes in report.jsp.
Supposedly, field does not have showInheader actually, inlineList does. 

Please, check the actual source code in intermine.

I guess one of your member put some tweaks there for some reasons. It would be nice to use a fresh clone of intermine and check if it's working first.

Cheers,
HongKee

On Feb 4, 2019, at 4:39 PM, Choi, Yongwook <[hidden email]> wrote:

Thank you for sharing your experience, HongKee.
 
I have checked our webconfig-model.xml file (https://github.com/ywchoi/medicmine/blob/upgrade-3.1/webapp/src/main/webapp/WEB-INF/webconfig-model.xml ). Indeed, all the showInHeader attributes were used in table entity, not in fieldconfig entity.
 
According to the Intermine document, showInHeader is an optional parameter, but from the following error message, it seems the parameter is expected:
“Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]”
 
The webconfig-model.xml file is the same one used with Intermine 1.x version. So I wonder if we need any updates in this file for upgrading to 2.x versions.
 
Thanks!
Yongwook
 
From: HongKee Moon <[hidden email]>
Date: Monday, February 4, 2019 at 4:28 AM
To: "Choi, Yongwook" <[hidden email]>
Cc: InterMine Devs <[hidden email]>, Julie Sullivan <[hidden email]>
Subject: Re: [InterMine Dev] Questions regarding JCVI MedicMine upgrade to 2.x
 
Hi Yongwook, 
 
Based on the error, I might be able to guess the wrong format of webconfig-model.xml located in webapp/resource/webapp/WEB-INF.
Usually, showInHeader attribute is used in table entity, not in the fieldconfig entity.
 
Please, refer the below pages.
 
Cheers,
HongKee
 
 
On Feb 1, 2019, at 9:24 AM, Julie Sullivan <[hidden email]> wrote:
 
1. The site is not working for report pages. Below are the URL and the error message saying “showInHeader” property is not found. Have you seen this type of errors? Do you have any suggestions on how to investigate this?
"GET /medicmine2/report.do?id=1000004&trail=%7c1000004 HTTP/1.1" 500 16592
SEVERE [http-nio-8080-exec-52] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [action] in context with path [/medicmine2] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: ServletException in '/report.jsp': Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]] with root cause
 javax.el.PropertyNotFoundException: Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]
 

--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany
 
Office: CSBD 008

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de
 


--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany

Office: CSBD 008

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Questions regarding JCVI MedicMine upgrade to 2.x

Choi, Yongwook

Hi HongKee,

 

Thank you very much for your help and suggestion. The issue was resolved by removing the added condition.

 

Thanks!

Yongwook

 

From: HongKee Moon <[hidden email]>
Date: Monday, February 4, 2019 at 11:27 AM
To: "Choi, Yongwook" <[hidden email]>
Cc: InterMine Devs <[hidden email]>, Julie Sullivan <[hidden email]>
Subject: Re: [InterMine Dev] Questions regarding JCVI MedicMine upgrade to 2.x

 

Dear Yongwook,

 

I do not think your webconfig-model.xml has a problem.

When I briefly checked your codes in report.jsp.

Supposedly, field does not have showInheader actually, inlineList does. 

 

Please, check the actual source code in intermine.

 

I guess one of your member put some tweaks there for some reasons. It would be nice to use a fresh clone of intermine and check if it's working first.

 

Cheers,

HongKee

 

On Feb 4, 2019, at 4:39 PM, Choi, Yongwook <[hidden email]> wrote:

 

Thank you for sharing your experience, HongKee.

 

I have checked our webconfig-model.xml file (https://github.com/ywchoi/medicmine/blob/upgrade-3.1/webapp/src/main/webapp/WEB-INF/webconfig-model.xml ). Indeed, all the showInHeader attributes were used in table entity, not in fieldconfig entity.

 

According to the Intermine document, showInHeader is an optional parameter, but from the following error message, it seems the parameter is expected:

“Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]”

 

The webconfig-model.xml file is the same one used with Intermine 1.x version. So I wonder if we need any updates in this file for upgrading to 2.x versions.

 

Thanks!

Yongwook

 

From: HongKee Moon <[hidden email]>
Date: Monday, February 4, 2019 at 4:28 AM
To: "Choi, Yongwook" <[hidden email]>
Cc: InterMine Devs <[hidden email]>, Julie Sullivan <[hidden email]>
Subject: Re: [InterMine Dev] Questions regarding JCVI MedicMine upgrade to 2.x

 

Hi Yongwook, 

 

Based on the error, I might be able to guess the wrong format of webconfig-model.xml located in webapp/resource/webapp/WEB-INF.

Usually, showInHeader attribute is used in table entity, not in the fieldconfig entity.

 

Please, refer the below pages.

 

Cheers,

HongKee

 

 

On Feb 1, 2019, at 9:24 AM, Julie Sullivan <[hidden email]> wrote:

 

1. The site is not working for report pages. Below are the URL and the error message saying “showInHeader” property is not found. Have you seen this type of errors? Do you have any suggestions on how to investigate this?
"GET /medicmine2/report.do?id=1000004&trail=%7c1000004 HTTP/1.1" 500 16592
SEVERE [http-nio-8080-exec-52] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [action] in context with path [/medicmine2] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: ServletException in '/report.jsp': Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]] with root cause
 javax.el.PropertyNotFoundException: Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]

 


--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany

 

Office: CSBD 008

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de

 

 


--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany

 

Office: CSBD 008

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de

 


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Questions regarding JCVI MedicMine upgrade to 2.x

Vivek Krishnakumar
Hi All,

Just wanted to chime in on this conversation! Back in 2015, I had added functionality to ThaleMine to enable controlling whether a particular field shows up in the header or not, by way of this commit: https://github.com/Arabidopsis-Information-Portal/intermine/commit/0907aa4716a12c19aaa28a265fcc4912423d54a8. This change also trickled down to MedicMine (since MedicMine forks ThaleMine).

These changes to the core FieldConfig, ReportObject* and ObjectViewController did not make its way back upstream, as such the report.jsp is no longer in sync with the rest of the code. Apologies for the incovenience caused!

Thank you.
Vivek

On Mon, Feb 4, 2019 at 8:56 AM Choi, Yongwook <[hidden email]> wrote:

Hi HongKee,

 

Thank you very much for your help and suggestion. The issue was resolved by removing the added condition.

 

Thanks!

Yongwook

 

From: HongKee Moon <[hidden email]>
Date: Monday, February 4, 2019 at 11:27 AM
To: "Choi, Yongwook" <[hidden email]>
Cc: InterMine Devs <[hidden email]>, Julie Sullivan <[hidden email]>
Subject: Re: [InterMine Dev] Questions regarding JCVI MedicMine upgrade to 2.x

 

Dear Yongwook,

 

I do not think your webconfig-model.xml has a problem.

When I briefly checked your codes in report.jsp.

Supposedly, field does not have showInheader actually, inlineList does. 

 

Please, check the actual source code in intermine.

 

I guess one of your member put some tweaks there for some reasons. It would be nice to use a fresh clone of intermine and check if it's working first.

 

Cheers,

HongKee

 

On Feb 4, 2019, at 4:39 PM, Choi, Yongwook <[hidden email]> wrote:

 

Thank you for sharing your experience, HongKee.

 

I have checked our webconfig-model.xml file (https://github.com/ywchoi/medicmine/blob/upgrade-3.1/webapp/src/main/webapp/WEB-INF/webconfig-model.xml ). Indeed, all the showInHeader attributes were used in table entity, not in fieldconfig entity.

 

According to the Intermine document, showInHeader is an optional parameter, but from the following error message, it seems the parameter is expected:

“Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]”

 

The webconfig-model.xml file is the same one used with Intermine 1.x version. So I wonder if we need any updates in this file for upgrading to 2.x versions.

 

Thanks!

Yongwook

 

From: HongKee Moon <[hidden email]>
Date: Monday, February 4, 2019 at 4:28 AM
To: "Choi, Yongwook" <[hidden email]>
Cc: InterMine Devs <[hidden email]>, Julie Sullivan <[hidden email]>
Subject: Re: [InterMine Dev] Questions regarding JCVI MedicMine upgrade to 2.x

 

Hi Yongwook, 

 

Based on the error, I might be able to guess the wrong format of webconfig-model.xml located in webapp/resource/webapp/WEB-INF.

Usually, showInHeader attribute is used in table entity, not in the fieldconfig entity.

 

Please, refer the below pages.

 

Cheers,

HongKee

 

 

On Feb 1, 2019, at 9:24 AM, Julie Sullivan <[hidden email]> wrote:

 

1. The site is not working for report pages. Below are the URL and the error message saying “showInHeader” property is not found. Have you seen this type of errors? Do you have any suggestions on how to investigate this?
"GET /medicmine2/report.do?id=1000004&trail=%7c1000004 HTTP/1.1" 500 16592
SEVERE [http-nio-8080-exec-52] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [action] in context with path [/medicmine2] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: ServletException in '/report.jsp': Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]] with root cause
 javax.el.PropertyNotFoundException: Property [showInHeader] not found on type [org.intermine.web.logic.results.ReportObjectField]

 


--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany

 

Office: CSBD 008

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de

 

 


--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany

 

Office: CSBD 008

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de

 

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev