Update Proccess...

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

Update Proccess...

Vallejos, Andrew

Alright, so I am up to step 10, and I am trying to build the model.  However, it keeps complaining:

 

/home/intermine/build/ratmine_current/imbuild/objectstore.xml:52: java.lang.IllegalArgumentException: No such field name primaryIdentifier in class org.intermine.model.bio.Gene for primary key key_primaryidentifier

        at org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)

        at org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java:65)

        at org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIndexesTask.java:409)

        at org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)

        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)

        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:597)

        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)

        at org.apache.tools.ant.Task.perform(Task.java:348)

        at org.apache.tools.ant.Target.execute(Target.java:390)

        at org.apache.tools.ant.Target.performTasks(Target.java:411)

        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)

        at org.apache.tools.ant.Project.executeTarget(Project.java:1366)

        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)

        at org.apache.tools.ant.Project.executeTargets(Project.java:1249)

        at org.apache.tools.ant.Main.runBuild(Main.java:801)

        at org.apache.tools.ant.Main.startAnt(Main.java:218)

        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)

        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

 

I keep commenting out the offending key, but it just picks another one.  I’ve updated a couple of the keys that I noticed needed updating from the core model updates page.

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Julie Sullivan
That sounds like your model is not being merged correctly.  Gene gets
primaryIdentifier from the so_additions.xml file.

Do you have that file?

        dbmodel/build/model/so_additions.xml

If not, try to run Step #8 again:

        ./update_to_0.94 build

That will update your build.xml file so that the SO additions file is created as
part of "build-db".  Then try again to run build-db again?

Let me know if that doesn't work.

Vallejos, Andrew wrote:

> Alright, so I am up to step 10, and I am trying to build the model.
> However, it keeps complaining:
>
>  
>
> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
> java.lang.IllegalArgumentException: No such field name primaryIdentifier
> in class org.intermine.model.bio.Gene for primary key
> key_primaryidentifier
>
>         at org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>
>         at
> org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
> :65)
>
>         at
> org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
> dexesTask.java:409)
>
>         at
> org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>
>         at java.lang.reflect.Method.invoke(Method.java:597)
>
>         at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 06)
>
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>
>         at org.apache.tools.ant.Target.execute(Target.java:390)
>
>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>
>         at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>
>         at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
>
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>
>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>
>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>
>         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>
>  
>
> I keep commenting out the offending key, but it just picks another one.
> I've updated a couple of the keys that I noticed needed updating from
> the core model updates page.
>
>  
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>  
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Vallejos, Andrew
Ha...looks like I skipped step 6.

-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Wednesday, October 06, 2010 4:19 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] Update Proccess...

That sounds like your model is not being merged correctly.  Gene gets
primaryIdentifier from the so_additions.xml file.

Do you have that file?

        dbmodel/build/model/so_additions.xml

If not, try to run Step #8 again:

        ./update_to_0.94 build

That will update your build.xml file so that the SO additions file is
created as
part of "build-db".  Then try again to run build-db again?

Let me know if that doesn't work.

Vallejos, Andrew wrote:
> Alright, so I am up to step 10, and I am trying to build the model.
> However, it keeps complaining:
>
>  
>
> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
> java.lang.IllegalArgumentException: No such field name
primaryIdentifier
> in class org.intermine.model.bio.Gene for primary key
> key_primaryidentifier
>
>         at
org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>
>         at
>
org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
> :65)
>
>         at
>
org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
> dexesTask.java:409)
>
>         at
>
org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>
>         at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>
>         at java.lang.reflect.Method.invoke(Method.java:597)
>
>         at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1

> 06)
>
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>
>         at org.apache.tools.ant.Target.execute(Target.java:390)
>
>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>
>         at
org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>
>         at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

> or.java:41)
>
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>
>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>
>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>
>         at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>
>  
>
> I keep commenting out the offending key, but it just picks another
one.

> I've updated a couple of the keys that I noticed needed updating from
> the core model updates page.
>
>  
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>  
>
>
>
>
>
------------------------------------------------------------------------
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Vallejos, Andrew
In reply to this post by Julie Sullivan
Alright, I created a so_terms_list.txt file, and went through the steps
again.  I am still lacking a so_additions.xml file.

-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Wednesday, October 06, 2010 4:19 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] Update Proccess...

That sounds like your model is not being merged correctly.  Gene gets
primaryIdentifier from the so_additions.xml file.

Do you have that file?

        dbmodel/build/model/so_additions.xml

If not, try to run Step #8 again:

        ./update_to_0.94 build

That will update your build.xml file so that the SO additions file is
created as
part of "build-db".  Then try again to run build-db again?

Let me know if that doesn't work.

Vallejos, Andrew wrote:
> Alright, so I am up to step 10, and I am trying to build the model.
> However, it keeps complaining:
>
>  
>
> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
> java.lang.IllegalArgumentException: No such field name
primaryIdentifier
> in class org.intermine.model.bio.Gene for primary key
> key_primaryidentifier
>
>         at
org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>
>         at
>
org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
> :65)
>
>         at
>
org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
> dexesTask.java:409)
>
>         at
>
org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>
>         at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>
>         at java.lang.reflect.Method.invoke(Method.java:597)
>
>         at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1

> 06)
>
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>
>         at org.apache.tools.ant.Target.execute(Target.java:390)
>
>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>
>         at
org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>
>         at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

> or.java:41)
>
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>
>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>
>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>
>         at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>
>  
>
> I keep commenting out the offending key, but it just picks another
one.

> I've updated a couple of the keys that I noticed needed updating from
> the core model updates page.
>
>  
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>  
>
>
>
>
>
------------------------------------------------------------------------
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Julie Sullivan
What happens when you run this in ratmine/dbmodel:

        ant create-so-model -v

Do you get an error?  Do you get something like this in your terminal?

  [so-model] Starting OboToModel conversion from
/home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
/home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.  Filtering on
47 obo terms from /home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt

The SO file generated will be placed here:

        ratmine/dbmodel/build/model/so_additions.xml



Vallejos, Andrew wrote:

> Alright, I created a so_terms_list.txt file, and went through the steps
> again.  I am still lacking a so_additions.xml file.
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 4:19 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> That sounds like your model is not being merged correctly.  Gene gets
> primaryIdentifier from the so_additions.xml file.
>
> Do you have that file?
>
> dbmodel/build/model/so_additions.xml
>
> If not, try to run Step #8 again:
>
> ./update_to_0.94 build
>
> That will update your build.xml file so that the SO additions file is
> created as
> part of "build-db".  Then try again to run build-db again?
>
> Let me know if that doesn't work.
>
> Vallejos, Andrew wrote:
>> Alright, so I am up to step 10, and I am trying to build the model.
>> However, it keeps complaining:
>>
>>  
>>
>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>> java.lang.IllegalArgumentException: No such field name
> primaryIdentifier
>> in class org.intermine.model.bio.Gene for primary key
>> key_primaryidentifier
>>
>>         at
> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>         at
>>
> org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>> :65)
>>
>>         at
>>
> org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>> dexesTask.java:409)
>>
>>         at
>>
> org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>         at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>
>>         at
>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>
>>         at
>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>> 06)
>>
>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>
>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>
>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>
>>         at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>
>>         at
> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>         at
>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>> or.java:41)
>>
>>         at
>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>
>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>
>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>
>>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>
>>         at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>  
>>
>> I keep commenting out the offending key, but it just picks another
> one.
>> I've updated a couple of the keys that I noticed needed updating from
>> the core model updates page.
>>
>>  
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>  
>>
>>
>>
>>
>>
> ------------------------------------------------------------------------
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Julie Sullivan
In reply to this post by Vallejos, Andrew
And you meant "so_term_list.txt" not "so_terms_list.txt", right?

Vallejos, Andrew wrote:

> Alright, I created a so_terms_list.txt file, and went through the steps
> again.  I am still lacking a so_additions.xml file.
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 4:19 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> That sounds like your model is not being merged correctly.  Gene gets
> primaryIdentifier from the so_additions.xml file.
>
> Do you have that file?
>
> dbmodel/build/model/so_additions.xml
>
> If not, try to run Step #8 again:
>
> ./update_to_0.94 build
>
> That will update your build.xml file so that the SO additions file is
> created as
> part of "build-db".  Then try again to run build-db again?
>
> Let me know if that doesn't work.
>
> Vallejos, Andrew wrote:
>> Alright, so I am up to step 10, and I am trying to build the model.
>> However, it keeps complaining:
>>
>>  
>>
>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>> java.lang.IllegalArgumentException: No such field name
> primaryIdentifier
>> in class org.intermine.model.bio.Gene for primary key
>> key_primaryidentifier
>>
>>         at
> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>         at
>>
> org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>> :65)
>>
>>         at
>>
> org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>> dexesTask.java:409)
>>
>>         at
>>
> org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>         at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>
>>         at
>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>
>>         at
>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>> 06)
>>
>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>
>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>
>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>
>>         at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>
>>         at
> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>         at
>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>> or.java:41)
>>
>>         at
>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>
>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>
>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>
>>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>
>>         at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>  
>>
>> I keep commenting out the offending key, but it just picks another
> one.
>> I've updated a couple of the keys that I noticed needed updating from
>> the core model updates page.
>>
>>  
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>  
>>
>>
>>
>>
>>
> ------------------------------------------------------------------------
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Vallejos, Andrew
Yes.  "so_term_list.txt".

Sadly, not so simple an error.  :)

-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Wednesday, October 06, 2010 9:42 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] Update Proccess...

And you meant "so_term_list.txt" not "so_terms_list.txt", right?

Vallejos, Andrew wrote:
> Alright, I created a so_terms_list.txt file, and went through the
steps

> again.  I am still lacking a so_additions.xml file.
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 4:19 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> That sounds like your model is not being merged correctly.  Gene gets
> primaryIdentifier from the so_additions.xml file.
>
> Do you have that file?
>
> dbmodel/build/model/so_additions.xml
>
> If not, try to run Step #8 again:
>
> ./update_to_0.94 build
>
> That will update your build.xml file so that the SO additions file is
> created as
> part of "build-db".  Then try again to run build-db again?
>
> Let me know if that doesn't work.
>
> Vallejos, Andrew wrote:
>> Alright, so I am up to step 10, and I am trying to build the model.
>> However, it keeps complaining:
>>
>>  
>>
>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>> java.lang.IllegalArgumentException: No such field name
> primaryIdentifier
>> in class org.intermine.model.bio.Gene for primary key
>> key_primaryidentifier
>>
>>         at
> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>         at
>>
>
org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>> :65)
>>
>>         at
>>
>
org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>> dexesTask.java:409)
>>
>>         at
>>
>
org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>         at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
Source)
>>
>>         at
>>
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>
>>         at
>>
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1

>> 06)
>>
>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>
>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>
>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>
>>         at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>
>>         at
> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>         at
>>
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

>> or.java:41)
>>
>>         at
>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>
>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>
>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>
>>         at
org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)

>>
>>         at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>  
>>
>> I keep commenting out the offending key, but it just picks another
> one.
>> I've updated a couple of the keys that I noticed needed updating from
>> the core model updates page.
>>
>>  
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>  
>>
>>
>>
>>
>>
>
------------------------------------------------------------------------
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Vallejos, Andrew
In reply to this post by Julie Sullivan

/home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:3:
Reference task.class.path not found.
        at
org.apache.tools.ant.types.Reference.getReferencedObject(Reference.java:
115)
        at
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
:144)
        at
org.apache.tools.ant.types.Path.dieOnCircularReference(Path.java:491)
        at
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
:115)
        at
org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:248)
        at
org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:214)
        at
org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:202)
        at
org.apache.tools.ant.types.Path.isFilesystemOnly(Path.java:714)
        at
org.apache.tools.ant.types.resources.BaseResourceCollectionContainer.isF
ilesystemOnly(BaseResourceCollectionContainer.java:169)
        at
org.apache.tools.ant.types.Path.assertFilesystemOnly(Path.java:728)
        at org.apache.tools.ant.types.Path.list(Path.java:372)
        at org.apache.tools.ant.types.Path.addExisting(Path.java:331)
        at org.apache.tools.ant.types.Path.addExisting(Path.java:319)
        at
org.apache.tools.ant.types.Path.concatSpecialPath(Path.java:566)
        at
org.apache.tools.ant.types.Path.concatSystemClasspath(Path.java:526)
        at
org.apache.tools.ant.AntClassLoader.setClassPath(AntClassLoader.java:351
)
        at
org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:265)
        at
org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:286)
        at
org.apache.tools.ant.loader.AntClassLoader5.<init>(AntClassLoader5.java:
49)
        at
sun.reflect.GeneratedConstructorAccessor13.newInstance(Unknown Source)
        at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
tructorAccessorImpl.java:27)
        at
java.lang.reflect.Constructor.newInstance(Constructor.java:513)
        at
org.apache.tools.ant.util.ReflectUtil.newInstance(ReflectUtil.java:49)
        at
org.apache.tools.ant.AntClassLoader.newAntClassLoader(AntClassLoader.jav
a:1551)
        at
org.apache.tools.ant.Project.createClassLoader(Project.java:339)
        at
org.apache.tools.ant.util.ClasspathUtils.getUniqueClassLoaderForPath(Cla
sspathUtils.java:206)
        at
org.apache.tools.ant.util.ClasspathUtils.getClassLoaderForPath(Classpath
Utils.java:183)
        at
org.apache.tools.ant.util.ClasspathUtils$Delegate.getClassLoader(Classpa
thUtils.java:411)
        at
org.apache.tools.ant.taskdefs.DefBase.createLoader(DefBase.java:142)
        at
org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:208)
        at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
06)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
        at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
or.java:41)
        at
org.apache.tools.ant.Project.executeTargets(Project.java:1249)
        at org.apache.tools.ant.Main.runBuild(Main.java:801)
        at org.apache.tools.ant.Main.startAnt(Main.java:218)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

Total time: 2 seconds
-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Wednesday, October 06, 2010 9:41 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] Update Proccess...

What happens when you run this in ratmine/dbmodel:

        ant create-so-model -v

Do you get an error?  Do you get something like this in your terminal?

  [so-model] Starting OboToModel conversion from
/home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
/home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.
Filtering on
47 obo terms from
/home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt

The SO file generated will be placed here:

        ratmine/dbmodel/build/model/so_additions.xml



Vallejos, Andrew wrote:
> Alright, I created a so_terms_list.txt file, and went through the
steps

> again.  I am still lacking a so_additions.xml file.
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 4:19 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> That sounds like your model is not being merged correctly.  Gene gets
> primaryIdentifier from the so_additions.xml file.
>
> Do you have that file?
>
> dbmodel/build/model/so_additions.xml
>
> If not, try to run Step #8 again:
>
> ./update_to_0.94 build
>
> That will update your build.xml file so that the SO additions file is
> created as
> part of "build-db".  Then try again to run build-db again?
>
> Let me know if that doesn't work.
>
> Vallejos, Andrew wrote:
>> Alright, so I am up to step 10, and I am trying to build the model.
>> However, it keeps complaining:
>>
>>  
>>
>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>> java.lang.IllegalArgumentException: No such field name
> primaryIdentifier
>> in class org.intermine.model.bio.Gene for primary key
>> key_primaryidentifier
>>
>>         at
> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>         at
>>
>
org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>> :65)
>>
>>         at
>>
>
org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>> dexesTask.java:409)
>>
>>         at
>>
>
org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>         at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
Source)
>>
>>         at
>>
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>
>>         at
>>
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1

>> 06)
>>
>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>
>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>
>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>
>>         at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>
>>         at
> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>         at
>>
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

>> or.java:41)
>>
>>         at
>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>
>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>
>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>
>>         at
org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)

>>
>>         at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>  
>>
>> I keep commenting out the offending key, but it just picks another
> one.
>> I've updated a couple of the keys that I noticed needed updating from
>> the core model updates page.
>>
>>  
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>  
>>
>>
>>
>>
>>
>
------------------------------------------------------------------------
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Julie Sullivan
What does your build file (ratmine/dbmodel/build.xml) look like?  I'm thinking
the script mucked it up.  The script is supposed to add the ant task, but since
it broke I bet the script added that ant task twice.

The build file should look like this:

<project name="flymine-dbmodel" default="default" basedir=".">

   <description>represents the production objectstore and the model
therein</description>
   <import file="../../imbuild/objectstore.xml"/>

   <target name="create-so-model" depends="init, -init-deps">
     <taskdef name="so-model" classname="org.intermine.bio.task.SOToModelTask">
       <classpath refid="task.class.path"/>
     </taskdef>
     <so-model
        soTermListFile="${so.termlist.file}"
        soFile="${so.obo.file}"
        outputFile="${so.output.file}"/>
   </target>

   <target name="-pre-init-merge" depends="create-so-model"/>

</project>

Can you verify that's what your build file looks like?  Or just send it to me?

Vallejos, Andrew wrote:

> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:3:
> Reference task.class.path not found.
>         at
> org.apache.tools.ant.types.Reference.getReferencedObject(Reference.java:
> 115)
>         at
> org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
> :144)
>         at
> org.apache.tools.ant.types.Path.dieOnCircularReference(Path.java:491)
>         at
> org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
> :115)
>         at
> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:248)
>         at
> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:214)
>         at
> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:202)
>         at
> org.apache.tools.ant.types.Path.isFilesystemOnly(Path.java:714)
>         at
> org.apache.tools.ant.types.resources.BaseResourceCollectionContainer.isF
> ilesystemOnly(BaseResourceCollectionContainer.java:169)
>         at
> org.apache.tools.ant.types.Path.assertFilesystemOnly(Path.java:728)
>         at org.apache.tools.ant.types.Path.list(Path.java:372)
>         at org.apache.tools.ant.types.Path.addExisting(Path.java:331)
>         at org.apache.tools.ant.types.Path.addExisting(Path.java:319)
>         at
> org.apache.tools.ant.types.Path.concatSpecialPath(Path.java:566)
>         at
> org.apache.tools.ant.types.Path.concatSystemClasspath(Path.java:526)
>         at
> org.apache.tools.ant.AntClassLoader.setClassPath(AntClassLoader.java:351
> )
>         at
> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:265)
>         at
> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:286)
>         at
> org.apache.tools.ant.loader.AntClassLoader5.<init>(AntClassLoader5.java:
> 49)
>         at
> sun.reflect.GeneratedConstructorAccessor13.newInstance(Unknown Source)
>         at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
> tructorAccessorImpl.java:27)
>         at
> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>         at
> org.apache.tools.ant.util.ReflectUtil.newInstance(ReflectUtil.java:49)
>         at
> org.apache.tools.ant.AntClassLoader.newAntClassLoader(AntClassLoader.jav
> a:1551)
>         at
> org.apache.tools.ant.Project.createClassLoader(Project.java:339)
>         at
> org.apache.tools.ant.util.ClasspathUtils.getUniqueClassLoaderForPath(Cla
> sspathUtils.java:206)
>         at
> org.apache.tools.ant.util.ClasspathUtils.getClassLoaderForPath(Classpath
> Utils.java:183)
>         at
> org.apache.tools.ant.util.ClasspathUtils$Delegate.getClassLoader(Classpa
> thUtils.java:411)
>         at
> org.apache.tools.ant.taskdefs.DefBase.createLoader(DefBase.java:142)
>         at
> org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:208)
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 06)
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>         at org.apache.tools.ant.Target.execute(Target.java:390)
>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>         at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>         at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>
> Total time: 2 seconds
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 9:41 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> What happens when you run this in ratmine/dbmodel:
>
> ant create-so-model -v
>
> Do you get an error?  Do you get something like this in your terminal?
>
>   [so-model] Starting OboToModel conversion from
> /home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
> /home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.
> Filtering on
> 47 obo terms from
> /home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt
>
> The SO file generated will be placed here:
>
> ratmine/dbmodel/build/model/so_additions.xml
>
>
>
> Vallejos, Andrew wrote:
>> Alright, I created a so_terms_list.txt file, and went through the
> steps
>> again.  I am still lacking a so_additions.xml file.
>>
>> -----Original Message-----
>> From: Julie Sullivan [mailto:[hidden email]]
>> Sent: Wednesday, October 06, 2010 4:19 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] Update Proccess...
>>
>> That sounds like your model is not being merged correctly.  Gene gets
>> primaryIdentifier from the so_additions.xml file.
>>
>> Do you have that file?
>>
>> dbmodel/build/model/so_additions.xml
>>
>> If not, try to run Step #8 again:
>>
>> ./update_to_0.94 build
>>
>> That will update your build.xml file so that the SO additions file is
>> created as
>> part of "build-db".  Then try again to run build-db again?
>>
>> Let me know if that doesn't work.
>>
>> Vallejos, Andrew wrote:
>>> Alright, so I am up to step 10, and I am trying to build the model.
>>> However, it keeps complaining:
>>>
>>>  
>>>
>>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>>> java.lang.IllegalArgumentException: No such field name
>> primaryIdentifier
>>> in class org.intermine.model.bio.Gene for primary key
>>> key_primaryidentifier
>>>
>>>         at
>> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>>         at
>>>
> org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>>> :65)
>>>
>>>         at
>>>
> org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>>> dexesTask.java:409)
>>>
>>>         at
>>>
> org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>>         at
>>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>
>>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
> Source)
>>>         at
>>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>> Impl.java:25)
>>>
>>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>>
>>>         at
>>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>>> 06)
>>>
>>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>>
>>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>>
>>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>
>>>         at
>>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>
>>>         at
>> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>         at
>>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>>> or.java:41)
>>>
>>>         at
>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>
>>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>
>>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>
>>>         at
> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>         at
>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>>  
>>>
>>> I keep commenting out the offending key, but it just picks another
>> one.
>>> I've updated a couple of the keys that I noticed needed updating from
>>> the core model updates page.
>>>
>>>  
>>>
>>> ======================
>>>
>>> Andrew Vallejos
>>>
>>> Web Developer II
>>>
>>> Biotechnology and Bioengineering Center
>>>
>>> Medical College of Wisconsin
>>>
>>> 414-955-4104
>>>
>>> [hidden email]
>>>
>>>  
>>>
>>>
>>>
>>>
>>>
> ------------------------------------------------------------------------
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Vallejos, Andrew
Diff of the new build vs my original

diff --git a/dbmodel/build.xml b/dbmodel/build.xml
index 7790689..6f910dc 100644
--- a/dbmodel/build.xml
+++ b/dbmodel/build.xml
@@ -1,4 +1,11 @@
 <project name="ratmine-dbmodel" default="default" basedir=".">
+<target name="create-so-model" depends="init, -init-deps">
+    <taskdef name="so-model"
classname="org.intermine.bio.task.SOToModelTask">
+        <classpath refid="task.class.path"/>
+    </taskdef>
+    <so-model soTermListFile="${so.termlist.file}"
soFile="${so.obo.file}" outputFile="${so.output.file}"/
+</target>
+
   <description>represents the production objectstore and the model
therein</description>
   <import file="../../imbuild/objectstore.xml"/>
 </project>


-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Wednesday, October 06, 2010 10:10 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] Update Proccess...

What does your build file (ratmine/dbmodel/build.xml) look like?  I'm
thinking
the script mucked it up.  The script is supposed to add the ant task,
but since
it broke I bet the script added that ant task twice.

The build file should look like this:

<project name="flymine-dbmodel" default="default" basedir=".">

   <description>represents the production objectstore and the model
therein</description>
   <import file="../../imbuild/objectstore.xml"/>

   <target name="create-so-model" depends="init, -init-deps">
     <taskdef name="so-model"
classname="org.intermine.bio.task.SOToModelTask">
       <classpath refid="task.class.path"/>
     </taskdef>
     <so-model
        soTermListFile="${so.termlist.file}"
        soFile="${so.obo.file}"
        outputFile="${so.output.file}"/>
   </target>

   <target name="-pre-init-merge" depends="create-so-model"/>

</project>

Can you verify that's what your build file looks like?  Or just send it
to me?

Vallejos, Andrew wrote:
> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:3:
> Reference task.class.path not found.
>         at
>
org.apache.tools.ant.types.Reference.getReferencedObject(Reference.java:
> 115)
>         at
>
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
> :144)
>         at
> org.apache.tools.ant.types.Path.dieOnCircularReference(Path.java:491)
>         at
>
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java

> :115)
>         at
> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:248)
>         at
> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:214)
>         at
> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:202)
>         at
> org.apache.tools.ant.types.Path.isFilesystemOnly(Path.java:714)
>         at
>
org.apache.tools.ant.types.resources.BaseResourceCollectionContainer.isF

> ilesystemOnly(BaseResourceCollectionContainer.java:169)
>         at
> org.apache.tools.ant.types.Path.assertFilesystemOnly(Path.java:728)
>         at org.apache.tools.ant.types.Path.list(Path.java:372)
>         at org.apache.tools.ant.types.Path.addExisting(Path.java:331)
>         at org.apache.tools.ant.types.Path.addExisting(Path.java:319)
>         at
> org.apache.tools.ant.types.Path.concatSpecialPath(Path.java:566)
>         at
> org.apache.tools.ant.types.Path.concatSystemClasspath(Path.java:526)
>         at
>
org.apache.tools.ant.AntClassLoader.setClassPath(AntClassLoader.java:351
> )
>         at
> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:265)
>         at
> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:286)
>         at
>
org.apache.tools.ant.loader.AntClassLoader5.<init>(AntClassLoader5.java:
> 49)
>         at
> sun.reflect.GeneratedConstructorAccessor13.newInstance(Unknown Source)
>         at
>
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
> tructorAccessorImpl.java:27)
>         at
> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>         at
> org.apache.tools.ant.util.ReflectUtil.newInstance(ReflectUtil.java:49)
>         at
>
org.apache.tools.ant.AntClassLoader.newAntClassLoader(AntClassLoader.jav
> a:1551)
>         at
> org.apache.tools.ant.Project.createClassLoader(Project.java:339)
>         at
>
org.apache.tools.ant.util.ClasspathUtils.getUniqueClassLoaderForPath(Cla
> sspathUtils.java:206)
>         at
>
org.apache.tools.ant.util.ClasspathUtils.getClassLoaderForPath(Classpath
> Utils.java:183)
>         at
>
org.apache.tools.ant.util.ClasspathUtils$Delegate.getClassLoader(Classpa

> thUtils.java:411)
>         at
> org.apache.tools.ant.taskdefs.DefBase.createLoader(DefBase.java:142)
>         at
> org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:208)
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 06)
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>         at org.apache.tools.ant.Target.execute(Target.java:390)
>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>         at
org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>         at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>         at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

>
> Total time: 2 seconds
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 9:41 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> What happens when you run this in ratmine/dbmodel:
>
> ant create-so-model -v
>
> Do you get an error?  Do you get something like this in your terminal?
>
>   [so-model] Starting OboToModel conversion from
> /home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
> /home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.
> Filtering on
> 47 obo terms from
> /home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt
>
> The SO file generated will be placed here:
>
> ratmine/dbmodel/build/model/so_additions.xml
>
>
>
> Vallejos, Andrew wrote:
>> Alright, I created a so_terms_list.txt file, and went through the
> steps
>> again.  I am still lacking a so_additions.xml file.
>>
>> -----Original Message-----
>> From: Julie Sullivan [mailto:[hidden email]]
>> Sent: Wednesday, October 06, 2010 4:19 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] Update Proccess...
>>
>> That sounds like your model is not being merged correctly.  Gene gets

>> primaryIdentifier from the so_additions.xml file.
>>
>> Do you have that file?
>>
>> dbmodel/build/model/so_additions.xml
>>
>> If not, try to run Step #8 again:
>>
>> ./update_to_0.94 build
>>
>> That will update your build.xml file so that the SO additions file is
>> created as
>> part of "build-db".  Then try again to run build-db again?
>>
>> Let me know if that doesn't work.
>>
>> Vallejos, Andrew wrote:
>>> Alright, so I am up to step 10, and I am trying to build the model.
>>> However, it keeps complaining:
>>>
>>>  
>>>
>>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>>> java.lang.IllegalArgumentException: No such field name
>> primaryIdentifier
>>> in class org.intermine.model.bio.Gene for primary key
>>> key_primaryidentifier
>>>
>>>         at
>> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>>         at
>>>
>
org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>>> :65)
>>>
>>>         at
>>>
>
org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>>> dexesTask.java:409)
>>>
>>>         at
>>>
>
org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>>         at
>>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>
>>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
> Source)
>>>         at
>>>
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>> Impl.java:25)
>>>
>>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>>
>>>         at
>>>
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1

>>> 06)
>>>
>>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>>
>>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>>
>>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>
>>>         at
>>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>
>>>         at
>> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>         at
>>>
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

>>> or.java:41)
>>>
>>>         at
>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>
>>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>
>>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>
>>>         at
> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>         at
>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>>  
>>>
>>> I keep commenting out the offending key, but it just picks another
>> one.
>>> I've updated a couple of the keys that I noticed needed updating
from

>>> the core model updates page.
>>>
>>>  
>>>
>>> ======================
>>>
>>> Andrew Vallejos
>>>
>>> Web Developer II
>>>
>>> Biotechnology and Bioengineering Center
>>>
>>> Medical College of Wisconsin
>>>
>>> 414-955-4104
>>>
>>> [hidden email]
>>>
>>>  
>>>
>>>
>>>
>>>
>>>
>
------------------------------------------------------------------------
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Richard Smith
It looks like the new target (create-so-model) is inserted
before the import of objectstore.xml.  It needs to be after the
import to pick up the class path it defines.

Sorry about that.  Moving this this to the top should fix it:

<description>represents the production objectstore and the model
    therein</description>
<import file="../../imbuild/objectstore.xml"/>


Cheers,
Richard.




Vallejos, Andrew wrote:

> Diff of the new build vs my original
>
> diff --git a/dbmodel/build.xml b/dbmodel/build.xml
> index 7790689..6f910dc 100644
> --- a/dbmodel/build.xml
> +++ b/dbmodel/build.xml
> @@ -1,4 +1,11 @@
>  <project name="ratmine-dbmodel" default="default" basedir=".">
> +<target name="create-so-model" depends="init, -init-deps">
> +    <taskdef name="so-model"
> classname="org.intermine.bio.task.SOToModelTask">
> +        <classpath refid="task.class.path"/>
> +    </taskdef>
> +    <so-model soTermListFile="${so.termlist.file}"
> soFile="${so.obo.file}" outputFile="${so.output.file}"/
> +</target>
> +
>    <description>represents the production objectstore and the model
> therein</description>
>    <import file="../../imbuild/objectstore.xml"/>
>  </project>
>
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 10:10 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> What does your build file (ratmine/dbmodel/build.xml) look like?  I'm
> thinking
> the script mucked it up.  The script is supposed to add the ant task,
> but since
> it broke I bet the script added that ant task twice.
>
> The build file should look like this:
>
> <project name="flymine-dbmodel" default="default" basedir=".">
>
>    <description>represents the production objectstore and the model
> therein</description>
>    <import file="../../imbuild/objectstore.xml"/>
>
>    <target name="create-so-model" depends="init, -init-deps">
>      <taskdef name="so-model"
> classname="org.intermine.bio.task.SOToModelTask">
>        <classpath refid="task.class.path"/>
>      </taskdef>
>      <so-model
>         soTermListFile="${so.termlist.file}"
>         soFile="${so.obo.file}"
>         outputFile="${so.output.file}"/>
>    </target>
>
>    <target name="-pre-init-merge" depends="create-so-model"/>
>
> </project>
>
> Can you verify that's what your build file looks like?  Or just send it
> to me?
>
> Vallejos, Andrew wrote:
>> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:3:
>> Reference task.class.path not found.
>>         at
>>
> org.apache.tools.ant.types.Reference.getReferencedObject(Reference.java:
>> 115)
>>         at
>>
> org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
>> :144)
>>         at
>> org.apache.tools.ant.types.Path.dieOnCircularReference(Path.java:491)
>>         at
>>
> org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
>> :115)
>>         at
>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:248)
>>         at
>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:214)
>>         at
>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:202)
>>         at
>> org.apache.tools.ant.types.Path.isFilesystemOnly(Path.java:714)
>>         at
>>
> org.apache.tools.ant.types.resources.BaseResourceCollectionContainer.isF
>> ilesystemOnly(BaseResourceCollectionContainer.java:169)
>>         at
>> org.apache.tools.ant.types.Path.assertFilesystemOnly(Path.java:728)
>>         at org.apache.tools.ant.types.Path.list(Path.java:372)
>>         at org.apache.tools.ant.types.Path.addExisting(Path.java:331)
>>         at org.apache.tools.ant.types.Path.addExisting(Path.java:319)
>>         at
>> org.apache.tools.ant.types.Path.concatSpecialPath(Path.java:566)
>>         at
>> org.apache.tools.ant.types.Path.concatSystemClasspath(Path.java:526)
>>         at
>>
> org.apache.tools.ant.AntClassLoader.setClassPath(AntClassLoader.java:351
>> )
>>         at
>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:265)
>>         at
>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:286)
>>         at
>>
> org.apache.tools.ant.loader.AntClassLoader5.<init>(AntClassLoader5.java:
>> 49)
>>         at
>> sun.reflect.GeneratedConstructorAccessor13.newInstance(Unknown Source)
>>         at
>>
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
>> tructorAccessorImpl.java:27)
>>         at
>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>         at
>> org.apache.tools.ant.util.ReflectUtil.newInstance(ReflectUtil.java:49)
>>         at
>>
> org.apache.tools.ant.AntClassLoader.newAntClassLoader(AntClassLoader.jav
>> a:1551)
>>         at
>> org.apache.tools.ant.Project.createClassLoader(Project.java:339)
>>         at
>>
> org.apache.tools.ant.util.ClasspathUtils.getUniqueClassLoaderForPath(Cla
>> sspathUtils.java:206)
>>         at
>>
> org.apache.tools.ant.util.ClasspathUtils.getClassLoaderForPath(Classpath
>> Utils.java:183)
>>         at
>>
> org.apache.tools.ant.util.ClasspathUtils$Delegate.getClassLoader(Classpa
>> thUtils.java:411)
>>         at
>> org.apache.tools.ant.taskdefs.DefBase.createLoader(DefBase.java:142)
>>         at
>> org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:208)
>>         at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>         at
>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>         at
>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>> 06)
>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>         at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>         at
> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>         at
>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>> or.java:41)
>>         at
>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>         at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>> Total time: 2 seconds
>> -----Original Message-----
>> From: Julie Sullivan [mailto:[hidden email]]
>> Sent: Wednesday, October 06, 2010 9:41 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] Update Proccess...
>>
>> What happens when you run this in ratmine/dbmodel:
>>
>> ant create-so-model -v
>>
>> Do you get an error?  Do you get something like this in your terminal?
>>
>>   [so-model] Starting OboToModel conversion from
>> /home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
>> /home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.
>> Filtering on
>> 47 obo terms from
>> /home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt
>>
>> The SO file generated will be placed here:
>>
>> ratmine/dbmodel/build/model/so_additions.xml
>>
>>
>>
>> Vallejos, Andrew wrote:
>>> Alright, I created a so_terms_list.txt file, and went through the
>> steps
>>> again.  I am still lacking a so_additions.xml file.
>>>
>>> -----Original Message-----
>>> From: Julie Sullivan [mailto:[hidden email]]
>>> Sent: Wednesday, October 06, 2010 4:19 AM
>>> To: Vallejos, Andrew
>>> Cc: [hidden email]
>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>
>>> That sounds like your model is not being merged correctly.  Gene gets
>
>>> primaryIdentifier from the so_additions.xml file.
>>>
>>> Do you have that file?
>>>
>>> dbmodel/build/model/so_additions.xml
>>>
>>> If not, try to run Step #8 again:
>>>
>>> ./update_to_0.94 build
>>>
>>> That will update your build.xml file so that the SO additions file is
>>> created as
>>> part of "build-db".  Then try again to run build-db again?
>>>
>>> Let me know if that doesn't work.
>>>
>>> Vallejos, Andrew wrote:
>>>> Alright, so I am up to step 10, and I am trying to build the model.
>>>> However, it keeps complaining:
>>>>
>>>>  
>>>>
>>>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>>>> java.lang.IllegalArgumentException: No such field name
>>> primaryIdentifier
>>>> in class org.intermine.model.bio.Gene for primary key
>>>> key_primaryidentifier
>>>>
>>>>         at
>>> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>>>         at
>>>>
> org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>>>> :65)
>>>>
>>>>         at
>>>>
> org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>>>> dexesTask.java:409)
>>>>
>>>>         at
>>>>
> org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>>>         at
>>>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>>
>>>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>> Source)
>>>>         at
>>>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>>> Impl.java:25)
>>>>
>>>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>>>
>>>>         at
>>>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>>>> 06)
>>>>
>>>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>>>
>>>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>>>
>>>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>>
>>>>         at
>>>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>>
>>>>         at
>>> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>>         at
>>>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>>>> or.java:41)
>>>>
>>>>         at
>>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>>
>>>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>>
>>>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>>
>>>>         at
>> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>>         at
>>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>>>  
>>>>
>>>> I keep commenting out the offending key, but it just picks another
>>> one.
>>>> I've updated a couple of the keys that I noticed needed updating
> from
>>>> the core model updates page.
>>>>
>>>>  
>>>>
>>>> ======================
>>>>
>>>> Andrew Vallejos
>>>>
>>>> Web Developer II
>>>>
>>>> Biotechnology and Bioengineering Center
>>>>
>>>> Medical College of Wisconsin
>>>>
>>>> 414-955-4104
>>>>
>>>> [hidden email]
>>>>
>>>>  
>>>>
>>>>
>>>>
>>>>
>>>>
> ------------------------------------------------------------------------
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Vallejos, Andrew
In reply to this post by Julie Sullivan
Current error:

create-so-model:
 [so-model] Starting OboToModel conversion from
/home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo
to
/home/intermine/build/ratmine_current/ratmine/dbmodel/build/model/so_add
itions.xml.  Filtering on 19 obo terms from
/home/intermine/build/ratmine_current/ratmine/dbmodel/resources/so_term_
list.txt

BUILD FAILED
/home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:9:
java.lang.RuntimeException: The following terms specified in
so_term_list.txt are not valid Sequence Ontology terms according to:
/home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo:
Allele, SSLP, Gene, Exon, SequenceVariant, Transcript, Chromosome,
SequenceFeature, Probe, Strain, Genotype, IntergenicRegion,
SequenceCollection, Sequence and Protein
        at
org.intermine.bio.ontology.OboToModelProcessor.validateTermsToKeep(OboTo
ModelProcessor.java:629)
        at
org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:259)
        at
org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.jav
a:98)
        at
org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68)
        at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
06)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
        at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
or.java:41)
        at
org.apache.tools.ant.Project.executeTargets(Project.java:1249)
        at org.apache.tools.ant.Main.runBuild(Main.java:801)
        at org.apache.tools.ant.Main.startAnt(Main.java:218)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)


-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Wednesday, October 06, 2010 10:54 AM
To: Vallejos, Andrew
Subject: Re: [InterMine Dev] Update Proccess...

Can you send me ratmine/dbmodel/project.properties?

Vallejos, Andrew wrote:
> Here is the build file.  Sorry for the double email, but that's what I
get for using two computers.  
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wed 10/6/2010 10:09 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>  
> What does your build file (ratmine/dbmodel/build.xml) look like?  I'm
thinking
> the script mucked it up.  The script is supposed to add the ant task,
but since

> it broke I bet the script added that ant task twice.
>
> The build file should look like this:
>
> <project name="flymine-dbmodel" default="default" basedir=".">
>
>    <description>represents the production objectstore and the model
> therein</description>
>    <import file="../../imbuild/objectstore.xml"/>
>
>    <target name="create-so-model" depends="init, -init-deps">
>      <taskdef name="so-model"
classname="org.intermine.bio.task.SOToModelTask">

>        <classpath refid="task.class.path"/>
>      </taskdef>
>      <so-model
>         soTermListFile="${so.termlist.file}"
>         soFile="${so.obo.file}"
>         outputFile="${so.output.file}"/>
>    </target>
>
>    <target name="-pre-init-merge" depends="create-so-model"/>
>
> </project>
>
> Can you verify that's what your build file looks like?  Or just send
it to me?
>
> Vallejos, Andrew wrote:
>> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:3:
>> Reference task.class.path not found.
>>         at
>>
org.apache.tools.ant.types.Reference.getReferencedObject(Reference.java:
>> 115)
>>         at
>>
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
>> :144)
>>         at
>> org.apache.tools.ant.types.Path.dieOnCircularReference(Path.java:491)
>>         at
>>
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java

>> :115)
>>         at
>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:248)
>>         at
>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:214)
>>         at
>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:202)
>>         at
>> org.apache.tools.ant.types.Path.isFilesystemOnly(Path.java:714)
>>         at
>>
org.apache.tools.ant.types.resources.BaseResourceCollectionContainer.isF

>> ilesystemOnly(BaseResourceCollectionContainer.java:169)
>>         at
>> org.apache.tools.ant.types.Path.assertFilesystemOnly(Path.java:728)
>>         at org.apache.tools.ant.types.Path.list(Path.java:372)
>>         at org.apache.tools.ant.types.Path.addExisting(Path.java:331)
>>         at org.apache.tools.ant.types.Path.addExisting(Path.java:319)
>>         at
>> org.apache.tools.ant.types.Path.concatSpecialPath(Path.java:566)
>>         at
>> org.apache.tools.ant.types.Path.concatSystemClasspath(Path.java:526)
>>         at
>>
org.apache.tools.ant.AntClassLoader.setClassPath(AntClassLoader.java:351
>> )
>>         at
>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:265)
>>         at
>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:286)
>>         at
>>
org.apache.tools.ant.loader.AntClassLoader5.<init>(AntClassLoader5.java:
>> 49)
>>         at
>> sun.reflect.GeneratedConstructorAccessor13.newInstance(Unknown
Source)
>>         at
>>
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
>> tructorAccessorImpl.java:27)
>>         at
>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>         at
>>
org.apache.tools.ant.util.ReflectUtil.newInstance(ReflectUtil.java:49)
>>         at
>>
org.apache.tools.ant.AntClassLoader.newAntClassLoader(AntClassLoader.jav
>> a:1551)
>>         at
>> org.apache.tools.ant.Project.createClassLoader(Project.java:339)
>>         at
>>
org.apache.tools.ant.util.ClasspathUtils.getUniqueClassLoaderForPath(Cla
>> sspathUtils.java:206)
>>         at
>>
org.apache.tools.ant.util.ClasspathUtils.getClassLoaderForPath(Classpath
>> Utils.java:183)
>>         at
>>
org.apache.tools.ant.util.ClasspathUtils$Delegate.getClassLoader(Classpa
>> thUtils.java:411)
>>         at
>> org.apache.tools.ant.taskdefs.DefBase.createLoader(DefBase.java:142)
>>         at
>> org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:208)
>>         at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
Source)
>>         at
>>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>         at
>>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>> 06)
>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>         at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>         at
org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>         at
>>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>> or.java:41)
>>         at
>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>         at
org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>         at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

>>
>> Total time: 2 seconds
>> -----Original Message-----
>> From: Julie Sullivan [mailto:[hidden email]]
>> Sent: Wednesday, October 06, 2010 9:41 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] Update Proccess...
>>
>> What happens when you run this in ratmine/dbmodel:
>>
>> ant create-so-model -v
>>
>> Do you get an error?  Do you get something like this in your
terminal?

>>
>>   [so-model] Starting OboToModel conversion from
>> /home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
>> /home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.
>> Filtering on
>> 47 obo terms from
>> /home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt
>>
>> The SO file generated will be placed here:
>>
>> ratmine/dbmodel/build/model/so_additions.xml
>>
>>
>>
>> Vallejos, Andrew wrote:
>>> Alright, I created a so_terms_list.txt file, and went through the
>> steps
>>> again.  I am still lacking a so_additions.xml file.
>>>
>>> -----Original Message-----
>>> From: Julie Sullivan [mailto:[hidden email]]
>>> Sent: Wednesday, October 06, 2010 4:19 AM
>>> To: Vallejos, Andrew
>>> Cc: [hidden email]
>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>
>>> That sounds like your model is not being merged correctly.  Gene
gets

>>> primaryIdentifier from the so_additions.xml file.
>>>
>>> Do you have that file?
>>>
>>> dbmodel/build/model/so_additions.xml
>>>
>>> If not, try to run Step #8 again:
>>>
>>> ./update_to_0.94 build
>>>
>>> That will update your build.xml file so that the SO additions file
is

>>> created as
>>> part of "build-db".  Then try again to run build-db again?
>>>
>>> Let me know if that doesn't work.
>>>
>>> Vallejos, Andrew wrote:
>>>> Alright, so I am up to step 10, and I am trying to build the model.
>>>> However, it keeps complaining:
>>>>
>>>>  
>>>>
>>>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>>>> java.lang.IllegalArgumentException: No such field name
>>> primaryIdentifier
>>>> in class org.intermine.model.bio.Gene for primary key
>>>> key_primaryidentifier
>>>>
>>>>         at
>>> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>>>         at
>>>>
>>
org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>>>> :65)
>>>>
>>>>         at
>>>>
>>
org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>>>> dexesTask.java:409)
>>>>
>>>>         at
>>>>
>>
org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>>>         at
>>>>
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>>
>>>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>> Source)
>>>>         at
>>>>
>>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>>> Impl.java:25)
>>>>
>>>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>>>
>>>>         at
>>>>
>>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>>>> 06)
>>>>
>>>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>>>
>>>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>>>
>>>>         at
org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>>
>>>>         at
>>>>
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>>
>>>>         at
>>> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>>         at
>>>>
>>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

>>>> or.java:41)
>>>>
>>>>         at
>>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>>
>>>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>>
>>>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>>
>>>>         at
>> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>>         at
>>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>>>  
>>>>
>>>> I keep commenting out the offending key, but it just picks another
>>> one.
>>>> I've updated a couple of the keys that I noticed needed updating
from

>>>> the core model updates page.
>>>>
>>>>  
>>>>
>>>> ======================
>>>>
>>>> Andrew Vallejos
>>>>
>>>> Web Developer II
>>>>
>>>> Biotechnology and Bioengineering Center
>>>>
>>>> Medical College of Wisconsin
>>>>
>>>> 414-955-4104
>>>>
>>>> [hidden email]
>>>>
>>>>  
>>>>
>>>>
>>>>
>>>>
>>>>
>>
------------------------------------------------------------------------
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Vallejos, Andrew
Oh...looking at FlyMine, it looks like the list should not be
capitalized.

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Vallejos, Andrew
Sent: Wednesday, October 06, 2010 11:47 AM
To: Julie Sullivan
Cc: [hidden email]
Subject: Re: [InterMine Dev] Update Proccess...

Current error:

create-so-model:
 [so-model] Starting OboToModel conversion from
/home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo
to
/home/intermine/build/ratmine_current/ratmine/dbmodel/build/model/so_add
itions.xml.  Filtering on 19 obo terms from
/home/intermine/build/ratmine_current/ratmine/dbmodel/resources/so_term_
list.txt

BUILD FAILED
/home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:9:
java.lang.RuntimeException: The following terms specified in
so_term_list.txt are not valid Sequence Ontology terms according to:
/home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo:
Allele, SSLP, Gene, Exon, SequenceVariant, Transcript, Chromosome,
SequenceFeature, Probe, Strain, Genotype, IntergenicRegion,
SequenceCollection, Sequence and Protein
        at
org.intermine.bio.ontology.OboToModelProcessor.validateTermsToKeep(OboTo
ModelProcessor.java:629)
        at
org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:259)
        at
org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.jav
a:98)
        at
org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68)
        at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
06)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
        at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
or.java:41)
        at
org.apache.tools.ant.Project.executeTargets(Project.java:1249)
        at org.apache.tools.ant.Main.runBuild(Main.java:801)
        at org.apache.tools.ant.Main.startAnt(Main.java:218)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)


-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Wednesday, October 06, 2010 10:54 AM
To: Vallejos, Andrew
Subject: Re: [InterMine Dev] Update Proccess...

Can you send me ratmine/dbmodel/project.properties?

Vallejos, Andrew wrote:
> Here is the build file.  Sorry for the double email, but that's what I
get for using two computers.  
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wed 10/6/2010 10:09 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>  
> What does your build file (ratmine/dbmodel/build.xml) look like?  I'm
thinking
> the script mucked it up.  The script is supposed to add the ant task,
but since

> it broke I bet the script added that ant task twice.
>
> The build file should look like this:
>
> <project name="flymine-dbmodel" default="default" basedir=".">
>
>    <description>represents the production objectstore and the model
> therein</description>
>    <import file="../../imbuild/objectstore.xml"/>
>
>    <target name="create-so-model" depends="init, -init-deps">
>      <taskdef name="so-model"
classname="org.intermine.bio.task.SOToModelTask">

>        <classpath refid="task.class.path"/>
>      </taskdef>
>      <so-model
>         soTermListFile="${so.termlist.file}"
>         soFile="${so.obo.file}"
>         outputFile="${so.output.file}"/>
>    </target>
>
>    <target name="-pre-init-merge" depends="create-so-model"/>
>
> </project>
>
> Can you verify that's what your build file looks like?  Or just send
it to me?
>
> Vallejos, Andrew wrote:
>> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:3:
>> Reference task.class.path not found.
>>         at
>>
org.apache.tools.ant.types.Reference.getReferencedObject(Reference.java:
>> 115)
>>         at
>>
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
>> :144)
>>         at
>> org.apache.tools.ant.types.Path.dieOnCircularReference(Path.java:491)
>>         at
>>
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java

>> :115)
>>         at
>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:248)
>>         at
>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:214)
>>         at
>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:202)
>>         at
>> org.apache.tools.ant.types.Path.isFilesystemOnly(Path.java:714)
>>         at
>>
org.apache.tools.ant.types.resources.BaseResourceCollectionContainer.isF

>> ilesystemOnly(BaseResourceCollectionContainer.java:169)
>>         at
>> org.apache.tools.ant.types.Path.assertFilesystemOnly(Path.java:728)
>>         at org.apache.tools.ant.types.Path.list(Path.java:372)
>>         at org.apache.tools.ant.types.Path.addExisting(Path.java:331)
>>         at org.apache.tools.ant.types.Path.addExisting(Path.java:319)
>>         at
>> org.apache.tools.ant.types.Path.concatSpecialPath(Path.java:566)
>>         at
>> org.apache.tools.ant.types.Path.concatSystemClasspath(Path.java:526)
>>         at
>>
org.apache.tools.ant.AntClassLoader.setClassPath(AntClassLoader.java:351
>> )
>>         at
>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:265)
>>         at
>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:286)
>>         at
>>
org.apache.tools.ant.loader.AntClassLoader5.<init>(AntClassLoader5.java:
>> 49)
>>         at
>> sun.reflect.GeneratedConstructorAccessor13.newInstance(Unknown
Source)
>>         at
>>
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
>> tructorAccessorImpl.java:27)
>>         at
>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>         at
>>
org.apache.tools.ant.util.ReflectUtil.newInstance(ReflectUtil.java:49)
>>         at
>>
org.apache.tools.ant.AntClassLoader.newAntClassLoader(AntClassLoader.jav
>> a:1551)
>>         at
>> org.apache.tools.ant.Project.createClassLoader(Project.java:339)
>>         at
>>
org.apache.tools.ant.util.ClasspathUtils.getUniqueClassLoaderForPath(Cla
>> sspathUtils.java:206)
>>         at
>>
org.apache.tools.ant.util.ClasspathUtils.getClassLoaderForPath(Classpath
>> Utils.java:183)
>>         at
>>
org.apache.tools.ant.util.ClasspathUtils$Delegate.getClassLoader(Classpa
>> thUtils.java:411)
>>         at
>> org.apache.tools.ant.taskdefs.DefBase.createLoader(DefBase.java:142)
>>         at
>> org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:208)
>>         at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
Source)
>>         at
>>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>         at
>>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>> 06)
>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>         at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>         at
org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>         at
>>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>> or.java:41)
>>         at
>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>         at
org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>         at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

>>
>> Total time: 2 seconds
>> -----Original Message-----
>> From: Julie Sullivan [mailto:[hidden email]]
>> Sent: Wednesday, October 06, 2010 9:41 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] Update Proccess...
>>
>> What happens when you run this in ratmine/dbmodel:
>>
>> ant create-so-model -v
>>
>> Do you get an error?  Do you get something like this in your
terminal?

>>
>>   [so-model] Starting OboToModel conversion from
>> /home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
>> /home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.
>> Filtering on
>> 47 obo terms from
>> /home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt
>>
>> The SO file generated will be placed here:
>>
>> ratmine/dbmodel/build/model/so_additions.xml
>>
>>
>>
>> Vallejos, Andrew wrote:
>>> Alright, I created a so_terms_list.txt file, and went through the
>> steps
>>> again.  I am still lacking a so_additions.xml file.
>>>
>>> -----Original Message-----
>>> From: Julie Sullivan [mailto:[hidden email]]
>>> Sent: Wednesday, October 06, 2010 4:19 AM
>>> To: Vallejos, Andrew
>>> Cc: [hidden email]
>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>
>>> That sounds like your model is not being merged correctly.  Gene
gets

>>> primaryIdentifier from the so_additions.xml file.
>>>
>>> Do you have that file?
>>>
>>> dbmodel/build/model/so_additions.xml
>>>
>>> If not, try to run Step #8 again:
>>>
>>> ./update_to_0.94 build
>>>
>>> That will update your build.xml file so that the SO additions file
is

>>> created as
>>> part of "build-db".  Then try again to run build-db again?
>>>
>>> Let me know if that doesn't work.
>>>
>>> Vallejos, Andrew wrote:
>>>> Alright, so I am up to step 10, and I am trying to build the model.
>>>> However, it keeps complaining:
>>>>
>>>>  
>>>>
>>>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>>>> java.lang.IllegalArgumentException: No such field name
>>> primaryIdentifier
>>>> in class org.intermine.model.bio.Gene for primary key
>>>> key_primaryidentifier
>>>>
>>>>         at
>>> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>>>         at
>>>>
>>
org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>>>> :65)
>>>>
>>>>         at
>>>>
>>
org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>>>> dexesTask.java:409)
>>>>
>>>>         at
>>>>
>>
org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>>>         at
>>>>
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>>
>>>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>> Source)
>>>>         at
>>>>
>>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>>> Impl.java:25)
>>>>
>>>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>>>
>>>>         at
>>>>
>>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>>>> 06)
>>>>
>>>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>>>
>>>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>>>
>>>>         at
org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>>
>>>>         at
>>>>
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>>
>>>>         at
>>> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>>         at
>>>>
>>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

>>>> or.java:41)
>>>>
>>>>         at
>>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>>
>>>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>>
>>>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>>
>>>>         at
>> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>>         at
>>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>>>  
>>>>
>>>> I keep commenting out the offending key, but it just picks another
>>> one.
>>>> I've updated a couple of the keys that I noticed needed updating
from

>>>> the core model updates page.
>>>>
>>>>  
>>>>
>>>> ======================
>>>>
>>>> Andrew Vallejos
>>>>
>>>> Web Developer II
>>>>
>>>> Biotechnology and Bioengineering Center
>>>>
>>>> Medical College of Wisconsin
>>>>
>>>> 414-955-4104
>>>>
>>>> [hidden email]
>>>>
>>>>  
>>>>
>>>>
>>>>
>>>>
>>>>
>>
------------------------------------------------------------------------
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Julie Sullivan
Yes, sorry.  Here are the naming conventions for SO:

        * lower case
        * underscores between words
        * eg. sequenceFeature

Check sequenceontology.org for the exact term names.
       

Vallejos, Andrew wrote:

> Oh...looking at FlyMine, it looks like the list should not be
> capitalized.
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On
> Behalf Of Vallejos, Andrew
> Sent: Wednesday, October 06, 2010 11:47 AM
> To: Julie Sullivan
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> Current error:
>
> create-so-model:
>  [so-model] Starting OboToModel conversion from
> /home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo
> to
> /home/intermine/build/ratmine_current/ratmine/dbmodel/build/model/so_add
> itions.xml.  Filtering on 19 obo terms from
> /home/intermine/build/ratmine_current/ratmine/dbmodel/resources/so_term_
> list.txt
>
> BUILD FAILED
> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:9:
> java.lang.RuntimeException: The following terms specified in
> so_term_list.txt are not valid Sequence Ontology terms according to:
> /home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo:
> Allele, SSLP, Gene, Exon, SequenceVariant, Transcript, Chromosome,
> SequenceFeature, Probe, Strain, Genotype, IntergenicRegion,
> SequenceCollection, Sequence and Protein
>         at
> org.intermine.bio.ontology.OboToModelProcessor.validateTermsToKeep(OboTo
> ModelProcessor.java:629)
>         at
> org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:259)
>         at
> org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.jav
> a:98)
>         at
> org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68)
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 06)
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>         at org.apache.tools.ant.Target.execute(Target.java:390)
>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>         at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>         at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 10:54 AM
> To: Vallejos, Andrew
> Subject: Re: [InterMine Dev] Update Proccess...
>
> Can you send me ratmine/dbmodel/project.properties?
>
> Vallejos, Andrew wrote:
>> Here is the build file.  Sorry for the double email, but that's what I
> get for using two computers.  
>> -----Original Message-----
>> From: Julie Sullivan [mailto:[hidden email]]
>> Sent: Wed 10/6/2010 10:09 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] Update Proccess...
>>  
>> What does your build file (ratmine/dbmodel/build.xml) look like?  I'm
> thinking
>> the script mucked it up.  The script is supposed to add the ant task,
> but since
>> it broke I bet the script added that ant task twice.
>>
>> The build file should look like this:
>>
>> <project name="flymine-dbmodel" default="default" basedir=".">
>>
>>    <description>represents the production objectstore and the model
>> therein</description>
>>    <import file="../../imbuild/objectstore.xml"/>
>>
>>    <target name="create-so-model" depends="init, -init-deps">
>>      <taskdef name="so-model"
> classname="org.intermine.bio.task.SOToModelTask">
>>        <classpath refid="task.class.path"/>
>>      </taskdef>
>>      <so-model
>>         soTermListFile="${so.termlist.file}"
>>         soFile="${so.obo.file}"
>>         outputFile="${so.output.file}"/>
>>    </target>
>>
>>    <target name="-pre-init-merge" depends="create-so-model"/>
>>
>> </project>
>>
>> Can you verify that's what your build file looks like?  Or just send
> it to me?
>> Vallejos, Andrew wrote:
>>> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:3:
>>> Reference task.class.path not found.
>>>         at
>>>
> org.apache.tools.ant.types.Reference.getReferencedObject(Reference.java:
>>> 115)
>>>         at
>>>
> org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
>>> :144)
>>>         at
>>> org.apache.tools.ant.types.Path.dieOnCircularReference(Path.java:491)
>>>         at
>>>
> org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
>>> :115)
>>>         at
>>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:248)
>>>         at
>>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:214)
>>>         at
>>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:202)
>>>         at
>>> org.apache.tools.ant.types.Path.isFilesystemOnly(Path.java:714)
>>>         at
>>>
> org.apache.tools.ant.types.resources.BaseResourceCollectionContainer.isF
>>> ilesystemOnly(BaseResourceCollectionContainer.java:169)
>>>         at
>>> org.apache.tools.ant.types.Path.assertFilesystemOnly(Path.java:728)
>>>         at org.apache.tools.ant.types.Path.list(Path.java:372)
>>>         at org.apache.tools.ant.types.Path.addExisting(Path.java:331)
>>>         at org.apache.tools.ant.types.Path.addExisting(Path.java:319)
>>>         at
>>> org.apache.tools.ant.types.Path.concatSpecialPath(Path.java:566)
>>>         at
>>> org.apache.tools.ant.types.Path.concatSystemClasspath(Path.java:526)
>>>         at
>>>
> org.apache.tools.ant.AntClassLoader.setClassPath(AntClassLoader.java:351
>>> )
>>>         at
>>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:265)
>>>         at
>>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:286)
>>>         at
>>>
> org.apache.tools.ant.loader.AntClassLoader5.<init>(AntClassLoader5.java:
>>> 49)
>>>         at
>>> sun.reflect.GeneratedConstructorAccessor13.newInstance(Unknown
> Source)
>>>         at
>>>
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
>>> tructorAccessorImpl.java:27)
>>>         at
>>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>>         at
>>>
> org.apache.tools.ant.util.ReflectUtil.newInstance(ReflectUtil.java:49)
>>>         at
>>>
> org.apache.tools.ant.AntClassLoader.newAntClassLoader(AntClassLoader.jav
>>> a:1551)
>>>         at
>>> org.apache.tools.ant.Project.createClassLoader(Project.java:339)
>>>         at
>>>
> org.apache.tools.ant.util.ClasspathUtils.getUniqueClassLoaderForPath(Cla
>>> sspathUtils.java:206)
>>>         at
>>>
> org.apache.tools.ant.util.ClasspathUtils.getClassLoaderForPath(Classpath
>>> Utils.java:183)
>>>         at
>>>
> org.apache.tools.ant.util.ClasspathUtils$Delegate.getClassLoader(Classpa
>>> thUtils.java:411)
>>>         at
>>> org.apache.tools.ant.taskdefs.DefBase.createLoader(DefBase.java:142)
>>>         at
>>> org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:208)
>>>         at
>>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
> Source)
>>>         at
>>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>> Impl.java:25)
>>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>>         at
>>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>>> 06)
>>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>         at
>>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>         at
> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>         at
>>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>>> or.java:41)
>>>         at
>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>         at
> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>         at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>> Total time: 2 seconds
>>> -----Original Message-----
>>> From: Julie Sullivan [mailto:[hidden email]]
>>> Sent: Wednesday, October 06, 2010 9:41 AM
>>> To: Vallejos, Andrew
>>> Cc: [hidden email]
>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>
>>> What happens when you run this in ratmine/dbmodel:
>>>
>>> ant create-so-model -v
>>>
>>> Do you get an error?  Do you get something like this in your
> terminal?
>>>   [so-model] Starting OboToModel conversion from
>>> /home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
>>> /home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.
>>> Filtering on
>>> 47 obo terms from
>>> /home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt
>>>
>>> The SO file generated will be placed here:
>>>
>>> ratmine/dbmodel/build/model/so_additions.xml
>>>
>>>
>>>
>>> Vallejos, Andrew wrote:
>>>> Alright, I created a so_terms_list.txt file, and went through the
>>> steps
>>>> again.  I am still lacking a so_additions.xml file.
>>>>
>>>> -----Original Message-----
>>>> From: Julie Sullivan [mailto:[hidden email]]
>>>> Sent: Wednesday, October 06, 2010 4:19 AM
>>>> To: Vallejos, Andrew
>>>> Cc: [hidden email]
>>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>>
>>>> That sounds like your model is not being merged correctly.  Gene
> gets
>>>> primaryIdentifier from the so_additions.xml file.
>>>>
>>>> Do you have that file?
>>>>
>>>> dbmodel/build/model/so_additions.xml
>>>>
>>>> If not, try to run Step #8 again:
>>>>
>>>> ./update_to_0.94 build
>>>>
>>>> That will update your build.xml file so that the SO additions file
> is
>>>> created as
>>>> part of "build-db".  Then try again to run build-db again?
>>>>
>>>> Let me know if that doesn't work.
>>>>
>>>> Vallejos, Andrew wrote:
>>>>> Alright, so I am up to step 10, and I am trying to build the model.
>>>>> However, it keeps complaining:
>>>>>
>>>>>  
>>>>>
>>>>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>>>>> java.lang.IllegalArgumentException: No such field name
>>>> primaryIdentifier
>>>>> in class org.intermine.model.bio.Gene for primary key
>>>>> key_primaryidentifier
>>>>>
>>>>>         at
>>>> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>>>>         at
>>>>>
> org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>>>>> :65)
>>>>>
>>>>>         at
>>>>>
> org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>>>>> dexesTask.java:409)
>>>>>
>>>>>         at
>>>>>
> org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>>>>         at
>>>>>
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>>> Source)
>>>>>         at
>>>>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>>>> Impl.java:25)
>>>>>
>>>>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>>>>
>>>>>         at
>>>>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>>>>> 06)
>>>>>
>>>>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>>>>
>>>>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>>>>
>>>>>         at
> org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>>>         at
>>>>>
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>>>         at
>>>> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>>>         at
>>>>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>>>>> or.java:41)
>>>>>
>>>>>         at
>>>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>>>
>>>>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>>>
>>>>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>>>
>>>>>         at
>>> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>>>         at
>>>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>>>>  
>>>>>
>>>>> I keep commenting out the offending key, but it just picks another
>>>> one.
>>>>> I've updated a couple of the keys that I noticed needed updating
> from
>>>>> the core model updates page.
>>>>>
>>>>>  
>>>>>
>>>>> ======================
>>>>>
>>>>> Andrew Vallejos
>>>>>
>>>>> Web Developer II
>>>>>
>>>>> Biotechnology and Bioengineering Center
>>>>>
>>>>> Medical College of Wisconsin
>>>>>
>>>>> 414-955-4104
>>>>>
>>>>> [hidden email]
>>>>>
>>>>>  
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
> ------------------------------------------------------------------------
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Vallejos, Andrew
Thanks Julie, Richard, Kalpana, and whomever else I am forgetting.  I
finally got RatMine to build.  

Now to see how many of my sources I can actually get to integrate...

-Andrew

-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Wednesday, October 06, 2010 11:58 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] Update Proccess...

Yes, sorry.  Here are the naming conventions for SO:

        * lower case
        * underscores between words
        * eg. sequenceFeature

Check sequenceontology.org for the exact term names.
       

Vallejos, Andrew wrote:

> Oh...looking at FlyMine, it looks like the list should not be
> capitalized.
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On
> Behalf Of Vallejos, Andrew
> Sent: Wednesday, October 06, 2010 11:47 AM
> To: Julie Sullivan
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> Current error:
>
> create-so-model:
>  [so-model] Starting OboToModel conversion from
> /home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo
> to
>
/home/intermine/build/ratmine_current/ratmine/dbmodel/build/model/so_add
> itions.xml.  Filtering on 19 obo terms from
>
/home/intermine/build/ratmine_current/ratmine/dbmodel/resources/so_term_
> list.txt
>
> BUILD FAILED
> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:9:
> java.lang.RuntimeException: The following terms specified in
> so_term_list.txt are not valid Sequence Ontology terms according to:
>
/home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo:
> Allele, SSLP, Gene, Exon, SequenceVariant, Transcript, Chromosome,
> SequenceFeature, Probe, Strain, Genotype, IntergenicRegion,
> SequenceCollection, Sequence and Protein
>         at
>
org.intermine.bio.ontology.OboToModelProcessor.validateTermsToKeep(OboTo
> ModelProcessor.java:629)
>         at
>
org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:259)
>         at
>
org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.jav
> a:98)
>         at
> org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68)
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 06)
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>         at org.apache.tools.ant.Target.execute(Target.java:390)
>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>         at
org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>         at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>         at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

>
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 10:54 AM
> To: Vallejos, Andrew
> Subject: Re: [InterMine Dev] Update Proccess...
>
> Can you send me ratmine/dbmodel/project.properties?
>
> Vallejos, Andrew wrote:
>> Here is the build file.  Sorry for the double email, but that's what
I

> get for using two computers.  
>> -----Original Message-----
>> From: Julie Sullivan [mailto:[hidden email]]
>> Sent: Wed 10/6/2010 10:09 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] Update Proccess...
>>  
>> What does your build file (ratmine/dbmodel/build.xml) look like?  I'm
> thinking
>> the script mucked it up.  The script is supposed to add the ant task,
> but since
>> it broke I bet the script added that ant task twice.
>>
>> The build file should look like this:
>>
>> <project name="flymine-dbmodel" default="default" basedir=".">
>>
>>    <description>represents the production objectstore and the model
>> therein</description>
>>    <import file="../../imbuild/objectstore.xml"/>
>>
>>    <target name="create-so-model" depends="init, -init-deps">
>>      <taskdef name="so-model"
> classname="org.intermine.bio.task.SOToModelTask">
>>        <classpath refid="task.class.path"/>
>>      </taskdef>
>>      <so-model
>>         soTermListFile="${so.termlist.file}"
>>         soFile="${so.obo.file}"
>>         outputFile="${so.output.file}"/>
>>    </target>
>>
>>    <target name="-pre-init-merge" depends="create-so-model"/>
>>
>> </project>
>>
>> Can you verify that's what your build file looks like?  Or just send
> it to me?
>> Vallejos, Andrew wrote:
>>> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:3:
>>> Reference task.class.path not found.
>>>         at
>>>
>
org.apache.tools.ant.types.Reference.getReferencedObject(Reference.java:
>>> 115)
>>>         at
>>>
>
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
>>> :144)
>>>         at
>>>
org.apache.tools.ant.types.Path.dieOnCircularReference(Path.java:491)
>>>         at
>>>
>
org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java

>>> :115)
>>>         at
>>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:248)
>>>         at
>>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:214)
>>>         at
>>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:202)
>>>         at
>>> org.apache.tools.ant.types.Path.isFilesystemOnly(Path.java:714)
>>>         at
>>>
>
org.apache.tools.ant.types.resources.BaseResourceCollectionContainer.isF
>>> ilesystemOnly(BaseResourceCollectionContainer.java:169)
>>>         at
>>> org.apache.tools.ant.types.Path.assertFilesystemOnly(Path.java:728)
>>>         at org.apache.tools.ant.types.Path.list(Path.java:372)
>>>         at
org.apache.tools.ant.types.Path.addExisting(Path.java:331)
>>>         at
org.apache.tools.ant.types.Path.addExisting(Path.java:319)
>>>         at
>>> org.apache.tools.ant.types.Path.concatSpecialPath(Path.java:566)
>>>         at
>>> org.apache.tools.ant.types.Path.concatSystemClasspath(Path.java:526)
>>>         at
>>>
>
org.apache.tools.ant.AntClassLoader.setClassPath(AntClassLoader.java:351
>>> )
>>>         at
>>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:265)
>>>         at
>>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:286)
>>>         at
>>>
>
org.apache.tools.ant.loader.AntClassLoader5.<init>(AntClassLoader5.java:
>>> 49)
>>>         at
>>> sun.reflect.GeneratedConstructorAccessor13.newInstance(Unknown
> Source)
>>>         at
>>>
>
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
>>> tructorAccessorImpl.java:27)
>>>         at
>>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>>         at
>>>
> org.apache.tools.ant.util.ReflectUtil.newInstance(ReflectUtil.java:49)
>>>         at
>>>
>
org.apache.tools.ant.AntClassLoader.newAntClassLoader(AntClassLoader.jav
>>> a:1551)
>>>         at
>>> org.apache.tools.ant.Project.createClassLoader(Project.java:339)
>>>         at
>>>
>
org.apache.tools.ant.util.ClasspathUtils.getUniqueClassLoaderForPath(Cla
>>> sspathUtils.java:206)
>>>         at
>>>
>
org.apache.tools.ant.util.ClasspathUtils.getClassLoaderForPath(Classpath
>>> Utils.java:183)
>>>         at
>>>
>
org.apache.tools.ant.util.ClasspathUtils$Delegate.getClassLoader(Classpa

>>> thUtils.java:411)
>>>         at
>>> org.apache.tools.ant.taskdefs.DefBase.createLoader(DefBase.java:142)
>>>         at
>>> org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:208)
>>>         at
>>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
> Source)
>>>         at
>>>
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>> Impl.java:25)
>>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>>         at
>>>
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1

>>> 06)
>>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>         at
>>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>         at
> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>         at
>>>
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

>>> or.java:41)
>>>         at
>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>         at
> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>         at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>> Total time: 2 seconds
>>> -----Original Message-----
>>> From: Julie Sullivan [mailto:[hidden email]]
>>> Sent: Wednesday, October 06, 2010 9:41 AM
>>> To: Vallejos, Andrew
>>> Cc: [hidden email]
>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>
>>> What happens when you run this in ratmine/dbmodel:
>>>
>>> ant create-so-model -v
>>>
>>> Do you get an error?  Do you get something like this in your
> terminal?
>>>   [so-model] Starting OboToModel conversion from
>>> /home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
>>> /home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.
>>> Filtering on
>>> 47 obo terms from
>>> /home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt
>>>
>>> The SO file generated will be placed here:
>>>
>>> ratmine/dbmodel/build/model/so_additions.xml
>>>
>>>
>>>
>>> Vallejos, Andrew wrote:
>>>> Alright, I created a so_terms_list.txt file, and went through the
>>> steps
>>>> again.  I am still lacking a so_additions.xml file.
>>>>
>>>> -----Original Message-----
>>>> From: Julie Sullivan [mailto:[hidden email]]
>>>> Sent: Wednesday, October 06, 2010 4:19 AM
>>>> To: Vallejos, Andrew
>>>> Cc: [hidden email]
>>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>>
>>>> That sounds like your model is not being merged correctly.  Gene
> gets
>>>> primaryIdentifier from the so_additions.xml file.
>>>>
>>>> Do you have that file?
>>>>
>>>> dbmodel/build/model/so_additions.xml
>>>>
>>>> If not, try to run Step #8 again:
>>>>
>>>> ./update_to_0.94 build
>>>>
>>>> That will update your build.xml file so that the SO additions file
> is
>>>> created as
>>>> part of "build-db".  Then try again to run build-db again?
>>>>
>>>> Let me know if that doesn't work.
>>>>
>>>> Vallejos, Andrew wrote:
>>>>> Alright, so I am up to step 10, and I am trying to build the
model.

>>>>> However, it keeps complaining:
>>>>>
>>>>>  
>>>>>
>>>>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>>>>> java.lang.IllegalArgumentException: No such field name
>>>> primaryIdentifier
>>>>> in class org.intermine.model.bio.Gene for primary key
>>>>> key_primaryidentifier
>>>>>
>>>>>         at
>>>> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>>>>         at
>>>>>
>
org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>>>>> :65)
>>>>>
>>>>>         at
>>>>>
>
org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>>>>> dexesTask.java:409)
>>>>>
>>>>>         at
>>>>>
>
org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>>>>         at
>>>>>
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>>> Source)
>>>>>         at
>>>>>
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>>>> Impl.java:25)
>>>>>
>>>>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>>>>
>>>>>         at
>>>>>
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1

>>>>> 06)
>>>>>
>>>>>         at org.apache.tools.ant.Task.perform(Task.java:348)
>>>>>
>>>>>         at org.apache.tools.ant.Target.execute(Target.java:390)
>>>>>
>>>>>         at
> org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>>>         at
>>>>>
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>>>         at
>>>> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>>>         at
>>>>>
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

>>>>> or.java:41)
>>>>>
>>>>>         at
>>>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>>>
>>>>>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>>>
>>>>>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>>>
>>>>>         at
>>> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>>>         at
>>>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>>>>  
>>>>>
>>>>> I keep commenting out the offending key, but it just picks another
>>>> one.
>>>>> I've updated a couple of the keys that I noticed needed updating
> from
>>>>> the core model updates page.
>>>>>
>>>>>  
>>>>>
>>>>> ======================
>>>>>
>>>>> Andrew Vallejos
>>>>>
>>>>> Web Developer II
>>>>>
>>>>> Biotechnology and Bioengineering Center
>>>>>
>>>>> Medical College of Wisconsin
>>>>>
>>>>> 414-955-4104
>>>>>
>>>>> [hidden email]
>>>>>
>>>>>  
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>
------------------------------------------------------------------------

>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Update Proccess...

Richard Smith
Great stuff!

Richard.



On 06/10/2010 20:07, Vallejos, Andrew wrote:

> Thanks Julie, Richard, Kalpana, and whomever else I am forgetting.  I
> finally got RatMine to build.
>
> Now to see how many of my sources I can actually get to integrate...
>
> -Andrew
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Wednesday, October 06, 2010 11:58 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Update Proccess...
>
> Yes, sorry.  Here are the naming conventions for SO:
>
> * lower case
> * underscores between words
> * eg. sequenceFeature
>
> Check sequenceontology.org for the exact term names.
>
>
> Vallejos, Andrew wrote:
>> Oh...looking at FlyMine, it looks like the list should not be
>> capitalized.
>>
>> -----Original Message-----
>> From: [hidden email] [mailto:[hidden email]] On
>> Behalf Of Vallejos, Andrew
>> Sent: Wednesday, October 06, 2010 11:47 AM
>> To: Julie Sullivan
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] Update Proccess...
>>
>> Current error:
>>
>> create-so-model:
>>   [so-model] Starting OboToModel conversion from
>> /home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo
>> to
>>
> /home/intermine/build/ratmine_current/ratmine/dbmodel/build/model/so_add
>> itions.xml.  Filtering on 19 obo terms from
>>
> /home/intermine/build/ratmine_current/ratmine/dbmodel/resources/so_term_
>> list.txt
>>
>> BUILD FAILED
>> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:9:
>> java.lang.RuntimeException: The following terms specified in
>> so_term_list.txt are not valid Sequence Ontology terms according to:
>>
> /home/intermine/build/ratmine_current/bio/sources/so/data/so_2_4_2.obo:
>> Allele, SSLP, Gene, Exon, SequenceVariant, Transcript, Chromosome,
>> SequenceFeature, Probe, Strain, Genotype, IntergenicRegion,
>> SequenceCollection, Sequence and Protein
>>          at
>>
> org.intermine.bio.ontology.OboToModelProcessor.validateTermsToKeep(OboTo
>> ModelProcessor.java:629)
>>          at
>>
> org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:259)
>>          at
>>
> org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.jav
>> a:98)
>>          at
>> org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68)
>>          at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>          at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>          at
>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>          at
>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>> 06)
>>          at org.apache.tools.ant.Task.perform(Task.java:348)
>>          at org.apache.tools.ant.Target.execute(Target.java:390)
>>          at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>          at
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>          at
> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>          at
>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>> or.java:41)
>>          at
>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>          at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>          at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>          at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>          at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>
>>
>> -----Original Message-----
>> From: Julie Sullivan [mailto:[hidden email]]
>> Sent: Wednesday, October 06, 2010 10:54 AM
>> To: Vallejos, Andrew
>> Subject: Re: [InterMine Dev] Update Proccess...
>>
>> Can you send me ratmine/dbmodel/project.properties?
>>
>> Vallejos, Andrew wrote:
>>> Here is the build file.  Sorry for the double email, but that's what
> I
>> get for using two computers.
>>> -----Original Message-----
>>> From: Julie Sullivan [mailto:[hidden email]]
>>> Sent: Wed 10/6/2010 10:09 AM
>>> To: Vallejos, Andrew
>>> Cc: [hidden email]
>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>
>>> What does your build file (ratmine/dbmodel/build.xml) look like?  I'm
>> thinking
>>> the script mucked it up.  The script is supposed to add the ant task,
>> but since
>>> it broke I bet the script added that ant task twice.
>>>
>>> The build file should look like this:
>>>
>>> <project name="flymine-dbmodel" default="default" basedir=".">
>>>
>>>     <description>represents the production objectstore and the model
>>> therein</description>
>>>     <import file="../../imbuild/objectstore.xml"/>
>>>
>>>     <target name="create-so-model" depends="init, -init-deps">
>>>       <taskdef name="so-model"
>> classname="org.intermine.bio.task.SOToModelTask">
>>>         <classpath refid="task.class.path"/>
>>>       </taskdef>
>>>       <so-model
>>>          soTermListFile="${so.termlist.file}"
>>>          soFile="${so.obo.file}"
>>>          outputFile="${so.output.file}"/>
>>>     </target>
>>>
>>>     <target name="-pre-init-merge" depends="create-so-model"/>
>>>
>>> </project>
>>>
>>> Can you verify that's what your build file looks like?  Or just send
>> it to me?
>>> Vallejos, Andrew wrote:
>>>> /home/intermine/build/ratmine_current/ratmine/dbmodel/build.xml:3:
>>>> Reference task.class.path not found.
>>>>          at
>>>>
>>
> org.apache.tools.ant.types.Reference.getReferencedObject(Reference.java:
>>>> 115)
>>>>          at
>>>>
>>
> org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
>>>> :144)
>>>>          at
>>>>
> org.apache.tools.ant.types.Path.dieOnCircularReference(Path.java:491)
>>>>          at
>>>>
>>
> org.apache.tools.ant.types.DataType.dieOnCircularReference(DataType.java
>>>> :115)
>>>>          at
>>>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:248)
>>>>          at
>>>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:214)
>>>>          at
>>>> org.apache.tools.ant.types.DataType.getCheckedRef(DataType.java:202)
>>>>          at
>>>> org.apache.tools.ant.types.Path.isFilesystemOnly(Path.java:714)
>>>>          at
>>>>
>>
> org.apache.tools.ant.types.resources.BaseResourceCollectionContainer.isF
>>>> ilesystemOnly(BaseResourceCollectionContainer.java:169)
>>>>          at
>>>> org.apache.tools.ant.types.Path.assertFilesystemOnly(Path.java:728)
>>>>          at org.apache.tools.ant.types.Path.list(Path.java:372)
>>>>          at
> org.apache.tools.ant.types.Path.addExisting(Path.java:331)
>>>>          at
> org.apache.tools.ant.types.Path.addExisting(Path.java:319)
>>>>          at
>>>> org.apache.tools.ant.types.Path.concatSpecialPath(Path.java:566)
>>>>          at
>>>> org.apache.tools.ant.types.Path.concatSystemClasspath(Path.java:526)
>>>>          at
>>>>
>>
> org.apache.tools.ant.AntClassLoader.setClassPath(AntClassLoader.java:351
>>>> )
>>>>          at
>>>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:265)
>>>>          at
>>>> org.apache.tools.ant.AntClassLoader.<init>(AntClassLoader.java:286)
>>>>          at
>>>>
>>
> org.apache.tools.ant.loader.AntClassLoader5.<init>(AntClassLoader5.java:
>>>> 49)
>>>>          at
>>>> sun.reflect.GeneratedConstructorAccessor13.newInstance(Unknown
>> Source)
>>>>          at
>>>>
>>
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
>>>> tructorAccessorImpl.java:27)
>>>>          at
>>>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>>>          at
>>>>
>> org.apache.tools.ant.util.ReflectUtil.newInstance(ReflectUtil.java:49)
>>>>          at
>>>>
>>
> org.apache.tools.ant.AntClassLoader.newAntClassLoader(AntClassLoader.jav
>>>> a:1551)
>>>>          at
>>>> org.apache.tools.ant.Project.createClassLoader(Project.java:339)
>>>>          at
>>>>
>>
> org.apache.tools.ant.util.ClasspathUtils.getUniqueClassLoaderForPath(Cla
>>>> sspathUtils.java:206)
>>>>          at
>>>>
>>
> org.apache.tools.ant.util.ClasspathUtils.getClassLoaderForPath(Classpath
>>>> Utils.java:183)
>>>>          at
>>>>
>>
> org.apache.tools.ant.util.ClasspathUtils$Delegate.getClassLoader(Classpa
>>>> thUtils.java:411)
>>>>          at
>>>> org.apache.tools.ant.taskdefs.DefBase.createLoader(DefBase.java:142)
>>>>          at
>>>> org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:208)
>>>>          at
>>>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>>          at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>> Source)
>>>>          at
>>>>
>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>>> Impl.java:25)
>>>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>>>          at
>>>>
>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>>>> 06)
>>>>          at org.apache.tools.ant.Task.perform(Task.java:348)
>>>>          at org.apache.tools.ant.Target.execute(Target.java:390)
>>>>          at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>>          at
>>>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>>          at
>> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>>          at
>>>>
>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>>>> or.java:41)
>>>>          at
>>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>>          at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>>          at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>>          at
>> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>>          at
>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>>> Total time: 2 seconds
>>>> -----Original Message-----
>>>> From: Julie Sullivan [mailto:[hidden email]]
>>>> Sent: Wednesday, October 06, 2010 9:41 AM
>>>> To: Vallejos, Andrew
>>>> Cc: [hidden email]
>>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>>
>>>> What happens when you run this in ratmine/dbmodel:
>>>>
>>>> ant create-so-model -v
>>>>
>>>> Do you get an error?  Do you get something like this in your
>> terminal?
>>>>    [so-model] Starting OboToModel conversion from
>>>> /home/julie/svn/dev/bio/sources/so/data/so_2_4_2.obo to
>>>> /home/julie/svn/dev/flymine/dbmodel/build/model/so_additions.xml.
>>>> Filtering on
>>>> 47 obo terms from
>>>> /home/julie/svn/dev/flymine/dbmodel/resources/so_term_list.txt
>>>>
>>>> The SO file generated will be placed here:
>>>>
>>>> ratmine/dbmodel/build/model/so_additions.xml
>>>>
>>>>
>>>>
>>>> Vallejos, Andrew wrote:
>>>>> Alright, I created a so_terms_list.txt file, and went through the
>>>> steps
>>>>> again.  I am still lacking a so_additions.xml file.
>>>>>
>>>>> -----Original Message-----
>>>>> From: Julie Sullivan [mailto:[hidden email]]
>>>>> Sent: Wednesday, October 06, 2010 4:19 AM
>>>>> To: Vallejos, Andrew
>>>>> Cc: [hidden email]
>>>>> Subject: Re: [InterMine Dev] Update Proccess...
>>>>>
>>>>> That sounds like your model is not being merged correctly.  Gene
>> gets
>>>>> primaryIdentifier from the so_additions.xml file.
>>>>>
>>>>> Do you have that file?
>>>>>
>>>>> dbmodel/build/model/so_additions.xml
>>>>>
>>>>> If not, try to run Step #8 again:
>>>>>
>>>>> ./update_to_0.94 build
>>>>>
>>>>> That will update your build.xml file so that the SO additions file
>> is
>>>>> created as
>>>>> part of "build-db".  Then try again to run build-db again?
>>>>>
>>>>> Let me know if that doesn't work.
>>>>>
>>>>> Vallejos, Andrew wrote:
>>>>>> Alright, so I am up to step 10, and I am trying to build the
> model.
>>>>>> However, it keeps complaining:
>>>>>>
>>>>>>
>>>>>>
>>>>>> /home/intermine/build/ratmine_current/imbuild/objectstore.xml:52:
>>>>>> java.lang.IllegalArgumentException: No such field name
>>>>> primaryIdentifier
>>>>>> in class org.intermine.model.bio.Gene for primary key
>>>>>> key_primaryidentifier
>>>>>>
>>>>>>          at
>>>>> org.intermine.metadata.PrimaryKey.<init>(PrimaryKey.java:45)
>>>>>>          at
>>>>>>
>>
> org.intermine.metadata.PrimaryKeyUtil.getPrimaryKeys(PrimaryKeyUtil.java
>>>>>> :65)
>>>>>>
>>>>>>          at
>>>>>>
>>
> org.intermine.task.CreateIndexesTask.getStandardIndexStatements(CreateIn
>>>>>> dexesTask.java:409)
>>>>>>
>>>>>>          at
>>>>>>
>>
> org.intermine.task.CreateIndexesTask.execute(CreateIndexesTask.java:173)
>>>>>>          at
>>>>>>
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>>>>          at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>>>> Source)
>>>>>>          at
>>>>>>
>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>>>>>> Impl.java:25)
>>>>>>
>>>>>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>>>>>
>>>>>>          at
>>>>>>
>>
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
>>>>>> 06)
>>>>>>
>>>>>>          at org.apache.tools.ant.Task.perform(Task.java:348)
>>>>>>
>>>>>>          at org.apache.tools.ant.Target.execute(Target.java:390)
>>>>>>
>>>>>>          at
>> org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>>>>          at
>>>>>>
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>>>>          at
>>>>> org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>>>>          at
>>>>>>
>>
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
>>>>>> or.java:41)
>>>>>>
>>>>>>          at
>>>>>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>>>>
>>>>>>          at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>>>>
>>>>>>          at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>>>>
>>>>>>          at
>>>> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>>>>          at
>>>>> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>>>>>
>>>>>>
>>>>>> I keep commenting out the offending key, but it just picks another
>>>>> one.
>>>>>> I've updated a couple of the keys that I noticed needed updating
>> from
>>>>>> the core model updates page.
>>>>>>
>>>>>>
>>>>>>
>>>>>> ======================
>>>>>>
>>>>>> Andrew Vallejos
>>>>>>
>>>>>> Web Developer II
>>>>>>
>>>>>> Biotechnology and Bioengineering Center
>>>>>>
>>>>>> Medical College of Wisconsin
>>>>>>
>>>>>> 414-955-4104
>>>>>>
>>>>>> [hidden email]
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>
> ------------------------------------------------------------------------
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email]
>>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev