[Fwd: Re: Upgrade_094 Update..]

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[Fwd: Re: Upgrade_094 Update..]

Julie Sullivan


Kalpana Karra wrote:
> Hi,
>
> Some notes..
>
> 1) For the SO addition stuff to work for me.   I had to edit so_2_4_2.obo to remove the extra space in Y_prime_element (there was a space in front of element)

I'll email the SO people.

> 2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in sgd_additions file.

The SO file we are using was generated 12 April and that term was added to SO 21
April.

> 3) Had to comment out class MRNA in genomic_additions.xml (was causing merging error due to fivePrimeUTR in my model)

I have made this change also, do an "svn update" and you should get the
corrected file.

> 4) To get over errors in Step 10  ant -Drelease=dev clean build-db -v
>
>     - Had to edit class_keys to change to
>          DataSet = name
>        Ontology.key_name=name  (was title)
>
>     - Had to edit genomic_keyDefs to
>         remove 'source' from Comment
>         remove 'type' from Synonym
>
>     -  Had to comment out
>        #Chromosome.key_primaryidentifier = primaryIdentifier, organism
>        #Location.key_all = subject, object, end, start, strand, startIsPartial, endIsPartial
>
>     - Had to add -- Gene extends BioEntity -- (it is not defined in core as suggested)
>
> I am not sure if all of the above was necessary, but, thats what I had to to to keep moving. I did get a successful build at Step 10. after that.
>

Yes, this is correct.  Sorry for the confusion.

> 5) Step 11: For the > ./update_to_0.94 paths
>
> 1)  The script gave me errors and failed. I had to print the file it was processing in path_updater.pl (after line 806) to see which file it did not like.

  Turns out it did not like commented out classes in my webconfig-model.xml.

Thanks for the note.  Alex, can you print out the file being processed like
Kalpana did for debugging purposes?  Also, can you ignore commented out classes?

> 2) Lastly, I got the error below. So, I copied datasets.xml file from flymine and commented out a major chunk and ran the paths task and it finished without errors!
>
>
> Cannot open /Users/kkarra/Dev/intermine_src/intermine_0_94/yeastmine/integrate/datasets.xml, No such file or directory - skipping
>  at path_updater.pl line 8
> main::__ANON__('\x{d}Cannot open /Users/kkarra/Dev/intermine_src/intermine_0_94/y...') called at path_updater.pl line 799
> Processing element       1676Path update failed 512 at ./update_to_0.94 line 55.
>
>
> I am stopping at this point (Step 11).
>

I see this error:
Cannot open
/Users/kkarra/Dev/intermine_src/intermine_0_94/yeastmine/integrate/datasets.xml

If you don't have that file, then remove it from the config.  Then the script
won't process that file.  I'm not sure that's the issue though.

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


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Re: [Fwd: Re: Upgrade_094 Update..]

Alex Kalderimis
On Wed, Oct 06, 2010 at 04:43:24PM +0100, Julie Sullivan wrote:

>
>
> Kalpana Karra wrote:
> >Hi,
> >
> >Some notes..
> >
> >1) For the SO addition stuff to work for me.   I had to edit so_2_4_2.obo to remove the extra space in Y_prime_element (there was a space in front of element)
>
> I'll email the SO people.
>
> >2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in sgd_additions file.
>
> The SO file we are using was generated 12 April and that term was added to SO 21
> April.
>
> >3) Had to comment out class MRNA in genomic_additions.xml (was causing merging error due to fivePrimeUTR in my model)
>
> I have made this change also, do an "svn update" and you should get the
> corrected file.
>
> >4) To get over errors in Step 10  ant -Drelease=dev clean build-db -v
> >
> >    - Had to edit class_keys to change to          DataSet = name
> >       Ontology.key_name=name  (was title)
> >
> >    - Had to edit genomic_keyDefs to         remove 'source' from
> >Comment
> >        remove 'type' from Synonym
> >
> >    -  Had to comment out        #Chromosome.key_primaryidentifier
> >= primaryIdentifier, organism
> >       #Location.key_all = subject, object, end, start, strand, startIsPartial, endIsPartial
> >
> >    - Had to add -- Gene extends BioEntity -- (it is not defined in core as suggested)
> >
> >I am not sure if all of the above was necessary, but, thats what I had to to to keep moving. I did get a successful build at Step 10. after that.
> >
>
> Yes, this is correct.  Sorry for the confusion.
>
> >5) Step 11: For the > ./update_to_0.94 paths
> >
> >1)  The script gave me errors and failed. I had to print the file
> >it was processing in path_updater.pl (after line 806) to see which
> >file it did not like.
>
>  Turns out it did not like commented out classes in my webconfig-model.xml.
>
> Thanks for the note.  Alex, can you print out the file being processed like
> Kalpana did for debugging purposes?  Also, can you ignore commented out classes?
>

Sure thing. I'll try and get it to ignore commented out xml sections.

As for printing the file, I assume you mean the file name?

Alex

> >2) Lastly, I got the error below. So, I copied datasets.xml file from flymine and commented out a major chunk and ran the paths task and it finished without errors!
> >
> >
> >Cannot open /Users/kkarra/Dev/intermine_src/intermine_0_94/yeastmine/integrate/datasets.xml, No such file or directory - skipping
> > at path_updater.pl line 8
> > main::__ANON__('\x{d}Cannot open /Users/kkarra/Dev/intermine_src/intermine_0_94/y...') called at path_updater.pl line 799
> >Processing element       1676Path update failed 512 at ./update_to_0.94 line 55.
> >
> >
> >I am stopping at this point (Step 11).
> >
>
> I see this error:
> Cannot open
> /Users/kkarra/Dev/intermine_src/intermine_0_94/yeastmine/integrate/datasets.xml
>
> If you don't have that file, then remove it from the config.  Then the script
> won't process that file.  I'm not sure that's the issue though.
>
> >-Kalpana
> >
> >
> >
> >
> >
> >
> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >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