Upgrade_094 Update..

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Upgrade_094 Update..

kkarra@stanford.edu
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)

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

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

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.


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.

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).


-Kalpana





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Re: Upgrade_094 Update..

Vallejos, Andrew

I received a similar error message.

 

[intermine@stearman scripts]$ perl update_to_0.94 paths

Cannot open /home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml, No such file or directory - skipping

 at path_updater.pl line 8

        main::__ANON__('\x{d}Cannot open /home/intermine/build/ratmine_current/ratmine/in...') called at path_updater.pl line 798

Processing element        740Path update failed 512 at update_to_0.94 line 57.

 

Any word on the cause?

 

-Andrew


From: [hidden email] [mailto:[hidden email]] On Behalf Of Kalpana Karra
Sent: Tuesday, October 05, 2010 4:53 PM
To: Intermine
Subject: [InterMine Dev] Upgrade_094 Update..

 

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)

 

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

 

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

 

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.

 

 

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.

 

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).

 

 

-Kalpana

 

 

 

 


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Re: Upgrade_094 Update..

kkarra@stanford.edu
<base href="x-msg://2/">

Julie says to remove it from the updater.config file...
>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.
~/svn/intermine/scripts/resources/updater.config


On Oct 6, 2010, at 1:24 PM, Vallejos, Andrew wrote:

I received a similar error message.
 
[intermine@stearman scripts]$ perl update_to_0.94 paths
Cannot open /home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml, No such file or directory - skipping
 at path_updater.pl line 8
        main::__ANON__('\x{d}Cannot open /home/intermine/build/ratmine_current/ratmine/in...') called at path_updater.pl line 798
Processing element        740Path update failed 512 at update_to_0.94 line 57.
 
Any word on the cause?
 
-Andrew

From: [hidden email] [mailto:[hidden email]] On Behalf Of Kalpana Karra
Sent: Tuesday, October 05, 2010 4:53 PM
To: Intermine
Subject: [InterMine Dev] Upgrade_094 Update..
 
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)
 
2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in sgd_additions file.
 
3) Had to comment out class MRNA in genomic_additions.xml (was causing merging error due to fivePrimeUTR in my model)
 
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.
 
 
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.
 
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).
 
 
-Kalpana
 
 
 
 


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Re: Upgrade_094 Update..

Richard Smith
In reply to this post by Vallejos, Andrew
It looks like this is a FlyMine thing - we have a datasets.xml file in
the integrate directory that needed updating.  Other mines don't have
one.

The fix is to delete this line:

inputfile = $svndirectory/$mine/integrate/datasets.xml

 From intermine/scripts/resources/updater.config.

Cheers,
Richard.



On 06/10/2010 21:24, Vallejos, Andrew wrote:

> I received a similar error message.
>
> [intermine@stearman scripts]$ perl update_to_0.94 paths
>
> Cannot open
> /home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml, No
> such file or directory - skipping
>
> at path_updater.pl line 8
>
> main::__ANON__('\x{d}Cannot open
> /home/intermine/build/ratmine_current/ratmine/in...') called at
> path_updater.pl line 798
>
> Processing element 740Path update failed 512 at update_to_0.94 line 57.
>
> Any word on the cause?
>
> -Andrew
>
> ------------------------------------------------------------------------
>
> *From:* [hidden email] [mailto:[hidden email]] *On
> Behalf Of *Kalpana Karra
> *Sent:* Tuesday, October 05, 2010 4:53 PM
> *To:* Intermine
> *Subject:* [InterMine Dev] Upgrade_094 Update..
>
> 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)
>
> 2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in
> sgd_additions file.
>
> 3) Had to comment out class MRNA in genomic_additions.xml (was causing
> merging error due to fivePrimeUTR in my model)
>
> 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.
>
> 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.
>
> 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).
>
> -Kalpana
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: Upgrade_094 Update..

Vallejos, Andrew
So, it looks like changes that I made to my model are causing the script
to gag on the userprofile.xml.  Which I guess should be expected.  

RatMine contains a few legacy classes that do not conform to the SO
standards, despite being SO objects (aka synonym).  Anyway, I should be
able to do a search/replace on the offending class names and get that
righted.

Example:
Old --> New

Qtl --> QTL
SSLP --> SimpleSequenceLengthVariance
SSLPAllele --> Allele

-----Original Message-----
From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex
Kalderimis
Sent: Thursday, October 07, 2010 6:25 AM
To: Richard Smith
Cc: Vallejos, Andrew; Julie Sullivan
Subject: Re: [InterMine Dev] Upgrade_094 Update..

This looks like we are trying to process an undefined element of a
pathstring. This really shouldn't happen, so I've put in a warning
againt undefined bits. I'll continue to investigate and try and work
out where this comes from.

Alex

On Wed, Oct 06, 2010 at 10:03:30PM +0100, Richard Smith wrote:
> It looks like something has turned up in some query XML that the
script

> wasn't expecting.  We'll have to let Alex take a look at it tomorrow.
>
> If you could gzip the userprofile.xml and send it over that would be a
> big help.  But it's probably too big for e-mail?  Maybe it's possible
> to extract just the profile it failed on?
>
> Cheers,
> Richard.
>
>
>
> On 06/10/2010 21:44, Vallejos, Andrew wrote:
> >[intermine@stearman scripts]$ perl update_to_0.94 paths
> >ProcessUse of uninitialized value in string eq at path_updater.pl
line
> >149,<$INFH>  line 35443.
> >  at path_updater.pl line 8
> >         main::__ANON__('Use of uninitialized value in string eq at
> >path_updater.pl li...') called at path_updater.pl line 149
> >         main::update_path('Chromosome.genes.primaryIdentifier',
> >'HASH(0x12222780)') called at path_updater.pl line 242
> >
>
>main::update_view('Webservice::InterMine::Query::Template=HASH(0x118d9c
b
> >0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...')
> >called at path_updater.pl line 299
> >
>
>main::update_query('Webservice::InterMine::Query::Template=HASH(0x118d9
c

> >b0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
> >"jrsm...') called at path_updater.pl line 363
> >         main::translate_query('template', '<template name="genes on
> >chromosome" title="Chromosome --&gt;...',
> >'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> >'[hidden email]') called at path_updater.pl line 333
> >         main::update_buffer('<template name="genes on chromosome"
> >title="Chromosome --&gt;...', 'template',
> >'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> >'[hidden email]') called at path_updater.pl line 769
> >         main::process_xml_line('</items><bags><bag
> >name="All_peptidase_genes" type="Gene" dat...',
> >'/home/intermine/userprofile.xml') called at path_updater.pl line 806
> >Processing element      44163Path update failed 2304 at
update_to_0.94

> >line 57.
> >
> >Got another error.
> >
> >-----Original Message-----
> >From: [hidden email] [mailto:[hidden email]] On
> >Behalf Of Richard Smith
> >Sent: Wednesday, October 06, 2010 3:42 PM
> >To: [hidden email]
> >Subject: Re: [InterMine Dev] Upgrade_094 Update..
> >
> >It looks like this is a FlyMine thing - we have a datasets.xml file
in

> >the integrate directory that needed updating.  Other mines don't have
> >one.
> >
> >The fix is to delete this line:
> >
> >inputfile = $svndirectory/$mine/integrate/datasets.xml
> >
> >  From intermine/scripts/resources/updater.config.
> >
> >Cheers,
> >Richard.
> >
> >
> >
> >On 06/10/2010 21:24, Vallejos, Andrew wrote:
> >>I received a similar error message.
> >>
> >>[intermine@stearman scripts]$ perl update_to_0.94 paths
> >>
> >>Cannot open
>
>>/home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml,
> >No
> >>such file or directory - skipping
> >>
> >>at path_updater.pl line 8
> >>
> >>main::__ANON__('\x{d}Cannot open
> >>/home/intermine/build/ratmine_current/ratmine/in...') called at
> >>path_updater.pl line 798
> >>
> >>Processing element 740Path update failed 512 at update_to_0.94 line
> >57.
> >>
> >>Any word on the cause?
> >>
> >>-Andrew
> >>
> >>
>
>-----------------------------------------------------------------------
-

> >>
> >>*From:* [hidden email] [mailto:[hidden email]]
> >*On
> >>Behalf Of *Kalpana Karra
> >>*Sent:* Tuesday, October 05, 2010 4:53 PM
> >>*To:* Intermine
> >>*Subject:* [InterMine Dev] Upgrade_094 Update..
> >>
> >>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)
> >>
> >>2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in
> >>sgd_additions file.
> >>
> >>3) Had to comment out class MRNA in genomic_additions.xml (was
causing

> >>merging error due to fivePrimeUTR in my model)
> >>
> >>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.
> >>
> >>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.
> >>
> >>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/data
s

> >ets.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).
> >>
> >>-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
> >
>

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Re: Upgrade_094 Update..

Alex Kalderimis
On Thu, Oct 07, 2010 at 08:35:14AM -0500, Vallejos, Andrew wrote:

> So, it looks like changes that I made to my model are causing the script
> to gag on the userprofile.xml.  Which I guess should be expected.  
>
> RatMine contains a few legacy classes that do not conform to the SO
> standards, despite being SO objects (aka synonym).  Anyway, I should be
> able to do a search/replace on the offending class names and get that
> righted.
>
> Example:
> Old --> New
>
> Qtl --> QTL
> SSLP --> SimpleSequenceLengthVariance
> SSLPAllele --> Allele
>
As mentioned on the call, the best way to do this is to use the
model_changes.0.94.yaml file, since it will also follow references to
these classes, as well as when they are the root class of a path:

in the second section of the yaml add:

"Qtl":QTL
"SSLP":SimpleSequenceLengthVariance
"SSLPAllele":Allele

As always with Yaml, be careful when adding lines to keep the
indentation consistent.

Alex

> -----Original Message-----
> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex
> Kalderimis
> Sent: Thursday, October 07, 2010 6:25 AM
> To: Richard Smith
> Cc: Vallejos, Andrew; Julie Sullivan
> Subject: Re: [InterMine Dev] Upgrade_094 Update..
>
> This looks like we are trying to process an undefined element of a
> pathstring. This really shouldn't happen, so I've put in a warning
> againt undefined bits. I'll continue to investigate and try and work
> out where this comes from.
>
> Alex
>
> On Wed, Oct 06, 2010 at 10:03:30PM +0100, Richard Smith wrote:
> > It looks like something has turned up in some query XML that the
> script
> > wasn't expecting.  We'll have to let Alex take a look at it tomorrow.
> >
> > If you could gzip the userprofile.xml and send it over that would be a
> > big help.  But it's probably too big for e-mail?  Maybe it's possible
> > to extract just the profile it failed on?
> >
> > Cheers,
> > Richard.
> >
> >
> >
> > On 06/10/2010 21:44, Vallejos, Andrew wrote:
> > >[intermine@stearman scripts]$ perl update_to_0.94 paths
> > >ProcessUse of uninitialized value in string eq at path_updater.pl
> line
> > >149,<$INFH>  line 35443.
> > >  at path_updater.pl line 8
> > >         main::__ANON__('Use of uninitialized value in string eq at
> > >path_updater.pl li...') called at path_updater.pl line 149
> > >         main::update_path('Chromosome.genes.primaryIdentifier',
> > >'HASH(0x12222780)') called at path_updater.pl line 242
> > >
> >
> >main::update_view('Webservice::InterMine::Query::Template=HASH(0x118d9c
> b
> > >0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
> "jrsm...')
> > >called at path_updater.pl line 299
> > >
> >
> >main::update_query('Webservice::InterMine::Query::Template=HASH(0x118d9
> c
> > >b0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
> > >"jrsm...') called at path_updater.pl line 363
> > >         main::translate_query('template', '<template name="genes on
> > >chromosome" title="Chromosome --&gt;...',
> > >'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> > >'[hidden email]') called at path_updater.pl line 333
> > >         main::update_buffer('<template name="genes on chromosome"
> > >title="Chromosome --&gt;...', 'template',
> > >'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> > >'[hidden email]') called at path_updater.pl line 769
> > >         main::process_xml_line('</items><bags><bag
> > >name="All_peptidase_genes" type="Gene" dat...',
> > >'/home/intermine/userprofile.xml') called at path_updater.pl line 806
> > >Processing element      44163Path update failed 2304 at
> update_to_0.94
> > >line 57.
> > >
> > >Got another error.
> > >
> > >-----Original Message-----
> > >From: [hidden email] [mailto:[hidden email]] On
> > >Behalf Of Richard Smith
> > >Sent: Wednesday, October 06, 2010 3:42 PM
> > >To: [hidden email]
> > >Subject: Re: [InterMine Dev] Upgrade_094 Update..
> > >
> > >It looks like this is a FlyMine thing - we have a datasets.xml file
> in
> > >the integrate directory that needed updating.  Other mines don't have
> > >one.
> > >
> > >The fix is to delete this line:
> > >
> > >inputfile = $svndirectory/$mine/integrate/datasets.xml
> > >
> > >  From intermine/scripts/resources/updater.config.
> > >
> > >Cheers,
> > >Richard.
> > >
> > >
> > >
> > >On 06/10/2010 21:24, Vallejos, Andrew wrote:
> > >>I received a similar error message.
> > >>
> > >>[intermine@stearman scripts]$ perl update_to_0.94 paths
> > >>
> > >>Cannot open
> >
> >>/home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml,
> > >No
> > >>such file or directory - skipping
> > >>
> > >>at path_updater.pl line 8
> > >>
> > >>main::__ANON__('\x{d}Cannot open
> > >>/home/intermine/build/ratmine_current/ratmine/in...') called at
> > >>path_updater.pl line 798
> > >>
> > >>Processing element 740Path update failed 512 at update_to_0.94 line
> > >57.
> > >>
> > >>Any word on the cause?
> > >>
> > >>-Andrew
> > >>
> > >>
> >
> >-----------------------------------------------------------------------
> -
> > >>
> > >>*From:* [hidden email] [mailto:[hidden email]]
> > >*On
> > >>Behalf Of *Kalpana Karra
> > >>*Sent:* Tuesday, October 05, 2010 4:53 PM
> > >>*To:* Intermine
> > >>*Subject:* [InterMine Dev] Upgrade_094 Update..
> > >>
> > >>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)
> > >>
> > >>2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in
> > >>sgd_additions file.
> > >>
> > >>3) Had to comment out class MRNA in genomic_additions.xml (was
> causing
> > >>merging error due to fivePrimeUTR in my model)
> > >>
> > >>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.
> > >>
> > >>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.
> > >>
> > >>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/data
> s
> > >ets.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).
> > >>
> > >>-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
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http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: Upgrade_094 Update..

Vallejos, Andrew

[intermine@stearman scripts]$ perl update_to_0.94 paths
ProcessUse of uninitialized value in string eq at path_updater.pl line
149, <$INFH> line 35443.
 at path_updater.pl line 8
        main::__ANON__('Use of uninitialized value in string eq at
path_updater.pl li...') called at path_updater.pl line 149
        main::update_path('Chromosome.genes.primaryIdentifier',
'HASH(0x7c22360)') called at path_updater.pl line 242
 
main::update_view('Webservice::InterMine::Query::Template=HASH(0x7b76d60
)', '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...')
called at path_updater.pl line 299
 
main::update_query('Webservice::InterMine::Query::Template=HASH(0x7b76d6
0)', '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...')
called at path_updater.pl line 363
        main::translate_query('template', '<template name="genes on
chromosome" title="Chromosome --&gt;...',
'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
'[hidden email]') called at path_updater.pl line 333
        main::update_buffer('<template name="genes on chromosome"
title="Chromosome --&gt;...', 'template',
'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
'[hidden email]') called at path_updater.pl line 769
        main::process_xml_line('</items><bags><bag
name="All_peptidase_genes" type="Gene" dat...',
'/home/intermine/userprofile.xml') called at path_updater.pl line 806
Processing element      44163Path update failed 2304 at update_to_0.94
line 57.

Any idea what this error means?  


-----Original Message-----
From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex
Kalderimis
Sent: Thursday, October 07, 2010 11:30 AM
To: Vallejos, Andrew
Cc: Intermine
Subject: Re: [InterMine Dev] Upgrade_094 Update..

On Thu, Oct 07, 2010 at 08:35:14AM -0500, Vallejos, Andrew wrote:
> So, it looks like changes that I made to my model are causing the
script
> to gag on the userprofile.xml.  Which I guess should be expected.  
>
> RatMine contains a few legacy classes that do not conform to the SO
> standards, despite being SO objects (aka synonym).  Anyway, I should
be

> able to do a search/replace on the offending class names and get that
> righted.
>
> Example:
> Old --> New
>
> Qtl --> QTL
> SSLP --> SimpleSequenceLengthVariance
> SSLPAllele --> Allele
>
As mentioned on the call, the best way to do this is to use the
model_changes.0.94.yaml file, since it will also follow references to
these classes, as well as when they are the root class of a path:

in the second section of the yaml add:

"Qtl":QTL
"SSLP":SimpleSequenceLengthVariance
"SSLPAllele":Allele

As always with Yaml, be careful when adding lines to keep the
indentation consistent.

Alex

> -----Original Message-----
> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of
Alex

> Kalderimis
> Sent: Thursday, October 07, 2010 6:25 AM
> To: Richard Smith
> Cc: Vallejos, Andrew; Julie Sullivan
> Subject: Re: [InterMine Dev] Upgrade_094 Update..
>
> This looks like we are trying to process an undefined element of a
> pathstring. This really shouldn't happen, so I've put in a warning
> againt undefined bits. I'll continue to investigate and try and work
> out where this comes from.
>
> Alex
>
> On Wed, Oct 06, 2010 at 10:03:30PM +0100, Richard Smith wrote:
> > It looks like something has turned up in some query XML that the
> script
> > wasn't expecting.  We'll have to let Alex take a look at it
tomorrow.
> >
> > If you could gzip the userprofile.xml and send it over that would be
a
> > big help.  But it's probably too big for e-mail?  Maybe it's
possible

> > to extract just the profile it failed on?
> >
> > Cheers,
> > Richard.
> >
> >
> >
> > On 06/10/2010 21:44, Vallejos, Andrew wrote:
> > >[intermine@stearman scripts]$ perl update_to_0.94 paths
> > >ProcessUse of uninitialized value in string eq at path_updater.pl
> line
> > >149,<$INFH>  line 35443.
> > >  at path_updater.pl line 8
> > >         main::__ANON__('Use of uninitialized value in string eq at
> > >path_updater.pl li...') called at path_updater.pl line 149
> > >         main::update_path('Chromosome.genes.primaryIdentifier',
> > >'HASH(0x12222780)') called at path_updater.pl line 242
> > >
> >
>
>main::update_view('Webservice::InterMine::Query::Template=HASH(0x118d9c
> b
> > >0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
> "jrsm...')
> > >called at path_updater.pl line 299
> > >
> >
>
>main::update_query('Webservice::InterMine::Query::Template=HASH(0x118d9
> c
> > >b0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
> > >"jrsm...') called at path_updater.pl line 363
> > >         main::translate_query('template', '<template name="genes
on

> > >chromosome" title="Chromosome --&gt;...',
> > >'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> > >'[hidden email]') called at path_updater.pl line 333
> > >         main::update_buffer('<template name="genes on chromosome"
> > >title="Chromosome --&gt;...', 'template',
> > >'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> > >'[hidden email]') called at path_updater.pl line 769
> > >         main::process_xml_line('</items><bags><bag
> > >name="All_peptidase_genes" type="Gene" dat...',
> > >'/home/intermine/userprofile.xml') called at path_updater.pl line
806
> > >Processing element      44163Path update failed 2304 at
> update_to_0.94
> > >line 57.
> > >
> > >Got another error.
> > >
> > >-----Original Message-----
> > >From: [hidden email] [mailto:[hidden email]]
On
> > >Behalf Of Richard Smith
> > >Sent: Wednesday, October 06, 2010 3:42 PM
> > >To: [hidden email]
> > >Subject: Re: [InterMine Dev] Upgrade_094 Update..
> > >
> > >It looks like this is a FlyMine thing - we have a datasets.xml file
> in
> > >the integrate directory that needed updating.  Other mines don't
have

> > >one.
> > >
> > >The fix is to delete this line:
> > >
> > >inputfile = $svndirectory/$mine/integrate/datasets.xml
> > >
> > >  From intermine/scripts/resources/updater.config.
> > >
> > >Cheers,
> > >Richard.
> > >
> > >
> > >
> > >On 06/10/2010 21:24, Vallejos, Andrew wrote:
> > >>I received a similar error message.
> > >>
> > >>[intermine@stearman scripts]$ perl update_to_0.94 paths
> > >>
> > >>Cannot open
> >
>
>>/home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml,
> > >No
> > >>such file or directory - skipping
> > >>
> > >>at path_updater.pl line 8
> > >>
> > >>main::__ANON__('\x{d}Cannot open
> > >>/home/intermine/build/ratmine_current/ratmine/in...') called at
> > >>path_updater.pl line 798
> > >>
> > >>Processing element 740Path update failed 512 at update_to_0.94
line

> > >57.
> > >>
> > >>Any word on the cause?
> > >>
> > >>-Andrew
> > >>
> > >>
> >
>
>-----------------------------------------------------------------------
> -
> > >>
> > >>*From:* [hidden email]
[mailto:[hidden email]]

> > >*On
> > >>Behalf Of *Kalpana Karra
> > >>*Sent:* Tuesday, October 05, 2010 4:53 PM
> > >>*To:* Intermine
> > >>*Subject:* [InterMine Dev] Upgrade_094 Update..
> > >>
> > >>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)
> > >>
> > >>2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in
> > >>sgd_additions file.
> > >>
> > >>3) Had to comment out class MRNA in genomic_additions.xml (was
> causing
> > >>merging error due to fivePrimeUTR in my model)
> > >>
> > >>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.
> > >>
> > >>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.
> > >>
> > >>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/data
> s
> > >ets.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).
> > >>
> > >>-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
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Re: Upgrade_094 Update..

Alex Kalderimis
I put a new version of path_updater on the branch yesterday which should
give a more informative error message for this - If you could
update to that and run again, that would be very helpful in diagnosing
this issue. It is a very odd one as there clearly is a defined value
being passed ('Chromosome.genes.primaryIdentifier'), so at some point
the @bits array is getting undefined. It would also be helpful if you
could grep the log for 'Chromosome.genes.primaryIdentifier'.

Alex.


On Fri, Oct 08, 2010 at 10:49:46AM -0500, Vallejos, Andrew wrote:

>
> [intermine@stearman scripts]$ perl update_to_0.94 paths
> ProcessUse of uninitialized value in string eq at path_updater.pl line
> 149, <$INFH> line 35443.
>  at path_updater.pl line 8
>         main::__ANON__('Use of uninitialized value in string eq at
> path_updater.pl li...') called at path_updater.pl line 149
>         main::update_path('Chromosome.genes.primaryIdentifier',
> 'HASH(0x7c22360)') called at path_updater.pl line 242
>  
> main::update_view('Webservice::InterMine::Query::Template=HASH(0x7b76d60
> )', '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...')
> called at path_updater.pl line 299
>  
> main::update_query('Webservice::InterMine::Query::Template=HASH(0x7b76d6
> 0)', '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...')
> called at path_updater.pl line 363
>         main::translate_query('template', '<template name="genes on
> chromosome" title="Chromosome --&gt;...',
> '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> '[hidden email]') called at path_updater.pl line 333
>         main::update_buffer('<template name="genes on chromosome"
> title="Chromosome --&gt;...', 'template',
> '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> '[hidden email]') called at path_updater.pl line 769
>         main::process_xml_line('</items><bags><bag
> name="All_peptidase_genes" type="Gene" dat...',
> '/home/intermine/userprofile.xml') called at path_updater.pl line 806
> Processing element      44163Path update failed 2304 at update_to_0.94
> line 57.
>
> Any idea what this error means?  
>
>
> -----Original Message-----
> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex
> Kalderimis
> Sent: Thursday, October 07, 2010 11:30 AM
> To: Vallejos, Andrew
> Cc: Intermine
> Subject: Re: [InterMine Dev] Upgrade_094 Update..
>
> On Thu, Oct 07, 2010 at 08:35:14AM -0500, Vallejos, Andrew wrote:
> > So, it looks like changes that I made to my model are causing the
> script
> > to gag on the userprofile.xml.  Which I guess should be expected.  
> >
> > RatMine contains a few legacy classes that do not conform to the SO
> > standards, despite being SO objects (aka synonym).  Anyway, I should
> be
> > able to do a search/replace on the offending class names and get that
> > righted.
> >
> > Example:
> > Old --> New
> >
> > Qtl --> QTL
> > SSLP --> SimpleSequenceLengthVariance
> > SSLPAllele --> Allele
> >
> As mentioned on the call, the best way to do this is to use the
> model_changes.0.94.yaml file, since it will also follow references to
> these classes, as well as when they are the root class of a path:
>
> in the second section of the yaml add:
>
> "Qtl":QTL
> "SSLP":SimpleSequenceLengthVariance
> "SSLPAllele":Allele
>
> As always with Yaml, be careful when adding lines to keep the
> indentation consistent.
>
> Alex
>
> > -----Original Message-----
> > From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of
> Alex
> > Kalderimis
> > Sent: Thursday, October 07, 2010 6:25 AM
> > To: Richard Smith
> > Cc: Vallejos, Andrew; Julie Sullivan
> > Subject: Re: [InterMine Dev] Upgrade_094 Update..
> >
> > This looks like we are trying to process an undefined element of a
> > pathstring. This really shouldn't happen, so I've put in a warning
> > againt undefined bits. I'll continue to investigate and try and work
> > out where this comes from.
> >
> > Alex
> >
> > On Wed, Oct 06, 2010 at 10:03:30PM +0100, Richard Smith wrote:
> > > It looks like something has turned up in some query XML that the
> > script
> > > wasn't expecting.  We'll have to let Alex take a look at it
> tomorrow.
> > >
> > > If you could gzip the userprofile.xml and send it over that would be
> a
> > > big help.  But it's probably too big for e-mail?  Maybe it's
> possible
> > > to extract just the profile it failed on?
> > >
> > > Cheers,
> > > Richard.
> > >
> > >
> > >
> > > On 06/10/2010 21:44, Vallejos, Andrew wrote:
> > > >[intermine@stearman scripts]$ perl update_to_0.94 paths
> > > >ProcessUse of uninitialized value in string eq at path_updater.pl
> > line
> > > >149,<$INFH>  line 35443.
> > > >  at path_updater.pl line 8
> > > >         main::__ANON__('Use of uninitialized value in string eq at
> > > >path_updater.pl li...') called at path_updater.pl line 149
> > > >         main::update_path('Chromosome.genes.primaryIdentifier',
> > > >'HASH(0x12222780)') called at path_updater.pl line 242
> > > >
> > >
> >
> >main::update_view('Webservice::InterMine::Query::Template=HASH(0x118d9c
> > b
> > > >0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
> > "jrsm...')
> > > >called at path_updater.pl line 299
> > > >
> > >
> >
> >main::update_query('Webservice::InterMine::Query::Template=HASH(0x118d9
> > c
> > > >b0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
> > > >"jrsm...') called at path_updater.pl line 363
> > > >         main::translate_query('template', '<template name="genes
> on
> > > >chromosome" title="Chromosome --&gt;...',
> > > >'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> > > >'[hidden email]') called at path_updater.pl line 333
> > > >         main::update_buffer('<template name="genes on chromosome"
> > > >title="Chromosome --&gt;...', 'template',
> > > >'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> > > >'[hidden email]') called at path_updater.pl line 769
> > > >         main::process_xml_line('</items><bags><bag
> > > >name="All_peptidase_genes" type="Gene" dat...',
> > > >'/home/intermine/userprofile.xml') called at path_updater.pl line
> 806
> > > >Processing element      44163Path update failed 2304 at
> > update_to_0.94
> > > >line 57.
> > > >
> > > >Got another error.
> > > >
> > > >-----Original Message-----
> > > >From: [hidden email] [mailto:[hidden email]]
> On
> > > >Behalf Of Richard Smith
> > > >Sent: Wednesday, October 06, 2010 3:42 PM
> > > >To: [hidden email]
> > > >Subject: Re: [InterMine Dev] Upgrade_094 Update..
> > > >
> > > >It looks like this is a FlyMine thing - we have a datasets.xml file
> > in
> > > >the integrate directory that needed updating.  Other mines don't
> have
> > > >one.
> > > >
> > > >The fix is to delete this line:
> > > >
> > > >inputfile = $svndirectory/$mine/integrate/datasets.xml
> > > >
> > > >  From intermine/scripts/resources/updater.config.
> > > >
> > > >Cheers,
> > > >Richard.
> > > >
> > > >
> > > >
> > > >On 06/10/2010 21:24, Vallejos, Andrew wrote:
> > > >>I received a similar error message.
> > > >>
> > > >>[intermine@stearman scripts]$ perl update_to_0.94 paths
> > > >>
> > > >>Cannot open
> > >
> >
> >>/home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml,
> > > >No
> > > >>such file or directory - skipping
> > > >>
> > > >>at path_updater.pl line 8
> > > >>
> > > >>main::__ANON__('\x{d}Cannot open
> > > >>/home/intermine/build/ratmine_current/ratmine/in...') called at
> > > >>path_updater.pl line 798
> > > >>
> > > >>Processing element 740Path update failed 512 at update_to_0.94
> line
> > > >57.
> > > >>
> > > >>Any word on the cause?
> > > >>
> > > >>-Andrew
> > > >>
> > > >>
> > >
> >
> >-----------------------------------------------------------------------
> > -
> > > >>
> > > >>*From:* [hidden email]
> [mailto:[hidden email]]
> > > >*On
> > > >>Behalf Of *Kalpana Karra
> > > >>*Sent:* Tuesday, October 05, 2010 4:53 PM
> > > >>*To:* Intermine
> > > >>*Subject:* [InterMine Dev] Upgrade_094 Update..
> > > >>
> > > >>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)
> > > >>
> > > >>2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in
> > > >>sgd_additions file.
> > > >>
> > > >>3) Had to comment out class MRNA in genomic_additions.xml (was
> > causing
> > > >>merging error due to fivePrimeUTR in my model)
> > > >>
> > > >>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.
> > > >>
> > > >>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.
> > > >>
> > > >>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/data
> > s
> > > >ets.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).
> > > >>
> > > >>-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
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Re: Upgrade_094 Update..

Vallejos, Andrew
Processundefined bit of the path string
Chromosome.genes.primaryIdentifier - translated so far to Chromosome at
path_updater.pl line 148
        main::update_path('Chromosome.genes.primaryIdentifier',
'HASH(0x13c9c8c0)') called at path_updater.pl line 243
 
main::update_view('Webservice::InterMine::Query::Template=HASH(0x133504f
0)', '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...')
called at path_updater.pl line 300
 
main::update_query('Webservice::InterMine::Query::Template=HASH(0x133504
f0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...') called at path_updater.pl line 364
        main::translate_query('template', '<template name="genes on
chromosome" title="Chromosome --&gt;...',
'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
'[hidden email]') called at path_updater.pl line 334
        main::update_buffer('<template name="genes on chromosome"
title="Chromosome --&gt;...', 'template',
'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
'[hidden email]') called at path_updater.pl line 770
        main::process_xml_line('</items><bags><bag
name="All_peptidase_genes" type="Gene" dat...',
'/home/intermine/userprofile.xml') called at path_updater.pl line 808
Processing element      44163Path update failed 2304 at update_to_0.94
line 60.

Here is what I got from the updated script.  I tried grepping the log
and it did not return any results.  I am going to grepping different
words.

-----Original Message-----
From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex
Kalderimis
Sent: Friday, October 08, 2010 11:12 AM
To: Vallejos, Andrew
Cc: Intermine
Subject: Re: [InterMine Dev] Upgrade_094 Update..

I put a new version of path_updater on the branch yesterday which should
give a more informative error message for this - If you could
update to that and run again, that would be very helpful in diagnosing
this issue. It is a very odd one as there clearly is a defined value
being passed ('Chromosome.genes.primaryIdentifier'), so at some point
the @bits array is getting undefined. It would also be helpful if you
could grep the log for 'Chromosome.genes.primaryIdentifier'.

Alex.


On Fri, Oct 08, 2010 at 10:49:46AM -0500, Vallejos, Andrew wrote:

>
> [intermine@stearman scripts]$ perl update_to_0.94 paths
> ProcessUse of uninitialized value in string eq at path_updater.pl line
> 149, <$INFH> line 35443.
>  at path_updater.pl line 8
>         main::__ANON__('Use of uninitialized value in string eq at
> path_updater.pl li...') called at path_updater.pl line 149
>         main::update_path('Chromosome.genes.primaryIdentifier',
> 'HASH(0x7c22360)') called at path_updater.pl line 242
>  
>
main::update_view('Webservice::InterMine::Query::Template=HASH(0x7b76d60
> )', '/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...')
> called at path_updater.pl line 299
>  
>
main::update_query('Webservice::InterMine::Query::Template=HASH(0x7b76d6
> 0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...')

> called at path_updater.pl line 363
>         main::translate_query('template', '<template name="genes on
> chromosome" title="Chromosome --&gt;...',
> '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> '[hidden email]') called at path_updater.pl line 333
>         main::update_buffer('<template name="genes on chromosome"
> title="Chromosome --&gt;...', 'template',
> '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
> '[hidden email]') called at path_updater.pl line 769
>         main::process_xml_line('</items><bags><bag
> name="All_peptidase_genes" type="Gene" dat...',
> '/home/intermine/userprofile.xml') called at path_updater.pl line 806
> Processing element      44163Path update failed 2304 at update_to_0.94
> line 57.
>
> Any idea what this error means?  
>
>
> -----Original Message-----
> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of
Alex

> Kalderimis
> Sent: Thursday, October 07, 2010 11:30 AM
> To: Vallejos, Andrew
> Cc: Intermine
> Subject: Re: [InterMine Dev] Upgrade_094 Update..
>
> On Thu, Oct 07, 2010 at 08:35:14AM -0500, Vallejos, Andrew wrote:
> > So, it looks like changes that I made to my model are causing the
> script
> > to gag on the userprofile.xml.  Which I guess should be expected.  
> >
> > RatMine contains a few legacy classes that do not conform to the SO
> > standards, despite being SO objects (aka synonym).  Anyway, I should
> be
> > able to do a search/replace on the offending class names and get
that

> > righted.
> >
> > Example:
> > Old --> New
> >
> > Qtl --> QTL
> > SSLP --> SimpleSequenceLengthVariance
> > SSLPAllele --> Allele
> >
> As mentioned on the call, the best way to do this is to use the
> model_changes.0.94.yaml file, since it will also follow references to
> these classes, as well as when they are the root class of a path:
>
> in the second section of the yaml add:
>
> "Qtl":QTL
> "SSLP":SimpleSequenceLengthVariance
> "SSLPAllele":Allele
>
> As always with Yaml, be careful when adding lines to keep the
> indentation consistent.
>
> Alex
>
> > -----Original Message-----
> > From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of
> Alex
> > Kalderimis
> > Sent: Thursday, October 07, 2010 6:25 AM
> > To: Richard Smith
> > Cc: Vallejos, Andrew; Julie Sullivan
> > Subject: Re: [InterMine Dev] Upgrade_094 Update..
> >
> > This looks like we are trying to process an undefined element of a
> > pathstring. This really shouldn't happen, so I've put in a warning
> > againt undefined bits. I'll continue to investigate and try and work
> > out where this comes from.
> >
> > Alex
> >
> > On Wed, Oct 06, 2010 at 10:03:30PM +0100, Richard Smith wrote:
> > > It looks like something has turned up in some query XML that the
> > script
> > > wasn't expecting.  We'll have to let Alex take a look at it
> tomorrow.
> > >
> > > If you could gzip the userprofile.xml and send it over that would
be

> a
> > > big help.  But it's probably too big for e-mail?  Maybe it's
> possible
> > > to extract just the profile it failed on?
> > >
> > > Cheers,
> > > Richard.
> > >
> > >
> > >
> > > On 06/10/2010 21:44, Vallejos, Andrew wrote:
> > > >[intermine@stearman scripts]$ perl update_to_0.94 paths
> > > >ProcessUse of uninitialized value in string eq at path_updater.pl
> > line
> > > >149,<$INFH>  line 35443.
> > > >  at path_updater.pl line 8
> > > >         main::__ANON__('Use of uninitialized value in string eq
at

> > > >path_updater.pl li...') called at path_updater.pl line 149
> > > >         main::update_path('Chromosome.genes.primaryIdentifier',
> > > >'HASH(0x12222780)') called at path_updater.pl line 242
> > > >
> > >
> >
>
>main::update_view('Webservice::InterMine::Query::Template=HASH(0x118d9c
> > b
> > > >0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
> > "jrsm...')
> > > >called at path_updater.pl line 299
> > > >
> > >
> >
>
>main::update_query('Webservice::InterMine::Query::Template=HASH(0x118d9
> > c
> > > >b0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
> > > >"jrsm...') called at path_updater.pl line 363
> > > >         main::translate_query('template', '<template name="genes
> on
> > > >chromosome" title="Chromosome --&gt;...',
> > > >'/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...',
> > > >'[hidden email]') called at path_updater.pl line 333
> > > >         main::update_buffer('<template name="genes on
chromosome"
> > > >title="Chromosome --&gt;...', 'template',
> > > >'/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...',

> > > >'[hidden email]') called at path_updater.pl line 769
> > > >         main::process_xml_line('</items><bags><bag
> > > >name="All_peptidase_genes" type="Gene" dat...',
> > > >'/home/intermine/userprofile.xml') called at path_updater.pl line
> 806
> > > >Processing element      44163Path update failed 2304 at
> > update_to_0.94
> > > >line 57.
> > > >
> > > >Got another error.
> > > >
> > > >-----Original Message-----
> > > >From: [hidden email]
[mailto:[hidden email]]
> On
> > > >Behalf Of Richard Smith
> > > >Sent: Wednesday, October 06, 2010 3:42 PM
> > > >To: [hidden email]
> > > >Subject: Re: [InterMine Dev] Upgrade_094 Update..
> > > >
> > > >It looks like this is a FlyMine thing - we have a datasets.xml
file

> > in
> > > >the integrate directory that needed updating.  Other mines don't
> have
> > > >one.
> > > >
> > > >The fix is to delete this line:
> > > >
> > > >inputfile = $svndirectory/$mine/integrate/datasets.xml
> > > >
> > > >  From intermine/scripts/resources/updater.config.
> > > >
> > > >Cheers,
> > > >Richard.
> > > >
> > > >
> > > >
> > > >On 06/10/2010 21:24, Vallejos, Andrew wrote:
> > > >>I received a similar error message.
> > > >>
> > > >>[intermine@stearman scripts]$ perl update_to_0.94 paths
> > > >>
> > > >>Cannot open
> > >
> >
>
>>/home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml,
> > > >No
> > > >>such file or directory - skipping
> > > >>
> > > >>at path_updater.pl line 8
> > > >>
> > > >>main::__ANON__('\x{d}Cannot open
> > > >>/home/intermine/build/ratmine_current/ratmine/in...') called at
> > > >>path_updater.pl line 798
> > > >>
> > > >>Processing element 740Path update failed 512 at update_to_0.94
> line
> > > >57.
> > > >>
> > > >>Any word on the cause?
> > > >>
> > > >>-Andrew
> > > >>
> > > >>
> > >
> >
>
>-----------------------------------------------------------------------
> > -
> > > >>
> > > >>*From:* [hidden email]
> [mailto:[hidden email]]
> > > >*On
> > > >>Behalf Of *Kalpana Karra
> > > >>*Sent:* Tuesday, October 05, 2010 4:53 PM
> > > >>*To:* Intermine
> > > >>*Subject:* [InterMine Dev] Upgrade_094 Update..
> > > >>
> > > >>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)
> > > >>
> > > >>2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in
> > > >>sgd_additions file.
> > > >>
> > > >>3) Had to comment out class MRNA in genomic_additions.xml (was
> > causing
> > > >>merging error due to fivePrimeUTR in my model)
> > > >>
> > > >>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.
> > > >>
> > > >>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.
> > > >>
> > > >>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/data
> > s
> > > >ets.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).
> > > >>
> > > >>-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
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http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: Upgrade_094 Update..

Sierra Moxon
Do you have the script that updates the UUID for SVN yet?

From my 0.94 checkout:

-bash-3.00$ svn up
svn: Repository UUID '37e1b716-f2f3-0310-95ce-c813c9c44928' doesn't match expected UUID 'fe4c2b01-3cf8-46b5-8a92-cfa53fcdf647'

Sierra




-----Original Message-----
From: A.J. Kalderimis [[hidden email]] On Behalf Of Alex
Kalderimis
Sent: Friday, October 08, 2010 11:12 AM
To: Vallejos, Andrew
Cc: Intermine
Subject: Re: [InterMine Dev] Upgrade_094 Update..

I put a new version of path_updater on the branch yesterday which should
give a more informative error message for this - If you could
update to that and run again, that would be very helpful in diagnosing
this issue. It is a very odd one as there clearly is a defined value
being passed ('Chromosome.genes.primaryIdentifier'), so at some point
the @bits array is getting undefined. It would also be helpful if you
could grep the log for 'Chromosome.genes.primaryIdentifier'.

Alex.


On Fri, Oct 08, 2010 at 10:49:46AM -0500, Vallejos, Andrew wrote:

[intermine@stearman scripts]$ perl update_to_0.94 paths
ProcessUse of uninitialized value in string eq at path_updater.pl line
149, <$INFH> line 35443.
at path_updater.pl line 8
       main::__ANON__('Use of uninitialized value in string eq at
path_updater.pl li...') called at path_updater.pl line 149
       main::update_path('Chromosome.genes.primaryIdentifier',
'HASH(0x7c22360)') called at path_updater.pl line 242


main::update_view('Webservice::InterMine::Query::Template=HASH(0x7b76d60
)', '/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...')
called at path_updater.pl line 299


main::update_query('Webservice::InterMine::Query::Template=HASH(0x7b76d6
0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...')
called at path_updater.pl line 363
       main::translate_query('template', '<template name="genes on
chromosome" title="Chromosome --&gt;...',
'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
[hidden email]') called at path_updater.pl line 333
       main::update_buffer('<template name="genes on chromosome"
title="Chromosome --&gt;...', 'template',
'/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
[hidden email]') called at path_updater.pl line 769
       main::process_xml_line('</items><bags><bag
name="All_peptidase_genes" type="Gene" dat...',
'/home/intermine/userprofile.xml') called at path_updater.pl line 806
Processing element      44163Path update failed 2304 at update_to_0.94
line 57.

Any idea what this error means?  


-----Original Message-----
From: A.J. Kalderimis [[hidden email]] On Behalf Of
Alex
Kalderimis
Sent: Thursday, October 07, 2010 11:30 AM
To: Vallejos, Andrew
Cc: Intermine
Subject: Re: [InterMine Dev] Upgrade_094 Update..

On Thu, Oct 07, 2010 at 08:35:14AM -0500, Vallejos, Andrew wrote:
So, it looks like changes that I made to my model are causing the
script
to gag on the userprofile.xml.  Which I guess should be expected.  

RatMine contains a few legacy classes that do not conform to the SO
standards, despite being SO objects (aka synonym).  Anyway, I should
be
able to do a search/replace on the offending class names and get
that
righted.

Example:
Old --> New

Qtl --> QTL
SSLP --> SimpleSequenceLengthVariance
SSLPAllele --> Allele

As mentioned on the call, the best way to do this is to use the
model_changes.0.94.yaml file, since it will also follow references to
these classes, as well as when they are the root class of a path:

in the second section of the yaml add:

"Qtl":QTL
"SSLP":SimpleSequenceLengthVariance
"SSLPAllele":Allele

As always with Yaml, be careful when adding lines to keep the
indentation consistent.

Alex

-----Original Message-----
From: A.J. Kalderimis [[hidden email]] On Behalf Of
Alex
Kalderimis
Sent: Thursday, October 07, 2010 6:25 AM
To: Richard Smith
Cc: Vallejos, Andrew; Julie Sullivan
Subject: Re: [InterMine Dev] Upgrade_094 Update..

This looks like we are trying to process an undefined element of a
pathstring. This really shouldn't happen, so I've put in a warning
againt undefined bits. I'll continue to investigate and try and work
out where this comes from.

Alex

On Wed, Oct 06, 2010 at 10:03:30PM +0100, Richard Smith wrote:
It looks like something has turned up in some query XML that the
script
wasn't expecting.  We'll have to let Alex take a look at it
tomorrow.

If you could gzip the userprofile.xml and send it over that would
be
a
big help.  But it's probably too big for e-mail?  Maybe it's
possible
to extract just the profile it failed on?

Cheers,
Richard.



On 06/10/2010 21:44, Vallejos, Andrew wrote:
[intermine@stearman scripts]$ perl update_to_0.94 paths
ProcessUse of uninitialized value in string eq at path_updater.pl
line
149,<$INFH>  line 35443.
at path_updater.pl line 8
       main::__ANON__('Use of uninitialized value in string eq
at
path_updater.pl li...') called at path_updater.pl line 149
       main::update_path('Chromosome.genes.primaryIdentifier',
'HASH(0x12222780)') called at path_updater.pl line 242




main::update_view('Webservice::InterMine::Query::Template=HASH(0x118d9c
b
0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...')
called at path_updater.pl line 299




main::update_query('Webservice::InterMine::Query::Template=HASH(0x118d9
c
b0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...') called at path_updater.pl line 363
       main::translate_query('template', '<template name="genes
on
chromosome" title="Chromosome --&gt;...',
'/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...',
[hidden email]') called at path_updater.pl line 333
       main::update_buffer('<template name="genes on
chromosome"
title="Chromosome --&gt;...', 'template',
'/home/intermine/userprofile.xml ll. 35443 in profile of
"jrsm...',
[hidden email]') called at path_updater.pl line 769
       main::process_xml_line('</items><bags><bag
name="All_peptidase_genes" type="Gene" dat...',
'/home/intermine/userprofile.xml') called at path_updater.pl line
806
Processing element      44163Path update failed 2304 at
update_to_0.94
line 57.

Got another error.

-----Original Message-----
From: [hidden email]
[[hidden email]]
On
Behalf Of Richard Smith
Sent: Wednesday, October 06, 2010 3:42 PM
To: [hidden email]
Subject: Re: [InterMine Dev] Upgrade_094 Update..

It looks like this is a FlyMine thing - we have a datasets.xml
file
in
the integrate directory that needed updating.  Other mines don't
have
one.

The fix is to delete this line:

inputfile = $svndirectory/$mine/integrate/datasets.xml

From intermine/scripts/resources/updater.config.

Cheers,
Richard.



On 06/10/2010 21:24, Vallejos, Andrew wrote:
I received a similar error message.

[intermine@stearman scripts]$ perl update_to_0.94 paths

Cannot open



/home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml,
No
such file or directory - skipping

at path_updater.pl line 8

main::__ANON__('\x{d}Cannot open
/home/intermine/build/ratmine_current/ratmine/in...') called at
path_updater.pl line 798

Processing element 740Path update failed 512 at update_to_0.94
line
57.

Any word on the cause?

-Andrew





-----------------------------------------------------------------------
-

*From:* [hidden email]
[[hidden email]]
*On
Behalf Of *Kalpana Karra
*Sent:* Tuesday, October 05, 2010 4:53 PM
*To:* Intermine
*Subject:* [InterMine Dev] Upgrade_094 Update..

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)

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

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

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.

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.

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/data
s
ets.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).

-Kalpana



_______________________________________________
dev mailing list
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_______________________________________________
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


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Re: Upgrade_094 Update..

Richard Smith
Yes, see here:

        http://www.intermine.org/wiki/SvnFix

Cheers,
Richard.



On 18/10/2010 19:56, Sierra Moxon wrote:

> Do you have the script that updates the UUID for SVN yet?
>
>  From my 0.94 checkout:
>
> -bash-3.00$ svn up
> svn: Repository UUID '37e1b716-f2f3-0310-95ce-c813c9c44928' doesn't
> match expected UUID 'fe4c2b01-3cf8-46b5-8a92-cfa53fcdf647'
>
> Sierra
>
>>
>>
>>
>> -----Original Message-----
>> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of Alex
>> Kalderimis
>> Sent: Friday, October 08, 2010 11:12 AM
>> To: Vallejos, Andrew
>> Cc: Intermine
>> Subject: Re: [InterMine Dev] Upgrade_094 Update..
>>
>> I put a new version of path_updater on the branch yesterday which should
>> give a more informative error message for this - If you could
>> update to that and run again, that would be very helpful in diagnosing
>> this issue. It is a very odd one as there clearly is a defined value
>> being passed ('Chromosome.genes.primaryIdentifier'), so at some point
>> the @bits array is getting undefined. It would also be helpful if you
>> could grep the log for 'Chromosome.genes.primaryIdentifier'.
>>
>> Alex.
>>
>>
>> On Fri, Oct 08, 2010 at 10:49:46AM -0500, Vallejos, Andrew wrote:
>>>
>>> [intermine@stearman scripts]$ perl update_to_0.94 paths
>>> ProcessUse of uninitialized value in string eq at path_updater.pl line
>>> 149, <$INFH> line 35443.
>>> at path_updater.pl line 8
>>> main::__ANON__('Use of uninitialized value in string eq at
>>> path_updater.pl li...') called at path_updater.pl line 149
>>> main::update_path('Chromosome.genes.primaryIdentifier',
>>> 'HASH(0x7c22360)') called at path_updater.pl line 242
>>>
>>>
>> main::update_view('Webservice::InterMine::Query::Template=HASH(0x7b76d60
>>> )', '/home/intermine/userprofile.xml ll. 35443 in profile of
>> "jrsm...')
>>> called at path_updater.pl line 299
>>>
>>>
>> main::update_query('Webservice::InterMine::Query::Template=HASH(0x7b76d6
>>> 0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
>> "jrsm...')
>>> called at path_updater.pl line 363
>>> main::translate_query('template', '<template name="genes on
>>> chromosome" title="Chromosome --&gt;...',
>>> '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
>>> '[hidden email] <mailto:'[hidden email]>') called at
>>> path_updater.pl line 333
>>> main::update_buffer('<template name="genes on chromosome"
>>> title="Chromosome --&gt;...', 'template',
>>> '/home/intermine/userprofile.xml ll. 35443 in profile of "jrsm...',
>>> '[hidden email] <mailto:'[hidden email]>') called at
>>> path_updater.pl line 769
>>> main::process_xml_line('</items><bags><bag
>>> name="All_peptidase_genes" type="Gene" dat...',
>>> '/home/intermine/userprofile.xml') called at path_updater.pl line 806
>>> Processing element 44163Path update failed 2304 at update_to_0.94
>>> line 57.
>>>
>>> Any idea what this error means?
>>>
>>>
>>> -----Original Message-----
>>> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of
>> Alex
>>> Kalderimis
>>> Sent: Thursday, October 07, 2010 11:30 AM
>>> To: Vallejos, Andrew
>>> Cc: Intermine
>>> Subject: Re: [InterMine Dev] Upgrade_094 Update..
>>>
>>> On Thu, Oct 07, 2010 at 08:35:14AM -0500, Vallejos, Andrew wrote:
>>>> So, it looks like changes that I made to my model are causing the
>>> script
>>>> to gag on the userprofile.xml. Which I guess should be expected.
>>>>
>>>> RatMine contains a few legacy classes that do not conform to the SO
>>>> standards, despite being SO objects (aka synonym). Anyway, I should
>>> be
>>>> able to do a search/replace on the offending class names and get
>> that
>>>> righted.
>>>>
>>>> Example:
>>>> Old --> New
>>>>
>>>> Qtl --> QTL
>>>> SSLP --> SimpleSequenceLengthVariance
>>>> SSLPAllele --> Allele
>>>>
>>> As mentioned on the call, the best way to do this is to use the
>>> model_changes.0.94.yaml file, since it will also follow references to
>>> these classes, as well as when they are the root class of a path:
>>>
>>> in the second section of the yaml add:
>>>
>>> "Qtl":QTL
>>> "SSLP":SimpleSequenceLengthVariance
>>> "SSLPAllele":Allele
>>>
>>> As always with Yaml, be careful when adding lines to keep the
>>> indentation consistent.
>>>
>>> Alex
>>>
>>>> -----Original Message-----
>>>> From: A.J. Kalderimis [mailto:[hidden email]] On Behalf Of
>>> Alex
>>>> Kalderimis
>>>> Sent: Thursday, October 07, 2010 6:25 AM
>>>> To: Richard Smith
>>>> Cc: Vallejos, Andrew; Julie Sullivan
>>>> Subject: Re: [InterMine Dev] Upgrade_094 Update..
>>>>
>>>> This looks like we are trying to process an undefined element of a
>>>> pathstring. This really shouldn't happen, so I've put in a warning
>>>> againt undefined bits. I'll continue to investigate and try and work
>>>> out where this comes from.
>>>>
>>>> Alex
>>>>
>>>> On Wed, Oct 06, 2010 at 10:03:30PM +0100, Richard Smith wrote:
>>>>> It looks like something has turned up in some query XML that the
>>>> script
>>>>> wasn't expecting. We'll have to let Alex take a look at it
>>> tomorrow.
>>>>>
>>>>> If you could gzip the userprofile.xml and send it over that would
>> be
>>> a
>>>>> big help. But it's probably too big for e-mail? Maybe it's
>>> possible
>>>>> to extract just the profile it failed on?
>>>>>
>>>>> Cheers,
>>>>> Richard.
>>>>>
>>>>>
>>>>>
>>>>> On 06/10/2010 21:44, Vallejos, Andrew wrote:
>>>>>> [intermine@stearman scripts]$ perl update_to_0.94 paths
>>>>>> ProcessUse of uninitialized value in string eq at path_updater.pl
>>>> line
>>>>>> 149,<$INFH> line 35443.
>>>>>> at path_updater.pl line 8
>>>>>> main::__ANON__('Use of uninitialized value in string eq
>> at
>>>>>> path_updater.pl li...') called at path_updater.pl line 149
>>>>>> main::update_path('Chromosome.genes.primaryIdentifier',
>>>>>> 'HASH(0x12222780)') called at path_updater.pl line 242
>>>>>>
>>>>>
>>>>
>>>
>>> main::update_view('Webservice::InterMine::Query::Template=HASH(0x118d9c
>>>> b
>>>>>> 0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
>>>> "jrsm...')
>>>>>> called at path_updater.pl line 299
>>>>>>
>>>>>
>>>>
>>>
>>> main::update_query('Webservice::InterMine::Query::Template=HASH(0x118d9
>>>> c
>>>>>> b0)', '/home/intermine/userprofile.xml ll. 35443 in profile of
>>>>>> "jrsm...') called at path_updater.pl line 363
>>>>>> main::translate_query('template', '<template name="genes
>>> on
>>>>>> chromosome" title="Chromosome --&gt;...',
>>>>>> '/home/intermine/userprofile.xml ll. 35443 in profile of
>> "jrsm...',
>>>>>> '[hidden email] <mailto:'[hidden email]>') called at
>>>>>> path_updater.pl line 333
>>>>>> main::update_buffer('<template name="genes on
>> chromosome"
>>>>>> title="Chromosome --&gt;...', 'template',
>>>>>> '/home/intermine/userprofile.xml ll. 35443 in profile of
>> "jrsm...',
>>>>>> '[hidden email] <mailto:'[hidden email]>') called at
>>>>>> path_updater.pl line 769
>>>>>> main::process_xml_line('</items><bags><bag
>>>>>> name="All_peptidase_genes" type="Gene" dat...',
>>>>>> '/home/intermine/userprofile.xml') called at path_updater.pl line
>>> 806
>>>>>> Processing element 44163Path update failed 2304 at
>>>> update_to_0.94
>>>>>> line 57.
>>>>>>
>>>>>> Got another error.
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: [hidden email] <mailto:[hidden email]>
>> [mailto:[hidden email]]
>>> On
>>>>>> Behalf Of Richard Smith
>>>>>> Sent: Wednesday, October 06, 2010 3:42 PM
>>>>>> To: [hidden email] <mailto:[hidden email]>
>>>>>> Subject: Re: [InterMine Dev] Upgrade_094 Update..
>>>>>>
>>>>>> It looks like this is a FlyMine thing - we have a datasets.xml
>> file
>>>> in
>>>>>> the integrate directory that needed updating. Other mines don't
>>> have
>>>>>> one.
>>>>>>
>>>>>> The fix is to delete this line:
>>>>>>
>>>>>> inputfile = $svndirectory/$mine/integrate/datasets.xml
>>>>>>
>>>>>> From intermine/scripts/resources/updater.config.
>>>>>>
>>>>>> Cheers,
>>>>>> Richard.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 06/10/2010 21:24, Vallejos, Andrew wrote:
>>>>>>> I received a similar error message.
>>>>>>>
>>>>>>> [intermine@stearman scripts]$ perl update_to_0.94 paths
>>>>>>>
>>>>>>> Cannot open
>>>>>
>>>>
>>>
>>>> /home/intermine/build/ratmine_current/ratmine/integrate/datasets.xml,
>>>>>> No
>>>>>>> such file or directory - skipping
>>>>>>>
>>>>>>> at path_updater.pl line 8
>>>>>>>
>>>>>>> main::__ANON__('\x{d}Cannot open
>>>>>>> /home/intermine/build/ratmine_current/ratmine/in...') called at
>>>>>>> path_updater.pl line 798
>>>>>>>
>>>>>>> Processing element 740Path update failed 512 at update_to_0.94
>>> line
>>>>>> 57.
>>>>>>>
>>>>>>> Any word on the cause?
>>>>>>>
>>>>>>> -Andrew
>>>>>>>
>>>>>>>
>>>>>
>>>>
>>>
>>> -----------------------------------------------------------------------
>>>> -
>>>>>>>
>>>>>>> *From:* [hidden email] <mailto:[hidden email]>
>>> [mailto:[hidden email]]
>>>>>> *On
>>>>>>> Behalf Of *Kalpana Karra
>>>>>>> *Sent:* Tuesday, October 05, 2010 4:53 PM
>>>>>>> *To:* Intermine
>>>>>>> *Subject:* [InterMine Dev] Upgrade_094 Update..
>>>>>>>
>>>>>>> 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)
>>>>>>>
>>>>>>> 2) rRNA_gene is not in so_2_4_2.obo, so I had to leave it in
>>>>>>> sgd_additions file.
>>>>>>>
>>>>>>> 3) Had to comment out class MRNA in genomic_additions.xml (was
>>>> causing
>>>>>>> merging error due to fivePrimeUTR in my model)
>>>>>>>
>>>>>>> 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.
>>>>>>>
>>>>>>> 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.
>>>>>>>
>>>>>>> 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/data
>>>> s
>>>>>> ets.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).
>>>>>>>
>>>>>>> -Kalpana
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> dev mailing list
>>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>>>
>>>>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email] <mailto:[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


_______________________________________________
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[hidden email]
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