Problems mith make onthology

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Problems mith make onthology

Marcel Kerkveld
Hi,

While trying to install chado 1.22, I get into troubles when importing onthologies.
I don't seem to be able to do make onthologies, getting the following output.

./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4,5
fetching files for Plant Ontology
  +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
    updated
    loading...Cannot quote a reference at /home/mke/perl5/lib/perl5/DBIx/DBStag.pm line 3736.
System call 'stag-storenode.pl -d 'dbi:Pg:dbname=mkechado;host=localhost;port=5432' --user chadotest  --password 'mypassword'  tmp/po/po_anatomy.oboxml' failed: 256
failed: 256 at lib/Bio/Chado/Builder.pm line 367, <STDIN> line 1.
make: *** [ontologies] Error 2




Marcel Kerkveld

Analist Bioinformatics




Rijk Zwaan Breeding B.V.

Bio-Informatics

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Re: Problems mith make onthology

Scott Cain
Hi Marcel,

I just tried to reproduce this and failed (that is, I was able to successfully load PO after squashing a bug that causes a problem between Tripal and dBIx::DBSchema--unrelated to your problem though).

I wonder if either the download of PO was truncated or its conversion to oboxml was truncated, resulting in a corrupted file.  Take a look at the two po_anatomy files in tmp/po (.obo and .oboxml).  At the end of the obo file, I have:

[Typedef]
id: participates_in
name: participates_in
holds_over_chain: part_of participates_in

and at the end of the oboxml file I have:

  <cvterm_relationship>
    <type_id>part_of</type_id>
    <subject_id>PO:0030087</subject_id>
    <object_id>PO:0030018</object_id>
  </cvterm_relationship>
  <!--is_a relationship types between typedefs-->
  <!--cvterm metadata-->
  <!--instance-level relations-->
</chado>

(hmm, hopefully, the xml snippet I just pasted will render in your mail client; it ends with a closing "chado" tag; if not, let me know and I'll find somewhere else for it.)

If both of those look ok, I'm not sure what the problem is.  The first obvious thing to try is to remove the tmp/po directory and try the load again.  Also, if it doesn't work, can you tell me what is on and around line 3736 of DBStag.pm (the line where the error occurs)?

Thanks and good luck,
Scott



On Fri, May 31, 2013 at 5:58 AM, Marcel Kerkveld <[hidden email]> wrote:
Hi,

While trying to install chado 1.22, I get into troubles when importing onthologies.
I don't seem to be able to do make onthologies, getting the following output.

./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4,5
fetching files for Plant Ontology
  +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
    updated
    loading...Cannot quote a reference at /home/mke/perl5/lib/perl5/DBIx/DBStag.pm line 3736.
System call 'stag-storenode.pl -d 'dbi:Pg:dbname=mkechado;host=localhost;port=5432' --user chadotest  --password 'mypassword'  tmp/po/po_anatomy.oboxml' failed: 256
failed: 256 at lib/Bio/Chado/Builder.pm line 367, <STDIN> line 1.
make: *** [ontologies] Error 2




Marcel Kerkveld

Analist Bioinformatics




Rijk Zwaan Breeding B.V.

Bio-Informatics

P.O. Box 40 | 2678 ZG | De Lier | The Netherlands
T: <a href="tel:%2B31%20%280%29174%20532%20300" value="+31174532300" target="_blank">+31 (0)174 532 300 | F: <a href="tel:%2B31%20%280%29174%20515%20334" value="+31174515334" target="_blank">+31 (0)174 515 334 | E:
[hidden email]
W:
http://www.rijkzwaan.com
Chamber of Commerce Haaglanden: 24126474 0000


The information contained in this e-mail (and attachments if any) is exclusively intended for the recipient(s) named above and may be confidential, proprietary, and/or legally privileged.

Unintentional disclosure of this e-mail does not constitute a waiver of any right or privilege. Please notify us if you are not the intended recipient and do not use, print, copy, forward,

or disclose (any part of) this e-mail, but delete it (and attachments and copies if any) subsequently. Thank you.

You can find disclaimer translations in different languages by visiting our website http://www.rijkzwaan.com/edisclaimer

The registration number of each Rijk Zwaan company can be found using the following link:

http://www.rijkzwaan.com/registrationnumbers

 

 

 


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Ontario Institute for Cancer Research

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