tutorial post processing

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tutorial post processing

JD Wong

I ran ant -v in the postprocess folder of malariamine to successful completion, but it seems like post processing did not correctly process the data in postgres.

select distinct geneid from exon;
gives me an empty set


select primaryidentifier, exon.length, residues from exon, intermine_sequence where sequenceid = intermine_sequence.id and exon.primaryidentifier = 'exon.32017';
gives me:
 primaryidentifier | length |                               residues
 exon.32017        |     14 | 3000006,1838895,14,org.intermine.bio.util.ClobAccessReverseComplement

where it should give me the sequence itself, right?

All steps before this have run smoothly, and the malarmine/project.xml contains
    <post-process name="create-references"/>
    <post-process name="transfer-sequences" dump="true"/>

    <!-- this runs the postprocessing steps in all sources -->
    <post-process name="do-sources"/>

    <post-process name="summarise-objectstore"/>
    <post-process name="create-autocomplete-index"/>
    <post-process name="create-search-index"/>

My output file is here: http://nutria.bio.indiana.edu:8080/output/postprocessing_output.txt
(line 4668): it looks like it is performing these actions... but I don't see the results

The tutorial suggests I should have received differing results for the tests I ran after post processing.  Am I doing this correctly?


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