tripal pub cvterm not populated on site install

Created on 7 May 2018  路  4Comments  路  Source: tripal/tripal

recreated by @laceysanderson

The publicaiton bundle type field does not display any options.
For some reason this statement returns no results in schema__additional_type_widget.

      $sql = "
          SELECT
            CVTS.cvterm_id, CVTS.name
          FROM {cvtermpath} CVTP
            INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
            INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
            INNER JOIN {cvterm} CVTT ON CVTP.type_id = CVTT.cvterm_id
            INNER JOIN {dbxref} DBXO ON DBXO.dbxref_id = CVTO.dbxref_id
            INNER JOIN {db} DBO      ON DBO.db_id = DBXO.db_id
          WHERE
            DBO.name = :vocabulary AND DBXO.accession = :accession AND
            (CVTT.name = 'is a' OR CVTT.name = 'is_a') AND
            CVTS.name != CVTO.name AND
            NOT CVTS.is_obsolete = 1
          ORDER BY CVTS.name ASC
       ";

We do have tripal_pub cvterms. however this is is looking basd on db:accession, for TPUB: 0000015. I htink my terms all have db = tripal... this might be the problem?

edit: nah terms are there http://localhost:8083/cv/lookup/TPUB ...

bug tripal-7.x-3.x

All 4 comments

cvterm path isnt populate for this CV.

manually populating the cvtermpath for pubs fixes the issues.

Why doesnt cvtermpath populate for tripalpub on install?

Confirmed that new installs of tripal don't have publication types available and that populating cvtermpath for tripal_pub fixes the issue.

I think this has been fixed. I have recently installed a new Tripal instance and the publication types are present. I'm sure we fixed this along the way and forgot to update this issue.

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