OBOLoader error when trying to install on Tripal 3

[carolyncaron]

I received the following error message:

Warning: array_key_exists(): The first argument should be either a string or an integer in OBOImporter->addDB() (line 2217 of /home/ubuntu/workspace/sites/all/modules/tripal/tripal_chado/includes/TripalImporter/OBOImporter.inc).
Exception: Cannot cache terms without a default DB.Array ( [id] => Array ( [0] => CO_020:0000000 ) [name] => Array ( [0] => multicrop passport ontology ) [comment] => Array ( [0] => release date: June 30, 2015\nversion: 2.1. Adapted from FAO/Bioversity Multi-Crop Passport Descriptors, December 2015\ncoverage: Multi-Crop Passport Descriptors\ncreator: Jeffrey Detras, Tom Hazekamp and Richard Bruskiewich, updated by Leo Valette\npublisher: Bioversity International and IRRI under the Generation Challenge Program ) [xref] => Array ( [0] => GCPDomainModel:CO_000:0000165 ) ) in OBOImporter->cacheTermStanza() (line 1721 of /home/ubuntu/workspace/sites/all/modules/tripal/tripal_chado/includes/TripalImporter/OBOImporter.inc).

[laceysanderson]

I retrieved the same error. I was able to move forward by downgrading to 7.x-3.0-rc2, loading the ontology and then re-upgrading:

1. git status to see your current version
2. git checkout 7.x-3.0-rc2 to check out the 2nd release candidate
3. Navigate to admin/tripal/loaders/chado_vocabs/obo_loader in your site
4. Select “Multi-crop Passport Descriptors Ontology” from the drop-down
5. Click “Import OBO File” and run the job
6. Then switch back to your previous tripal version using git checkout [previous version]

[guignonv]

Several issues remains in the obo file but we can remove in the end of the file, the term:

[Term]
id: ID:0000000
name: persistent unique identifier
comment: Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. \n\nThe Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of  a DOI, to PGRFA at the accession level (http://www.planttreaty.org/doi). \nGenebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier \nsimilar in most respects to the PUID whenever they exchange information on accessions with third parties (e.g. NOR017:NGB17773:ALLIUM).
synonym: "PUID" RELATED []
is_a: CO_020:0000074 ! multicrop passport descriptor
created_by: lvalette
creation_date: 2015-12-15T09:38:00Z

[guignonv]

Complementary info:

Step 1: Preloading File sites/v3.chadocontroller.info/modules/brapi/cv/mcpd_v2.1_151215.obo...
array_key_exists(): The first argument should be either a string or an integer OBOImporter.inc:2217                                                                                                  [warning]
Cannot cache terms without a default DB.Array
(
    [id] => Array
        (
            [0] => CO_020:0000000
        )

    [name] => Array
        (
            [0] => multicrop passport ontology
        )

    [comment] => Array
        (
            [0] => release date: June 30, 2015\nversion: 2.1. Adapted from FAO/Bioversity Multi-Crop Passport Descriptors, December 2015\ncoverage: Multi-Crop Passport Descriptors\ncreator: Jeffrey Detras, Tom Hazekamp and Richard Bruskiewich, updated by Leo Valette\npublisher: Bioversity International and IRRI under the Generation Challenge Program
        )

    [xref] => Array
        (
            [0] => GCPDomainModel:CO_000\:0000165
        )

)

[site http://v3.chadocontroller.info] [TRIPAL ERROR] [TRIPAL_JOB] Cannot cache terms without a default DB.Array(    [id] => Array        (            [0] => CO_020:0000000        )    [name] => Array        (            [0] => multicrop passport ontology        )    [comment] => Array        (            [0] => release date: June 30, 2015\nversion: 2.1. Adapted from FAO/Bioversity Multi-Crop Passport Descriptors, December 2015\ncoverage: Multi-Crop Passport Descriptors\ncreator: Jeffrey Detras, Tom Hazekamp and Richard Bruskiewich, updated by Leo Valette\npublisher: Bioversity International and IRRI under the Generation Challenge Program        )    [xref] => Array        (            [0] => GCPDomainModel:CO_000\:0000165        ))