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Manages site-wide files and associates them with content in a Tripal site.
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Load EDAM Vocabulary - incorrect response from EBI #8

Closed Ferrisx4 closed 3 years ago

Ferrisx4 commented 4 years ago

When launching the job to load the EDAM vocabulary, the server gets a bad response from EBI:

Cannot find the ontology via an EBI OLS lookup: EDAM_data. \nWe tried to access: http://www.ebi.ac.uk/ols/api/ontologies/EDAM_dataEBI Reported: Resource not found. Consider finding the OBO file for this ontology and manually loading it first.
Cannot find the term via an EBI OLS lookup: EDAM_data:0005. We tried to access: "http://www.ebi.ac.uk/ols/api/ontologies//terms/0005" EBI Reported: No message available. Consider finding the OBO file for this ontology and manually loading it first.
Performing EBI OLS Lookup for: EDAM_data:0006
Cannot find the term via an EBI OLS lookup: EDAM_data:0006. We tried to access: "http://www.ebi.ac.uk/ols/api/ontologies//terms/0006" EBI Reported: No message available. Consider finding the OBO file for this ontology and manually loading it first.
Performing EBI OLS Lookup for: EDAM_data:0007
Cannot find the term via an EBI OLS lookup: EDAM_data:0007. We tried to access: "http://www.ebi.ac.uk/ols/api/ontologies//terms/0007" EBI Reported: No message available. Consider finding the OBO file for this ontology and manually loading it first.

This continues on for every term (~3000 - http://edamontology.org/EDAM.obo), and then the same for 'format', 'operation', and 'topic'.

Letting it run to completion (instead of cancelling it) results in a Division by Zero error from TripalImporter.inc:646 followed by evidently not loading any type defs or terms:

Step 3: Loading type defs...
Step 4: Loading terms... %. Memory: 46,783,152 bytes.

The double slash in the URL does not seem to be the cause.

spficklin commented 4 years ago

Oh @Ferrisx4 . I'm sorry. The problems here are related to the OBO Loader. There is a PR to fix it here: https://github.com/tripal/tripal/pull/1117.

Perhaps you could now, pull that code from the PR and retest it? That would be sufficient as a functional test for that PR

Ferrisx4 commented 4 years ago

Hi @spficklin, I pulled the PR and tested it. It was successful other than a few warnings during step #4:


Step 4: Loading terms... %. Memory: 59,168,560 bytes.
Cannot add an Alt ID without an accession: 'topic_0197'
Cannot add an Alt ID without an accession: 'topic_3076'
Cannot add an Alt ID without an accession: 'topic_3040'
Step 5: Cleanup...100.00 %. Memory: 59,433,896 bytes. ```
spficklin commented 4 years ago

Yeah, those warnings are from badly formatted alt_ids in the OBO. I'm not sure if those were historically made incorrectly or if there were entered into the OBO incorrect. But it doesn't inhibit loading of the vocabulary.

spficklin commented 4 years ago

Would you mind leaving a comment about the successful test on the PR? I'll mark it has having been approved and that should just trigger one more code review.

spficklin commented 3 years ago

I think this issue is now resolved.