Go site 2210 gorule 0000027 must check dbs are in the db xref file #677
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Linking to geneontology/go-site#2210 |
ontobio/io/gpadparser.py
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| @@ -235,6 +239,8 @@ def parse_line(self, line): | |||
| references = self.validate_curie_ids(assoc.evidence.has_supporting_reference, split_line) | |||
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@mugitty Is there any overlap of logic between self.validate_curie_ids here and self._validate_curie_using_db_xrefs just below? Could self._validate_curie_using_db_xrefs be incorporated into self.validate_curie_ids?
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@dustine32 , validate_curie_ids calls _validate_id . This checks for things like "DB:id" or for annotations, prefix has to be in GO id space. However, it does not validate against the syntax pattern specified in the db-xrefs file. This is meant as a catch-all for any identifier in the GAF line that has a database field and id_syntax
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@mugitty Would there be any issue if you incorporated this db-xrefs syntax pattern checking inside _validate_id? It looks like _validate_id assumes every id is a CURIE, which by definition should always have colon-separated database field and id_syntax (else an error will be reported). The only complication I could think of is if a metadata/db-xrefs is not supplied when _validate_id is called but you could just make this optional in _validate_id (i.e., if self.config.db_type_name_regex_id_syntax is not None).
I guess my main concern is separating validation logic throughout the code that really should be in the same place.
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@dustine32, as you suggested, I could incorporate in _validate_id and add a check for self.config.db_type_name_regex_id_syntax is not None.
Let me update
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@mugitty Do we already have a test for gorule 0000027 somewhere? |
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@dustine32 , I pushed updates to combine id syntax change into _validate_id method |
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@mugitty Awesome, thank you so much! Do we have a test for wrong IDs that should return that "does not match any id_syntax patterns" warning message? It would be good to confirm your new code can be triggered by this. |
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I ran it through https://github.com/geneontology/go-site/blob/master/docs/gorules_test_errors.gaf . The output error.json file contains things such as This update outputs warnings. Groups can update the id_syntax and or ids based on these errors |
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@mugitty Thanks again! It's great that you confirmed the |
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@dustine32, since these are validation tests, I added tests to both test_gafparser.py and test_gpad_parser.py |
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