RichardBruskiewich
commented
2 years ago Strange bug reported by @kevinschaper:
ERROR:koza.app:Validation error while processing:
{
'DB': 'WB',
'DB_Object_ID': 'WBGene00000013',
'DB_Object_Symbol': 'abf-2',
'Qualifier': 'involved_in',
'GO_ID': 'GO:0050830',
'DB_Reference': 'WB_REF:WBPaper00045314|PMID:24882217',
'Evidence_Code': 'IEP',
'With_or_From': '', 'Aspect': 'P',
'DB_Object_Name': '',
'DB_Object_Synonym': 'C50F2.10|C50F2.e',
'DB_Object_Type': 'gene', 'Taxon': 'taxon:6239|taxon:46170', 'Date': '20140827',
'Assigned_By': 'WB',
'Annotation_Extension': '',
'Gene_Product_Form_ID': ''
}Traceback (most recent call last):
...
File "pydantic/dataclasses.py", line 99, in pydantic.dataclasses._generate_pydantic_post_init._pydantic_post_init
# +=======+=======+=======+
pydantic.error_wrappers.ValidationError: 4 validation errors for Gene
in_taxon
value is not a valid list (type=type_error.list)
in_taxon
string does not match regex "^[a-zA-Z_]?[a-zA-Z_0-9-]*:([A-Za-z0-9_][A-Za-z0-9_.-]*[A-Za-z0-9./\(\)\-><_:;]*)?$" (type=value_error.str.regex; pattern=^[a-zA-Z_]?[a-zA-Z_0-9-]*:([A-Za-z0-9_][A-Za-z0-9_.-]*[A-Za-z0-9./\(\)\-><_:;]*)?$)
in_taxon
string does not match regex "^(http|ftp)" (type=value_error.str.regex; pattern=^(http|ftp))
in_taxon
instance of OrganismTaxon, tuple or dict expected (type=type_error.dataclass; class_name=OrganismTaxon)The PubMed reference is PMID:24882217 which talks about an interaction between C. elegans and S. aureus (which is why the value in the field is a piped string list).
Might not be a common occurrence, but perhaps, one to support. I'll modify the code accordingly. DONE: Commit https://github.com/monarch-initiative/monarch-ingest/pull/152/commits/c658aae1174bc7c108f745a68a233edb70331260.
Note that along the way, a flaw was discovered in the unit tests: the tests only run the last row of data in the test_rows() fixture. I ended up commenting/uncommenting individual entries to run every test row separately to ensure that the underlying test passed. But, the test pattern needs to be fixed.
kevinschaper
GOA ingest is substantially complete, ready for stress testing on full datasets. Resolves Monarch Ingest issue https://github.com/monarch-initiative/monarch-ingest/issues/64.