harm-EB

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Workflow

The following workflow defines all tasks necessary to upload, preprocess, share, and map a new data dictionary.

Upload cohort data
Open Google Sheet
Run automated mapping for new data dictionary
Share Google Sheet with submitter
Prepare data dictionary for build
Run automated validation
Build data dictionary
View results
Add data dictionary to Version Control
Prepare git commit (click on Commit in Version menu)
Push changes to GitHub (click on Push in Version menu), and make pull request.
Delete Google sheet (Caution, cannot be undone)

IHCC Data Admin Tasks

Console

Action automated_mapping started at 2022-12-01T13:05:49.961Z (2022-12-01T13:05:49.961Z)

ERROR: Exit code 2

$ make -f Makefile automated_mapping

make cogs_pull
make[1]: Entering directory '/workspace'
cogs fetch
cogs pull
make[1]: Leaving directory '/workspace'
cp build/terminology.tsv templates/cogs.tsv
make build/suggestions_cogs.tsv
make[1]: Entering directory '/workspace'
python3 src/mapping-suggest/id-generator-templates.py -t templates/cogs.tsv -m build/metadata.tsv
Generating IDs for data dictionary: EB
python3 src/mapping-suggest/mapping-suggest-zooma.py -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -o build/intermediate/cogs_mapping_suggestions_zooma.tsv
Zooma config: {'zooma_annotate': 'http://192.168.0.199:8009/zooma/v2/api/services/annotate?propertyValue=', 'oxo_mapping': 'https://mapping.ihccglobal.app/api/mappings?fromId=', 'ols_term': 'https://registry.ihccglobal.app/api/terms?iri=', 'ols_oboid': 'https://registry.ihccglobal.app/api/terms?obo_id=', 'min_match_probability': 0.1, 'rescale_nlp_matches': {'low': 0, 'high': 0.9}, 'zooma_confidence_mappings': {'LOW': 0.51, 'MEDIUM': 0.76, 'GOOD': 0.98, 'HIGH': 1}}
Zooma matching successful. First two results:
     term          match  confidence
0  Person  GECKO:0000066        0.76
1  Person  GECKO:0000055        0.76
python3 src/mapping-suggest/mapping-suggest-nlp.py -z data/ihcc-mapping-suggestions-zooma.tsv -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -g build/intermediate/gecko-xrefs-sparql.csv -o build/intermediate/cogs_mapping_suggestions_nlp.tsv
/usr/local/lib/python3.8/dist-packages/sklearn/linear_model/_stochastic_gradient.py:173: FutureWarning: The loss 'log' was deprecated in v1.1 and will be removed in version 1.3. Use `loss='log_loss'` which is equivalent.
  warnings.warn(
NLP matching successful. First two results:
                          term        match  confidence
0  ObjectiveInformation.weight  CMO:0000012    0.838037
1     ObjectiveInformation.bmi  CMO:0000021    0.693854
python3 src/mapping-suggest/merge-mapping-suggestions.py -t templates/cogs.tsv  -s build/intermediate/cogs_mapping_suggestions_zooma.tsv  -s build/intermediate/cogs_mapping_suggestions_nlp.tsv -o build/suggestions_cogs.tsv
['build/intermediate/cogs_mapping_suggestions_zooma.tsv', 'build/intermediate/cogs_mapping_suggestions_nlp.tsv']
Traceback (most recent call last):
  File "src/mapping-suggest/merge-mapping-suggestions.py", line 59, in <module>
    dfs["Suggested Categories"] = dfs[["confidence", "match", "match_label"]].agg(" ".join, axis=1)
  File "/usr/local/lib/python3.8/dist-packages/pandas/core/frame.py", line 7586, in aggregate
    return self.apply(func, axis=axis, args=args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pandas/core/frame.py", line 7768, in apply
    return op.get_result()
  File "/usr/local/lib/python3.8/dist-packages/pandas/core/apply.py", line 185, in get_result
    return self.apply_standard()
  File "/usr/local/lib/python3.8/dist-packages/pandas/core/apply.py", line 276, in apply_standard
    results, res_index = self.apply_series_generator()
  File "/usr/local/lib/python3.8/dist-packages/pandas/core/apply.py", line 290, in apply_series_generator
    results[i] = self.f(v)
TypeError: sequence item 2: expected str instance, float found
make[1]: *** [Makefile:385: build/suggestions_cogs.tsv] Error 1
make[1]: Leaving directory '/workspace'
make: *** [Makefile:423: automated_mapping] Error 2

ERROR: Exit code 2