CRDCDH 2431 #238
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CRDCDH 2431 #238
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vshand11
commented
Mar 11, 2025
vshand11
commented
- implemented CRDCDH2431.
- add index, synonym_1, in synonyms collection.
- updated mongo DAO function, find_pvs_by_synonym.
- updated mongo_db_script/restoreErrorCodeInQCResults.js
n2iw
requested changes
Mar 19, 2025
src/metadata_validator.py
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| self.log.error(msg) | ||
| return FAILED | ||
| self.study_name = study.get("studyName") | ||
| program = submission.get("organization") |
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"organization" property in Submission should be removed. Please find program via study_id only.
src/metadata_validator.py
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| @@ -322,6 +345,23 @@ def validate_required_props(self, data_record, msg_prefix): | |||
| if anode_definition["properties"][data_key]["required"]: | |||
| if data_value is None or not str(data_value).strip(): | |||
| result[ERRORS].append(create_error("M003",[msg_prefix, data_key], data_key, data_value)) | |||
| else: | |||
| # validate program name and study name required in CRDCDH-2431. Both are required properties. | |||
| if node_type == "program" and data_key == "program_name": | |||
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We should use entityType instead of node type, because node type can be different in different data commons. Same for the property name, we probably need to add some new configurations in model repo's content.json to configure property names.
src/metadata_validator.py
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| else: | ||
| data_record[PROPERTIES][data_key] = matched_val | ||
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|
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| if node_type in ["study"] and data_key in ["study_name", "clinical_study_name"]: |
There was a problem hiding this comment.
Similar to above comment, that study node name can be different among data commons, same as the name property.
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