Ccdidash 121#22
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Pull request overview
This PR updates the treatments_table index configuration in indices.yaml, migrating it from a single monolithic cypher_queries block to the repository’s initial_query + update_queries indexing pattern and expanding treatment sourcing across treatment subtypes.
Changes:
- Refactors
treatments_tableindexing to useinitial_queryseeding plus multipleupdate_queriesthat independently populate treatment/participant, study, survival, treatment response, and sample/diagnosis/GA/file facet fields. - Introduces subtype-qualified treatment document IDs (e.g.,
treatment_chemotherapy:<id>) and normalizes treatment subtype properties into common fields (treatment_type,treatment_agent, etc.). - Replaces the prior “many combinations” facet-building Cypher with a context-based approach for sample/model-linked sample traversal and associated files/diagnoses/genetic analyses.
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JoonLeeNIH
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JoonLeeNIH
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Needs changes where I commented. The sample_diagnosis_genetic_analysis_file_filters query looks good. It's the same as the one for the participants_table, but the treatment's ID is carried throughout.
| CASE | ||
| WHEN trad.radiation_therapy_type IS NULL OR trad.radiation_therapy_type = '' THEN [] | ||
| ELSE [trim(trad.radiation_therapy_type)] | ||
| END AS treatment_agent, | ||
| trad.radiation_therapy_type AS treatment_agent_str, |
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radiation_therapy is a list in the database.
| CASE | ||
| WHEN trad.treatment_type IS NULL OR trad.treatment_type = '' THEN ['radiation'] | ||
| ELSE [item IN split(trad.treatment_type, ';') | trim(item)] | ||
| END AS treatment_type, | ||
| CASE | ||
| WHEN trad.treatment_type IS NULL OR trad.treatment_type = '' THEN 'radiation' | ||
| ELSE trad.treatment_type | ||
| END AS treatment_type_str |
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treatment_type is a list in the database.
| (cg:consent_group)-[:of_participant]->(p), | ||
| (stu:study)-[:of_consent_group]->(cg) |
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The relationship arrows for these two lines in the query need to go the other direction.
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