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fix: resolving circular dependencies in MoA steps #69

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Merged
DSuveges merged 2 commits into from
Mar 2, 2026
Merged

fix: resolving circular dependencies in MoA steps #69

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c09c4e2
fix: circural dependencies resolved
DSuveges Mar 2, 2026
28b05e6
Update config.yaml
DSuveges Mar 2, 2026
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2 changes: 1 addition & 1 deletion config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -413,7 +413,7 @@ steps:
source:
chembl_mechanism: input/drug/chembl_mechanism.jsonl
chembl_target: input/drug/chembl_target.jsonl
target: output/target
target: intermediate/target/ensembl/homo_sapiens.parquet
destination: output/drug_mechanism_of_action
##################################################################################################

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2 changes: 1 addition & 1 deletion pyproject.toml
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@@ -1,6 +1,6 @@
[project]
name = "PTS"
version = "26.03.0-dev.14"
version = "26.03.0-dev.15"
description = "Open Targets Pipeline Transformation Stage"
readme = "README.md"
requires-python = ">=3.11,<3.14"
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5 changes: 2 additions & 3 deletions src/pts/pyspark/drug_mechanism_of_action.py
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Expand Up @@ -145,9 +145,8 @@ def _chembl_target(target_df: DataFrame, gene_df: DataFrame) -> DataFrame:

# Get gene IDs from gene data - explode proteinIds
genes = gene_df.select(
f.col('id').alias('geneId'),
f.explode('proteinIds.id').alias('uniprot_id'),
)
f.col('id').alias('geneId'), f.array_union('uniprot_trembl', 'uniprot_swissprot').alias('uniprotIds')
).select('geneId', f.explode('uniprotIds').alias('uniprot_id'))

# Join target with genes on uniprot_id or geneId
joined = target.join(
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