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chore: migrate etl_reactome → pts_reactome #175

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Merged
DSuveges merged 1 commit into from
May 11, 2026
Merged

chore: migrate etl_reactome → pts_reactome #175

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29 changes: 0 additions & 29 deletions src/orchestration/dags/config/etl.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -22,35 +22,6 @@ spark_settings: {

# ============================= STEP CONFIGURATION =============================
steps: {
reactome: {
input: {
pathways: {
format: "csv"
path: ${common.path}"/input/reactome/ReactomePathways.txt"
options: [
{ k: "sep", v: "\\t" }
{ k: "header", v: false }
{ k: "inferSchema", v: true }
]
}
relations: {
format: "csv"
path: ${common.path}"/input/reactome/ReactomePathwaysRelation.txt"
options: [
{ k: "sep", v: "\\t" }
{ k: "header", v: false }
{ k: "inferSchema", v: true }
]
}
}
output: {
reactome: {
format: ${common.output_format}
path: ${common.output_path}"/intermediate/reactome"
}
}
}

expression: {
input: {
rna: {
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10 changes: 10 additions & 0 deletions src/orchestration/dags/config/pts.yaml
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Expand Up @@ -38,6 +38,16 @@ steps:
destination: output/go/go.parquet
##################################################################################################

#: REACTOME STEP :################################################################################
reactome:
- name: pyspark reactome
pyspark: reactome
source:
pathways: input/reactome/ReactomePathways.txt
relations: input/reactome/ReactomePathwaysRelation.txt
destination: output/reactome
##################################################################################################

#: EXPRESSION STEP :##############################################################################
expression:
- name: unzip normal tissue
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9 changes: 4 additions & 5 deletions src/orchestration/dags/config/unified_pipeline.yaml
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Expand Up @@ -95,6 +95,9 @@ steps:
pis_target:
pis_target_prioritisation:
# PTS STEPS
pts_reactome:
depends_on:
- pis_reactome
pts_go:
depends_on:
- pis_go
Expand Down Expand Up @@ -406,10 +409,6 @@ steps:
num_partitions: 4
depends_on:
- pts_expression
etl_reactome:
num_partitions: 1
depends_on:
- pis_reactome
etl_otar:
ppp_only: true
depends_on:
Expand All @@ -420,7 +419,7 @@ steps:
depends_on:
- pts_disease
- pts_target
- etl_reactome
- pts_reactome
- pts_target_safety
- pts_target_gene_essentiality
etl_search_facet:
Expand Down
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