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Change context matrix to subtype matrix #246

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Change context matrix to subtype matrix #246

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c30e132
Custom rule for PedDep in 25Q2: Adding BALL and TALL subtypes underne…
acameron13 Apr 17, 2025
f44577f
Changing name of ContextMatrix to be SubtypeMatrix in the release fil…
acameron13 Apr 17, 2025
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2 changes: 1 addition & 1 deletion data-prep-pipeline/data_prep_pipeline/publish.conseq
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Expand Up @@ -83,4 +83,4 @@ rule publish_context_matrix:
update_taiga_script=fileref('upload_to_taiga.py')
outputs:{"type": "release_context_matrix_published"}

run "python3 {{inputs.update_taiga_script.filename}} {{inputs.release_taiga_id.dataset_id}} 'Created ContextMatrix for release' 'ContextMatrix' {{inputs.context_matrix.filename}} 'csv_matrix'"
run "python3 {{inputs.update_taiga_script.filename}} {{inputs.release_taiga_id.dataset_id}} 'Created ContextMatrix for release' 'SubtypeMatrix' {{inputs.context_matrix.filename}} 'csv_matrix'"
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Should we call it "Subtype Matrix" in context manager as well?

(Currently it's being called "Context Matrix")

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Yes, that's the plan. I'm making that part of the renaming changes

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Cool, thanks

4 changes: 4 additions & 0 deletions data-prep-pipeline/scripts/subtype_tree/create_subtype_tree.py
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Expand Up @@ -322,6 +322,10 @@ def add_non_cancerous_lineages(non_cancerous_types, oncotable):
## DECISION: Add cancerous nodes at level 1, right underneath lineage
parent_code = lin_node.DepmapModelType

## Hard-coded PedDep request for 25Q2: Add BALL and TALL under Lymphoid Neoplasm
if new_type.DepmapModelType in ['BALL', 'TALL']:
parent_code = 'LNM'

elif new_type.OncotreePrimaryDisease == "Non-Cancerous":
if lin_node.NodeSource == "Oncotree":
## DECISION: Add underneath the Non-Cancerous Level 1 node
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