diff --git a/data-prep-pipeline/data_prep_pipeline/publish.conseq b/data-prep-pipeline/data_prep_pipeline/publish.conseq index f197d68d..bfa2bd04 100644 --- a/data-prep-pipeline/data_prep_pipeline/publish.conseq +++ b/data-prep-pipeline/data_prep_pipeline/publish.conseq @@ -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'" diff --git a/data-prep-pipeline/scripts/subtype_tree/create_subtype_tree.py b/data-prep-pipeline/scripts/subtype_tree/create_subtype_tree.py index aad7d2fa..990cfd51 100644 --- a/data-prep-pipeline/scripts/subtype_tree/create_subtype_tree.py +++ b/data-prep-pipeline/scripts/subtype_tree/create_subtype_tree.py @@ -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