make_compound_summary_table.conseq

rule get_rep_all_single_pt_compound_doses:
    inputs: treatment_metadata={'type' : 'raw-treatment_metadata', 'label' : 'Rep_all_single_pt'},
        script=fileref("scripts/rep_all_single_pt_cpd_doses_from_treatment_metadata.py")
    outputs: {
        'type': 'dataset-compound-doses',
        'dataset': 'Rep_all_single_pt',
        'filename': {'$filename': 'rep_all_single_pt_compound_doses.csv'},
    }
    run "python3 {{ inputs.script.filename }} {{ inputs.treatment_metadata.dataset_id }} rep_all_single_pt_compound_doses.csv"

rule get_oncref_compound_doses:
    inputs: treatment_metadata={'type' : 'raw-treatment_metadata', 'label' : 'Prism_oncology_AUC'},
        script=fileref("scripts/oncref_cpd_doses_from_treatment_metadata.py")
    outputs: {
        'type': 'dataset-compound-doses',
        'dataset': 'Prism_oncology_AUC',
        'filename': {'$filename': 'oncref_compound_doses.csv'},
    }
    run "python3 {{ inputs.script.filename }} {{ inputs.treatment_metadata.dataset_id }} oncref_compound_doses.csv"

rule expand_drug_metadata:
    inputs: drug_metadata={'type': 'drug-metadata', 'name': 'merged-drugs'},
        script=fileref('scripts/expand_drug_metadata.py')
    outputs: {
        'type': 'expanded-drug-metadata',
        'name': 'merged-drugs',
        'filename': {'$filename': 'expand_drug_metadata.csv'}
    }
    run "python3 {{ inputs.script.filename }} {{ inputs.drug_metadata.filename }} expand_drug_metadata.csv"

rule merge_predictability_into_compound_summary:
    inputs: predictions={'type': 'pred-models-csv', 'dataset': dataset}, #'[Prism_oncology_AUC, Rep_all_single_pt, RNAi_merged, Chronos_Combined] where only first 2 are compound-related'
        dataset_matrix={'type': 'dep-matrix', 'label': dataset}, # originally {'type':'raw-compound-summary', 'dataset': dataset'} where dataset is ['Rep_all_single_pt']
        dataset_for_compound_dashboard={'type': 'needs-compound-dashboard', 'dataset': dataset},    # The number of times this rule is run is limited by this artifact type's datasets
        drug_metadata={'type': 'expanded-drug-metadata', 'name': 'merged-drugs'},
        dose_data={'type': 'dataset-compound-doses', 'dataset': dataset},
        script=fileref("scripts/compound_summary_merge.py"),
        hdf5_utils=fileref('scripts/hdf5_utils.py')
    outputs: {
        'type': 'compound-summary',
        'dataset': "{{ inputs.predictions.dataset }}",
        'filename': {"$filename": "compound_summary_table.csv"}
    }
     run "cp {{ inputs.hdf5_utils.filename }} hdf5_utils.py"
     run "python3 {{ inputs.script.filename }} {{ inputs.predictions.filename }} {{ inputs.dataset_matrix.filename }} '{{inputs.dataset_for_compound_dashboard.units}}' {{ inputs.drug_metadata.filename }} {{ inputs.dose_data.filename }} compound_summary_table.csv"