nci-cidc-schemas 0.27.8__tar.gz → 0.27.9__tar.gz
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- {nci_cidc_schemas-0.27.8/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.27.9}/PKG-INFO +1 -1
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/__init__.py +1 -1
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/sample.json +4 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/shipping_core.json +3 -3
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/h_and_e_template.json +5 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +5 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +5 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json +5 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/pbmc_template.json +5 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/plasma_template.json +5 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/tissue_slide_template.json +5 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json +5 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json +5 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9/nci_cidc_schemas.egg-info}/PKG-INFO +1 -1
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_1.json +7 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_1PA_multiWES.json +6 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_cytof_with_analysis.json +6 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_ihc.json +4 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_minimal.json +2 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/cidc_test_data/manifest_data.py +5 -4
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/cidc_test_data/utils.py +1 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_json_validation.py +2 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_trial_core.py +3 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_unprism.py +8 -8
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/LICENSE +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/MANIFEST.in +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/README.md +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/cli.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/constants.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/json_validation.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/metaschema/strict_meta_schema.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/migrations.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2 +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/prism/__init__.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/prism/constants.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/prism/core.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/prism/extra_metadata.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/prism/merger.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/prism/pipelines.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/aliquot.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_bam.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_bam_bai.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_bed.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_bigwig.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_binary.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_clinical_csv.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_clinical_docx.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_clinical_xlsx.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_cncf.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_cns.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_core.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_csv.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_elisa_xlsx.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_fastq_gz.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_fcs.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_file.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_gz.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_image.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_jpg.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_json.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_junction.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_log.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_maf.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_narrowPeak.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_npx.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_ome_tiff.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_pdf.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_png.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_rcc.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_rdata.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_tbi.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_text.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_tsv.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_vcf.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_vcf_gz.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_xlsx.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_yaml.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_zip.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/atacseq_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/antibody.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/assay_core.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/available_assays.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/available_ngs_analyses.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/composite_image.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/controls.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/enrichment_core.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/excluded_samples.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/hande_local_file.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/image.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/imaging/mif_entry.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/imaging/mif_export.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/imaging/mif_input.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/imaging/mif_roi.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/imaging_data.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/local_file.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/mapping.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/mibi_antibody.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/mibi_imaging/mibi_files.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/mif_antibody.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/multiple_local_files.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/ngs_assay_record.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/fusion.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/microbiome.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/msisensor.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/neoantigen.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/rna_analysis.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/rna_level1_analysis.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/rseqc.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/salmon.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/star.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs/rna/trust4.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs_assay_core.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/ngs_assay_record.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/reads_core.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/components/reads_with_index.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/ctdna_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/cytof_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/cytof_assay_core.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/elisa_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/hande_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/ihc_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/mibi_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/microbiome_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/mif_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/misc_data.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/nanostring_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/olink_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/rna_assay-v0.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/rna_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/tcr_analysis.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/tcr_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/wes_analysis.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/wes_assay.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/wes_core.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/assays/wes_tumor_only_analysis.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/clinical_data.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/clinical_trial.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/participant.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/analyses/wes_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/clinical_data_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/ctdna_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/cytof_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/elisa_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/hande_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/ihc_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/mibi_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/microbiome_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/mif_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/misc_data_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/nanostring_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/olink_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/rna_bam_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/rna_fastq_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/tcr_fastq_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/wes_bam_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/assays/wes_fastq_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/template.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/template_reader.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/template_writer.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/unprism.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/util.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/nci_cidc_schemas.egg-info/SOURCES.txt +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/nci_cidc_schemas.egg-info/dependency_links.txt +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/nci_cidc_schemas.egg-info/entry_points.txt +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/nci_cidc_schemas.egg-info/not-zip-safe +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/nci_cidc_schemas.egg-info/requires.txt +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/nci_cidc_schemas.egg-info/top_level.txt +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/requirements.txt +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/setup.cfg +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/setup.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/__init__.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/conftest.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/constants.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinical_test_file.1.csv +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinical_test_file.1.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinical_test_file.2.bom.csv +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinical_test_file.2.csv +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinical_test_file.2.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinical_test_file.3.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinical_test_file.docx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/date_examples.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/elisa_test_file.1.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/elisa_test_file.2.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/hande_err_template.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/olink/invalid_olink_assay_1_NPX.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/olink/olink_assay_1_NPX.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/olink/olink_assay_2_NPX.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/olink/olink_assay_combined.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/pbmc_invalid.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/pbmc_manifest_valid.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/1.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/a.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/b.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/c.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/d1/3.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/d1/d2/2.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/invalid_ref.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/target-templates/atacseq_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/target-templates/rna_level1_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/target-templates/wes_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/schemas/target-templates/wes_tumor_only_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/tiny_invalid_manifest.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/tiny_valid_manifest.xlsx +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/__init__.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/cidc_test_data/__init__.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/cidc_test_data/analysis_data.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/cidc_test_data/assay_data.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/schema/test_schema.json +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/test_cidc_data_model.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/test_constants.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/test_core.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/test_extra_metadata.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/test_merger.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/test_pipelines.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_artifacts.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_assays.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_clinicaltrial_examples.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_migrations.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_schemas.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_strict_meta_schema.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_template.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_template_reader.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_template_writer.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_templates.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/test_util.py +0 -0
- {nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/utils/test_template_generator.py +0 -0
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{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_1.json
RENAMED
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{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_ihc.json
RENAMED
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{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/tests/prism/cidc_test_data/manifest_data.py
RENAMED
|
@@ -32,7 +32,7 @@ def plasma() -> PrismTestData:
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@@ -822,6 +822,7 @@ def normal_blood_dna() -> PrismTestData:
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822
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823
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@@ -1293,7 +1294,7 @@ def tumor_tissue_dna() -> PrismTestData:
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@@ -1714,7 +1715,7 @@ def tumor_tissue_rna() -> PrismTestData:
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1714
1715
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1715
1716
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@@ -128,6 +128,7 @@ def test_trial_core():
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128
128
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|
@@ -142,6 +143,7 @@ def test_trial_core():
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143
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+
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145
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|
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|
|
146
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|
sm_validator.validate(sample2)
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|
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|
@@ -75,6 +75,7 @@ def test_clinicaltrial_simple():
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75
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|
@@ -112,6 +113,7 @@ def test_clinicaltrial_olink():
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|
@@ -125,6 +127,7 @@ def test_clinicaltrial_olink():
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|
@@ -75,14 +75,14 @@ def test_derive_files_shipping_manifest(ct, upload_type):
|
|
|
75
75
|
file_type="samples info",
|
|
76
76
|
data_format="csv",
|
|
77
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|
data=(
|
|
78
|
-
f"cimac_id,parent_sample_id,collection_event_name,sample_location,type_of_sample,type_of_primary_container,sample_volume_units,material_used,material_remaining,quality_of_sample,{PROTOCOL_ID_FIELD_NAME},participants.cimac_participant_id\n"
|
|
79
|
-
"CTTTPP1S1.00,SA.1.1,Baseline,---,Other,Other,Other,1,0,Pass at Risk,10021,CTTTPP1\n"
|
|
80
|
-
"CTTTPP1S1.01,SA.1.1,Baseline,---,Other,Other,Other,1,0,Pass at Risk,10021,CTTTPP1\n"
|
|
81
|
-
"CTTTPP1S2.00,SA.1.2,Baseline,---,Other,Other,Other,1,0,Pass at Risk,10021,CTTTPP1\n"
|
|
82
|
-
"CTTTPP2S1.00,SA.2.1,Baseline,---,Other,Other,Other,1,0,Pass at Risk,10021,CTTTPP2\n"
|
|
83
|
-
"CTTTPP2S1.01,SA.2.1,Baseline,---,Other,Other,Other,1,0,Pass at Risk,10021,CTTTPP2\n"
|
|
84
|
-
"CTTTPP2S2.00,SA.2.2,Baseline,---,Other,Other,Other,1,0,Pass at Risk,10021,CTTTPP2\n"
|
|
85
|
-
"CTTTPP2S2.01,SA.2.2,Baseline,---,Other,Other,Other,1,0,Pass at Risk,10021,CTTTPP2\n"
|
|
78
|
+
f"cimac_id,parent_sample_id,collection_event_name,sample_location,type_of_sample,type_of_sample_other,type_of_primary_container,sample_volume_units,material_used,material_remaining,quality_of_sample,{PROTOCOL_ID_FIELD_NAME},participants.cimac_participant_id\n"
|
|
79
|
+
"CTTTPP1S1.00,SA.1.1,Baseline,---,Other,other_sample,Other,Other,1,0,Pass at Risk,10021,CTTTPP1\n"
|
|
80
|
+
"CTTTPP1S1.01,SA.1.1,Baseline,---,Other,other_sample,Other,Other,1,0,Pass at Risk,10021,CTTTPP1\n"
|
|
81
|
+
"CTTTPP1S2.00,SA.1.2,Baseline,---,Other,other_sample,Other,Other,1,0,Pass at Risk,10021,CTTTPP1\n"
|
|
82
|
+
"CTTTPP2S1.00,SA.2.1,Baseline,---,Other,other_sample,Other,Other,1,0,Pass at Risk,10021,CTTTPP2\n"
|
|
83
|
+
"CTTTPP2S1.01,SA.2.1,Baseline,---,Other,other_sample,Other,Other,1,0,Pass at Risk,10021,CTTTPP2\n"
|
|
84
|
+
"CTTTPP2S2.00,SA.2.2,Baseline,---,Other,other_sample,Other,Other,1,0,Pass at Risk,10021,CTTTPP2\n"
|
|
85
|
+
"CTTTPP2S2.01,SA.2.2,Baseline,---,Other,other_sample,Other,Other,1,0,Pass at Risk,10021,CTTTPP2\n"
|
|
86
86
|
),
|
|
87
87
|
metadata=None,
|
|
88
88
|
),
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/metaschema/strict_meta_schema.json
RENAMED
|
File without changes
|
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File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
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File without changes
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File without changes
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File without changes
|
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File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_bam.json
RENAMED
|
File without changes
|
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File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_bed.json
RENAMED
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File without changes
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{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_cns.json
RENAMED
|
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File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_csv.json
RENAMED
|
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File without changes
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{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_fcs.json
RENAMED
|
File without changes
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File without changes
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{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_gz.json
RENAMED
|
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File without changes
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{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_jpg.json
RENAMED
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File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_log.json
RENAMED
|
File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_maf.json
RENAMED
|
File without changes
|
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File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_npx.json
RENAMED
|
File without changes
|
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File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_pdf.json
RENAMED
|
File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_png.json
RENAMED
|
File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_rcc.json
RENAMED
|
File without changes
|
|
File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_tbi.json
RENAMED
|
File without changes
|
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File without changes
|
{nci_cidc_schemas-0.27.8 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/artifacts/artifact_tsv.json
RENAMED
|
File without changes
|