nci-cidc-schemas 0.26.37__tar.gz → 0.26.38__tar.gz

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  1. {nci_cidc_schemas-0.26.37/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.26.38}/PKG-INFO +1 -1
  2. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/__init__.py +1 -1
  3. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/unprism.py +4 -0
  4. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38/nci_cidc_schemas.egg-info}/PKG-INFO +1 -1
  5. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_unprism.py +6 -0
  6. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/LICENSE +0 -0
  7. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/MANIFEST.in +0 -0
  8. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/README.md +0 -0
  9. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/cli.py +0 -0
  10. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/constants.py +0 -0
  11. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/json_validation.py +0 -0
  12. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/metaschema/strict_meta_schema.json +0 -0
  13. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/migrations.py +0 -0
  14. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2 +0 -0
  15. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/prism/__init__.py +0 -0
  16. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/prism/constants.py +0 -0
  17. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/prism/core.py +0 -0
  18. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/prism/extra_metadata.py +0 -0
  19. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/prism/merger.py +0 -0
  20. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/prism/pipelines.py +0 -0
  21. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/aliquot.json +0 -0
  22. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_bam.json +0 -0
  23. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_bam_bai.json +0 -0
  24. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_bed.json +0 -0
  25. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_bigwig.json +0 -0
  26. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_binary.json +0 -0
  27. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_clinical_csv.json +0 -0
  28. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_clinical_docx.json +0 -0
  29. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_clinical_xlsx.json +0 -0
  30. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_cncf.json +0 -0
  31. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_cns.json +0 -0
  32. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_core.json +0 -0
  33. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_csv.json +0 -0
  34. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_elisa_xlsx.json +0 -0
  35. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_fastq_gz.json +0 -0
  36. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_fcs.json +0 -0
  37. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_file.json +0 -0
  38. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_gz.json +0 -0
  39. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_image.json +0 -0
  40. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_jpg.json +0 -0
  41. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_json.json +0 -0
  42. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_junction.json +0 -0
  43. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_log.json +0 -0
  44. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_maf.json +0 -0
  45. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_narrowPeak.json +0 -0
  46. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_npx.json +0 -0
  47. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_ome_tiff.json +0 -0
  48. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_pdf.json +0 -0
  49. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_png.json +0 -0
  50. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_rcc.json +0 -0
  51. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_rdata.json +0 -0
  52. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_tbi.json +0 -0
  53. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_text.json +0 -0
  54. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_tsv.json +0 -0
  55. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_vcf.json +0 -0
  56. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_vcf_gz.json +0 -0
  57. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_xlsx.json +0 -0
  58. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_yaml.json +0 -0
  59. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/artifacts/artifact_zip.json +0 -0
  60. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/atacseq_assay.json +0 -0
  61. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/antibody.json +0 -0
  62. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/assay_core.json +0 -0
  63. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/available_assays.json +0 -0
  64. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/available_ngs_analyses.json +0 -0
  65. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/composite_image.json +0 -0
  66. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/controls.json +0 -0
  67. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/enrichment_core.json +0 -0
  68. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/excluded_samples.json +0 -0
  69. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/hande_local_file.json +0 -0
  70. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/image.json +0 -0
  71. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/imaging/mif_entry.json +0 -0
  72. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/imaging/mif_export.json +0 -0
  73. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/imaging/mif_input.json +0 -0
  74. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/imaging/mif_roi.json +0 -0
  75. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/imaging_data.json +0 -0
  76. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/local_file.json +0 -0
  77. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/mapping.json +0 -0
  78. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/mibi_antibody.json +0 -0
  79. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/mibi_imaging/mibi_files.json +0 -0
  80. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json +0 -0
  81. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/mif_antibody.json +0 -0
  82. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/multiple_local_files.json +0 -0
  83. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json +0 -0
  84. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/ngs_assay_record.json +0 -0
  85. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/fusion.json +0 -0
  86. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/microbiome.json +0 -0
  87. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/msisensor.json +0 -0
  88. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/neoantigen.json +0 -0
  89. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/rna_analysis.json +0 -0
  90. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/rna_level1_analysis.json +0 -0
  91. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/rseqc.json +0 -0
  92. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/salmon.json +0 -0
  93. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/star.json +0 -0
  94. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs/rna/trust4.json +0 -0
  95. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs_assay_core.json +0 -0
  96. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/ngs_assay_record.json +0 -0
  97. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/reads_core.json +0 -0
  98. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/components/reads_with_index.json +0 -0
  99. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/ctdna_assay.json +0 -0
  100. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/cytof_assay.json +0 -0
  101. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/cytof_assay_core.json +0 -0
  102. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/elisa_assay.json +0 -0
  103. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/hande_assay.json +0 -0
  104. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/ihc_assay.json +0 -0
  105. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/mibi_assay.json +0 -0
  106. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/microbiome_assay.json +0 -0
  107. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/mif_assay.json +0 -0
  108. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/misc_data.json +0 -0
  109. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/nanostring_assay.json +0 -0
  110. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/olink_assay.json +0 -0
  111. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/rna_assay-v0.json +0 -0
  112. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/rna_assay.json +0 -0
  113. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/tcr_analysis.json +0 -0
  114. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/tcr_assay.json +0 -0
  115. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/wes_analysis.json +0 -0
  116. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/wes_assay.json +0 -0
  117. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/wes_core.json +0 -0
  118. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/assays/wes_tumor_only_analysis.json +0 -0
  119. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/clinical_data.json +0 -0
  120. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/clinical_trial.json +0 -0
  121. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/participant.json +0 -0
  122. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/sample.json +0 -0
  123. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/shipping_core.json +0 -0
  124. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json +0 -0
  125. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json +0 -0
  126. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json +0 -0
  127. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json +0 -0
  128. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/analyses/wes_analysis_template.json +0 -0
  129. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json +0 -0
  130. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json +0 -0
  131. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/clinical_data_template.json +0 -0
  132. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/ctdna_template.json +0 -0
  133. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/cytof_template.json +0 -0
  134. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/elisa_template.json +0 -0
  135. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/hande_template.json +0 -0
  136. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/ihc_template.json +0 -0
  137. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/mibi_template.json +0 -0
  138. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/microbiome_template.json +0 -0
  139. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/mif_template.json +0 -0
  140. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/misc_data_template.json +0 -0
  141. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/nanostring_template.json +0 -0
  142. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/olink_template.json +0 -0
  143. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/rna_bam_template.json +0 -0
  144. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/rna_fastq_template.json +0 -0
  145. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json +0 -0
  146. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/tcr_fastq_template.json +0 -0
  147. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/wes_bam_template.json +0 -0
  148. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/assays/wes_fastq_template.json +0 -0
  149. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/h_and_e_template.json +0 -0
  150. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +0 -0
  151. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +0 -0
  152. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json +0 -0
  153. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/pbmc_template.json +0 -0
  154. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/plasma_template.json +0 -0
  155. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/tissue_slide_template.json +0 -0
  156. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json +0 -0
  157. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json +0 -0
  158. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json +0 -0
  159. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/template.py +0 -0
  160. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/template_reader.py +0 -0
  161. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/template_writer.py +0 -0
  162. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/util.py +0 -0
  163. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/nci_cidc_schemas.egg-info/SOURCES.txt +0 -0
  164. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/nci_cidc_schemas.egg-info/dependency_links.txt +0 -0
  165. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/nci_cidc_schemas.egg-info/entry_points.txt +0 -0
  166. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/nci_cidc_schemas.egg-info/not-zip-safe +0 -0
  167. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/nci_cidc_schemas.egg-info/requires.txt +0 -0
  168. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/nci_cidc_schemas.egg-info/top_level.txt +0 -0
  169. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/requirements.txt +0 -0
  170. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/setup.cfg +0 -0
  171. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/setup.py +0 -0
  172. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/__init__.py +0 -0
  173. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/conftest.py +0 -0
  174. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/constants.py +0 -0
  175. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinical_test_file.1.csv +0 -0
  176. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinical_test_file.1.xlsx +0 -0
  177. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinical_test_file.2.bom.csv +0 -0
  178. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinical_test_file.2.csv +0 -0
  179. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinical_test_file.2.xlsx +0 -0
  180. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinical_test_file.3.xlsx +0 -0
  181. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinical_test_file.docx +0 -0
  182. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinicaltrial_examples/CT_1.json +0 -0
  183. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinicaltrial_examples/CT_1PA_multiWES.json +0 -0
  184. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinicaltrial_examples/CT_cytof_with_analysis.json +0 -0
  185. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinicaltrial_examples/CT_ihc.json +0 -0
  186. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/clinicaltrial_examples/CT_minimal.json +0 -0
  187. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/date_examples.xlsx +0 -0
  188. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/elisa_test_file.1.xlsx +0 -0
  189. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/elisa_test_file.2.xlsx +0 -0
  190. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/hande_err_template.xlsx +0 -0
  191. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/olink/invalid_olink_assay_1_NPX.xlsx +0 -0
  192. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/olink/olink_assay_1_NPX.xlsx +0 -0
  193. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/olink/olink_assay_2_NPX.xlsx +0 -0
  194. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/olink/olink_assay_combined.xlsx +0 -0
  195. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/pbmc_invalid.xlsx +0 -0
  196. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/1.json +0 -0
  197. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/a.json +0 -0
  198. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/b.json +0 -0
  199. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/c.json +0 -0
  200. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/d1/3.json +0 -0
  201. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/d1/d2/2.json +0 -0
  202. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/invalid_ref.json +0 -0
  203. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/target-templates/atacseq_analysis_template.json +0 -0
  204. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/target-templates/rna_level1_analysis_template.json +0 -0
  205. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/target-templates/wes_analysis_template.json +0 -0
  206. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/schemas/target-templates/wes_tumor_only_analysis_template.json +0 -0
  207. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/tiny_invalid_manifest.xlsx +0 -0
  208. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/data/tiny_valid_manifest.xlsx +0 -0
  209. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/__init__.py +0 -0
  210. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/cidc_test_data/__init__.py +0 -0
  211. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/cidc_test_data/analysis_data.py +0 -0
  212. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/cidc_test_data/assay_data.py +0 -0
  213. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/cidc_test_data/manifest_data.py +0 -0
  214. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/cidc_test_data/utils.py +0 -0
  215. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/schema/test_schema.json +0 -0
  216. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/test_cidc_data_model.py +0 -0
  217. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/test_constants.py +0 -0
  218. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/test_core.py +0 -0
  219. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/test_extra_metadata.py +0 -0
  220. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/test_merger.py +0 -0
  221. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/prism/test_pipelines.py +0 -0
  222. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_artifacts.py +0 -0
  223. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_assays.py +0 -0
  224. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_clinicaltrial_examples.py +0 -0
  225. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_json_validation.py +0 -0
  226. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_migrations.py +0 -0
  227. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_schemas.py +0 -0
  228. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_strict_meta_schema.py +0 -0
  229. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_template.py +0 -0
  230. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_template_reader.py +0 -0
  231. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_template_writer.py +0 -0
  232. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_templates.py +0 -0
  233. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_trial_core.py +0 -0
  234. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_util.py +0 -0
  235. {nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/utils/test_template_generator.py +0 -0
{nci_cidc_schemas-0.26.37/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.26.38}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: nci_cidc_schemas
3
- Version: 0.26.37
3
+ Version: 0.26.38
4
4
  Summary: The CIDC data model and tools for working with it.
5
5
  Home-page: https://github.com/NCI-CIDC/cidc-schemas
6
6
  Author: NCI
{nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/__init__.py RENAMED
@@ -2,4 +2,4 @@
2
2
 
3
3
  __author__ = """NCI"""
4
4
  __email__ = "nci-cidc-tools-admin@mail.nih.gov"
5
- __version__ = "0.26.37"
5
+ __version__ = "0.26.38"
{nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/cidc_schemas/unprism.py RENAMED
@@ -3,6 +3,7 @@
3
3
  from io import StringIO, BytesIO
4
4
  from typing import Callable, Dict, List, NamedTuple, Optional, Union
5
5
 
6
+ import math
6
7
  import pandas as pd
7
8
 
8
9
  from . import prism
@@ -332,6 +333,9 @@ def _cytof_analysis_derivation(context: DeriveFilesContext) -> DeriveFilesResult
332
333
  res_df = pd.DataFrame()
333
334
  for index, row in cell_counts_analysis_csvs.iterrows():
334
335
  obj_url = row[f"output_files.{combined_f_kind}.object_url"]
336
+ if isinstance(obj_url, float) and math.isnan(obj_url):
337
+ # output file does not exist - continue (don't fail when a cytof assay is not included in analysis)
338
+ continue
335
339
 
336
340
  cell_counts_csv = context.fetch_artifact(obj_url, True)
337
341
 
{nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38/nci_cidc_schemas.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: nci_cidc_schemas
3
- Version: 0.26.37
3
+ Version: 0.26.38
4
4
  Summary: The CIDC data model and tools for working with it.
5
5
  Home-page: https://github.com/NCI-CIDC/cidc-schemas
6
6
  Author: NCI
{nci_cidc_schemas-0.26.37 → nci_cidc_schemas-0.26.38}/tests/test_unprism.py RENAMED
@@ -296,3 +296,9 @@ def test_derive_files_CyTOF_analysis():
296
296
  assert sorted([r["cimac_participant_id"] for r in recs]) == sorted(
297
297
  list(map(participant_id_from_cimac, cimac_ids))
298
298
  )
299
+
300
+ # remove 'output_files' from first cytof assay (simulate not included in analysis)
301
+ ct["assays"]["cytof"][0]["records"][0].pop("output_files", None)
302
+ # ensure still able to successfully retrieve result even if cytof assay output_files do not exist
303
+ result = derive_files(DeriveFilesContext(ct, "cytof_analysis", fetch_artifact))
304
+ assert len(result.artifacts) == 3