nci-cidc-schemas 0.28.7__py2.py3-none-any.whl → 0.28.13__py2.py3-none-any.whl

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Files changed (83) hide show
  1. cidc_schemas/__init__.py +1 -1
  2. cidc_schemas/ngs_pipeline_api/__init__.py +0 -1
  3. cidc_schemas/ngs_pipeline_api/wes/wes_output_API.py +1 -1
  4. cidc_schemas/prism/constants.py +5 -8
  5. cidc_schemas/prism/pipelines.py +2 -24
  6. cidc_schemas/schemas/artifacts/artifact_parquet.json +51 -0
  7. cidc_schemas/schemas/assays/atacseq_assay.json +4 -0
  8. cidc_schemas/schemas/assays/components/available_assays.json +23 -2
  9. cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json +4 -0
  10. cidc_schemas/schemas/assays/components/ngs/rna/rna_analysis.json +10 -1
  11. cidc_schemas/schemas/assays/components/ngs_assay_core.json +2 -1
  12. cidc_schemas/schemas/assays/ctdna_assay.json +4 -0
  13. cidc_schemas/schemas/assays/cytof_assay.json +4 -0
  14. cidc_schemas/schemas/assays/cytof_assay_core.json +4 -0
  15. cidc_schemas/schemas/assays/elisa_assay.json +8 -4
  16. cidc_schemas/schemas/assays/hande_assay.json +10 -1
  17. cidc_schemas/schemas/assays/ihc_assay.json +9 -1
  18. cidc_schemas/schemas/assays/maldi_glycan_assay.json +4 -0
  19. cidc_schemas/schemas/assays/mibi_assay.json +4 -0
  20. cidc_schemas/schemas/assays/microbiome_assay.json +5 -1
  21. cidc_schemas/schemas/assays/mif_assay.json +10 -3
  22. cidc_schemas/schemas/assays/mihc_assay.json +4 -1
  23. cidc_schemas/schemas/assays/misc_data.json +9 -1
  24. cidc_schemas/schemas/assays/nanostring_assay.json +5 -1
  25. cidc_schemas/schemas/assays/nulisa_assay.json +4 -0
  26. cidc_schemas/schemas/assays/olink_assay.json +4 -0
  27. cidc_schemas/schemas/assays/olink_ht_assay.json +100 -0
  28. cidc_schemas/schemas/assays/rna_assay-v0.json +9 -0
  29. cidc_schemas/schemas/assays/scrnaseq_analysis.json +4 -0
  30. cidc_schemas/schemas/assays/scrnaseq_assay.json +4 -0
  31. cidc_schemas/schemas/assays/tcr_analysis.json +4 -0
  32. cidc_schemas/schemas/assays/tcr_assay.json +4 -0
  33. cidc_schemas/schemas/assays/tcrseq_rna_assay.json +64 -0
  34. cidc_schemas/schemas/assays/visium_analysis.json +4 -0
  35. cidc_schemas/schemas/assays/visium_assay.json +4 -0
  36. cidc_schemas/schemas/assays/wes_analysis.json +9 -1
  37. cidc_schemas/schemas/assays/wes_assay.json +25 -3
  38. cidc_schemas/schemas/assays/wes_tumor_only_analysis.json +9 -1
  39. cidc_schemas/schemas/clinical_data.json +8 -0
  40. cidc_schemas/schemas/shipping_core.json +3 -2
  41. cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json +6 -2
  42. cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json +16 -12
  43. cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json +9 -1
  44. cidc_schemas/schemas/templates/analyses/scrnaseq_analysis_template.json +32 -28
  45. cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json +9 -5
  46. cidc_schemas/schemas/templates/analyses/visium_analysis_template.json +11 -7
  47. cidc_schemas/schemas/templates/analyses/wes_analysis_template.json +9 -1
  48. cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json +9 -1
  49. cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json +6 -2
  50. cidc_schemas/schemas/templates/assays/clinical_data_template.json +8 -0
  51. cidc_schemas/schemas/templates/assays/ctdna_template.json +15 -11
  52. cidc_schemas/schemas/templates/assays/cytof_template.json +9 -4
  53. cidc_schemas/schemas/templates/assays/elisa_template.json +8 -4
  54. cidc_schemas/schemas/templates/assays/hande_template.json +8 -0
  55. cidc_schemas/schemas/templates/assays/ihc_template.json +8 -0
  56. cidc_schemas/schemas/templates/assays/maldi_glycan_template.json +11 -7
  57. cidc_schemas/schemas/templates/assays/mibi_template.json +8 -4
  58. cidc_schemas/schemas/templates/assays/microbiome_template.json +12 -8
  59. cidc_schemas/schemas/templates/assays/mif_template.json +8 -0
  60. cidc_schemas/schemas/templates/assays/mihc_template.json +6 -2
  61. cidc_schemas/schemas/templates/assays/misc_data_template.json +8 -0
  62. cidc_schemas/schemas/templates/assays/nanostring_template.json +10 -6
  63. cidc_schemas/schemas/templates/assays/nulisa_template.json +8 -4
  64. cidc_schemas/schemas/templates/assays/olink_ht_template.json +86 -0
  65. cidc_schemas/schemas/templates/assays/olink_template.json +8 -4
  66. cidc_schemas/schemas/templates/assays/rna_bam_template.json +9 -1
  67. cidc_schemas/schemas/templates/assays/rna_fastq_template.json +9 -1
  68. cidc_schemas/schemas/templates/assays/scrnaseq_template.json +8 -4
  69. cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json +9 -5
  70. cidc_schemas/schemas/templates/assays/tcr_fastq_template.json +10 -6
  71. cidc_schemas/schemas/templates/assays/tcrseq_rna_template.json +59 -0
  72. cidc_schemas/schemas/templates/assays/visium_template.json +13 -9
  73. cidc_schemas/schemas/templates/assays/wes_bam_template.json +8 -0
  74. cidc_schemas/schemas/templates/assays/wes_fastq_template.json +8 -0
  75. cidc_schemas/template.py +0 -4
  76. cidc_schemas/unprism.py +3 -3
  77. {nci_cidc_schemas-0.28.7.dist-info → nci_cidc_schemas-0.28.13.dist-info}/METADATA +12 -12
  78. {nci_cidc_schemas-0.28.7.dist-info → nci_cidc_schemas-0.28.13.dist-info}/RECORD +82 -78
  79. {nci_cidc_schemas-0.28.7.dist-info → nci_cidc_schemas-0.28.13.dist-info}/WHEEL +1 -1
  80. cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json +0 -63
  81. {nci_cidc_schemas-0.28.7.dist-info → nci_cidc_schemas-0.28.13.dist-info}/entry_points.txt +0 -0
  82. {nci_cidc_schemas-0.28.7.dist-info → nci_cidc_schemas-0.28.13.dist-info}/licenses/LICENSE +0 -0
  83. {nci_cidc_schemas-0.28.7.dist-info → nci_cidc_schemas-0.28.13.dist-info}/top_level.txt +0 -0
cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json DELETED
@@ -1,63 +0,0 @@
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- {
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- "title": "Metadata manifest for WES analysis pairing",
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- "description": "Metadata manifest for tumor / normal pairing for WES assay analysis.",
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- "properties": {
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- "worksheets": {
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-
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- "Pairing": {
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- "prism_preamble_object_schema": "clinical_trial.json",
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- "prism_preamble_object_pointer": "#",
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- "preamble_rows": {
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- "protocol identifier": {
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- "merge_pointer": "/protocol_identifier",
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- "type_ref": "clinical_trial.json#properties/protocol_identifier"
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- }
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- },
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- "prism_data_object_pointer": "/analysis/wes_analysis/pair_runs/-",
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- "data_columns": {
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- "Pair": {
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- "tumor sample CIMAC ID": {
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- "merge_pointer": "/tumor/cimac_id",
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- "type_ref": "sample.json#properties/cimac_id",
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- "process_as": [
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- {
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- "merge_pointer": "/run_id",
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- "type_ref": "assays/wes_analysis.json#definitions/pair_analysis/properties/run_id"
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- }
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- ]
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- },
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- "normal sample CIMAC ID": {
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- "merge_pointer": "/normal/cimac_id",
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- "type_ref": "sample.json#properties/cimac_id"
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- }
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- }
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- }
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- },
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- "Tumor-only": {
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- "prism_preamble_object_schema": "clinical_trial.json",
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- "prism_preamble_object_pointer": "#",
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- "preamble_rows": {
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- "protocol identifier": {
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- "merge_pointer": "/protocol_identifier",
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- "type_ref": "clinical_trial.json#properties/protocol_identifier"
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- }
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- },
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- "prism_data_object_pointer": "/analysis/wes_tumor_only_analysis/runs/-",
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- "data_columns": {
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- "Tumor-only": {
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- "tumor sample CIMAC ID": {
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- "merge_pointer": "/tumor/cimac_id",
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- "type_ref": "sample.json#properties/cimac_id",
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- "process_as": [
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- {
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- "merge_pointer": "/run_id",
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- "type_ref": "assays/wes_tumor_only_analysis.json#definitions/sample_analysis/properties/run_id"
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- }
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- ]
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- }
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- }
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- }
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- }
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- }
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- }
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- }