nci-cidc-schemas 0.27.22__tar.gz → 0.27.25__tar.gz

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  1. {nci_cidc_schemas-0.27.22/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.27.25}/PKG-INFO +1 -1
  2. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/__init__.py +1 -1
  3. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/prism/constants.py +48 -0
  4. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/artifacts/artifact_html.json +51 -0
  5. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/artifacts/artifact_mtx.json +51 -0
  6. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/artifacts/artifact_out.json +51 -0
  7. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/artifacts/artifact_rds.json +51 -0
  8. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/artifacts/artifact_stats.json +51 -0
  9. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/artifacts/artifact_tab.json +51 -0
  10. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/artifacts/artifact_tiff.json +51 -0
  11. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/artifacts/artifact_txt.json +51 -0
  12. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/available_assays.json +11 -0
  13. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/available_ngs_analyses.json +22 -0
  14. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/assays/components/visium_input.json +60 -0
  15. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/assays/components/visium_preamble.json +27 -0
  16. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/assays/scrnaseq_analysis.json +102 -0
  17. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/assays/visium_analysis.json +62 -0
  18. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/assays/visium_assay.json +68 -0
  19. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/templates/analyses/scrnaseq_analysis_template.json +238 -0
  20. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/templates/analyses/visium_analysis_template.json +103 -0
  21. nci_cidc_schemas-0.27.25/cidc_schemas/schemas/templates/assays/visium_template.json +150 -0
  22. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25/nci_cidc_schemas.egg-info}/PKG-INFO +1 -1
  23. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/nci_cidc_schemas.egg-info/SOURCES.txt +16 -0
  24. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/cidc_test_data/analysis_data.py +402 -0
  25. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/cidc_test_data/assay_data.py +135 -0
  26. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/LICENSE +0 -0
  27. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/MANIFEST.in +0 -0
  28. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/README.md +0 -0
  29. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/cli.py +0 -0
  30. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/constants.py +0 -0
  31. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/json_validation.py +0 -0
  32. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/metaschema/strict_meta_schema.json +0 -0
  33. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/migrations.py +0 -0
  34. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2 +0 -0
  35. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/prism/__init__.py +0 -0
  36. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/prism/core.py +0 -0
  37. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/prism/extra_metadata.py +0 -0
  38. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/prism/merger.py +0 -0
  39. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/prism/pipelines.py +0 -0
  40. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/aliquot.json +0 -0
  41. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_bam.json +0 -0
  42. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_bam_bai.json +0 -0
  43. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_bed.json +0 -0
  44. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_bigwig.json +0 -0
  45. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_binary.json +0 -0
  46. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_clinical_csv.json +0 -0
  47. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_clinical_docx.json +0 -0
  48. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_clinical_xlsx.json +0 -0
  49. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_cncf.json +0 -0
  50. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_cns.json +0 -0
  51. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_core.json +0 -0
  52. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_csv.json +0 -0
  53. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_elisa_xlsx.json +0 -0
  54. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_fastq_gz.json +0 -0
  55. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_fcs.json +0 -0
  56. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_file.json +0 -0
  57. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_gz.json +0 -0
  58. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_h5ad.json +0 -0
  59. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_image.json +0 -0
  60. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_jpg.json +0 -0
  61. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_json.json +0 -0
  62. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_junction.json +0 -0
  63. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_log.json +0 -0
  64. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_maf.json +0 -0
  65. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_narrowPeak.json +0 -0
  66. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_npx.json +0 -0
  67. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_ome_tiff.json +0 -0
  68. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_pdf.json +0 -0
  69. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_png.json +0 -0
  70. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_rcc.json +0 -0
  71. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_rdata.json +0 -0
  72. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_tbi.json +0 -0
  73. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_text.json +0 -0
  74. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_tsv.json +0 -0
  75. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_vcf.json +0 -0
  76. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_vcf_gz.json +0 -0
  77. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_xlsx.json +0 -0
  78. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_yaml.json +0 -0
  79. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/artifacts/artifact_zip.json +0 -0
  80. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/atacseq_assay.json +0 -0
  81. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/antibody.json +0 -0
  82. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/assay_core.json +0 -0
  83. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/composite_image.json +0 -0
  84. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/controls.json +0 -0
  85. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/enrichment_core.json +0 -0
  86. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/excluded_samples.json +0 -0
  87. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/hande_local_file.json +0 -0
  88. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/image.json +0 -0
  89. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/imaging/mif_entry.json +0 -0
  90. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/imaging/mif_export.json +0 -0
  91. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/imaging/mif_input.json +0 -0
  92. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/imaging/mif_roi.json +0 -0
  93. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/imaging_data.json +0 -0
  94. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/local_file.json +0 -0
  95. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/mapping.json +0 -0
  96. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/mibi_antibody.json +0 -0
  97. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json +0 -0
  98. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/mif_antibody.json +0 -0
  99. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/mihc_antibody.json +0 -0
  100. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/mihc_input.json +0 -0
  101. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/multiple_local_files.json +0 -0
  102. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json +0 -0
  103. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/ngs_assay_record.json +0 -0
  104. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/fusion.json +0 -0
  105. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/microbiome.json +0 -0
  106. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/msisensor.json +0 -0
  107. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/neoantigen.json +0 -0
  108. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/rna_analysis.json +0 -0
  109. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/rna_level1_analysis.json +0 -0
  110. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/rseqc.json +0 -0
  111. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/salmon.json +0 -0
  112. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/star.json +0 -0
  113. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs/rna/trust4.json +0 -0
  114. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs_assay_core.json +0 -0
  115. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/ngs_assay_record.json +0 -0
  116. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/reads_core.json +0 -0
  117. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/reads_with_index.json +0 -0
  118. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/scrnaseq_input.json +0 -0
  119. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/components/scrnaseq_preamble.json +0 -0
  120. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/ctdna_assay.json +0 -0
  121. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/cytof_assay.json +0 -0
  122. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/cytof_assay_core.json +0 -0
  123. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/elisa_assay.json +0 -0
  124. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/hande_assay.json +0 -0
  125. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/ihc_assay.json +0 -0
  126. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/mibi_assay.json +0 -0
  127. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/microbiome_assay.json +0 -0
  128. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/mif_assay.json +0 -0
  129. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/mihc_assay.json +0 -0
  130. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/misc_data.json +0 -0
  131. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/nanostring_assay.json +0 -0
  132. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/olink_assay.json +0 -0
  133. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/rna_assay-v0.json +0 -0
  134. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/rna_assay.json +0 -0
  135. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/scrnaseq_assay.json +0 -0
  136. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/tcr_analysis.json +0 -0
  137. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/tcr_assay.json +0 -0
  138. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/wes_analysis.json +0 -0
  139. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/wes_assay.json +0 -0
  140. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/wes_core.json +0 -0
  141. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/assays/wes_tumor_only_analysis.json +0 -0
  142. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/clinical_data.json +0 -0
  143. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/clinical_trial.json +0 -0
  144. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/participant.json +0 -0
  145. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/sample.json +0 -0
  146. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/shipping_core.json +0 -0
  147. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json +0 -0
  148. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json +0 -0
  149. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json +0 -0
  150. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json +0 -0
  151. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/analyses/wes_analysis_template.json +0 -0
  152. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json +0 -0
  153. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json +0 -0
  154. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/clinical_data_template.json +0 -0
  155. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/ctdna_template.json +0 -0
  156. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/cytof_template.json +0 -0
  157. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/elisa_template.json +0 -0
  158. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/hande_template.json +0 -0
  159. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/ihc_template.json +0 -0
  160. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/mibi_template.json +0 -0
  161. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/microbiome_template.json +0 -0
  162. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/mif_template.json +0 -0
  163. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/mihc_template.json +0 -0
  164. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/misc_data_template.json +0 -0
  165. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/nanostring_template.json +0 -0
  166. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/olink_template.json +0 -0
  167. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/rna_bam_template.json +0 -0
  168. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/rna_fastq_template.json +0 -0
  169. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/scrnaseq_template.json +0 -0
  170. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json +0 -0
  171. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/tcr_fastq_template.json +0 -0
  172. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/wes_bam_template.json +0 -0
  173. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/assays/wes_fastq_template.json +0 -0
  174. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/h_and_e_template.json +0 -0
  175. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +0 -0
  176. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +0 -0
  177. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json +0 -0
  178. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/pbmc_template.json +0 -0
  179. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/plasma_template.json +0 -0
  180. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/tissue_slide_template.json +0 -0
  181. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json +0 -0
  182. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json +0 -0
  183. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json +0 -0
  184. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/template.py +0 -0
  185. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/template_reader.py +0 -0
  186. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/template_writer.py +0 -0
  187. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/unprism.py +0 -0
  188. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/cidc_schemas/util.py +0 -0
  189. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/nci_cidc_schemas.egg-info/dependency_links.txt +0 -0
  190. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/nci_cidc_schemas.egg-info/entry_points.txt +0 -0
  191. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/nci_cidc_schemas.egg-info/not-zip-safe +0 -0
  192. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/nci_cidc_schemas.egg-info/requires.txt +0 -0
  193. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/nci_cidc_schemas.egg-info/top_level.txt +0 -0
  194. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/requirements.txt +0 -0
  195. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/setup.cfg +0 -0
  196. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/setup.py +0 -0
  197. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/__init__.py +0 -0
  198. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/conftest.py +0 -0
  199. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/constants.py +0 -0
  200. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinical_test_file.1.csv +0 -0
  201. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinical_test_file.1.xlsx +0 -0
  202. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinical_test_file.2.bom.csv +0 -0
  203. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinical_test_file.2.csv +0 -0
  204. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinical_test_file.2.xlsx +0 -0
  205. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinical_test_file.3.xlsx +0 -0
  206. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinical_test_file.docx +0 -0
  207. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinicaltrial_examples/CT_1.json +0 -0
  208. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinicaltrial_examples/CT_1PA_multiWES.json +0 -0
  209. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinicaltrial_examples/CT_cytof_with_analysis.json +0 -0
  210. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinicaltrial_examples/CT_ihc.json +0 -0
  211. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/clinicaltrial_examples/CT_minimal.json +0 -0
  212. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/date_examples.xlsx +0 -0
  213. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/elisa_test_file.1.xlsx +0 -0
  214. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/elisa_test_file.2.xlsx +0 -0
  215. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/hande_err_template.xlsx +0 -0
  216. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/olink/invalid_olink_assay_1_NPX.xlsx +0 -0
  217. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/olink/olink_assay_1_NPX.xlsx +0 -0
  218. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/olink/olink_assay_2_NPX.xlsx +0 -0
  219. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/olink/olink_assay_combined.xlsx +0 -0
  220. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/pbmc_invalid.xlsx +0 -0
  221. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/pbmc_manifest_valid.xlsx +0 -0
  222. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/1.json +0 -0
  223. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/a.json +0 -0
  224. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/b.json +0 -0
  225. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/c.json +0 -0
  226. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/d1/3.json +0 -0
  227. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/d1/d2/2.json +0 -0
  228. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/invalid_ref.json +0 -0
  229. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/target-templates/atacseq_analysis_template.json +0 -0
  230. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/target-templates/rna_level1_analysis_template.json +0 -0
  231. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/target-templates/wes_analysis_template.json +0 -0
  232. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/schemas/target-templates/wes_tumor_only_analysis_template.json +0 -0
  233. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/tiny_invalid_manifest.xlsx +0 -0
  234. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/data/tiny_valid_manifest.xlsx +0 -0
  235. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/__init__.py +0 -0
  236. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/cidc_test_data/__init__.py +0 -0
  237. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/cidc_test_data/manifest_data.py +0 -0
  238. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/cidc_test_data/utils.py +0 -0
  239. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/schema/test_schema.json +0 -0
  240. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/test_cidc_data_model.py +0 -0
  241. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/test_constants.py +0 -0
  242. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/test_core.py +0 -0
  243. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/test_extra_metadata.py +0 -0
  244. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/test_merger.py +0 -0
  245. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/prism/test_pipelines.py +0 -0
  246. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_artifacts.py +0 -0
  247. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_assays.py +0 -0
  248. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_clinicaltrial_examples.py +0 -0
  249. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_json_validation.py +0 -0
  250. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_migrations.py +0 -0
  251. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_schemas.py +0 -0
  252. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_strict_meta_schema.py +0 -0
  253. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_template.py +0 -0
  254. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_template_reader.py +0 -0
  255. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_template_writer.py +0 -0
  256. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_templates.py +0 -0
  257. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_trial_core.py +0 -0
  258. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_unprism.py +0 -0
  259. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/test_util.py +0 -0
  260. {nci_cidc_schemas-0.27.22 → nci_cidc_schemas-0.27.25}/tests/utils/test_template_generator.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: nci_cidc_schemas
3
- Version: 0.27.22
3
+ Version: 0.27.25
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
@@ -2,4 +2,4 @@
2
2
 
3
3
  __author__ = """NCI"""
4
4
  __email__ = "nci-cidc-tools-admin@mail.nih.gov"
5
- __version__ = "0.27.22"
5
+ __version__ = "0.27.25"
@@ -27,6 +27,7 @@ SUPPORTED_ASSAYS = [
27
27
  "microbiome",
28
28
  "mihc",
29
29
  "scrnaseq",
30
+ "visium",
30
31
  ]
31
32
 
32
33
  SUPPORTED_SHIPPING_MANIFESTS = [
@@ -53,8 +54,52 @@ SUPPORTED_ANALYSES = [
53
54
  "tcr_analysis",
54
55
  "wes_analysis",
55
56
  "wes_tumor_only_analysis",
57
+ "scrnaseq_analysis",
58
+ "visium_analysis",
56
59
  ]
57
60
 
61
+ """
62
+ Since most of the definitions are json files which don't allow comments, I'm putting
63
+ our scrnaseq_analysis documentation here. These are the files (and folder structure) that are expected in the gcloud
64
+ directory to fully create a record for scRNA analysis:
65
+ ./sample_metadata.csv
66
+ ./config.yaml
67
+ ./R_package_versions.csv
68
+ ./clustering/SRR8318954_clustering.rds
69
+ ./integration/integrated.rds
70
+ ./integration/heatmap_plots.zip
71
+ ./integration/markers.zip
72
+ ./integration/split_percent_plots.zip
73
+ ./integration/split_umap_plots.zip
74
+ ./integration/umap_plots.zip
75
+ ./report/SRR8318954_report.html
76
+ ./star/SRR8318954.Aligned.sortedByCoord.out.bam
77
+ ./star/SRR8318954.Aligned.sortedByCoord.out.bam.bai
78
+ ./star/SRR8318954.Log.final.out
79
+ ./star/SRR8318954.Log.out
80
+ ./star/SRR8318954.Log.progress.out
81
+ ./star/SRR8318954.SJ.out.tab
82
+ ./star/SRR8318954.Solo.out/Barcodes.stats
83
+ ./star/SRR8318954.Solo.out/Gene/Features.stats
84
+ ./star/SRR8318954.Solo.out/Gene/Summary.csv
85
+ ./star/SRR8318954.Solo.out/Gene/UMIperCellSorted.txt
86
+ ./star/SRR8318954.Solo.out/Gene/filtered/features.tsv
87
+ ./star/SRR8318954.Solo.out/Gene/filtered/barcodes.tsv
88
+ ./star/SRR8318954.Solo.out/Gene/filtered/matrix.mtx
89
+ ./star/SRR8318954.Solo.out/Gene/raw/features.tsv
90
+ ./star/SRR8318954.Solo.out/Gene/raw/barcodes.tsv
91
+ ./star/SRR8318954.Solo.out/Gene/raw/matrix.mtx
92
+
93
+ These are the files required for visium analysis:
94
+ ./sample_metadata.csv
95
+ ./config.yaml
96
+ ./R_package_versions.csv
97
+ ./spatial_variable_features/{id}_spatial_variable_features.rds
98
+ ./report/{id}_report.html
99
+ ./merge/merged.rds
100
+ ./{id}_spaceranger.zip
101
+ """
102
+
58
103
  SUPPORTED_TEMPLATES = SUPPORTED_ASSAYS + SUPPORTED_MANIFESTS + SUPPORTED_ANALYSES
59
104
 
60
105
  # provide a way to get file-path prefix for each upload_type
@@ -95,6 +140,9 @@ ASSAY_TO_FILEPATH: Dict[str, str] = {
95
140
  "olink",
96
141
  "mihc",
97
142
  "scrnaseq",
143
+ "scrnaseq_analysis",
144
+ "visium",
145
+ "visium_analysis",
98
146
  ]
99
147
  },
100
148
  }
@@ -0,0 +1,51 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "html_artifact",
4
+ "title": "HTML Artifact",
5
+ "type": "object",
6
+ "description": "Information about a HTML file.",
7
+ "additionalProperties": false,
8
+ "properties": {
9
+ "data_format": {
10
+ "description": "Data format.",
11
+ "const": "HTML"
12
+ },
13
+ "upload_placeholder": {
14
+ "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
15
+ },
16
+ "artifact_creator": {
17
+ "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
18
+ },
19
+ "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
20
+ "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
21
+ "file_name": {
22
+ "$ref": "artifacts/artifact_core.json#properties/file_name"
23
+ },
24
+ "object_url": {
25
+ "$ref": "artifacts/artifact_core.json#properties/object_url"
26
+ },
27
+ "uploaded_timestamp": {
28
+ "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
29
+ },
30
+ "file_size_bytes": {
31
+ "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
32
+ },
33
+ "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
34
+ "crc32c_hash": {
35
+ "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
36
+ },
37
+ "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
38
+ "artifact_category": {
39
+ "$ref": "artifacts/artifact_core.json#properties/artifact_category"
40
+ },
41
+ "facet_group": {
42
+ "$ref": "artifacts/artifact_core.json#properties/facet_group"
43
+ }
44
+ },
45
+ "allOf": [
46
+ {
47
+ "$ref": "artifacts/artifact_core.json"
48
+ }
49
+ ],
50
+ "mergeStrategy": "objectMerge"
51
+ }
@@ -0,0 +1,51 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "mtx_artifact",
4
+ "title": "MTX Artifact",
5
+ "type": "object",
6
+ "description": "Information about a MTX file.",
7
+ "additionalProperties": false,
8
+ "properties": {
9
+ "data_format": {
10
+ "description": "Data format.",
11
+ "const": "MTX"
12
+ },
13
+ "upload_placeholder": {
14
+ "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
15
+ },
16
+ "artifact_creator": {
17
+ "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
18
+ },
19
+ "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
20
+ "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
21
+ "file_name": {
22
+ "$ref": "artifacts/artifact_core.json#properties/file_name"
23
+ },
24
+ "object_url": {
25
+ "$ref": "artifacts/artifact_core.json#properties/object_url"
26
+ },
27
+ "uploaded_timestamp": {
28
+ "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
29
+ },
30
+ "file_size_bytes": {
31
+ "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
32
+ },
33
+ "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
34
+ "crc32c_hash": {
35
+ "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
36
+ },
37
+ "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
38
+ "artifact_category": {
39
+ "$ref": "artifacts/artifact_core.json#properties/artifact_category"
40
+ },
41
+ "facet_group": {
42
+ "$ref": "artifacts/artifact_core.json#properties/facet_group"
43
+ }
44
+ },
45
+ "allOf": [
46
+ {
47
+ "$ref": "artifacts/artifact_core.json"
48
+ }
49
+ ],
50
+ "mergeStrategy": "objectMerge"
51
+ }
@@ -0,0 +1,51 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "out_artifact",
4
+ "title": "OUT Artifact",
5
+ "type": "object",
6
+ "description": "Information about a OUT file.",
7
+ "additionalProperties": false,
8
+ "properties": {
9
+ "data_format": {
10
+ "description": "Data format.",
11
+ "const": "OUT"
12
+ },
13
+ "upload_placeholder": {
14
+ "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
15
+ },
16
+ "artifact_creator": {
17
+ "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
18
+ },
19
+ "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
20
+ "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
21
+ "file_name": {
22
+ "$ref": "artifacts/artifact_core.json#properties/file_name"
23
+ },
24
+ "object_url": {
25
+ "$ref": "artifacts/artifact_core.json#properties/object_url"
26
+ },
27
+ "uploaded_timestamp": {
28
+ "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
29
+ },
30
+ "file_size_bytes": {
31
+ "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
32
+ },
33
+ "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
34
+ "crc32c_hash": {
35
+ "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
36
+ },
37
+ "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
38
+ "artifact_category": {
39
+ "$ref": "artifacts/artifact_core.json#properties/artifact_category"
40
+ },
41
+ "facet_group": {
42
+ "$ref": "artifacts/artifact_core.json#properties/facet_group"
43
+ }
44
+ },
45
+ "allOf": [
46
+ {
47
+ "$ref": "artifacts/artifact_core.json"
48
+ }
49
+ ],
50
+ "mergeStrategy": "objectMerge"
51
+ }
@@ -0,0 +1,51 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "rds_artifact",
4
+ "title": "RDS Artifact",
5
+ "type": "object",
6
+ "description": "Information about a rds file.",
7
+ "additionalProperties": false,
8
+ "properties": {
9
+ "data_format": {
10
+ "description": "Data format.",
11
+ "const": "RDS"
12
+ },
13
+ "upload_placeholder": {
14
+ "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
15
+ },
16
+ "artifact_creator": {
17
+ "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
18
+ },
19
+ "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
20
+ "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
21
+ "file_name": {
22
+ "$ref": "artifacts/artifact_core.json#properties/file_name"
23
+ },
24
+ "object_url": {
25
+ "$ref": "artifacts/artifact_core.json#properties/object_url"
26
+ },
27
+ "uploaded_timestamp": {
28
+ "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
29
+ },
30
+ "file_size_bytes": {
31
+ "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
32
+ },
33
+ "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
34
+ "crc32c_hash": {
35
+ "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
36
+ },
37
+ "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
38
+ "artifact_category": {
39
+ "$ref": "artifacts/artifact_core.json#properties/artifact_category"
40
+ },
41
+ "facet_group": {
42
+ "$ref": "artifacts/artifact_core.json#properties/facet_group"
43
+ }
44
+ },
45
+ "allOf": [
46
+ {
47
+ "$ref": "artifacts/artifact_core.json"
48
+ }
49
+ ],
50
+ "mergeStrategy": "objectMerge"
51
+ }
@@ -0,0 +1,51 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "stats_artifact",
4
+ "title": "Stats Artifact",
5
+ "type": "object",
6
+ "description": "Information about a STATS file.",
7
+ "additionalProperties": false,
8
+ "properties": {
9
+ "data_format": {
10
+ "description": "Data format.",
11
+ "const": "STATS"
12
+ },
13
+ "upload_placeholder": {
14
+ "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
15
+ },
16
+ "artifact_creator": {
17
+ "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
18
+ },
19
+ "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
20
+ "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
21
+ "file_name": {
22
+ "$ref": "artifacts/artifact_core.json#properties/file_name"
23
+ },
24
+ "object_url": {
25
+ "$ref": "artifacts/artifact_core.json#properties/object_url"
26
+ },
27
+ "uploaded_timestamp": {
28
+ "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
29
+ },
30
+ "file_size_bytes": {
31
+ "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
32
+ },
33
+ "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
34
+ "crc32c_hash": {
35
+ "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
36
+ },
37
+ "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
38
+ "artifact_category": {
39
+ "$ref": "artifacts/artifact_core.json#properties/artifact_category"
40
+ },
41
+ "facet_group": {
42
+ "$ref": "artifacts/artifact_core.json#properties/facet_group"
43
+ }
44
+ },
45
+ "allOf": [
46
+ {
47
+ "$ref": "artifacts/artifact_core.json"
48
+ }
49
+ ],
50
+ "mergeStrategy": "objectMerge"
51
+ }
@@ -0,0 +1,51 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "tab_artifact",
4
+ "title": "TAB Artifact",
5
+ "type": "object",
6
+ "description": "Information about a TAB file.",
7
+ "additionalProperties": false,
8
+ "properties": {
9
+ "data_format": {
10
+ "description": "Data format.",
11
+ "const": "TAB"
12
+ },
13
+ "upload_placeholder": {
14
+ "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
15
+ },
16
+ "artifact_creator": {
17
+ "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
18
+ },
19
+ "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
20
+ "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
21
+ "file_name": {
22
+ "$ref": "artifacts/artifact_core.json#properties/file_name"
23
+ },
24
+ "object_url": {
25
+ "$ref": "artifacts/artifact_core.json#properties/object_url"
26
+ },
27
+ "uploaded_timestamp": {
28
+ "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
29
+ },
30
+ "file_size_bytes": {
31
+ "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
32
+ },
33
+ "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
34
+ "crc32c_hash": {
35
+ "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
36
+ },
37
+ "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
38
+ "artifact_category": {
39
+ "$ref": "artifacts/artifact_core.json#properties/artifact_category"
40
+ },
41
+ "facet_group": {
42
+ "$ref": "artifacts/artifact_core.json#properties/facet_group"
43
+ }
44
+ },
45
+ "allOf": [
46
+ {
47
+ "$ref": "artifacts/artifact_core.json"
48
+ }
49
+ ],
50
+ "mergeStrategy": "objectMerge"
51
+ }
@@ -0,0 +1,51 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "tiff_artifact",
4
+ "title": "Tiff Artifact",
5
+ "type": "object",
6
+ "description": "Information about a tiff file.",
7
+ "additionalProperties": false,
8
+ "properties": {
9
+ "data_format": {
10
+ "description": "Data format.",
11
+ "const": "TIFF"
12
+ },
13
+ "upload_placeholder": {
14
+ "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
15
+ },
16
+ "artifact_creator": {
17
+ "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
18
+ },
19
+ "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
20
+ "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
21
+ "file_name": {
22
+ "$ref": "artifacts/artifact_core.json#properties/file_name"
23
+ },
24
+ "object_url": {
25
+ "$ref": "artifacts/artifact_core.json#properties/object_url"
26
+ },
27
+ "uploaded_timestamp": {
28
+ "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
29
+ },
30
+ "file_size_bytes": {
31
+ "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
32
+ },
33
+ "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
34
+ "crc32c_hash": {
35
+ "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
36
+ },
37
+ "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
38
+ "artifact_category": {
39
+ "$ref": "artifacts/artifact_core.json#properties/artifact_category"
40
+ },
41
+ "facet_group": {
42
+ "$ref": "artifacts/artifact_core.json#properties/facet_group"
43
+ }
44
+ },
45
+ "allOf": [
46
+ {
47
+ "$ref": "artifacts/artifact_core.json"
48
+ }
49
+ ],
50
+ "mergeStrategy": "objectMerge"
51
+ }
@@ -0,0 +1,51 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "txt_artifact",
4
+ "title": "Txt Artifact",
5
+ "type": "object",
6
+ "description": "Information about a txt file.",
7
+ "additionalProperties": false,
8
+ "properties": {
9
+ "data_format": {
10
+ "description": "Data format.",
11
+ "const": "TXT"
12
+ },
13
+ "upload_placeholder": {
14
+ "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
15
+ },
16
+ "artifact_creator": {
17
+ "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
18
+ },
19
+ "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
20
+ "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
21
+ "file_name": {
22
+ "$ref": "artifacts/artifact_core.json#properties/file_name"
23
+ },
24
+ "object_url": {
25
+ "$ref": "artifacts/artifact_core.json#properties/object_url"
26
+ },
27
+ "uploaded_timestamp": {
28
+ "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
29
+ },
30
+ "file_size_bytes": {
31
+ "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
32
+ },
33
+ "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
34
+ "crc32c_hash": {
35
+ "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
36
+ },
37
+ "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
38
+ "artifact_category": {
39
+ "$ref": "artifacts/artifact_core.json#properties/artifact_category"
40
+ },
41
+ "facet_group": {
42
+ "$ref": "artifacts/artifact_core.json#properties/facet_group"
43
+ }
44
+ },
45
+ "allOf": [
46
+ {
47
+ "$ref": "artifacts/artifact_core.json"
48
+ }
49
+ ],
50
+ "mergeStrategy": "objectMerge"
51
+ }
@@ -141,6 +141,17 @@
141
141
  "idRef": "batch_id"
142
142
  }
143
143
  },
144
+ "visium": {
145
+ "type": "array",
146
+ "description": "Visium",
147
+ "items": {
148
+ "$ref": "assays/visium_assay.json"
149
+ },
150
+ "mergeStrategy": "arrayMergeById",
151
+ "mergeOptions": {
152
+ "idRef": "batch_id"
153
+ }
154
+ },
144
155
  "nanostring": {
145
156
  "type": "array",
146
157
  "description": "Nanostring",
@@ -35,6 +35,28 @@
35
35
  "mergeOptions": {
36
36
  "idRef": "batch_id"
37
37
  }
38
+ },
39
+ "scrnaseq_analysis": {
40
+ "type": "array",
41
+ "description": "Analysis for Assay for scRNA.",
42
+ "items": {
43
+ "$ref": "assays/scrnaseq_analysis.json"
44
+ },
45
+ "mergeStrategy": "arrayMergeById",
46
+ "mergeOptions": {
47
+ "idRef": "batch_id"
48
+ }
49
+ },
50
+ "visium_analysis": {
51
+ "type": "array",
52
+ "description": "Analysis for Assay for visium.",
53
+ "items": {
54
+ "$ref": "assays/visium_analysis.json"
55
+ },
56
+ "mergeStrategy": "arrayMergeById",
57
+ "mergeOptions": {
58
+ "idRef": "batch_id"
59
+ }
38
60
  }
39
61
  }
40
62
  }
@@ -0,0 +1,60 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "visium_input",
4
+ "title": "Visium Input Files and Data",
5
+ "type": "object",
6
+ "description": "Visium assay input files and data",
7
+ "inheritableBase": true,
8
+ "properties": {
9
+ "lane": {
10
+ "description": "Lane used for this run from 1-9",
11
+ "type": "integer",
12
+ "exclusiveMinimum": 0,
13
+ "maximum": 9
14
+ },
15
+ "read_1_fastq_gz": {
16
+ "$ref": "artifacts/artifact_gz.json"
17
+ },
18
+ "read_2_fastq_gz": {
19
+ "$ref": "artifacts/artifact_gz.json"
20
+ },
21
+ "loupe_alignment_file": {
22
+ "$ref": "artifacts/artifact_json.json"
23
+ },
24
+ "slide_serial_code": {
25
+ "type": "string",
26
+ "description": "Visium slide serial number"
27
+ },
28
+ "slide_capture_area": {
29
+ "type": "string",
30
+ "description": "Visium capture area identifier"
31
+ },
32
+ "library_yield_ng": {
33
+ "description": "Resulting yield (in ng) from library construction.",
34
+ "type": "number"
35
+ },
36
+ "dv200": {
37
+ "description": "The percentage of fragments > 200 nucleotides. (0-1)",
38
+ "type": "number",
39
+ "minimum": 0,
40
+ "maximum": 1
41
+ },
42
+ "brightfield_image": { "$ref": "artifacts/artifact_tiff.json"},
43
+ "dark_image": { "$ref": "artifacts/artifact_tiff.json"},
44
+ "colorized_image": { "$ref": "artifacts/artifact_tiff.json"},
45
+ "cytassist_image": { "$ref": "artifacts/artifact_tiff.json"},
46
+ "dapi_index": {
47
+ "type": "integer",
48
+ "description": "Index of DAPI channel (1-indexed) of fluorescence image."
49
+ },
50
+ "comments": {
51
+ "type": "string",
52
+ "description": "Comments on visium run"
53
+ }
54
+ },
55
+ "required": [
56
+ "lane",
57
+ "read_1_fastq_gz",
58
+ "read_2_fastq_gz"
59
+ ]
60
+ }
@@ -0,0 +1,27 @@
1
+ {
2
+ "$schema": "metaschema/strict_meta_schema.json#",
3
+ "$id": "visium_preamble",
4
+ "title": "Visium Preamble",
5
+ "description": "Preamble information in a visium assay",
6
+ "type": "object",
7
+ "inheritableBase": true,
8
+ "properties": {
9
+ "spatial_gene_expression_platform": {
10
+ "description": "Visium spatial gene expression platform",
11
+ "type": "string",
12
+ "enum": [
13
+ "Visium Spatial Gene Expression for FFPE",
14
+ "Visium CytAssist Spatial Gene Expression for FFPE",
15
+ "Visium HD Spatial Gene Expression for FFPE"
16
+ ]
17
+ },
18
+ "human_transcriptome_probe_set_version": {
19
+ "description": "Visium human transcriptome probe set version",
20
+ "type": "string",
21
+ "enum": [
22
+ "Visium Human Transcriptome Probe Set v1.0",
23
+ "Visium Human Transcriptome Probe Set v2.0"
24
+ ]
25
+ }
26
+ }
27
+ }