nci-cidc-schemas 0.27.1__py2.py3-none-any.whl → 0.27.4__py2.py3-none-any.whl

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Files changed (11) hide show
  1. cidc_schemas/__init__.py +1 -1
  2. cidc_schemas/schemas/templates/analyses/wes_analysis_template.json +5 -5
  3. cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json +4 -4
  4. cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +4 -0
  5. cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +4 -0
  6. {nci_cidc_schemas-0.27.1.dist-info → nci_cidc_schemas-0.27.4.dist-info}/METADATA +1 -1
  7. {nci_cidc_schemas-0.27.1.dist-info → nci_cidc_schemas-0.27.4.dist-info}/RECORD +11 -11
  8. {nci_cidc_schemas-0.27.1.dist-info → nci_cidc_schemas-0.27.4.dist-info}/WHEEL +1 -1
  9. {nci_cidc_schemas-0.27.1.dist-info → nci_cidc_schemas-0.27.4.dist-info}/LICENSE +0 -0
  10. {nci_cidc_schemas-0.27.1.dist-info → nci_cidc_schemas-0.27.4.dist-info}/entry_points.txt +0 -0
  11. {nci_cidc_schemas-0.27.1.dist-info → nci_cidc_schemas-0.27.4.dist-info}/top_level.txt +0 -0
cidc_schemas/__init__.py CHANGED
@@ -2,4 +2,4 @@
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  __author__ = """NCI"""
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  __email__ = "nci-cidc-tools-admin@mail.nih.gov"
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- __version__ = "0.27.01"
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+ __version__ = "0.27.04"
cidc_schemas/schemas/templates/analyses/wes_analysis_template.json CHANGED
@@ -187,35 +187,35 @@
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  "is_artifact": 1
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  },
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  {
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- "parse_through": "lambda run: f'{folder or \"\"}analysis/report.tar.gz'",
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+ "parse_through": "lambda run: f'{folder or \"\"}analysis/{run}.report.tar.gz'",
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  "merge_pointer": "/report/report",
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  "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/report.tar.gz",
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  "type_ref": "assays/components/local_file.json#properties/file_path",
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  "is_artifact": 1
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  },
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  {
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- "parse_through": "lambda run: f'{folder or \"\"}analysis/report/somatic_variants/05_tumor_germline_overlap.tsv'",
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+ "parse_through": "lambda run: f'{folder or \"\"}analysis/report/somatic_variants/{run}.05_tumor_germline_overlap.tsv'",
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  "merge_pointer": "/report/tumor_germline_overlap",
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  "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor_germline_overlap.tsv",
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  "type_ref": "assays/components/local_file.json#properties/file_path",
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  "is_artifact": 1
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  },
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  {
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- "parse_through": "lambda run: f'{folder or \"\"}analysis/report/WES_Meta/02_WES_Run_Version.tsv'",
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+ "parse_through": "lambda run: f'{folder or \"\"}analysis/report/WES_Meta/{run}.02_WES_Run_Version.tsv'",
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  "merge_pointer": "/report/wes_run_version",
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  "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/wes_run_version.tsv",
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  "type_ref": "assays/components/local_file.json#properties/file_path",
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  "is_artifact": 1
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  },
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  {
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- "parse_through": "lambda run: f'{folder or \"\"}analysis/report/config.yaml'",
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+ "parse_through": "lambda run: f'{folder or \"\"}analysis/report/{run}.config.yaml'",
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  "merge_pointer": "/report/config",
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  "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/config.yaml",
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  "type_ref": "assays/components/local_file.json#properties/file_path",
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  "is_artifact": 1
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  },
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  {
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- "parse_through": "lambda run: f'{folder or \"\"}analysis/report/metasheet.csv'",
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+ "parse_through": "lambda run: f'{folder or \"\"}analysis/report/{run}.metasheet.csv'",
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  "merge_pointer": "/report/metasheet",
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  "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/metasheet.csv",
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  "type_ref": "assays/components/local_file.json#properties/file_path",
cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json CHANGED
@@ -47,28 +47,28 @@
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  "is_artifact": 1
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  },
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  {
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- "parse_through": "lambda run: f'{folder or \"\"}analysis/report.tar.gz'",
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+ "parse_through": "lambda run: f'{folder or \"\"}analysis/{run}.report.tar.gz'",
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  "merge_pointer": "/report/report",
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  "gcs_uri_format": "{protocol identifier}/wes_tumor_only/{run id}/analysis/report.tar.gz",
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  "type_ref": "assays/components/local_file.json#properties/file_path",
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  "is_artifact": 1
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  },
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  {
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- "parse_through": "lambda run: f'{folder or \"\"}analysis/report/WES_Meta/02_WES_Run_Version.tsv'",
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+ "parse_through": "lambda run: f'{folder or \"\"}analysis/report/WES_Meta/{run}.02_WES_Run_Version.tsv'",
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  "merge_pointer": "/report/wes_run_version",
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  "gcs_uri_format": "{protocol identifier}/wes_tumor_only/{run id}/analysis/wes_run_version.tsv",
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  "type_ref": "assays/components/local_file.json#properties/file_path",
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  "is_artifact": 1
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  },
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  {
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- "parse_through": "lambda run: f'{folder or \"\"}analysis/report/config.yaml'",
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+ "parse_through": "lambda run: f'{folder or \"\"}analysis/report/{run}.config.yaml'",
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  "merge_pointer": "/report/config",
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  "gcs_uri_format": "{protocol identifier}/wes_tumor_only/{run id}/analysis/config.yaml",
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  "type_ref": "assays/components/local_file.json#properties/file_path",
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  "is_artifact": 1
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  },
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  {
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- "parse_through": "lambda run: f'{folder or \"\"}analysis/report/metasheet.csv'",
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+ "parse_through": "lambda run: f'{folder or \"\"}analysis/report/{run}.metasheet.csv'",
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  "merge_pointer": "/report/metasheet",
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  "gcs_uri_format": "{protocol identifier}/wes_tumor_only/{run id}/analysis/metasheet.csv",
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  "type_ref": "assays/components/local_file.json#properties/file_path",
cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json CHANGED
@@ -217,6 +217,10 @@
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  "merge_pointer": "/type_of_sample",
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  "type_ref": "sample.json#properties/type_of_sample"
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  },
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+ "type of tumor sample": {
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+ "merge_pointer": "/type_of_tumor_sample",
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+ "type_ref": "sample.json#properties/type_of_tumor_sample"
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+ },
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  "sample collection procedure": {
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  "merge_pointer": "/sample_collection_procedure",
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  "type_ref": "sample.json#properties/sample_collection_procedure"
cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json CHANGED
@@ -212,6 +212,10 @@
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  "merge_pointer": "/type_of_sample",
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  "type_ref": "sample.json#properties/type_of_sample"
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  },
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+ "type of tumor sample": {
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+ "merge_pointer": "/type_of_tumor_sample",
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+ "type_ref": "sample.json#properties/type_of_tumor_sample"
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+ },
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  "sample collection procedure": {
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  "merge_pointer": "/sample_collection_procedure",
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  "type_ref": "sample.json#properties/sample_collection_procedure"
{nci_cidc_schemas-0.27.1.dist-info → nci_cidc_schemas-0.27.4.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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  Name: nci_cidc_schemas
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- Version: 0.27.1
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+ Version: 0.27.4
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  Summary: The CIDC data model and tools for working with it.
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  Home-page: https://github.com/NCI-CIDC/cidc-schemas
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  Author: NCI
{nci_cidc_schemas-0.27.1.dist-info → nci_cidc_schemas-0.27.4.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
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- cidc_schemas/__init__.py,sha256=VcAwWzIL8eZjFMd1X0wzH9VJFMPjpfGxv5Vkdpxw2GU,136
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+ cidc_schemas/__init__.py,sha256=sJ-Bh9kRVMNMFxLIU3uhRndR7gShN0nXOyrqKWRJqPo,136
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  cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
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  cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
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  cidc_schemas/json_validation.py,sha256=nHkSfTmBN7EeTrZVdbb8h6A64lWrJe5z0AIHiIy-YB0,22552
@@ -123,8 +123,8 @@ cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json,sha256=7v
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  cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json,sha256=d6qOGbYXXx1c8rb-saM4D_tMuK8n4ydbyW9_xaW6xhk,6381
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  cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json,sha256=vMHXSQNZz8sFxwiBUnRXb5o08GxgbKZjMu8ZPjNn4TI,15944
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  cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json,sha256=ai5KUp6q5GGTxDybOHBaseOnvQCVqIRh4SurETz5Vx0,3054
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- cidc_schemas/schemas/templates/analyses/wes_analysis_template.json,sha256=V5RRZ39u9mNt29vlzAIPx6uojDKU3i7qLWGPy6Qanbs,35033
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- cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json,sha256=oHQ89pnzqGWE2sfb5sYGYhyknyd0pr0dTEGTYn2y_tQ,16240
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+ cidc_schemas/schemas/templates/analyses/wes_analysis_template.json,sha256=wp0Iop9V8zpy8pM7JGBRhGzF6QoNs743Z5K89IQA7PA,35063
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+ cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json,sha256=hhWA6mBPVBIM9QFg0C7CkimD9fcFXXtFSSkvo0lvnro,16264
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  cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json,sha256=7WygawkxnhFu5xBAuIhSOBD8TwCqDgINjC-HIYeCf4Q,3928
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  cidc_schemas/schemas/templates/assays/clinical_data_template.json,sha256=1luQXzyqbAKKiNVwVQFeZ4dwzVpnTeGAropzd_mYmx4,2193
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  cidc_schemas/schemas/templates/assays/ctdna_template.json,sha256=KDyOPbBh0dytlZRJVKNuaGEB8MAyq6Ls1CvI8d2wF3o,6151
@@ -145,8 +145,8 @@ cidc_schemas/schemas/templates/assays/tcr_fastq_template.json,sha256=7Qq4ssI8ErD
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  cidc_schemas/schemas/templates/assays/wes_bam_template.json,sha256=nxbb_lNPi-5cdAlwmSBvn7cS_8gMjROOz7wBWk6ev0Y,2724
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  cidc_schemas/schemas/templates/assays/wes_fastq_template.json,sha256=vuwuIpqXyqpGxCunpjbHKaBQhfKFnr2R-wMkXDiJdKM,3143
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  cidc_schemas/schemas/templates/manifests/h_and_e_template.json,sha256=ttdf1U9ENF1U6cn4jG6pLB0hqIVignaa8UfmyPwLuTY,17726
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- cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json,sha256=y88bHiUDoSvpgA1poHSOfwa4K-TLUjemnZ-qghibteY,17333
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- cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=wuDJrzC-f1jtTWt_tAeamIVd92QqItD24bnnpSj_ZM4,18416
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+ cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json,sha256=VavO5lg52VEXbdXS_pqsYRwCdjjk4wQuzrgaIOlwiU8,17566
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+ cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=nmr3DCCFzpAT_SdEfSTCWIga48z4PwnoSodBbnZvNAE,18649
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  cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json,sha256=GUtdrieD8vwoUMRs9ePzDHCrN2sbgDx81-R1K2PBzsI,18387
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  cidc_schemas/schemas/templates/manifests/pbmc_template.json,sha256=b72ng2fU2tEYTye_Na5bsHv7dxNS9sPciIQqznhHZ7s,18241
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  cidc_schemas/schemas/templates/manifests/plasma_template.json,sha256=sQR_ayLKgxzrkjC-PC7eCmEyV6dQzQr-boZAtDBgbx8,15856
@@ -154,9 +154,9 @@ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=jwyXO
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  cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json,sha256=lVJrGb28n-vyfjGBzhrzjn1lMKw1b4HXXmWtwA603v0,2797
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  cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=eoX_YIl1HfQXiL7Q6ybIuOLs85Nbn7EylJ8dzXKiMZw,18674
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  cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=HK2Q2VQcDhP8FZDZapk04Qx2-Tji9dCMH1UpkVhU3Vs,17819
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- nci_cidc_schemas-0.27.1.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
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- nci_cidc_schemas-0.27.1.dist-info/METADATA,sha256=S8HqjcNvuIkrdWflFo_Y2NfypLGiemRsrdRhZsmVmqc,4531
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- nci_cidc_schemas-0.27.1.dist-info/WHEEL,sha256=9Hm2OB-j1QcCUq9Jguht7ayGIIZBRTdOXD1qg9cCgPM,109
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- nci_cidc_schemas-0.27.1.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
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- nci_cidc_schemas-0.27.1.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
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- nci_cidc_schemas-0.27.1.dist-info/RECORD,,
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+ nci_cidc_schemas-0.27.4.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
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+ nci_cidc_schemas-0.27.4.dist-info/METADATA,sha256=qA1pzMsBtx7m2RIf5PBcSuXFUdhFz1pIsua6KyXLvoE,4531
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+ nci_cidc_schemas-0.27.4.dist-info/WHEEL,sha256=rF4EZyR2XVS6irmOHQIJx2SUqXLZKRMUrjsg8UwN-XQ,109
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+ nci_cidc_schemas-0.27.4.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
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+ nci_cidc_schemas-0.27.4.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
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+ nci_cidc_schemas-0.27.4.dist-info/RECORD,,
{nci_cidc_schemas-0.27.1.dist-info → nci_cidc_schemas-0.27.4.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (75.8.0)
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+ Generator: setuptools (75.8.2)
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  Root-Is-Purelib: true
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  Tag: py2-none-any
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  Tag: py3-none-any