nci-cidc-schemas 0.27.1__tar.gz → 0.27.5__tar.gz

{nci_cidc_schemas-0.27.1/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.27.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nci_cidc_schemas
-Version: 0.27.1
+Version: 0.27.5
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI

{nci_cidc_schemas-0.27.1 → nci_cidc_schemas-0.27.5}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.27.01"
+__version__ = "0.27.05"

{nci_cidc_schemas-0.27.1 → nci_cidc_schemas-0.27.5}/cidc_schemas/schemas/sample.json

@@ -195,8 +195,8 @@
             "type": "string",
             "enum": [
                 "Ficoll",
-                "Formulin Fixation",
-                "Formulin-Fixed Paraffin-Embedded (FFPE)",
+                "Formalin Fixation",
+                "Formalin-Fixed Paraffin-Embedded (FFPE)",
                 "Frozen",
                 "70% Ethanol",
                 "H&E",

{nci_cidc_schemas-0.27.1 → nci_cidc_schemas-0.27.5}/cidc_schemas/schemas/templates/analyses/wes_analysis_template.json

@@ -187,35 +187,35 @@
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report.tar.gz'",
+                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/{run}.report.tar.gz'",
                                     "merge_pointer": "/report/report",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/report.tar.gz",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/somatic_variants/05_tumor_germline_overlap.tsv'",
+                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/somatic_variants/{run}.05_tumor_germline_overlap.tsv'",
                                     "merge_pointer": "/report/tumor_germline_overlap",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor_germline_overlap.tsv",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/WES_Meta/02_WES_Run_Version.tsv'",
+                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/WES_Meta/{run}.02_WES_Run_Version.tsv'",
                                     "merge_pointer": "/report/wes_run_version",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/wes_run_version.tsv",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/config.yaml'",
+                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/{run}.config.yaml'",
                                     "merge_pointer": "/report/config",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/config.yaml",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/metasheet.csv'",
+                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/{run}.metasheet.csv'",
                                     "merge_pointer": "/report/metasheet",
                                     "gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/metasheet.csv",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",

{nci_cidc_schemas-0.27.1 → nci_cidc_schemas-0.27.5}/cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json

@@ -47,28 +47,28 @@
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report.tar.gz'",
+                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/{run}.report.tar.gz'",
                                     "merge_pointer": "/report/report",
                                     "gcs_uri_format": "{protocol identifier}/wes_tumor_only/{run id}/analysis/report.tar.gz",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/WES_Meta/02_WES_Run_Version.tsv'",
+                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/WES_Meta/{run}.02_WES_Run_Version.tsv'",
                                     "merge_pointer": "/report/wes_run_version",
                                     "gcs_uri_format": "{protocol identifier}/wes_tumor_only/{run id}/analysis/wes_run_version.tsv",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/config.yaml'",
+                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/{run}.config.yaml'",
                                     "merge_pointer": "/report/config",
                                     "gcs_uri_format": "{protocol identifier}/wes_tumor_only/{run id}/analysis/config.yaml",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
                                 },
                                 {
-                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/metasheet.csv'",
+                                    "parse_through": "lambda run: f'{folder or \"\"}analysis/report/{run}.metasheet.csv'",
                                     "merge_pointer": "/report/metasheet",
                                     "gcs_uri_format": "{protocol identifier}/wes_tumor_only/{run id}/analysis/metasheet.csv",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",

{nci_cidc_schemas-0.27.1 → nci_cidc_schemas-0.27.5}/cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json

@@ -217,6 +217,10 @@
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
                         },
+                        "type of tumor sample": {
+                            "merge_pointer": "/type_of_tumor_sample",
+                            "type_ref": "sample.json#properties/type_of_tumor_sample"
+                        },
                         "sample collection procedure": {
                             "merge_pointer": "/sample_collection_procedure",
                             "type_ref": "sample.json#properties/sample_collection_procedure"

{nci_cidc_schemas-0.27.1 → nci_cidc_schemas-0.27.5}/cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json

@@ -212,6 +212,10 @@
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
                         },
+                        "type of tumor sample": {
+                            "merge_pointer": "/type_of_tumor_sample",
+                            "type_ref": "sample.json#properties/type_of_tumor_sample"
+                        },
                         "sample collection procedure": {
                             "merge_pointer": "/sample_collection_procedure",
                             "type_ref": "sample.json#properties/sample_collection_procedure"

{nci_cidc_schemas-0.27.1 → nci_cidc_schemas-0.27.5/nci_cidc_schemas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nci_cidc_schemas
-Version: 0.27.1
+Version: 0.27.5
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI

{nci_cidc_schemas-0.27.1 → nci_cidc_schemas-0.27.5}/tests/data/clinicaltrial_examples/CT_cytof_with_analysis.json

@@ -282,7 +282,7 @@
           "material_remaining_units": "Slides",
           "processed_sample_quantity": 4,
           "material_storage_condition": "Ambient",
-          "fixation_stabilization_type": "Formulin-Fixed Paraffin-Embedded (FFPE)",
+          "fixation_stabilization_type": "Formalin-Fixed Paraffin-Embedded (FFPE)",
           "sample_collection_procedure": "Core Biopsy"
         },
         {

{nci_cidc_schemas-0.27.1 → nci_cidc_schemas-0.27.5}/tests/prism/cidc_test_data/manifest_data.py

@@ -617,7 +617,7 @@ def tissue_slide() -> PrismTestData:
                         "description_of_sample": "Normal",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 4.0,
                         "material_used": 3.0,
@@ -780,7 +780,7 @@ def normal_blood_dna() -> PrismTestData:
                     {
                         "shipping_entry_number": 1,
                         "collection_event_name": "Baseline",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 1')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP01N1.00",
@@ -815,7 +815,7 @@ def normal_blood_dna() -> PrismTestData:
                     {
                         "shipping_entry_number": 2,
                         "collection_event_name": "Baseline",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 2')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP01N2.00",
@@ -850,7 +850,7 @@ def normal_blood_dna() -> PrismTestData:
                     {
                         "shipping_entry_number": 3,
                         "collection_event_name": "Baseline",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 3')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP01N3.00",
@@ -891,7 +891,7 @@ def normal_blood_dna() -> PrismTestData:
                     {
                         "shipping_entry_number": 4,
                         "collection_event_name": "Baseline",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 4')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP02N1.00",
@@ -925,7 +925,7 @@ def normal_blood_dna() -> PrismTestData:
                     {
                         "shipping_entry_number": 5,
                         "collection_event_name": "Baseline",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 5')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP02N2.00",
@@ -959,7 +959,7 @@ def normal_blood_dna() -> PrismTestData:
                     {
                         "shipping_entry_number": 6,
                         "collection_event_name": "Baseline",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 6')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP02N3.00",
@@ -1100,7 +1100,7 @@ def normal_tissue_dna() -> PrismTestData:
                         "type_of_sample": "Skin Tissue",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 1.0,
                         "processed_sample_derivative": "Germline DNA",
@@ -1132,7 +1132,7 @@ def normal_tissue_dna() -> PrismTestData:
                         "type_of_sample": "Skin Tissue",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 2.0,
                         "processed_sample_derivative": "Germline DNA",
@@ -1332,7 +1332,7 @@ def tumor_tissue_dna() -> PrismTestData:
                         "description_of_sample": "Normal",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 1.0,
                         "processed_sample_derivative": "Germline DNA",
@@ -1363,7 +1363,7 @@ def tumor_tissue_dna() -> PrismTestData:
                         "description_of_sample": "Normal",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 1.0,
                         "processed_sample_derivative": "Germline DNA",
@@ -1397,7 +1397,7 @@ def tumor_tissue_dna() -> PrismTestData:
                         "description_of_sample": "Normal",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 2.0,
                         "processed_sample_derivative": "Germline DNA",
@@ -1752,7 +1752,7 @@ def tumor_tissue_rna() -> PrismTestData:
                         "description_of_sample": "Normal",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 1.0,
                         "processed_sample_derivative": "Germline RNA",
@@ -1783,7 +1783,7 @@ def tumor_tissue_rna() -> PrismTestData:
                         "description_of_sample": "Normal",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 1.0,
                         "processed_sample_derivative": "Germline RNA",
@@ -1814,7 +1814,7 @@ def tumor_tissue_rna() -> PrismTestData:
                         "description_of_sample": "Normal",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 2.0,
                         "processed_sample_derivative": "Germline RNA",
@@ -1851,7 +1851,7 @@ def tumor_tissue_rna() -> PrismTestData:
                         "description_of_sample": "Normal",
                         "sample_collection_procedure": "Core Biopsy",
                         "core_number": "1.0",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "processed_sample_type": "Bone Marrow Film",
                         "processed_sample_quantity": 1.0,
                         "processed_sample_derivative": "Germline RNA",
@@ -2067,7 +2067,7 @@ def microbiome_dna() -> PrismTestData:
                     {
                         "shipping_entry_number": 1,
                         "collection_event_name": "Baseline",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 1')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP08T3.00",
@@ -2095,7 +2095,7 @@ def microbiome_dna() -> PrismTestData:
                     {
                         "shipping_entry_number": 2,
                         "collection_event_name": "Pre_Day_1_Cycle_2",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 2')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP08T4.00",
@@ -2123,7 +2123,7 @@ def microbiome_dna() -> PrismTestData:
                     {
                         "shipping_entry_number": 3,
                         "collection_event_name": "Pre_Day_1_Cycle_2",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 3')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP08T5.00",
@@ -2156,7 +2156,7 @@ def microbiome_dna() -> PrismTestData:
                 "samples": [
                     {
                         "collection_event_name": "Baseline",
-                        "fixation_stabilization_type": "Formulin Fixation",
+                        "fixation_stabilization_type": "Formalin Fixation",
                         "parent_sample_id": "test_encrypted('TRIALGROUP 4')",
                         "processed_sample_id": "test_encrypted('BIOBANK 1')",
                         "cimac_id": "CTTTP09T1.00",