PyPI - nci-cidc-schemas - Versions diffs - 0.27.7__tar.gz → 0.27.9__tar.gz - Mend

nci-cidc-schemas 0.27.7tar.gz → 0.27.9tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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{nci_cidc_schemas-0.27.7/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.27.9}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.27.7
+Version: 0.27.9
 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-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/__init__.py RENAMED Viewed

@@ -2,4 +2,4 @@
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.27.07"
+__version__ = "0.27.09"

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/sample.json RENAMED Viewed

@@ -154,6 +154,10 @@
                 "Other"
             ]
         },
+        "type_of_sample_other": {
+            "description": "The description of the sample other.",
+            "type": "string"
+        },
         "description_of_sample": {
             "description": "The description of the sample.",
             "type": "string",
@@ -493,7 +497,7 @@
         "quality_of_sample": {
             "description": "Final status of sample after QC and pathology review.",
             "type": "string",
-            "enum": ["Pass", "Pass at Risk", "Fail"]
+            "enum": ["QC Pass", "Pass at Risk", "QC Failed", "QC Lost", "QC Not Shipped"]
         },
         "sample_replacement": {
             "description": "Indication if sample replacement is/was requested.",

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/shipping_core.json RENAMED Viewed

@@ -70,9 +70,9 @@
       "description": "Type of shipment made.",
       "type": "string",
       "enum": [
-        "Frozen_Dry_Ice",
-        "Frozen_Shipper",
-        "Ice_Pack",
+        "Frozen Dry Ice",
+        "Frozen Shipper",
+        "Ice/Cold Pack",
         "Ambient",
         "Not Reported",
         "Other"

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/h_and_e_template.json RENAMED Viewed

@@ -213,6 +213,11 @@
                         "type of sample": {
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
+                        },
+                         "type of sample other": {
+                            "merge_pointer": "/type_of_sample_other",
+                            "type_ref": "sample.json#properties/type_of_sample_other",
+                            "allow_empty": true
                         },
                         "type of tumor sample": {
                             "merge_pointer": "/type_of_tumor_sample",

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json RENAMED Viewed

@@ -217,6 +217,11 @@
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
                         },
+                        "type of sample other": {
+                            "merge_pointer": "/type_of_sample_other",
+                            "type_ref": "sample.json#properties/type_of_sample_other",
+                            "allow_empty": true
+                        },
                         "type of tumor sample": {
                             "merge_pointer": "/type_of_tumor_sample",
                             "type_ref": "sample.json#properties/type_of_tumor_sample"

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json RENAMED Viewed

@@ -212,6 +212,11 @@
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
                         },
+                        "type of sample other": {
+                            "merge_pointer": "/type_of_sample_other",
+                            "type_ref": "sample.json#properties/type_of_sample_other",
+                            "allow_empty": true
+                        },
                         "type of tumor sample": {
                             "merge_pointer": "/type_of_tumor_sample",
                             "type_ref": "sample.json#properties/type_of_tumor_sample"

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json RENAMED Viewed

@@ -220,6 +220,11 @@
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
                         },
+                        "type of sample other": {
+                            "merge_pointer": "/type_of_sample_other",
+                            "type_ref": "sample.json#properties/type_of_sample_other",
+                            "allow_empty": true
+                        },
                         "sample collection procedure": {
                             "merge_pointer": "/sample_collection_procedure",
                             "type_ref": "sample.json#properties/sample_collection_procedure"

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/pbmc_template.json RENAMED Viewed

@@ -213,6 +213,11 @@
                         "type of sample": {
                             "merge_pointer": "0/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
+                        },
+                         "type of sample other": {
+                            "merge_pointer": "/type_of_sample_other",
+                            "type_ref": "sample.json#properties/type_of_sample_other",
+                            "allow_empty": true
                         },
                         "sample collection procedure": {
                             "merge_pointer": "/sample_collection_procedure",

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/plasma_template.json RENAMED Viewed

@@ -215,6 +215,11 @@
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
                         },
+                        "type of sample other": {
+                            "merge_pointer": "/type_of_sample_other",
+                            "type_ref": "sample.json#properties/type_of_sample_other",
+                            "allow_empty": true
+                        },
                         "sample collection procedure": {
                             "merge_pointer": "/sample_collection_procedure",
                             "type_ref": "sample.json#properties/sample_collection_procedure"

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/tissue_slide_template.json RENAMED Viewed

@@ -215,6 +215,11 @@
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
                         },
+                        "type of sample other": {
+                            "merge_pointer": "/type_of_sample_other",
+                            "type_ref": "sample.json#properties/type_of_sample_other",
+                            "allow_empty": true
+                        },
                         "type of tumor sample": {
                             "merge_pointer": "/type_of_tumor_sample",
                             "type_ref": "sample.json#properties/type_of_tumor_sample"

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json RENAMED Viewed

@@ -215,6 +215,11 @@
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
                         },
+                        "type of sample other": {
+                            "merge_pointer": "/type_of_sample_other",
+                            "type_ref": "sample.json#properties/type_of_sample_other",
+                            "allow_empty": true
+                        },
                         "type of tumor sample": {
                             "merge_pointer": "/type_of_tumor_sample",
                             "type_ref": "sample.json#properties/type_of_tumor_sample"

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json RENAMED Viewed

@@ -215,6 +215,11 @@
                             "merge_pointer": "/type_of_sample",
                             "type_ref": "sample.json#properties/type_of_sample"
                         },
+                        "type of sample other": {
+                            "merge_pointer": "/type_of_sample_other",
+                            "type_ref": "sample.json#properties/type_of_sample_other",
+                            "allow_empty": true
+                        },
                         "type of tumor sample": {
                             "merge_pointer": "/type_of_tumor_sample",
                             "type_ref": "sample.json#properties/type_of_tumor_sample"

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9/nci_cidc_schemas.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.27.7
+Version: 0.27.9
 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-0.27.7 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_1.json RENAMED Viewed

@@ -14,6 +14,7 @@
           "collection_event_name": "Baseline",
           "sample_location": "---",
           "type_of_sample": "Other",
+          "type_of_sample_other": "other_sample",
           "type_of_primary_container": "Other",
           "sample_volume_units": "Other",
           "material_used": 1,
@@ -26,6 +27,7 @@
           "collection_event_name": "Baseline",
           "sample_location": "---",
           "type_of_sample": "Other",
+          "type_of_sample_other": "other_sample",
           "type_of_primary_container": "Other",
           "sample_volume_units": "Other",
           "material_used": 1,
@@ -38,6 +40,7 @@
           "collection_event_name": "Baseline",
           "sample_location": "---",
           "type_of_sample": "Other",
+          "type_of_sample_other": "other_sample",
           "type_of_primary_container": "Other",
           "sample_volume_units": "Other",
           "material_used": 1,
@@ -57,6 +60,7 @@
           "collection_event_name": "Baseline",
           "sample_location": "---",
           "type_of_sample": "Other",
+          "type_of_sample_other": "other_sample",
           "type_of_primary_container": "Other",
           "sample_volume_units": "Other",
           "material_used": 1,
@@ -69,6 +73,7 @@
           "collection_event_name": "Baseline",
           "sample_location": "---",
           "type_of_sample": "Other",
+          "type_of_sample_other": "other_sample",
           "type_of_primary_container": "Other",
           "sample_volume_units": "Other",
           "material_used": 1,
@@ -81,6 +86,7 @@
           "collection_event_name": "Baseline",
           "sample_location": "---",
           "type_of_sample": "Other",
+          "type_of_sample_other": "other_sample",
           "type_of_primary_container": "Other",
           "sample_volume_units": "Other",
           "material_used": 1,
@@ -93,6 +99,7 @@
           "collection_event_name": "Baseline",
           "sample_location": "---",
           "type_of_sample": "Other",
+          "type_of_sample_other": "other_sample",
           "type_of_primary_container": "Other",
           "sample_volume_units": "Other",
           "material_used": 1,

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_1PA_multiWES.json RENAMED Viewed

@@ -50,6 +50,7 @@
                     "collection_event_name": "Baseline",
                     "sample_location": "---",
                     "type_of_sample": "Other",
+                    "type_of_sample_other": "other_sample",
                     "type_of_primary_container": "Other",
                     "sample_volume_units": "Other",
                     "material_used": 1,
@@ -62,6 +63,7 @@
                     "collection_event_name": "Baseline",
                     "sample_location": "---",
                     "type_of_sample": "Other",
+                    "type_of_sample_other": "other_sample",
                     "type_of_primary_container": "Other",
                     "sample_volume_units": "Other",
                     "material_used": 1,
@@ -74,6 +76,7 @@
                     "collection_event_name": "Baseline",
                     "sample_location": "---",
                     "type_of_sample": "Other",
+                    "type_of_sample_other": "other_sample",
                     "type_of_primary_container": "Other",
                     "sample_volume_units": "Other",
                     "material_used": 1,
@@ -96,6 +99,7 @@
                     "box_number": "1",
                     "sample_location": "A4",
                     "type_of_sample": "Whole Blood",
+                    "type_of_sample_other": "other_sample",
                     "sample_collection_procedure": "Surgical Excision",
                     "type_of_primary_container": "EDTA Tube",
                     "type_of_primary_container_other": "Other",
@@ -116,7 +120,7 @@
                     "material_remaining": 0.0,
                     "material_remaining_units": "Milliliters",
                     "material_storage_condition": "Ambient",
-                    "quality_of_sample": "Pass",
+                    "quality_of_sample": "QC Pass",
                     "sample_replacement": "Replacement Not Requested",
                     "residual_sample_use": "Not Reported"
                 },
@@ -129,6 +133,7 @@
                     "box_number": "1",
                     "sample_location": "A5",
                     "type_of_sample": "Whole Blood",
+                    "type_of_sample_other": "other_sample",
                     "sample_collection_procedure": "Surgical Excision",
                     "type_of_primary_container": "EDTA Tube",
                     "type_of_primary_container_other": "Other",
@@ -149,7 +154,7 @@
                     "material_remaining": 0.0,
                     "material_remaining_units": "Milliliters",
                     "material_storage_condition": "Ambient",
-                    "quality_of_sample": "Pass",
+                    "quality_of_sample": "QC Pass",
                     "sample_replacement": "Replacement Not Requested",
                     "residual_sample_use": "Not Reported"
                 },
@@ -162,6 +167,7 @@
                     "box_number": "1",
                     "sample_location": "A6",
                     "type_of_sample": "Whole Blood",
+                    "type_of_sample_other": "other_sample",
                     "sample_collection_procedure": "Surgical Excision",
                     "type_of_primary_container": "EDTA Tube",
                     "type_of_primary_container_other": "Other",
@@ -182,7 +188,7 @@
                     "material_remaining": 0.0,
                     "material_remaining_units": "Milliliters",
                     "material_storage_condition": "Ambient",
-                    "quality_of_sample": "Pass",
+                    "quality_of_sample": "QC Pass",
                     "sample_replacement": "Replacement Not Requested",
                     "residual_sample_use": "Not Reported"
                 }

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_cytof_with_analysis.json RENAMED Viewed

@@ -183,9 +183,10 @@
           "box_number": "1",
           "material_used": 123,
           "type_of_sample": "Fresh Tissue",
+          "type_of_sample_other": "other_sample",
           "sample_location": "a1",
           "parent_sample_id": "qwe",
-          "quality_of_sample": "Pass",
+          "quality_of_sample": "QC Pass",
           "material_remaining": 0,
           "sample_replacement": "Replacement Not Requested",
           "material_used_units": "Microliters",
@@ -208,9 +209,10 @@
           "box_number": "1",
           "material_used": 123,
           "type_of_sample": "Fresh Tissue",
+          "type_of_sample_other": "other_sample",
           "sample_location": "a1",
           "parent_sample_id": "qwe",
-          "quality_of_sample": "Pass",
+          "quality_of_sample": "QC Pass",
           "material_remaining": 0,
           "sample_replacement": "Replacement Not Requested",
           "material_used_units": "Microliters",
@@ -240,9 +242,10 @@
           "core_number": "1",
           "material_used": 3,
           "type_of_sample": "Fresh Tissue",
+          "type_of_sample_other": "other_sample",
           "sample_location": "A1",
           "parent_sample_id": "TRIALGROUP 1",
-          "quality_of_sample": "Pass",
+          "quality_of_sample": "QC Pass",
           "material_remaining": 1,
           "sample_replacement": "Replacement Not Requested",
           "material_used_units": "Slides",
@@ -266,9 +269,10 @@
           "core_number": "a1",
           "material_used": 3,
           "type_of_sample": "Fresh Tissue",
+          "type_of_sample_other": "other_sample",
           "sample_location": "A2",
           "parent_sample_id": "TRIALGROUP 2",
-          "quality_of_sample": "Pass",
+          "quality_of_sample": "QC Pass",
           "material_remaining": 1,
           "sample_replacement": "Replacement Not Requested",
           "material_used_units": "Slides",
@@ -292,9 +296,10 @@
           "core_number": "1",
           "material_used": 1,
           "type_of_sample": "Fresh Tissue",
+          "type_of_sample_other": "other_sample",
           "sample_location": "A3",
           "parent_sample_id": "TRIALGROUP 3",
-          "quality_of_sample": "Pass",
+          "quality_of_sample": "QC Pass",
           "material_remaining": 0,
           "sample_replacement": "Replacement Not Requested",
           "material_used_units": "Slides",
@@ -325,9 +330,10 @@
           "core_number": "a",
           "material_used": 1,
           "type_of_sample": "Fresh Tissue",
+          "type_of_sample_other": "other_sample",
           "sample_location": "A4",
           "parent_sample_id": "TRIALGROUP 4",
-          "quality_of_sample": "Pass",
+          "quality_of_sample": "QC Pass",
           "material_remaining": 0,
           "sample_replacement": "Replacement Not Requested",
           "material_used_units": "Slides",

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_ihc.json RENAMED Viewed

@@ -18,6 +18,7 @@
                     "collection_event_name": "Baseline",
                     "sample_location": "---",
                     "type_of_sample": "Other",
+                    "type_of_sample_other": "other_sample",
                     "type_of_primary_container": "Other",
                     "type_of_primary_container_other": "Other",
                     "sample_volume_units": "Other",
@@ -31,6 +32,7 @@
                     "collection_event_name": "Baseline",
                     "sample_location": "---",
                     "type_of_sample": "Other",
+                    "type_of_sample_other": "other_sample",
                     "type_of_primary_container": "Other",
                     "type_of_primary_container_other": "Other",
                     "sample_volume_units": "Other",
@@ -51,6 +53,7 @@
                     "collection_event_name": "Baseline",
                     "sample_location": "---",
                     "type_of_sample": "Other",
+                    "type_of_sample_other": "other_sample",
                     "type_of_primary_container": "Other",
                     "type_of_primary_container_other": "Other",
                     "sample_volume_units": "Other",
@@ -64,6 +67,7 @@
                     "collection_event_name": "Baseline",
                     "sample_location": "---",
                     "type_of_sample": "Other",
+                    "type_of_sample_other": "other_sample",
                     "type_of_primary_container": "Other",
                     "type_of_primary_container_other": "Other",
                     "sample_volume_units": "Other",

{nci_cidc_schemas-0.27.7 → nci_cidc_schemas-0.27.9}/tests/data/clinicaltrial_examples/CT_minimal.json RENAMED Viewed

@@ -12,6 +12,7 @@
                     "collection_event_name": "Baseline",
                     "sample_location": "---",
                     "type_of_sample": "Other",
+                    "type_of_sample_other": "other_sample",
                     "type_of_primary_container": "Other",
                     "type_of_primary_container_other": "Other",
                     "sample_volume_units": "Other",
@@ -25,6 +26,7 @@
                     "collection_event_name": "Baseline",
                     "sample_location": "---",
                     "type_of_sample": "Other",
+                    "type_of_sample_other": "other_sample",
                     "type_of_primary_container": "Other",
                     "type_of_primary_container_other": "Other",
                     "sample_volume_units": "Other",

nci-cidc-schemas 0.27.7__tar.gz → 0.27.9__tar.gz

Potentially problematic release.

nci-cidc-schemas 0.27.7tar.gz → 0.27.9tar.gz