nci-cidc-schemas 0.27.4__tar.gz → 0.27.6__tar.gz

{nci_cidc_schemas-0.27.4/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.27.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nci_cidc_schemas
-Version: 0.27.4
+Version: 0.27.6
 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-0.27.4 → nci_cidc_schemas-0.27.6}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.27.04"
+__version__ = "0.27.06"

{nci_cidc_schemas-0.27.4 → nci_cidc_schemas-0.27.6}/cidc_schemas/schemas/sample.json

@@ -168,16 +168,30 @@
             "description": "Indicates the specimen source of the sample shipped. Example: Na Heparin blood draw aliquots (2 of three), FFPE block #52",
             "type": "string",
             "enum": [
-                "Blood Draw",
-                "Excision",
+                "Fine Needle Aspiration",
+                "Phlebotomy",
+                "Bone Marrow Aspiration",
+                "Bone Marrow Core Biopsy",
                 "Core Biopsy",
-                "Punch Biopsy",
                 "Endoscopic Biopsy",
-                "Bone Marrow Core Biopsy",
-                "Bone Marrow Aspirate",
+                "Surgical Excision",
+                "Fine Needle Aspiration",
                 "Lumbar Puncture",
-                "Aspirate",
-                "Fine-Needle Aspiration",
+                "FFPE Block Punch Biopsy",
+                "Skin Biopsy",
+                "Apheresis",
+                "Bone Biopsy",
+                "Bronchoalveolar Lavage",
+                "Buccal Swab",
+                "Leukapheresis",
+                "Mid Stream Urine Collection",
+                "Peritoneal Lavage",
+                "Peritoneal Paracentesis",
+                "Pleural Thoracentesis",
+                "Saliva Collection",
+                "Stool Collection",
+                "Surgical Incision",
+                "Urine Voiding",
                 "Not Reported",
                 "Other"
             ]
@@ -195,8 +209,8 @@
             "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-0.27.4 → nci_cidc_schemas-0.27.6/nci_cidc_schemas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nci_cidc_schemas
-Version: 0.27.4
+Version: 0.27.6
 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-0.27.4 → nci_cidc_schemas-0.27.6}/tests/data/clinicaltrial_examples/CT_1PA_multiWES.json

@@ -96,7 +96,7 @@
                     "box_number": "1",
                     "sample_location": "A4",
                     "type_of_sample": "Whole Blood",
-                    "sample_collection_procedure": "Blood Draw",
+                    "sample_collection_procedure": "Surgical Excision",
                     "type_of_primary_container": "EDTA Tube",
                     "type_of_primary_container_other": "Other",
                     "processed_sample_type": "Bone Marrow Film",
@@ -129,7 +129,7 @@
                     "box_number": "1",
                     "sample_location": "A5",
                     "type_of_sample": "Whole Blood",
-                    "sample_collection_procedure": "Blood Draw",
+                    "sample_collection_procedure": "Surgical Excision",
                     "type_of_primary_container": "EDTA Tube",
                     "type_of_primary_container_other": "Other",
                     "processed_sample_type": "Bone Marrow Film",
@@ -162,7 +162,7 @@
                     "box_number": "1",
                     "sample_location": "A6",
                     "type_of_sample": "Whole Blood",
-                    "sample_collection_procedure": "Blood Draw",
+                    "sample_collection_procedure": "Surgical Excision",
                     "type_of_primary_container": "EDTA Tube",
                     "type_of_primary_container_other": "Other",
                     "processed_sample_type": "Bone Marrow Film",

{nci_cidc_schemas-0.27.4 → nci_cidc_schemas-0.27.6}/tests/data/clinicaltrial_examples/CT_cytof_with_analysis.json

@@ -199,7 +199,7 @@
           "type_of_primary_container": "Sodium Heparin Tube",
           "type_of_primary_container_other": "Other",
           "material_storage_condition": "Ambient",
-          "sample_collection_procedure": "Blood Draw",
+          "sample_collection_procedure": "Surgical Excision",
           "processed_sample_volume_units": "Microliters"
         },
         {
@@ -223,7 +223,7 @@
           "type_of_primary_container": "Sodium Heparin Tube",
           "type_of_primary_container_other": "Other",
           "material_storage_condition": "Ambient",
-          "sample_collection_procedure": "Blood Draw",
+          "sample_collection_procedure": "Surgical Excision",
           "processed_sample_volume_units": "Microliters"
         }
       ],
@@ -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-0.27.4 → nci_cidc_schemas-0.27.6}/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,
@@ -780,14 +780,14 @@ 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",
                         "box_number": "1",
                         "sample_location": "A1",
                         "type_of_sample": "Whole Blood",
-                        "sample_collection_procedure": "Blood Draw",
+                        "sample_collection_procedure": "Surgical Excision",
                         "type_of_primary_container": "EDTA Tube",
                         "type_of_primary_container_other": "Other",
                         "processed_sample_type": "Bone Marrow Film",
@@ -815,14 +815,14 @@ 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",
                         "box_number": "1",
                         "sample_location": "A2",
                         "type_of_sample": "Whole Blood",
-                        "sample_collection_procedure": "Blood Draw",
+                        "sample_collection_procedure": "Surgical Excision",
                         "type_of_primary_container": "EDTA Tube",
                         "type_of_primary_container_other": "Other",
                         "processed_sample_type": "Bone Marrow Film",
@@ -850,14 +850,14 @@ 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",
                         "box_number": "1",
                         "sample_location": "A3",
                         "type_of_sample": "Whole Blood",
-                        "sample_collection_procedure": "Blood Draw",
+                        "sample_collection_procedure": "Surgical Excision",
                         "type_of_primary_container": "EDTA Tube",
                         "type_of_primary_container_other": "Other",
                         "processed_sample_type": "Bone Marrow Film",
@@ -891,14 +891,14 @@ 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",
                         "box_number": "1",
                         "sample_location": "A4",
                         "type_of_sample": "Whole Blood",
-                        "sample_collection_procedure": "Blood Draw",
+                        "sample_collection_procedure": "Surgical Excision",
                         "type_of_primary_container": "EDTA Tube",
                         "type_of_primary_container_other": "Other",
                         "processed_sample_type": "Bone Marrow Film",
@@ -925,14 +925,14 @@ 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",
                         "box_number": "1",
                         "sample_location": "A5",
                         "type_of_sample": "Whole Blood",
-                        "sample_collection_procedure": "Blood Draw",
+                        "sample_collection_procedure": "Surgical Excision",
                         "type_of_primary_container": "EDTA Tube",
                         "type_of_primary_container_other": "Other",
                         "processed_sample_type": "Bone Marrow Film",
@@ -959,14 +959,14 @@ 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",
                         "box_number": "1",
                         "sample_location": "A6",
                         "type_of_sample": "Whole Blood",
-                        "sample_collection_procedure": "Blood Draw",
+                        "sample_collection_procedure": "Surgical Excision",
                         "type_of_primary_container": "EDTA Tube",
                         "type_of_primary_container_other": "Other",
                         "processed_sample_type": "Bone Marrow Film",
@@ -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",