nci-cidc-schemas 0.28.6__tar.gz → 0.28.8__tar.gz

{nci_cidc_schemas-0.28.6/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.28.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.28.6
+Version: 0.28.8
 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-0.28.6 → nci_cidc_schemas-0.28.8}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.28.6"
+__version__ = "0.28.8"

{nci_cidc_schemas-0.28.6 → nci_cidc_schemas-0.28.8}/cidc_schemas/schemas/assays/hande_assay.json

@@ -27,6 +27,10 @@
             {
               "$comment": "Path to the H & E image in JPG format.",
               "$ref": "artifacts/artifact_jpg.json"
+            },
+            {
+              "$comment": "Path to the H & E image in OME-TIFF format.",
+              "$ref": "artifacts/artifact_jpg.json"
             }
           ]
         },
@@ -41,6 +45,10 @@
             {
               "$comment": "Path to the H & E annotated image in JPG format.",
               "$ref": "artifacts/artifact_jpg.json"
+            },
+            {
+              "$comment": "Path to the H & E annotated image in OME-TIFF format.",
+              "$ref": "artifacts/artifact_jpg.json"
             }
           ]
         }

{nci_cidc_schemas-0.28.6 → nci_cidc_schemas-0.28.8}/cidc_schemas/schemas/assays/wes_assay.json

@@ -72,12 +72,25 @@
       "sequencing_protocol": {
           "description": "Protocol and version used for the sequencing.",
           "type": "string",
-          "enum": ["Express Somatic Human WES (Deep Coverage) v1.1", "Somatic Human WES v6", "TWIST Custom Panel PN 101042", "TWIST"]
+          "enum": [
+            "Express Somatic Human WES (Deep Coverage) v1.1",
+            "Somatic Human WES v4",
+            "Somatic Human WES v6",
+            "TWIST Custom Panel PN 101042",
+            "TWIST"
+          ]
       },
       "bait_set": {
           "description": "Bait set ID.",
           "type": "string",
-          "enum": ["whole_exome_illumina_coding_v1","broad_custom_exome_v1","TWIST Dana Farber Custom Panel", "TWIST Custom Panel PN 101042", "TWIST Clin Research Exome PN 104033"]
+          "enum": [
+            "whole_exome_illumina_coding_v1",
+            "broad_custom_exome_v1",
+            "TWIST Dana Farber Custom Panel",
+            "TWIST Custom Panel PN 101042",
+            "TWIST Clin Research Exome PN 104033",
+            "Agilent SS Human All Exon V4"
+          ]
       },
       "read_length": {
           "description": "Number of cycles for each sequencing read.",

{nci_cidc_schemas-0.28.6 → nci_cidc_schemas-0.28.8}/cidc_schemas/schemas/templates/assays/hande_template.json

@@ -27,7 +27,7 @@
                           "do_not_merge": true,
                           "allow_empty": true,
                           "type": "string",
-                          "enum": ["svs", "jpg"]
+                          "enum": ["svs", "jpg", "ome.tiff"]
                       },
                       "image file": {
                         "merge_pointer": "0/files/image_file",
@@ -41,7 +41,7 @@
                         "do_not_merge": true,
                         "allow_empty": true,
                         "type": "string",
-                        "enum": ["svs", "jpg"]
+                        "enum": ["svs", "jpg", "ome.tiff"]
                     },
                       "annotated image": {
                           "merge_pointer": "0/files/annotated_image",

{nci_cidc_schemas-0.28.6 → nci_cidc_schemas-0.28.8/nci_cidc_schemas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.28.6
+Version: 0.28.8
 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-0.28.6 → nci_cidc_schemas-0.28.8}/tests/prism/cidc_test_data/assay_data.py

@@ -422,6 +422,21 @@ def hande() -> PrismTestData:
                             "necrosis_percentage": 0.0,
                             "fibrosis_percentage": 20.0,
                         },
+                        {
+                            "cimac_id": "CTTTPX121.00",
+                            "files": {
+                                "image_file": {
+                                    "upload_placeholder": "eedd-46aa-4329-a6fa-0bda83106461",
+                                },
+                                "annotated_image": {
+                                    "upload_placeholder": "ee1234-3517-4484-8f3a-eb0854f4d8b4",
+                                },
+                            },
+                            "tumor_tissue_percentage": 80.0,
+                            "viable_tumor_percentage": 50.0,
+                            "necrosis_percentage": 0.0,
+                            "fibrosis_percentage": 20.0,
+                        },
                     ],
                     "assay_creator": "DFCI",
                 }
@@ -471,6 +486,20 @@ def hande() -> PrismTestData:
             metadata_availability=False,
             allow_empty=False,
         ),
+        LocalFileUploadEntry(
+            local_path="image.ome.tiff",
+            gs_key="123/hande/CTTTPX121.00/image_file.ome.tiff",
+            upload_placeholder="eedd-46aa-4329-a6fa-0bda83106461",
+            metadata_availability=False,
+            allow_empty=False,
+        ),
+        LocalFileUploadEntry(
+            local_path="annotated.ome.tiff",
+            gs_key="123/hande/CTTTPX121.00/annotated_image.ome.tiff",
+            upload_placeholder="ee1234-3517-4484-8f3a-eb0854f4d8b4",
+            metadata_availability=False,
+            allow_empty=False,
+        ),
     ]
 
     cimac_ids = [