nci-cidc-schemas 0.26.24__tar.gz → 0.26.25__tar.gz

{nci_cidc_schemas-0.26.24 → nci_cidc_schemas-0.26.25}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_schemas
-Version: 0.26.24
+Version: 0.26.25
 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-0.26.24 → nci_cidc_schemas-0.26.25}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.26.24"
+__version__ = "0.26.25"

{nci_cidc_schemas-0.26.24 → nci_cidc_schemas-0.26.25}/cidc_schemas/schemas/assays/hande_assay.json

@@ -29,6 +29,20 @@
               "$ref": "artifacts/artifact_jpg.json"
             }
           ]
+        },
+        "annotated_image": {
+          "inheritableBase": true,
+          "mergeStrategy": "objectMerge",
+          "anyOf": [
+            {
+              "$comment": "Path to the H & E annotated image in SVS format.",
+              "$ref": "artifacts/artifact_image.json"
+            },
+            {
+              "$comment": "Path to the H & E annotated image in JPG format.",
+              "$ref": "artifacts/artifact_jpg.json"
+            }
+          ]
         }
       },
       "required": ["image_file"]

{nci_cidc_schemas-0.26.24 → nci_cidc_schemas-0.26.25}/cidc_schemas/schemas/templates/assays/hande_template.json

@@ -34,7 +34,13 @@
                           "gcs_uri_format": "{protocol identifier}/hande/{cimac id}/image_file.{file type}",
                           "type_ref": "assays/components/local_file.json#properties/file_path"
                       },
-
+                      "annotated image": {
+                          "merge_pointer": "0/files/annotated_image",
+                          "is_artifact": 1,
+                          "gcs_uri_format": "{protocol identifier}/hande/{cimac id}/annotated_image.{file type}",
+                          "type_ref": "assays/components/local_file.json#properties/file_path",
+                          "allow_empty": true
+                      },
                       "tumor tissue (% total area)": {
                         "merge_pointer": "0/tumor_tissue_percentage",
                         "type_ref": "assays/hande_assay.json#definitions/record/properties/tumor_tissue_percentage",

{nci_cidc_schemas-0.26.24 → nci_cidc_schemas-0.26.25}/nci_cidc_schemas.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci-cidc-schemas
-Version: 0.26.24
+Version: 0.26.25
 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-0.26.24 → nci_cidc_schemas-0.26.25}/tests/prism/cidc_test_data/assay_data.py

@@ -1,14 +1,13 @@
-from cidc_schemas.prism import SUPPORTED_ASSAYS, PROTOCOL_ID_FIELD_NAME
+from cidc_schemas.prism import PROTOCOL_ID_FIELD_NAME, SUPPORTED_ASSAYS
 
 from .utils import (
+    LocalFileUploadEntry,
+    PrismTestData,
     copy_dict_with_branch,
     get_prismify_args,
     get_test_trial,
-    LocalFileUploadEntry,
-    PrismTestData,
 )
 
-
 assay_data_generators = []
 
 
@@ -393,6 +392,36 @@ def hande() -> PrismTestData:
                             "fibrosis_percentage": 2.0,
                             "comment": "another comment",
                         },
+                        {
+                            "cimac_id": "CI2YI3D2U.00",
+                            "files": {
+                                "image_file": {
+                                    "upload_placeholder": "eeeeeeee-ad48-494e-b8f3-7be715faa3a3",
+                                },
+                                "annotated_image": {
+                                    "upload_placeholder": "eeeeeeee-eb69-4c4d-9c00-79204b20d823",
+                                },
+                            },
+                            "tumor_tissue_percentage": 70.0,
+                            "viable_tumor_percentage": 53.0,
+                            "necrosis_percentage": 0.0,
+                            "fibrosis_percentage": 20.0,
+                        },
+                        {
+                            "cimac_id": "CI2YY7SNE.00",
+                            "files": {
+                                "image_file": {
+                                    "upload_placeholder": "eeeeeeee-46aa-4329-a6fa-0bda83106461",
+                                },
+                                "annotated_image": {
+                                    "upload_placeholder": "eeeeeeee-3517-4484-8f3a-eb0854f4d8b4",
+                                },
+                            },
+                            "tumor_tissue_percentage": 70.0,
+                            "viable_tumor_percentage": 53.0,
+                            "necrosis_percentage": 0.0,
+                            "fibrosis_percentage": 20.0,
+                        },
                     ],
                     "assay_creator": "DFCI",
                 }
@@ -414,6 +443,34 @@ def hande() -> PrismTestData:
             metadata_availability=False,
             allow_empty=False,
         ),
+        LocalFileUploadEntry(
+            local_path="path/to/CI2YI3D2U.00.svs",
+            gs_key="123/hande/CI2YI3D2U.00/image_file.svs",
+            upload_placeholder="eeeeeeee-ad48-494e-b8f3-7be715faa3a3",
+            metadata_availability=False,
+            allow_empty=False,
+        ),
+        LocalFileUploadEntry(
+            local_path="path/to/CI2YI3D2U.00_annotated.svs",
+            gs_key="123/hande/CI2YI3D2U.00/annotated_image.svs",
+            upload_placeholder="eeeeeeee-eb69-4c4d-9c00-79204b20d823",
+            metadata_availability=False,
+            allow_empty=False,
+        ),
+        LocalFileUploadEntry(
+            local_path="path/to/CI2YY7SNE.00.svs",
+            gs_key="123/hande/CI2YY7SNE.00/image_file.svs",
+            upload_placeholder="eeeeeeee-46aa-4329-a6fa-0bda83106461",
+            metadata_availability=False,
+            allow_empty=False,
+        ),
+        LocalFileUploadEntry(
+            local_path="path/to/CI2YY7SNE.00_annotated.svs",
+            gs_key="123/hande/CI2YY7SNE.00/annotated_image.svs",
+            upload_placeholder="eeeeeeee-3517-4484-8f3a-eb0854f4d8b4",
+            metadata_availability=False,
+            allow_empty=False,
+        ),
     ]
 
     cimac_ids = [