conform to new callback format

docs/source/ImageSet.yaml

@@ -1,11 +1,11 @@
 type: object
 required:
-  - title
+  - imageName
   - assets
   - imageMetadata
 properties:
-  title:
-    description: Readable name or identifier of the asset
+  imageName:
+    description: Readable name or identifier of this ImageSet element.
   assets:
     description: List of generated image assets
     type: array

docs/source/PipelineCallback.yaml

@@ -16,7 +16,7 @@ properties:
     required:
       - primaryFilePath
       - thumbnailIndex
-      - sample
+      - title
       - fileMetadata
       - imageSet
 
@@ -29,8 +29,8 @@ properties:
         thumbnailIndex:
           description: The index of the image in imageSet which consists of the "label image" thumbnail
           type: integer
-        sample:
-          description: name of sample, usually file name minus path and extension.
+        title:
+          description: File specific, name of file minus path and extension. (Appears redundant.)
           type: string
         fileMetadata:
           description: >

docs/source/demo_callback.json

@@ -4,13 +4,13 @@
     {
       "primaryFilePath": "LNII/sbest/sbest-2023-0526-Rename/Spatial_example-2023-0526-Rename1/LNII/F13-TS005.czi",
       "thumbnailIndex": 0,
-      "sample": "Name of sample, usually file name minus path and extension",
+      "title": "Name of the file, file name minus path and extension",
       "fileMetadata": {
         "TBD": "TBD"
       },
       "imageSet": [
         {
-          "title": "Scene #1",
+          "imageName": "Scene #1",
           "imageMetadata": {
             "TBD": "TBD"
           },
@@ -33,7 +33,7 @@
           ]
         },
         {
-          "title": "image label",
+          "imageName": "image label",
           "imageMetadata": {
             "TBD": "TBD"
           },

em_workflows/file_path.py

@@ -167,6 +167,7 @@ def gen_asset(self, asset_type: str, asset_fp) -> Dict:
         :param asset_type: a string that details the type of output file
         :param asset_fp: the originating FilePath to "hang" the asset on
         :return: the resulting "asset" in the form of a dict
+        TODO: consider changings asset_type to newly created AssetType enum
         """
         assets_fp_no_root = asset_fp.relative_to(self.asset_root)
         asset = {"type": asset_type, "path": assets_fp_no_root.as_posix()}
@@ -184,16 +185,34 @@ def gen_prim_fp_elt(self) -> Dict:
             [
              {
               "primaryFilePath": "Lab/PI/Myproject/MySession/Sample1/file_a.mrc",
-              "title": "file_a",
-              "assets": []
+              "thumbnailIndex": 0,
+              "fileMetadata": {},
+              "imageSet": []
              }
             ]
 
         """
+        # TODO - update this for czi input, parse out title from OMEXML
         title = self.fp_in.stem
         primaryFilePath = self.fp_in.relative_to(self.proj_root)
+        # setting to zero here, most input files will only have a single image elt.
+        # will update val if czi
+        thumbnailIndex = 0
+        fileMetadata = {}
+        imageMetadata = {}
+        assets = []
+        imageSetElement = {
+            "imageName": title,
+            "imageMetadata": imageMetadata,
+            "assets": assets,
+        }
+        imageSet = [imageSetElement]
         return dict(
-            primaryFilePath=primaryFilePath.as_posix(), title=title, assets=list()
+            primaryFilePath=primaryFilePath.as_posix(),
+            thumbnailIndex=thumbnailIndex,
+            title=title,
+            fileMetadata=fileMetadata,
+            imageSet=imageSet,
         )
 
     def copy_workdir_to_assets(self) -> Path:

em_workflows/utils/utils.py

@@ -144,10 +144,12 @@ def add_asset(prim_fp: dict, asset: dict) -> dict:
     funtional style avoids this. This is why the callback data structure is not built inside
     the FilePath object at runtime.
     """
+    # TODO - at the moment we're assuming there's only a single image per file.
+    # when czi is implmented, we should pass which imageset to use.
     if type(asset) is list:
-        prim_fp["assets"].extend(asset)
+        prim_fp["imageSet"][0]["assets"].extend(asset)
     else:
-        prim_fp["assets"].append(asset)
+        prim_fp["imageSet"][0]["assets"].append(asset)
     log(f"Added fp elt {asset} to {prim_fp}.")
     return prim_fp