Merge pull request #2117 from fractal-analytics-platform/2116-tcompa-…

…could-we-add-some-metadata-to-fractal-tasks-mock-so-that-i-can-easily-test-the-filtering-end-to-end Add new metadata to fractal-tasks-mock
fractal-analytics-platform · Dec 2, 2024 · 6a98ca1 · 6a98ca1
2 parents 934f035 + f9f2048
commit 6a98ca1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,7 @@
 
 * Testing:
     * Re-include a specific test previously skipped for Python 3.12 (\#2114).
+    * Add metadata to `fractal-tasks-mock` package (\#2117).
 * Docs:
     * Add info about working versions.
 

diff --git a/tests/v2/fractal_tasks_mock/create_manifest.py b/tests/v2/fractal_tasks_mock/create_manifest.py
@@ -16,50 +16,78 @@
         executable="fill_cellvoyager_ome_zarr.py",
         meta_init={"key1": "value1"},
         meta={"key2": "value2"},
+        category="Conversion",
+        modality="HCS",
+        tags=["Yokogawa", "Cellvoyager"],
     ),
     CompoundTask(
         name="create_ome_zarr_multiplex_compound",
         executable_init="create_cellvoyager_ome_zarr_multiplex.py",
         executable="fill_cellvoyager_ome_zarr.py",
+        category="Conversion",
+        modality="HCS",
+        tags=["Yokogawa", "Cellvoyager"],
     ),
     CompoundTask(
         name="MIP_compound",
         input_types={"3D": True},
         executable_init="new_ome_zarr.py",
         executable="maximum_intensity_projection.py",
         output_types={"3D": False},
+        category="Image Processing",
+        modality="HCS",
+        tags=["Preprocessing"],
     ),
     ParallelTask(
         name="illumination_correction",
         input_types=dict(illumination_correction=False),
         executable="illumination_correction.py",
         output_types=dict(illumination_correction=True),
+        category="Image Processing",
+        tags=["Preprocessing"],
     ),
     CompoundTask(
         name="illumination_correction_compound",
         input_types=dict(illumination_correction=False),
         executable_init="illumination_correction_init.py",
         executable="illumination_correction_compute.py",
         output_types=dict(illumination_correction=True),
+        category="Image Processing",
+        tags=["Preprocessing"],
     ),
     ParallelTask(
         name="cellpose_segmentation",
         executable="cellpose_segmentation.py",
+        category="Segmentation",
+        tags=[
+            "Deep Learning",
+            "Convolutional Neural Network",
+            "Instance Segmentation",
+        ],
     ),
     CompoundTask(
         name="calculate_registration_compound",
         executable_init="calculate_registration_init.py",
         executable="calculate_registration_compute.py",
+        category="Registration",
+        modality="HCS",
+        tags=["Multiplexing"],
     ),
     NonParallelTask(
         name="find_registration_consensus",
         executable="find_registration_consensus.py",
+        category="Registration",
+        modality="HCS",
+        tags=["Multiplexing"],
     ),
     ParallelTask(
         name="apply_registration_to_image",
         input_types=dict(registration=False),
         executable="apply_registration_to_image.py",
         output_types=dict(registration=True),
+        category="Registration",
+        modality="HCS",
+        tags=["Multiplexing"],
     ),
     NonParallelTask(
         name="generic_task",
@@ -86,6 +114,7 @@
 
 
 PACKAGE = "fractal_tasks_mock"
+AUTHORS = "name1 surname1, name2 surname2"
 CUSTOM_PYDANTIC_MODELS = [
     ("fractal_tasks_mock", "input_models.py", "InitArgsRegistration"),
     ("fractal_tasks_mock", "input_models.py", "InitArgsCellVoyager"),
@@ -138,6 +167,7 @@
     task_list=TASK_LIST,
     has_args_schemas=True,
     args_schema_version="pydantic_v1",
+    authors=AUTHORS,
 )
 
 with open("src/fractal_tasks_mock/__FRACTAL_MANIFEST__.json", "w") as f:

diff --git a/tests/v2/fractal_tasks_mock/dist/fractal_tasks_mock-0.0.1-py3-none-any.whl b/tests/v2/fractal_tasks_mock/dist/fractal_tasks_mock-0.0.1-py3-none-any.whl
diff --git a/tests/v2/fractal_tasks_mock/src/fractal_tasks_mock/__FRACTAL_MANIFEST__.json b/tests/v2/fractal_tasks_mock/src/fractal_tasks_mock/__FRACTAL_MANIFEST__.json
@@ -1,5 +1,6 @@
 {
   "args_schema_version": "pydantic_v1",
+  "authors": "name1 surname1, name2 surname2",
   "has_args_schemas": true,
   "manifest_version": "2",
   "task_list": [
@@ -83,6 +84,7 @@
         "title": "FillCellvoyagerOmeZarr",
         "type": "object"
       },
+      "category": "Conversion",
       "docs_info": "This is task create_ome_zarr_compound.",
       "docs_link": "https://example.org",
       "executable_non_parallel": "create_cellvoyager_ome_zarr.py",
@@ -93,7 +95,12 @@
       "meta_parallel": {
         "key2": "value2"
       },
-      "name": "create_ome_zarr_compound"
+      "modality": "HCS",
+      "name": "create_ome_zarr_compound",
+      "tags": [
+        "Yokogawa",
+        "Cellvoyager"
+      ]
     },
     {
       "args_schema_non_parallel": {
@@ -169,11 +176,17 @@
         "title": "FillCellvoyagerOmeZarr",
         "type": "object"
       },
+      "category": "Conversion",
       "docs_info": "This is task create_ome_zarr_multiplex_compound.",
       "docs_link": "https://example.org",
       "executable_non_parallel": "create_cellvoyager_ome_zarr_multiplex.py",
       "executable_parallel": "fill_cellvoyager_ome_zarr.py",
-      "name": "create_ome_zarr_multiplex_compound"
+      "modality": "HCS",
+      "name": "create_ome_zarr_multiplex_compound",
+      "tags": [
+        "Yokogawa",
+        "Cellvoyager"
+      ]
     },
     {
       "args_schema_non_parallel": {
@@ -250,17 +263,22 @@
         "title": "MaximumIntensityProjection",
         "type": "object"
       },
+      "category": "Image Processing",
       "docs_info": "This is task MIP_compound.",
       "docs_link": "https://example.org",
       "executable_non_parallel": "new_ome_zarr.py",
       "executable_parallel": "maximum_intensity_projection.py",
       "input_types": {
         "3D": true
       },
+      "modality": "HCS",
       "name": "MIP_compound",
       "output_types": {
         "3D": false
-      }
+      },
+      "tags": [
+        "Preprocessing"
+      ]
     },
     {
       "args_schema_parallel": {
@@ -284,6 +302,7 @@
         "title": "IlluminationCorrection",
         "type": "object"
       },
+      "category": "Image Processing",
       "docs_info": "This is task illumination_correction.",
       "docs_link": "https://example.org",
       "executable_parallel": "illumination_correction.py",
@@ -293,7 +312,10 @@
       "name": "illumination_correction",
       "output_types": {
         "illumination_correction": true
-      }
+      },
+      "tags": [
+        "Preprocessing"
+      ]
     },
     {
       "args_schema_non_parallel": {
@@ -378,6 +400,7 @@
         "title": "IlluminationCorrectionCompute",
         "type": "object"
       },
+      "category": "Image Processing",
       "docs_info": "This is task illumination_correction_compound.",
       "docs_link": "https://example.org",
       "executable_non_parallel": "illumination_correction_init.py",
@@ -388,7 +411,10 @@
       "name": "illumination_correction_compound",
       "output_types": {
         "illumination_correction": true
-      }
+      },
+      "tags": [
+        "Preprocessing"
+      ]
     },
     {
       "args_schema_parallel": {
@@ -406,10 +432,16 @@
         "title": "CellposeSegmentation",
         "type": "object"
       },
+      "category": "Segmentation",
       "docs_info": "This is task cellpose_segmentation.",
       "docs_link": "https://example.org",
       "executable_parallel": "cellpose_segmentation.py",
-      "name": "cellpose_segmentation"
+      "name": "cellpose_segmentation",
+      "tags": [
+        "Deep Learning",
+        "Convolutional Neural Network",
+        "Instance Segmentation"
+      ]
     },
     {
       "args_schema_non_parallel": {
@@ -480,11 +512,16 @@
         "title": "CalculateRegistrationCompute",
         "type": "object"
       },
+      "category": "Registration",
       "docs_info": "This is task calculate_registration_compound.",
       "docs_link": "https://example.org",
       "executable_non_parallel": "calculate_registration_init.py",
       "executable_parallel": "calculate_registration_compute.py",
-      "name": "calculate_registration_compound"
+      "modality": "HCS",
+      "name": "calculate_registration_compound",
+      "tags": [
+        "Multiplexing"
+      ]
     },
     {
       "args_schema_non_parallel": {
@@ -511,10 +548,15 @@
         "title": "FindRegistrationConsensus",
         "type": "object"
       },
+      "category": "Registration",
       "docs_info": "This is task find_registration_consensus.",
       "docs_link": "https://example.org",
       "executable_non_parallel": "find_registration_consensus.py",
-      "name": "find_registration_consensus"
+      "modality": "HCS",
+      "name": "find_registration_consensus",
+      "tags": [
+        "Multiplexing"
+      ]
     },
     {
       "args_schema_parallel": {
@@ -538,16 +580,21 @@
         "title": "ApplyRegistrationToImage",
         "type": "object"
       },
+      "category": "Registration",
       "docs_info": "This is task apply_registration_to_image.",
       "docs_link": "https://example.org",
       "executable_parallel": "apply_registration_to_image.py",
       "input_types": {
         "registration": false
       },
+      "modality": "HCS",
       "name": "apply_registration_to_image",
       "output_types": {
         "registration": true
-      }
+      },
+      "tags": [
+        "Multiplexing"
+      ]
     },
     {
       "args_schema_non_parallel": {

diff --git a/tests/v2/fractal_tasks_mock/task_models.py b/tests/v2/fractal_tasks_mock/task_models.py
@@ -2,6 +2,7 @@
 from typing import Optional
 
 from pydantic import BaseModel
+from pydantic import Field
 
 
 class _BaseTask(BaseModel):
@@ -11,9 +12,12 @@ class Config:
 
     name: str
     executable: str
-    meta: Optional[dict[str, Any]]
-    input_types: Optional[dict[str, bool]]
-    output_types: Optional[dict[str, bool]]
+    meta: Optional[dict[str, Any]] = None
+    input_types: Optional[dict[str, bool]] = None
+    output_types: Optional[dict[str, bool]] = None
+    category: Optional[str] = None
+    modality: Optional[str] = None
+    tags: list[str] = Field(default_factory=list)
 
 
 class CompoundTask(_BaseTask):