Preliminary support for new task metadata

Author: tcompa

fractal_tasks_core/__FRACTAL_MANIFEST__.json

@@ -1,8 +1,11 @@
 {
   "manifest_version": "2",
+  "authors": "Name FIXME, Name FIXME, Name FIXME",
   "task_list": [
     {
       "name": "Convert Cellvoyager to OME-Zarr",
+      "category": "Conversion",
+      "modality": "HCS",
       "executable_non_parallel": "tasks/cellvoyager_to_ome_zarr_init.py",
       "executable_parallel": "tasks/cellvoyager_to_ome_zarr_compute.py",
       "meta_non_parallel": {
@@ -265,6 +268,8 @@
     },
     {
       "name": "Convert Cellvoyager Multiplexing to OME-Zarr",
+      "category": "Conversion",
+      "modality": "HCS",
       "executable_non_parallel": "tasks/cellvoyager_to_ome_zarr_init_multiplex.py",
       "executable_parallel": "tasks/cellvoyager_to_ome_zarr_compute.py",
       "meta_non_parallel": {
@@ -736,6 +741,7 @@
     },
     {
       "name": "Cellpose Segmentation",
+      "category": "Segmentation",
       "executable_parallel": "tasks/cellpose_segmentation.py",
       "meta_parallel": {
         "cpus_per_task": 4,
@@ -1030,6 +1036,7 @@
     },
     {
       "name": "Calculate Registration (image-based)",
+      "category": "Registration",
       "executable_non_parallel": "tasks/image_based_registration_hcs_init.py",
       "executable_parallel": "tasks/calculate_registration_image_based.py",
       "meta_non_parallel": {
@@ -1161,6 +1168,7 @@
     },
     {
       "name": "Find Registration Consensus",
+      "category": "Registration",
       "executable_non_parallel": "tasks/init_group_by_well_for_multiplexing.py",
       "executable_parallel": "tasks/find_registration_consensus.py",
       "meta_non_parallel": {
@@ -1263,6 +1271,7 @@
       "output_types": {
         "registered": true
       },
+      "category": "Registration",
       "executable_parallel": "tasks/apply_registration_to_image.py",
       "meta_parallel": {
         "cpus_per_task": 1,

fractal_tasks_core/dev/create_manifest.py

@@ -32,6 +32,7 @@
 
 def create_manifest(
     package: str = "fractal_tasks_core",
+    authors: Optional[str] = None,
     manifest_version: str = "2",
     has_args_schemas: bool = True,
     docs_link: Optional[str] = None,
@@ -71,6 +72,7 @@ def create_manifest(
     # Prepare an empty manifest
     manifest = dict(
         manifest_version=manifest_version,
+        authors=authors,
         task_list=[],
         has_args_schemas=has_args_schemas,
     )
@@ -148,4 +150,6 @@ def create_manifest(
 
 
 if __name__ == "__main__":
-    create_manifest()
+    PACKAGE = "fractal_tasks_core"
+    AUTHORS = "Name FIXME, Name FIXME, Name FIXME"
+    create_manifest(package=PACKAGE, authors=AUTHORS)

fractal_tasks_core/dev/task_list.py

@@ -22,13 +22,17 @@
         executable="tasks/cellvoyager_to_ome_zarr_compute.py",
         meta_init={"cpus_per_task": 1, "mem": 4000},
         meta={"cpus_per_task": 1, "mem": 4000},
+        category="Conversion",
+        modality="HCS",
     ),
     CompoundTask(
         name="Convert Cellvoyager Multiplexing to OME-Zarr",
         executable_init="tasks/cellvoyager_to_ome_zarr_init_multiplex.py",
         executable="tasks/cellvoyager_to_ome_zarr_compute.py",
         meta_init={"cpus_per_task": 1, "mem": 4000},
         meta={"cpus_per_task": 1, "mem": 4000},
+        category="Conversion",
+        modality="HCS",
     ),
     CompoundTask(
         name="Project Image (HCS Plate)",
@@ -50,27 +54,31 @@
         name="Cellpose Segmentation",
         executable="tasks/cellpose_segmentation.py",
         meta={"cpus_per_task": 4, "mem": 16000, "needs_gpu": True},
+        category="Segmentation",
     ),
     CompoundTask(
         name="Calculate Registration (image-based)",
         executable_init="tasks/image_based_registration_hcs_init.py",
         executable="tasks/calculate_registration_image_based.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 1, "mem": 8000},
+        category="Registration",
     ),
     CompoundTask(
         name="Find Registration Consensus",
         executable_init="tasks/init_group_by_well_for_multiplexing.py",
         executable="tasks/find_registration_consensus.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 1, "mem": 1000},
+        category="Registration",
     ),
     ParallelTask(
         name="Apply Registration to Image",
         input_types=dict(registered=False),
         executable="tasks/apply_registration_to_image.py",
         output_types=dict(registered=True),
         meta={"cpus_per_task": 1, "mem": 4000},
+        category="Registration",
     ),
     NonParallelTask(
         name="Import OME-Zarr",

fractal_tasks_core/dev/task_models.py

@@ -19,6 +19,7 @@
 from typing import Optional
 
 from pydantic import BaseModel
+from pydantic import Field
 
 
 class _BaseTask(BaseModel):
@@ -31,6 +32,9 @@ class Config:
     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):