Update manifest dev tool & manifest

fractal-analytics-platform · Sep 19, 2023 · b220c36 · b220c36
1 parent a5d9a27
commit b220c36
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Showing 2 changed files with 31 additions and 17 deletions.
diff --git a/src/fractal_faim_hcs/__FRACTAL_MANIFEST__.json b/src/fractal_faim_hcs/__FRACTAL_MANIFEST__.json
@@ -91,7 +91,9 @@
         "mem": 1000
       },
       "name": "Create OME-Zarr MD",
-      "output_type": "zarr"
+      "output_type": "zarr",
+      "docs_info": "Create OME-Zarr plate from MD Image Xpress files.",
+      "docs_link": "https://github.com/jluethi/fractal-faim-hcs"
     },
     {
       "args_schema": {
@@ -129,7 +131,7 @@
           },
           "memory_efficient": {
             "title": "Memory Efficient",
-            "default": true,
+            "default": false,
             "type": "boolean",
             "description": "Load images via dask (more memory efficient for 3D)"
           }
@@ -151,7 +153,9 @@
         "parallelization_level": "image"
       },
       "name": "Convert MD to OME-Zarr",
-      "output_type": "zarr"
+      "output_type": "zarr",
+      "docs_info": "Converts the image data from the MD image Xpress into OME-Zarr.",
+      "docs_link": "https://github.com/jluethi/fractal-faim-hcs"
     }
   ]
 }
diff --git a/src/fractal_faim_hcs/dev/new_args_schema.py b/src/fractal_faim_hcs/dev/new_args_schema.py
@@ -16,41 +16,51 @@
 """
 
 import json
+import logging
+from importlib import import_module
 from pathlib import Path
 
-import fractal_faim_hcs
 from fractal_tasks_core.dev.lib_args_schemas import (
     create_schema_for_single_task,
 )
+from fractal_tasks_core.dev.lib_task_docs import create_docs_info
+
+PACKAGE = "fractal_faim_hcs"
+
 
 if __name__ == "__main__":
     # Read manifest
-    manifest_path = Path(fractal_faim_hcs.__file__).parent / "__FRACTAL_MANIFEST__.json"
+    imported_package = import_module(PACKAGE)
+    manifest_path = Path(imported_package.__file__).parent / "__FRACTAL_MANIFEST__.json"
     with manifest_path.open("r") as f:
         manifest = json.load(f)
 
-    # Set or check global properties of manifest
+    # Set global properties of manifest
     manifest["has_args_schemas"] = True
     manifest["args_schema_version"] = "pydantic_v1"
 
-    # Loop over tasks and set or check args schemas
+    # Loop over tasks
     task_list = manifest["task_list"]
     for ind, task in enumerate(task_list):
         executable = task["executable"]
-        print(f"[{executable}] Start")
-        try:
-            schema = create_schema_for_single_task(
-                executable, package="fractal_faim_hcs"
-            )
-        except AttributeError as e:
-            print(f"[{executable}] Skip, due to AttributeError")
-            print(e)
-            continue
+        logging.info(f"[{executable}] START")
 
+        # Create new JSON Schema for task arguments
+        schema = create_schema_for_single_task(executable, package=PACKAGE)
         manifest["task_list"][ind]["args_schema"] = schema
-        print("Schema added to manifest")
+
+        # Update docs_info, based on task-function description
+        docs_info = create_docs_info(executable, package=PACKAGE)
+        docs_link = "https://github.com/jluethi/fractal-faim-hcs"
+        if docs_info:
+            manifest["task_list"][ind]["docs_info"] = docs_info
+        if docs_link:
+            manifest["task_list"][ind]["docs_link"] = docs_link
+
+        logging.info(f"[{executable}] END (new schema/description/link)")
         print()
 
     with manifest_path.open("w") as f:
         json.dump(manifest, f, indent=2)
         f.write("\n")
+    logging.info(f"Up-to-date manifest stored in {manifest_path.as_posix()}")