Update processing.json fields

.codeocean/secrets.json

@@ -0,0 +1,12 @@
+{
+	"version": 1,
+	"secrets": [
+		{
+			"type": "api-key",
+			"id": "UZZM1usjDUeETAGx",
+			"description": "Code Ocean API",
+			"key": "API_KEY",
+			"secret": "API_SECRET"
+		}
+	]
+}

code/02_update_metadata.py

@@ -12,11 +12,16 @@
 any schema violation raises and aborts the run.
 """
 
+import base64
+import json
+import os
 import shutil
+import urllib.error
+import urllib.request
 from datetime import datetime, timezone
 from pathlib import Path
 
-from aind_data_schema.components.identifiers import Code
+from aind_data_schema.components.identifiers import Code, DataAsset
 from aind_data_schema.core.data_description import DataDescription
 from aind_data_schema.core.processing import DataProcess, ProcessStage, Processing
 from aind_data_schema_models.process_names import ProcessName
@@ -26,10 +31,55 @@
 DATA_DIR = Path("/data")
 EXPERIMENTERS = ["Polina Kosillo"]
 
-# Code Ocean capsule URL recorded in processing.json. Hardcoded to the released
-# capsule so the published metadata always references the canonical capsule,
-# regardless of which working/test capsule is running this script.
-CAPSULE_URL = "https://codeocean.allenneuraldynamics.org/capsule/3953531/tree"
+CO_API_BASE = "https://codeocean.allenneuraldynamics.org/api/v1"
+CO_WEB_BASE = "https://codeocean.allenneuraldynamics.org/capsule"
+AIND_OPEN_DATA_BUCKET = "s3://aind-open-data"
+
+
+def fetch_co_provenance() -> tuple[str, str]:
+    """Return (capsule_url, version) for the running Code Ocean capsule.
+
+    Calls the Code Ocean REST API at runtime to look up the capsule's web URL
+    (built from the slug) and the release version of this run. ``version``
+    is ``"from non-release editable capsule"`` when running an editable
+    (non-release) capsule; otherwise it's a string like ``"v3.0"``.
+
+    Requires the "Code Ocean API Credentials" Secret to be attached to the
+    capsule (Capsule Settings -> Credentials), which exposes API_KEY at
+    runtime. Raises RuntimeError if any required env var is missing or the
+    API call fails -- the conversion can't produce valid metadata without
+    the capsule URL.
+    """
+    api_key = os.environ.get("API_KEY")
+    capsule_id = os.environ.get("CO_CAPSULE_ID")
+    computation_id = os.environ.get("CO_COMPUTATION_ID")
+    if not api_key or not capsule_id or not computation_id:
+        raise RuntimeError(
+            "Missing Code Ocean env vars (API_KEY / CO_CAPSULE_ID / "
+            "CO_COMPUTATION_ID). Attach the 'Code Ocean API Credentials' "
+            "Secret to the capsule (Capsule Settings -> Credentials)."
+        )
+
+    auth = base64.b64encode(f"{api_key}:".encode()).decode()
+    headers = {"Authorization": f"Basic {auth}"}
+
+    def _get(path: str) -> dict:
+        req = urllib.request.Request(f"{CO_API_BASE}{path}", headers=headers)
+        with urllib.request.urlopen(req, timeout=10) as resp:
+            return json.loads(resp.read())
+
+    try:
+        capsule = _get(f"/capsules/{capsule_id}")
+        computation = _get(f"/computations/{computation_id}")
+    except (urllib.error.URLError, json.JSONDecodeError) as e:
+        raise RuntimeError(f"Code Ocean API call failed: {e}") from e
+
+    capsule_url = f"{CO_WEB_BASE}/{capsule['slug']}/tree"
+    if "version" in computation:
+        version = f"v{computation['version']}.0"
+    else:
+        version = "from non-release editable capsule"
+    return capsule_url, version
 
 
 def find_output_dirs() -> list[Path]:
@@ -74,13 +124,16 @@ def write_data_description(input_dir: Path, out_dir: Path) -> None:
     print(f"  wrote derived data_description.json (source: {raw_dd.name})")
 
 
-def write_processing(out_dir: Path) -> None:
+def write_processing(out_dir: Path, input_asset: str) -> None:
     """Build and write a processing.json describing this conversion run."""
+    capsule_url, version = fetch_co_provenance()
     code = Code(
-        url=CAPSULE_URL,
+        url=capsule_url,
         name="LC-NE_BARseq_MAT-RDS_conversion",
+        version=version,
         run_script=Path("code/run"),
         language="R",
+        input_data=[DataAsset(url=f"{AIND_OPEN_DATA_BUCKET}/{input_asset}")],
     )
     process = DataProcess(
         process_type=ProcessName.FILE_FORMAT_CONVERSION,
@@ -106,13 +159,11 @@ def update_metadata_for_subject(out_dir: Path) -> None:
 
     copy_peer_metadata(input_dir, out_dir)
     write_data_description(input_dir, out_dir)
-    write_processing(out_dir)
+    write_processing(out_dir, input_asset)
 
 
 def main() -> None:
     """Discover output folders under /results/ and generate metadata for each."""
-    print(f"Capsule URL: {CAPSULE_URL}\n")
-
     out_dirs = find_output_dirs()
     if not out_dirs:
         raise RuntimeError(f"No output directories found under {RESULTS_DIR}")