9 session signature rework

act/tests/test_manifest_rebuild_from_lss.py

@@ -297,6 +297,66 @@ def test_rebuild_manifest_payload_from_lss_aggregates_strict_errors(tmp_path, mo
     assert "missing RedCap subject->lab mapping" in message
 
 
+def test_rebuild_manifest_payload_from_lss_ignores_9000_subject_missing_mapping(
+    tmp_path, monkeypatch
+):
+    save = _make_save_for_lss(tmp_path)
+
+    monkeypatch.setattr(
+        save,
+        "discover_lss_sessions",
+        lambda: (
+            {
+                "9000123": [
+                    {
+                        "subject_id": "9000123",
+                        "study": "int",
+                        "run": 1,
+                        "file_path": "/lss/int/sub-9000123/accel/ses-1/sub-9000123_ses-1_accel.csv",
+                    }
+                ]
+            },
+            {},
+        ),
+    )
+    monkeypatch.setattr(save, "_fetch_redcap_subject_lab_rows", lambda: [])
+    monkeypatch.setattr(save, "_list_rdss_metadata_rows", lambda: [])
+
+    payload = save.rebuild_manifest_payload_from_lss()
+
+    assert payload == {}
+
+
+def test_rebuild_manifest_payload_from_lss_ignores_4digit_9000_series_missing_mapping(
+    tmp_path, monkeypatch
+):
+    save = _make_save_for_lss(tmp_path)
+
+    monkeypatch.setattr(
+        save,
+        "discover_lss_sessions",
+        lambda: (
+            {
+                "9002": [
+                    {
+                        "subject_id": "9002",
+                        "study": "int",
+                        "run": 1,
+                        "file_path": "/lss/int/sub-9002/accel/ses-1/sub-9002_ses-1_accel.csv",
+                    }
+                ]
+            },
+            {},
+        ),
+    )
+    monkeypatch.setattr(save, "_fetch_redcap_subject_lab_rows", lambda: [])
+    monkeypatch.setattr(save, "_list_rdss_metadata_rows", lambda: [])
+
+    payload = save.rebuild_manifest_payload_from_lss()
+
+    assert payload == {}
+
+
 def test_atomic_manifest_write_preserves_existing_manifest_on_failure(tmp_path, monkeypatch):
     save = _make_save_for_lss(tmp_path)
     manifest_path = tmp_path / "res" / "data.json"

act/utils/save.py

@@ -340,6 +340,18 @@ def _subject_order_key(self, subject_id):
         except ValueError:
             return (1, subject)
 
+    def _subject_exempt_from_manifest_metadata_strictness(self, subject_id):
+        subject_text = str(subject_id).strip()
+        if subject_text.startswith("9000"):
+            return True
+
+        try:
+            subject_value = int(subject_text)
+        except (TypeError, ValueError):
+            return False
+
+        return 9000 <= subject_value <= 9999
+
     def _resolve_rdss_session_metadata_with_missing(
         self,
         discovered_sessions,
@@ -549,6 +561,8 @@ def rebuild_manifest_payload_from_lss(self):
             report_rows,
         )
         for subject_id in missing_subjects:
+            if self._subject_exempt_from_manifest_metadata_strictness(subject_id):
+                continue
             subject_errors.setdefault(subject_id, []).append(
                 "missing RedCap subject->lab mapping"
             )

cron.sh

@@ -9,7 +9,7 @@ conda activate act
 
 cd "${REPO_ROOT}"
 
-git pull --ff-only origin final-test
+git pull --ff-only
 
 if [[ -z "${BOOST_TOKEN:-}" ]]; then
   echo "BOOST_TOKEN is required. Aborting." >&2
@@ -22,7 +22,7 @@ DAYS_AGO="${DAYS_AGO:-30}"
 mkdir -p "logs/${SYSTEM}"
 LOG_FILE="logs/${SYSTEM}/$(date +%Y%m%d_%H%M%S).log"
 export LOG_FILE
-python -m act.main --daysago "${DAYS_AGO}" --token "${BOOST_TOKEN}" --system "${SYSTEM}" >> "${LOG_FILE}" 2>&1
+python -m act.main --daysago "${DAYS_AGO}" --token "${BOOST_TOKEN}" --system "${SYSTEM}" --rebuild-manifest-only >> "${LOG_FILE}" 2>&1
 
 if ! git diff --quiet; then
   git add .

data.json

@@ -232,6 +232,10 @@
       "8090": [
         "data/int/UI/8090/daily_plot.png",
         "data/int/UI/8090/summary_plot.png"
+      ],
+      "8085": [
+        "data/int/UI/8085/daily_plot.png",
+        "data/int/UI/8085/summary_plot.png"
       ]
     },
     "NE": {

features/FEATURE-cli-and-manifest-update/FIXES.md

@@ -0,0 +1,13 @@
+# Fixes for current logic issues in manifest // cli update
+
+## Current bugs // logic issues
+- Subjects starting with 9000 ids will not have a subject -> lab id mapping and will not be found in the rdss, remove warnings for these subjects that is causing strict conflict updates
+^^ Expanded below
+
+
+### 9000 IDs
+---
+***Dilemma***
+- 9000 IDs are pulled outside of this workflow from another data source, this logic is currently stable and will always end like this
+- Should these subjects even be added to the manifest if they are not truly required?
+- They are ran automatically through the GGIR script thus they should not be touched in this pipeline