Merge branch 'aviti-manifest-dev' of github.com:kedhammar/scilifelab_…

…epps into aviti-manifest-dev

VERSIONLOG.md

@@ -4,6 +4,10 @@
 
 For AVITI manifest generation: make PhiX manifest variant, fix udf typo, remove unused func, clarify var names
 
+## 20241011.1
+
+New project validator EPP
+
 ## 20241009.1
 
 Improve AVITI run manifest generation with sample-level settings. No longer produce submanifests.

scripts/project_validator.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+
+import re
+import sys
+from argparse import ArgumentParser
+
+import psycopg2
+import yaml
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.entities import Project
+from genologics.lims import Lims
+
+with open("/opt/gls/clarity/users/glsai/config/genosqlrc.yaml") as f:
+    config = yaml.safe_load(f)
+
+DESC = """EPP used to validate a project
+Author: Chuan Wang, Science for Life Laboratory, Stockholm, Sweden
+"""
+
+# Pre-compile regexes in global scope:
+NGISAMPLE_PAT = re.compile("P[0-9]+_[0-9]+")
+
+
+# Verify sample IDs
+def verify_sample_ids(project_id):
+    message = []
+    connection = psycopg2.connect(
+        user=config["username"],
+        host=config["url"],
+        database=config["db"],
+        password=config["password"],
+    )
+    cursor = connection.cursor()
+    query = (
+        "select sample.name from sample "
+        "inner join project on sample.projectid=project.projectid "
+        "where project.luid = '{}';"
+    )
+    cursor.execute(query.format(project_id))
+    query_output = cursor.fetchall()
+
+    for out in query_output:
+        sample_id = out[0]
+        if not NGISAMPLE_PAT.findall(sample_id):
+            message.append(f"SAMPLE NAME WARNING: Bad sample ID format {sample_id}")
+        else:
+            if sample_id.split("_")[0] != project_id:
+                message.append(
+                    f"SAMPLE NAME WARNING: Sample ID {sample_id} does not match project ID {project_id}"
+                )
+
+    # Close connections
+    if connection:
+        cursor.close()
+        connection.close()
+
+    return message
+
+
+def main(lims, pid):
+    message = []
+    project = Project(lims, id=pid)
+
+    # Validate sample IDs
+    message += verify_sample_ids(project.id)
+
+    if message:
+        sys.stderr.write("; ".join(message))
+        sys.exit(2)
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(description=DESC)
+    parser.add_argument("--pid", help="Project ID for current Project")
+    args = parser.parse_args()
+
+    lims = Lims(BASEURI, USERNAME, PASSWORD)
+    lims.check_version()
+    main(lims, args.pid)