Merge pull request #88 from aanil/master

Add script to update project closure in bioinfo_analysis db

Author: chuan-wang

scripts/bioinfo_project_status_update.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+import yaml
+from genologics.lims import Lims
+from genologics.entities import Project
+from genologics.config import BASEURI, USERNAME, PASSWORD
+import LIMS2DB.utils as lutils
+from requests.exceptions import HTTPError
+
+
+def main(args):
+    log = lutils.setupLog('bioinfologger', args.logfile)
+    lims = Lims(BASEURI, USERNAME, PASSWORD)
+    with open(args.conf) as conf_file:
+        conf = yaml.safe_load(conf_file)
+    bioinfodb = lutils.setupServer(conf)['bioinfo_analysis']
+    open_projects = bioinfodb.view('latest_data/sample_id_open')
+
+    for row in open_projects.rows:
+        project_id = row.key[0]
+        sample_id = row.key[3]
+        close_date = None
+        try:
+            close_date = Project(lims=lims, id=project_id).close_date
+        except HTTPError as e:
+            if '404: Project not found' in e.message:
+                log.error('Project '+project_id+' not found in LIMS')
+                continue
+        if close_date is not None:
+            try:
+                doc = bioinfodb.get(row.id)
+            except Exception as e:
+                log.error(e + 'in Project '+project_id+ ' Sample '+sample_id+ ' while accessing doc from statusdb')
+            doc['project_closed'] = True
+            try:
+                bioinfodb.save(doc)
+                log.info('Updated Project '+project_id+ ' Sample '+sample_id)
+            except Exception as e:
+                log.error(e + 'in Project '+project_id+ ' Sample '+sample_id+ ' while saving to statusdb')
+
+
+
+if __name__ == '__main__':
+    usage = "Usage:       python bioinfo_project_status_update.py [options]"
+    parser = argparse.ArgumentParser(description=usage)
+
+    parser.add_argument("-c", "--conf", dest="conf",
+    default=os.path.join(os.environ['HOME'],'opt/config/post_process.yaml'),
+    help = "Config file.  Default: ~/opt/config/post_process.yaml")
+
+    parser.add_argument("-l", "--log", dest="logfile",
+    default=os.path.join(os.environ['HOME'],'statusdb_bioinfo_closed.log'),
+    help = "log file.  Default: ~/statusdb_bioinfo_closed.log")
+    args = parser.parse_args()
+
+    main(args)