Merge pull request #366 from DESm1th/fixes

[FIX] Add small bug fixes + log message improvements
TIGRLab · Nov 11, 2024 · 40a6a58 · 40a6a58
2 parents dc73a79 + 31bc142
commit 40a6a58
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Showing 5 changed files with 21 additions and 8 deletions.
diff --git a/bin/dm_link.py b/bin/dm_link.py
@@ -205,7 +205,8 @@ def link_archive(archive_path, dicom_path, scanid_field, config):
         scanid = get_scanid_from_header(archive_path, scanid_field)
 
     if not scanid:
-        logger.error("Scanid not found for archive: {}".format(archive_path))
+        logger.error("Scanid not found for archive, please add intended ID "
+                     f"to 'scans.csv': {archive_path}")
         return
 
     try:

diff --git a/bin/dm_link_shared_ids.py b/bin/dm_link_shared_ids.py
@@ -186,7 +186,7 @@ def share_session(record, xnat_connection=None):
 
         target_cfg = datman.config.config(study=str(target))
         try:
-            target_tags = list(target_cfg.get_tags(site=source.site))
+            target_tags = list(target_cfg.get_tags(site=target.site))
         except Exception:
             target_tags = []
 

diff --git a/bin/dm_redcap_scan_completed.py b/bin/dm_redcap_scan_completed.py
@@ -89,12 +89,14 @@ def add_session_redcap(record, record_key):
         try:
             datman.scanid.is_scanid(subject_id)
         except datman.scanid.ParseException:
-            logger.error('Invalid session: {}, skipping'.format(subject_id))
+            logger.error(f'Invalid session {subject_id} in record {record_id}, '
+                         'skipping. Please fix ID on REDCap.')
             return
     try:
         ident = parse_id(subject_id)
     except datman.scanid.ParseException:
-        logger.error('Invalid session: {}, skipping'.format(subject_id))
+        logger.error(f'Invalid session {subject_id} in record {record_id}, '
+                     'skipping. Please fix ID on REDCap.')
         return
 
     session_date = record[get_setting('RedcapDate', default='date')]

diff --git a/bin/dm_xnat_extract.py b/bin/dm_xnat_extract.py
@@ -380,8 +380,8 @@ def get_experiment_identifier(config, project, experiment_id):
     try:
         ident = validate_subject_id(experiment_id, config)
     except datman.scanid.ParseException:
-        logger.error(f"Invalid experiment ID {experiment_id} in project "
-                     f"{project}.")
+        logger.error(f"Invalid XNAT experiment ID {experiment_id} in project "
+                     f"{project}. Please update XNAT with correct ID.")
         return
 
     if ident.session is None and not datman.scanid.is_phantom(ident):

diff --git a/datman/xnat.py b/datman/xnat.py
@@ -180,8 +180,9 @@ def __init__(self, server, username, password):
         self.auth = (username, password)
         try:
             self.open_session()
-        except Exception:
-            raise XnatException(f"Failed to open session with server {server}")
+        except Exception as e:
+            raise XnatException(
+                f"Failed to open session with server {server}. Reason - {e}")
 
     def __enter__(self):
         return self
@@ -206,6 +207,15 @@ def open_session(self):
             logger.debug("Username: {}")
             response.raise_for_status()
 
+        # If password is expired, XNAT returns status 200 and a sea of
+        # HTML causing later, unexpected, exceptions when using
+        # the connection. So! Check to see if we got HTML instead of a token.
+        if '<html' in response.text:
+            raise XnatException(
+                f"Password for user {self.auth[0]} on server {self.server} "
+                "has expired. Please update it."
+            )
+
         # Cookies are set automatically, don't manually set them or it wipes
         # out other session info
         self.session = s