wwpdb.apps.msgmodule 0.180.2__tar.gz → 0.181__tar.gz

{wwpdb_apps_msgmodule-0.180.2 → wwpdb_apps_msgmodule-0.181}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: wwpdb.apps.msgmodule
-Version: 0.180.2
+Version: 0.181
 Summary: wwPDB messaging module
 Home-page: https://github.com/rcsb/py-wwpdb_apps_ann_tasks_v2
 Author: Ezra Peisach

{wwpdb_apps_msgmodule-0.180.2 → wwpdb_apps_msgmodule-0.181}/wwpdb/apps/msgmodule/__init__.py

@@ -2,4 +2,4 @@ __docformat__ = "restructuredtext en"
 __author__ = "Ezra Peisach"
 __email__ = "ezra.peisach@rcsb.org"
 __license__ = "Apache 2.0"
-__version__ = "0.180.2"
+__version__ = "0.181"

{wwpdb_apps_msgmodule-0.180.2 → wwpdb_apps_msgmodule-0.181}/wwpdb/apps/msgmodule/db/DataAccessLayer.py

@@ -81,14 +81,18 @@ def _get_or_create_engine(db_config: Dict):
                 echo=False  # Set to True for SQL debugging
             )
 
-            # Test connection and set max_allowed_packet for large messages
+            # Test connection
+            # NOTE: Disabled SET SESSION max_allowed_packet due to permission restrictions in production.
+            # Production database users typically lack SUPER privilege required for session-level settings.
+            # The application relies on the server's GLOBAL max_allowed_packet setting configured by the DBA.
+            # If large message inserts fail due to packet size, the DBA must increase GLOBAL max_allowed_packet.
             with engine.connect() as conn:
                 conn.execute(text("SELECT 1"))
-                try:
-                    conn.execute(text("SET SESSION max_allowed_packet=67108864"))
-                    logger.info("Set SESSION max_allowed_packet to 64MB for large messages")
-                except Exception as e:
-                    logger.warning(f"Could not set max_allowed_packet (may require SUPER privilege): {e}")  # pylint: disable=logging-fstring-interpolation
+                # try:
+                #     conn.execute(text("SET SESSION max_allowed_packet=67108864"))
+                #     logger.info("Set SESSION max_allowed_packet to 64MB for large messages")
+                # except Exception as e:
+                #     logger.warning(f"Could not set max_allowed_packet (may require SUPER privilege): {e}")  # pylint: disable=logging-fstring-interpolation
 
                 logger.info("Database connection test successful")
 
@@ -236,18 +240,19 @@ class BaseDAO(Generic[ModelType]):
         Returns:
             bool: True if creation succeeded, False otherwise
 
-        Note:
-            Automatically sets SESSION max_allowed_packet to 64MB for large messages
         """
         max_retries = 3
         for attempt in range(max_retries):
             try:
                 with self.db_connection.get_session() as session:
-                    # Ensure max_allowed_packet is set for this session
-                    try:
-                        session.execute(text("SET SESSION max_allowed_packet=67108864"))
-                    except Exception:
-                        pass  # Ignore if we can't set it
+                    # NOTE: SET SESSION max_allowed_packet is disabled due to permission restrictions.
+                    # Production database users lack SUPER privilege. The application relies on the server's
+                    # GLOBAL max_allowed_packet setting. If inserts fail due to packet size, the DBA must
+                    # increase the global setting via: SET GLOBAL max_allowed_packet=...
+                    # try:
+                    #     session.execute(text("SET SESSION max_allowed_packet=67108864"))
+                    # except Exception:
+                    #     pass  # Ignore if we can't set it
 
                     session.add(obj)
                     session.commit()

{wwpdb_apps_msgmodule-0.180.2 → wwpdb_apps_msgmodule-0.181}/wwpdb/apps/msgmodule/depict/MessagingTemplates.py

@@ -68,16 +68,14 @@ Twitter: http://twitter.com/#!/buildmodels
 
     msgTmplt_site_contact_details_pdbe = """
 --------------------------------------------------------------------------------------------------------------
-Protein Data Bank in Europe (PDBe), a wwPDB partner site
-http://www.PDBe.org
-
+Protein Data Bank in Europe (PDBe) and Electron Microscopy Data Bank (EMDB), wwPDB partner sites
+https://www.PDBe.org | https://www.emdatabank.org
 EMBL's European Bioinformatics Institute
 Wellcome Trust Genome Campus
-Hinxton
-Cambridge CB10 1SD UK
-
-http://www.facebook.com/proteindatabank
-http://twitter.com/PDBeurope
+Hinxton, Cambridge, CB10 1SD, UK
+https://www.linkedin.com/company/pdbe/ | https://www.linkedin.com/company/emdatabank/
+https://bsky.app/profile/pdbeurope.bsky.social | https://bsky.app/profile/emdatabank.bsky.social
+https://x.com/PDBeurope | https://x.com/EMDB_EMPIAR
 --------------------------------------------------------------------------------------------------------------"""
 
     msgTmplt_site_contact_details_pdbj = """

{wwpdb_apps_msgmodule-0.180.2 → wwpdb_apps_msgmodule-0.181}/wwpdb/apps/msgmodule/io/MessagingIo.py

@@ -491,7 +491,7 @@ class MessagingIo(object):
 
                 # For database-backed storage (dummy paths), skip file existence checks
                 if self.__msgsFrmDpstrFilePath is not None and (self.__msgsFrmDpstrFilePath.startswith("/dummy") or os.access(self.__msgsFrmDpstrFilePath, os.R_OK)):
-                    pdbxMsgIo_frmDpstr = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                    pdbxMsgIo_frmDpstr = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                     try:
                         depId = str(self.__reqObj.getValue("identifier"))
                         ok = pdbxMsgIo_frmDpstr.read(self.__msgsFrmDpstrFilePath, deposition_id=depId)
@@ -504,7 +504,7 @@ class MessagingIo(object):
                             pdbxMsgIo_frmDpstr.close()  # Explicitly close to release database connections  # pylint: disable=no-member
 
                 if self.__msgsToDpstrFilePath is not None and (self.__msgsToDpstrFilePath.startswith("/dummy") or os.access(self.__msgsToDpstrFilePath, os.R_OK)):
-                    pdbxMsgIo_toDpstr = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                    pdbxMsgIo_toDpstr = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                     try:
                         depId = str(self.__reqObj.getValue("identifier"))
                         ok = pdbxMsgIo_toDpstr.read(self.__msgsToDpstrFilePath, deposition_id=depId)
@@ -521,7 +521,7 @@ class MessagingIo(object):
 
                 # For database-backed storage (dummy paths), skip file existence checks
                 if self.__notesFilePath is not None and (self.__notesFilePath.startswith("/dummy") or os.access(self.__notesFilePath, os.R_OK)):
-                    pdbxMsgIo_notes = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                    pdbxMsgIo_notes = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                     try:
                         depId = str(self.__reqObj.getValue("identifier"))
                         ok = pdbxMsgIo_notes.read(self.__notesFilePath, deposition_id=depId)
@@ -622,7 +622,7 @@ class MessagingIo(object):
 
                 # For database-backed storage (dummy paths), skip file existence checks
                 if self.__msgsFrmDpstrFilePath is not None and (self.__msgsFrmDpstrFilePath.startswith("/dummy") or os.access(self.__msgsFrmDpstrFilePath, os.R_OK)):
-                    pdbxMsgIo_frmDpstr = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                    pdbxMsgIo_frmDpstr = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                     depId = str(self.__reqObj.getValue("identifier"))
                     ok = pdbxMsgIo_frmDpstr.read(self.__msgsFrmDpstrFilePath, deposition_id=depId)
                     if ok:
@@ -634,7 +634,7 @@ class MessagingIo(object):
                             origCommsLst.extend(pdbxMsgIo_frmDpstr.getOrigCommReferenceInfo())
 
                 if self.__msgsToDpstrFilePath is not None and (self.__msgsToDpstrFilePath.startswith("/dummy") or os.access(self.__msgsToDpstrFilePath, os.R_OK)):
-                    pdbxMsgIo_toDpstr = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                    pdbxMsgIo_toDpstr = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                     depId = str(self.__reqObj.getValue("identifier"))
                     ok = pdbxMsgIo_toDpstr.read(self.__msgsToDpstrFilePath, deposition_id=depId)
                     if ok:
@@ -659,7 +659,7 @@ class MessagingIo(object):
 
                 # For database-backed storage (dummy paths), skip file existence checks
                 if self.__notesFilePath is not None and (self.__notesFilePath.startswith("/dummy") or os.access(self.__notesFilePath, os.R_OK)):
-                    pdbxMsgIo_notes = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                    pdbxMsgIo_notes = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                     depId = str(self.__reqObj.getValue("identifier"))
                     ok = pdbxMsgIo_notes.read(self.__notesFilePath, deposition_id=depId)
 
@@ -870,7 +870,7 @@ class MessagingIo(object):
 
             # For database-backed storage (dummy paths), skip file existence checks
             if self.__msgsFrmDpstrFilePath is not None and (self.__msgsFrmDpstrFilePath.startswith("/dummy") or os.access(self.__msgsFrmDpstrFilePath, os.R_OK)):
-                mIIo = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                mIIo = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                 with LockFile(
                     self.__msgsFrmDpstrFilePath, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__lfh
                 ) as _lf, FileSizeLogger(self.__msgsFrmDpstrFilePath, verbose=self.__verbose, log=self.__lfh) as _fsl:
@@ -882,7 +882,7 @@ class MessagingIo(object):
 
             # For database-backed storage (dummy paths), skip file existence checks
             if self.__msgsToDpstrFilePath is not None and (self.__msgsToDpstrFilePath.startswith("/dummy") or os.access(self.__msgsToDpstrFilePath, os.R_OK)):
-                mIIo2 = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                mIIo2 = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                 with LockFile(
                     self.__msgsToDpstrFilePath, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__lfh
                 ) as _lf, FileSizeLogger(  # noqa: F841
@@ -962,7 +962,7 @@ class MessagingIo(object):
 
             # For database-backed storage (dummy paths), skip file existence checks
             if self.__notesFilePath is not None and (self.__notesFilePath.startswith("/dummy") or os.access(self.__notesFilePath, os.R_OK)):
-                mIIo = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                mIIo = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                 with LockFile(
                     self.__notesFilePath, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__lfh
                 ) as _lf, FileSizeLogger(  # noqa: F841
@@ -1044,7 +1044,7 @@ class MessagingIo(object):
             else:
                 logger.info("Using database storage - skipping file operations for: %s", outputFilePth)
             #
-            mIIo = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+            mIIo = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             with LockFile(outputFilePth, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__lfh) as _lf, FileSizeLogger(
                 outputFilePth, verbose=self.__verbose, log=self.__lfh
             ) as _fsl:  # noqa: F841
@@ -1437,10 +1437,10 @@ class MessagingIo(object):
             elif p_tmpltType == "remind-unlocked":
                 msgTmplt = MessagingTemplates.msgTmplt_remindUnlocked
                 attachFiles = False
-                isNote = True
+                # isNote = True
                 # Need all ids
                 accstr = templateDict["accession_ids"]
-                subject = "ARCHIVED: Please attend to your unlocked deposition session - " + accstr
+                subject = "Please attend to your unlocked deposition session - " + accstr
             elif p_tmpltType == "approval-impl":  # CS 2024-04-04 change implicit-approved to approval-impl to match frontend drop-down
                 msgTmplt = MessagingTemplates.msgTmplt_approvalImplicit_em if p_isEmdbEntry else MessagingTemplates.msgTmplt_approvalImplicit
                 attachFiles = False
@@ -1468,14 +1468,14 @@ class MessagingIo(object):
             elif p_tmpltType == "reminder":  # CS 2024-04-04 change type from remind-feedback to reminder to match frontend drop-down
                 msgTmplt = MessagingTemplates.msgTmplt_reminder_em if p_isEmdbEntry else MessagingTemplates.msgTmplt_reminder
                 attachFiles = False
-                isNote = True
+                # isNote = True
                 # Need all ids
                 accstr = templateDict["accession_ids"]
                 subject = "REMINDER: Still awaiting feedback for " + accstr
             elif p_tmpltType == "reminder-auth-to-rel":  # CS 2024-09-09 add process to send reminder on AUTH entry deposited as REL
                 msgTmplt = MessagingTemplates.msgTmplt_reminder_auth_to_rel_em if p_isEmdbEntry else MessagingTemplates.msgTmplt_reminder_auth_to_rel
                 attachFiles = False
-                isNote = True
+                # isNote = True
                 accstr = templateDict["accession_ids"]
                 subject = "REMINDER: Upcoming release of " + accstr
             else:
@@ -1581,8 +1581,8 @@ class MessagingIo(object):
         # No files are being attached
         fileRefList = []
 
-        # We are archiving notes
-        isNote = True
+        # We are archiving notes -- not any more 3/30/26
+        isNote = False
 
         contextType = p_tmpltType  # CS 2024-04-04 record message type, following frontend message-to-depositor drop-down list, default at "other"
         contextVal = None
@@ -1654,7 +1654,7 @@ class MessagingIo(object):
         msgDI = MessagingDataImport(self.__reqObj, verbose=self.__verbose, log=self.__lfh)
         self.__msgsFrmDpstrFilePath = msgDI.getFilePath(contentType="messages-from-depositor", format="pdbx")
         logger.info("self.__msgsFromDpstrFilePath is: %s", self.__msgsFrmDpstrFilePath)
-        mIIo = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+        mIIo = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
         with LockFile(
             self.__msgsFrmDpstrFilePath, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__lfh
         ) as _lf, FileSizeLogger(  # noqa: F841
@@ -1726,7 +1726,7 @@ class MessagingIo(object):
                 except IOError:
                     pass
             #
-            mIIo = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+            mIIo = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             with LockFile(
                 self.__msgsToDpstrFilePath, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__lfh
             ) as _lf, FileSizeLogger(
@@ -1850,7 +1850,7 @@ class MessagingIo(object):
 
             # For database-backed storage (dummy paths), skip file existence checks
             if self.__notesFilePath is not None and (self.__notesFilePath.startswith("/dummy") or os.access(self.__notesFilePath, os.R_OK)):
-                pdbxMsgIo_notes = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                pdbxMsgIo_notes = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                 depId = str(self.__reqObj.getValue("identifier"))
                 bGotContent = pdbxMsgIo_notes.read(self.__notesFilePath, deposition_id=depId)
 
@@ -1927,7 +1927,7 @@ class MessagingIo(object):
                 except IOError:
                     pass
             #
-            mIIo = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+            mIIo = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             msgAlreadySeen = False
             with LockFile(
                 self.__msgsToDpstrFilePath, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__lfh
@@ -2002,8 +2002,8 @@ class MessagingIo(object):
         msgsFrmDpstrLst = []
         msgStatusLst = []
         fileSizeToDpstr = 0
-        mIIo = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
-        mIIo2 = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+        mIIo = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
+        mIIo2 = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
 
         try:
             # GET LIST OF IDS OF MSGS FROM DEPOSITOR
@@ -2152,7 +2152,7 @@ class MessagingIo(object):
             if self.__msgsToDpstrFilePath and (self.__msgsToDpstrFilePath.startswith("/dummy") or os.access(self.__msgsToDpstrFilePath, os.R_OK)):
                 fileSizeBytes = self.__getFileSizeBytes(self.__msgsToDpstrFilePath) if not self.__msgsToDpstrFilePath.startswith("/dummy") else 1
                 if fileSizeBytes > 0:
-                    mIIo = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                    mIIo = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                     with LockFile(
                         self.__msgsToDpstrFilePath, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__lfh
                     ) as _lf, FileSizeLogger(  # noqa: F841
@@ -2993,7 +2993,7 @@ class MessagingIo(object):
                 logger.info("self.__msgsToDpstrFilePath is: %s", self.__msgsToDpstrFilePath)
 
             if self.__msgsToDpstrFilePath is not None and os.access(self.__msgsToDpstrFilePath, os.R_OK):
-                mIIo = PdbxMessageIo(verbose=self.__verbose, log=self.__lfh)
+                mIIo = PdbxMessageIo(site_id=self.__siteId, verbose=self.__verbose, log=self.__lfh)
                 with LockFile(
                     self.__msgsToDpstrFilePath, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__lfh
                 ) as _lf, FileSizeLogger(  # noqa: F841

{wwpdb_apps_msgmodule-0.180.2 → wwpdb_apps_msgmodule-0.181}/wwpdb/apps/msgmodule/util/ExtractMessage.py

@@ -114,7 +114,9 @@ class ExtractMessage(object):
             logger.info("read message file for %s at %s", depid, filepath_msg)
 
             try:
-                pdbxMsgIo = PdbxMessageIo(verbose=self.__verbose, log=self.__log)
+                # Pass site_id explicitly to keep DB/file routing deterministic.
+                siteId = self.__siteId if self.__siteId is not None else getSiteId()
+                pdbxMsgIo = PdbxMessageIo(site_id=siteId, verbose=self.__verbose, log=self.__log)
                 with LockFile(filepath_msg, timeoutSeconds=self.__timeoutSeconds, retrySeconds=self.__retrySeconds, verbose=self.__verbose, log=self.__log):
                     ok = pdbxMsgIo.read(filepath_msg, deposition_id=depid)
                     if ok:
@@ -695,7 +697,9 @@ class ExtractMessage(object):
         dep_fpath = self.__getMsgFilePath(depid, "messages-from-depositor", test_folder=None)
         bio_fpath = self.__getMsgFilePath(depid, "messages-to-depositor", test_folder=None)
 
-        pdbxMsgIo_frmDpstr = PdbxMessageIo(verbose=self.__verbose, log=self.__log)
+        # Reuse one resolved site_id for both reads so they follow the same backend.
+        siteId = self.__siteId if self.__siteId is not None else getSiteId()
+        pdbxMsgIo_frmDpstr = PdbxMessageIo(site_id=siteId, verbose=self.__verbose, log=self.__log)
         ok = pdbxMsgIo_frmDpstr.read(dep_fpath, deposition_id=depid)
         if not ok:
             return []
@@ -704,7 +708,7 @@ class ExtractMessage(object):
             pdbxMsgIo_frmDpstr.getMessageInfo()
         )  # in recordSetLst we now have a list of dictionaries with item names as keys and respective data for values
 
-        pdbxMsgIo_toDpstr = PdbxMessageIo(verbose=self.__verbose, log=self.__log)
+        pdbxMsgIo_toDpstr = PdbxMessageIo(site_id=siteId, verbose=self.__verbose, log=self.__log)
         ok = pdbxMsgIo_toDpstr.read(bio_fpath, deposition_id=depid)
         if not ok:
             # Assume all messages unacknowledged

{wwpdb_apps_msgmodule-0.180.2 → wwpdb_apps_msgmodule-0.181}/wwpdb.apps.msgmodule.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: wwpdb.apps.msgmodule
-Version: 0.180.2
+Version: 0.181
 Summary: wwPDB messaging module
 Home-page: https://github.com/rcsb/py-wwpdb_apps_ann_tasks_v2
 Author: Ezra Peisach