wwpdb.apps.msgmodule 0.176.2__tar.gz → 0.177__tar.gz

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wwpdb.apps.msgmodule
-Version: 0.176.2
+Version: 0.177
 Summary: wwPDB messaging module
 Home-page: https://github.com/rcsb/py-wwpdb_apps_ann_tasks_v2
 Author: Ezra Peisach
@@ -15,8 +15,10 @@ Classifier: Programming Language :: Python :: 2.7
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.6
 Classifier: Programming Language :: Python :: 3.7
+Requires-Dist: oslo.concurrency
 Requires-Dist: wwpdb.io
 Requires-Dist: wwpdb.utils.config~=0.39
+Requires-Dist: wwpdb.utils.db
 Requires-Dist: wwpdb.utils.session
 Requires-Dist: wwpdb.utils.wf>=0.8
 Requires-Dist: mmcif

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/setup.py

@@ -42,8 +42,10 @@ setup(
     ],
     #
     install_requires=[
+        "oslo.concurrency",
         "wwpdb.io",
         "wwpdb.utils.config ~= 0.39",
+        "wwpdb.utils.db",
         "wwpdb.utils.session",
         "wwpdb.utils.wf >= 0.8",
         "mmcif",

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/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__ = "0.176.2"
+__version__ = "0.177"

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/wwpdb/apps/msgmodule/depict/MessagingTemplates.py

@@ -30,6 +30,7 @@
 #    2022-01-26    CS     update template
 #    2022-02-27    CS     add template for Map-only withdrawn
 #    2023-10-20    CS     add/modify various templates for superseding entry release, EM model-only and map-only
+#    2024-09-09    CS     add templates msgTmplt_reminder_auth_to_rel and msgTmplt_reminder_auth_to_rel_em
 ##
 """
 Convenience class to serve as source of message templates for dynamic population
@@ -165,6 +166,48 @@ In accordance with wwPDB policies (http://www.wwpdb.org/documentation/policy), i
 
 Thank you for your attention.
 
+%(msg_closing)s
+"""
+
+    msgTmplt_reminder_auth_to_rel = """Dear Depositors,
+
+This message is to inform you that your entry %(accession_ids)s (Deposition ID %(identifier)s) is scheduled for release. The entry is entitled:
+
+%(horiz_line)s
+%(title)s
+%(horiz_line)s
+
+Entry authors:
+
+%(entry_authors_newline_list)s
+
+Your entry was deposited with a request for immediate release.
+
+As we have not heard from you since we sent you the validation report and processed files on %(outbound_rprt_date)s, we consider your entry has been approved.
+
+Unless we hear from you otherwise, your entry will be set for release next week, in accordance with wwPDB policies (http://www.wwpdb.org/documentation/policy).
+
+%(msg_closing)s
+"""
+
+    msgTmplt_reminder_auth_to_rel_em = """Dear Depositors,
+
+This message is to inform you that your entry %(accession_ids)s (Deposition ID %(identifier)s) is scheduled for release. The entry is entitled:
+
+%(horiz_line)s
+%(em_title)s
+%(horiz_line)s
+
+Entry authors:
+
+%(em_entry_authors_newline_list)s
+
+Your entry was deposited with a request for immediate release.
+
+As we have not heard from you since we sent you the validation report and processed files on %(outbound_rprt_date)s, we consider your entry has been approved.
+
+Unless we hear from you otherwise, your entry will be set for release next week, in accordance with wwPDB policies (http://www.wwpdb.org/documentation/policy).
+
 %(msg_closing)s
 """
 
@@ -351,7 +394,7 @@ Thank you for your attention.
 
     msgTmplt_mapOnly_authStatus_em = """Dear Depositors,
 
-Your %(accession_ids)s which corresponds to Deposition ID %(identifier)s has been annotated and the status is now AUTH.
+Your %(accession_ids)s which corresponds to Deposition ID %(identifier)s has been annotated and the status is now %(status_code_em_map)s.
 
 %(horiz_line)s
 %(em_title)s
@@ -410,7 +453,7 @@ Thank you for your attention.
 
 Please acknowledge receipt of this message.
 
-This message is to inform you that your %(accession_ids)s (Deposition ID %(identifier)s) %(is_are)sstill awaiting your input. The entry is entitled:
+This message is to inform you that your %(accession_ids)s (Deposition ID %(identifier)s) %(is_are)s still awaiting your input. The entry is entitled:
 
 %(horiz_line)s
 %(em_title)s
@@ -418,8 +461,8 @@ This message is to inform you that your %(accession_ids)s (Deposition ID %(ident
 
 We have not heard from you since we sent you the %(vldtn_rprt)sprocessed files on %(outbound_rprt_date_em)s. Please respond to the questions raised in our previous correspondence as soon as possible.
 
-In accordance with wwPDB policies (http://www.wwpdb.org/documentation/policy.html), if we find a publication describing the %(entry_entries_comma)s%(it_they_lcase)swill be released%(caveat_records)s.
-If after %(expire_date_em_map)s (one year from the deposition date) we are unable to find a publication describing%(this_these)s%(entry_entries_comma)s the%(entry_entries)smay be withdrawn if there remain outstanding issues, otherwise the%(entry_entries)swill be released.
+In accordance with wwPDB policies (http://www.wwpdb.org/documentation/policy.html), if we find a publication describing the %(entry_entries_comma)s %(it_they_lcase)s will be released %(caveat_records)s.
+If after %(expire_date_em_map)s (one year from the deposition date) we are unable to find a publication describing %(this_these)s %(entry_entries_comma)s the %(entry_entries)s may be withdrawn if there remain outstanding issues, otherwise the %(entry_entries)s will be released.
 
 Thank you for your attention.
 

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/wwpdb/apps/msgmodule/io/MessagingIo.py

@@ -124,6 +124,8 @@
 #    2023-11-20    EP     Add anyUnactionApprovalWithoutCorrection() to determine if any pendingapproval without corrections that need to be acted upon
 #    2023-11-23    EP     autoMsg() add support for explicit-approved autogenerated message
 #    2024-04-04    CS     Add context_type to autoMsg() and sendSingle() to match frontend message-to-depositor drop-down list
+#    2024-09-09    CS     Add process to send reminder on AUTH entry deposited as REL
+#    2024-09-18    CS     Change statusCode selection in __getDefaultMsgTmpltType for map-only entries
 ##
 """
 Class to manage persistence/retrieval of messaging data
@@ -1407,7 +1409,13 @@ class MessagingIo(object):
                 isNote = True
                 # Need all ids
                 accstr = templateDict["accession_ids"]
-                subject = "ARCHIVED: Still awaiting feedback for " + accstr
+                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
+                accstr = templateDict["accession_ids"]
+                subject = "REMINDER: Upcoming release of " + accstr
             else:
                 logger.error("Unknown message template %s", p_tmpltType)
                 msgTmplt = "This is an unknown message template."
@@ -4871,7 +4879,7 @@ class MsgTmpltHlpr(object):
         If it is an EM map only entry --> if _pdbx_database_status.status_code= AUTH -> launch mapOnly-AuthStatus_letter_template
         """
 
-        # CS 2023-11-06 start change logic for default template, primary on statusCode dependency, impact EM entries only
+        # before 2023-11-06 start
         # if self.__emDeposition:
         #     statusCode = self.__statusCodeEmMap
         # else:
@@ -4880,15 +4888,33 @@ class MsgTmpltHlpr(object):
         #         statusCode = self.__postRelStatus
         #     else:
         #         statusCode = self.__statusCode
-        if self.__postRelStatus and len(self.__postRelStatus) > 1:
+        # before 2023-11-06 end
+
+        # CS 2023-11-06 start change logic for default template, primary on statusCode dependency, impact EM entries only
+        # if self.__postRelStatus and len(self.__postRelStatus) > 1:
+        #     statusCode = self.__postRelStatus
+        # elif self.__statusCode and len(self.__statusCode) > 1:
+        #     statusCode = self.__statusCode
+        # elif self.__emDeposition:
+        #     statusCode = self.__statusCodeEmMap
+        # else:
+        #     pass
+        # CS 2023-11-06 end
+
+        # CS 2024-09-18 start change logic again for statusCode on map-only entries
+        statusCode = None
+        if self.__emMapOnly and self.__emDeposition:
+            statusCode = self.__statusCodeEmMap
+        elif self.__postRelStatus and len(self.__postRelStatus) > 1:
             statusCode = self.__postRelStatus
         elif self.__statusCode and len(self.__statusCode) > 1:
             statusCode = self.__statusCode
-        elif self.__emDeposition:
-            statusCode = self.__statusCodeEmMap
         else:
             pass
-        # CS 2023-11-06 end
+        # CS 2024-09-18 end
+
+        logger.info("CStrack+++ statusCode = %s", statusCode)
+        logger.info("CStrack+++ self.__emDeposition = %s, self.__emMapOnly = %s", self.__emDeposition, self.__emMapOnly)
 
         if statusCode and len(statusCode) > 1:
             if statusCode == "HPUB" or statusCode == "HOLD":

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/wwpdb/apps/msgmodule/util/AutoMessage.py

@@ -3,6 +3,8 @@
 # Date:  28-Jun-2019 E. Peisach
 #
 # Update:
+#    2024-09-09    CS     Add function to send reminder on AUTH entry deposited as REL
+##
 """
 Support for automatic scripts to send template drive email messages and archive in normal message stream/notes
 Auto messages are archived in notes-from-annotator
@@ -63,6 +65,10 @@ class AutoMessage(object):
         """ Sends a reminder that depositor has not responded to validation report """
         self._sendReminderBulk(depidlist, p_tmplt="reminder")
 
+    def sendRemindAuthToRel(self, depidlist):  # CS 2024-09-09 Add function to send reminder on AUTH entry deposited as REL
+        """ Sends a reminder that depositor has not responded to validation report on AUTH entries deposited as REL """
+        self._sendReminderBulk(depidlist, p_tmplt="reminder-auth-to-rel")
+
     def sendImplicitApproved(self, depidlist):
         self._sendReminderBulk(depidlist, p_tmplt="approval-impl")  # CS 2024-04-04 change implicit-approved to approval-impl to match frontend drop-down
 

wwpdb_apps_msgmodule-0.177/wwpdb/apps/msgmodule/util/DaInternalDb.py

@@ -0,0 +1,167 @@
+# =============================================================================
+# Author:  Chenghua Shao
+# Date:    2024-08-30
+# Updates:
+#
+# =============================================================================
+"""
+DA_INTERNAL database utility
+"""
+
+from wwpdb.utils.db.MyConnectionBase import MyConnectionBase
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+class DaInternalDb(object):
+    """DA_INTERNAL DB class for data lookup
+
+    Args:
+        object (_type_): object
+    """
+    def __init__(self, siteId=None):
+        """Initiator
+
+        Args:
+            siteId (_type_, optional): SITE ID. Defaults to None that will use the SITE ID of the current server.
+        """
+        self.__mydb = None
+        self.__siteId = siteId
+        self.__open()
+
+    def __del__(self):
+        """Finalizer. Close DB connection when all references to the object have been deleted.
+        """
+        self.__close()
+
+    def __open(self, resource="DA_INTERNAL"):
+        """Open DB connection
+
+        Args:
+            resource (str, optional): DB name. Defaults to "DA_INTERNAL".
+
+        Returns:
+            _type_: True/False for DB connection
+        """
+        self.__mydb = MyConnectionBase(siteId=self.__siteId)
+        self.__mydb.setResource(resourceName=resource)
+        ok = self.__mydb.openConnection()
+        if not ok:
+            logger.error("Could not open resourve %s", resource)
+            self.__mydb = None
+            return False
+
+        return True
+
+    def __close(self):
+        """Proper DB closure
+        """
+        if self.__mydb:
+            self.__mydb.closeConnection()
+            self.__mydb = None
+
+    def run(self, query):
+        """Simplified query runner
+
+        Args:
+            query (_type_): Full text of a query
+
+        Returns:
+            _type_: raw query results as tuple of tuples, e.g. ((1,2),(3,4))
+        """
+        cur = self.__mydb.getCursor()
+        cur.execute(query)
+        rows = cur.fetchall()
+        cur.close()
+        return rows
+
+    def verifyDepId(self, dep_id):
+        """Verify if an id is deposition id
+
+        Args:
+            dep_id (_type_): presumed dep id input
+
+        Returns:
+            _type_: True/False
+        """
+        query = "select structure_id from rcsb_status where structure_id = '%s'" % dep_id
+        rows = self.run(query)
+        if rows:
+            return True
+        else:
+            return False
+
+    def verifyPdbId(self, pdb_id):
+        """Verify if an id is PDB ID
+
+        Args:
+            pdb_id (_type_): presumed PDB id input
+
+        Returns:
+            _type_: True/False
+        """
+        query = "select structure_id from rcsb_status where pdb_id = '%s'" % pdb_id
+        rows = self.run(query)
+        if rows:
+            return True
+        else:
+            return False
+
+    def verifyEmdbId(self, emdb_id):
+        """Verify if an id is EMDB ID
+
+        Args:
+            emdb_id (_type_): presumed EMDB ID input
+
+        Returns:
+            _type_: True/False
+        """
+        query = "select structure_id from database_2 where database_id = 'EMDB' and database_code = '%s'" % emdb_id
+        rows = self.run(query)
+        if rows:
+            return True
+        else:
+            return False
+
+    def convertPdbIdToDepId(self, pdb_id):
+        """Convert PDB ID to deposition id
+
+        Args:
+            pdb_id (_type_): presumed PDB ID
+
+        Returns:
+            _type_: valid deposition id at this site, or None
+        """
+        query = "select structure_id from rcsb_status where pdb_id = '%s'" % pdb_id
+        rows = self.run(query)
+        if rows:
+            return rows[0][0]
+        else:
+            return None
+
+    def convertEmdbIdToDepId(self, emdb_id):
+        """Convert EMDB ID to deposition id
+
+        Args:
+            pdb_id (_type_): presumed EMDB ID
+
+        Returns:
+            _type_: valid deposition id at this site, or None
+        """
+        query = "select structure_id from database_2 where database_id = 'EMDB' and database_code = '%s'" % emdb_id
+        rows = self.run(query)
+        if rows:
+            return rows[0][0]
+        else:
+            return None
+
+
+if __name__ == "__main__":
+    # Minimal temporary testing, cannot develop unit test because the IDs at the test sites are cleaned up regularly.
+    db_da_internal = DaInternalDb()
+    print(db_da_internal.verifyDepId("D_1000272951"))
+    print(db_da_internal.verifyPdbId("8GI8"))
+    print(db_da_internal.verifyEmdbId("EMD-40062"))
+    print(db_da_internal.convertPdbIdToDepId("8GI8"))
+    print(db_da_internal.convertEmdbIdToDepId("EMD-40062"))

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/wwpdb/apps/msgmodule/util/ExtractMessage.py

@@ -6,7 +6,7 @@
 #    2023-11-10    CS     Refactor code to add general process to parse message file; Add functions to retrieve datetime of last messages of various type.
 #    2023-11-23    EP     Add getApprovalNoCorrectSubjects() and getPendingDepositorMessages()
 #    2024-04-04    CS     Use context_type and context_value to find target message, and default to subject/title parsing as was used previously.
-#
+#    2024-09-09    CS     Update getLastAutoReminderDatetime() to include search on reminder-auth-to-rel
 ##
 """
 Support for automatic extracting information from send messages
@@ -256,7 +256,7 @@ class ExtractMessage(object):
         ret = None
         self.__readMsgFile(depid, contentType="notes-from-annotator", b_use_cache=b_use_cache, test_folder=test_folder)
         if len(self.__lc) >= 1:
-            ret_by_context_type = self.__selectLastMsgByContextType(["reminder"])  # CS 2024-04-04 search by context_type first
+            ret_by_context_type = self.__selectLastMsgByContextType(["reminder", "reminder-auth-to-rel"])  # CS 2024-09-09 add reminder-auth-to-rel
             if ret_by_context_type:
                 ret = ret_by_context_type
             else:

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/wwpdb/apps/msgmodule/webapp/MessagingWebApp.py

@@ -37,6 +37,7 @@
 # 2016-09-14    ZF     Added __checkGroupDeposition() function to support for group deposition
 # 2023-11-20    EP     Added __checkAnyApprovalFlags() and set approriate database flags if set
 # 2024-04-04    CS     Add process on context_type/context_value of message-to-depositor recorded by frontend JavaScript and passed here through wsgi message submit URL
+# 2024-08-30    CS     Add MessagingWebAppWorker._verifyOrConvertId() used by _propagateMsg("archive") to archive messages by PDB or EMDB IDs
 ##
 """
 wwPDB Messaging web request and response processing modules.
@@ -73,6 +74,7 @@ from wwpdb.apps.msgmodule.depict.MessagingDepict import MessagingDepict
 from wwpdb.apps.msgmodule.io.MessagingIo import MessagingIo
 from wwpdb.utils.wf.dbapi.StatusDbApi import StatusDbApi
 from wwpdb.apps.msgmodule.models.Message import Message
+from wwpdb.apps.msgmodule.util.DaInternalDb import DaInternalDb
 
 #
 # from wwpdb.apps.msgmodule.utils.WfTracking              import WfTracking
@@ -208,6 +210,9 @@ class MessagingWebAppWorker(object):
         # self.__rltvSessionPath = None
         self.__siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
         # self.__cI = ConfigInfo(self.__siteId)
+
+        # CS 2024-08-30 create class var for status DB api because such api is used multiple times
+        self.statusApi = StatusDbApi(siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
         #
         # Added by ZF
         #
@@ -881,8 +886,8 @@ class MessagingWebAppWorker(object):
             self.__reqObj.setValue("groupid", depId)
             return
         #
-        statusApi = StatusDbApi(siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
-        groupId = statusApi.getGroupId(depId)
+        # statusApi = StatusDbApi(siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
+        groupId = self.statusApi.getGroupId(depId)
         if groupId:
             self.__reqObj.setValue("groupid", groupId)
         #
@@ -1041,16 +1046,16 @@ class MessagingWebAppWorker(object):
             #
             # Added by ZF
             #
-            statusApi = StatusDbApi(siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
+            # statusApi = StatusDbApi(siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             groupId = str(self.__reqObj.getValue("groupid"))
             if groupId:
-                statusApi.runUpdate(table="batch_user_data", where={"dep_set_id": groupId.upper()}, data={"notify": p_status})
-                entryList = statusApi.getEntryIdList(groupId=groupId)
+                self.statusApi.runUpdate(table="batch_user_data", where={"dep_set_id": groupId.upper()}, data={"notify": p_status})
+                entryList = self.statusApi.getEntryIdList(groupId=groupId)
                 for entry in entryList:
-                    statusApi.runUpdate(table="deposition", where={"dep_set_id": entry}, data={"notify": p_status})
+                    self.statusApi.runUpdate(table="deposition", where={"dep_set_id": entry}, data={"notify": p_status})
                 #
             else:
-                statusApi.runUpdate(table="deposition", where={"dep_set_id": p_depId.upper()}, data={"notify": p_status})
+                self.statusApi.runUpdate(table="deposition", where={"dep_set_id": p_depId.upper()}, data={"notify": p_status})
             #
             bSuccess = True
         except:  # noqa: E722 pylint: disable=bare-except
@@ -1221,6 +1226,58 @@ class MessagingWebAppWorker(object):
     def _forwardMsg(self):
         return self._propagateMsg("forward")
 
+    def _verifyOrConvertId(self, id_to_check):  # CS 2024-08-30
+        """Verify whether an id is valid site-specific deposition id (D_##...) through DA_INTERNAL DB.
+        If the id is not a deposition id, verify whether it's PDB ID or EMDB ID, and if so, attempt to convert
+        such ids to valid deposition id, which aims to handle message archving based on PDB or EMDB ID.
+        The verification and conversion is site-id specific, and do NOT work cross sites or corss site-ids.
+        Because DA_INTERNAL DB doesn't record pdb extension id at the time this function is created,
+        extended pdb id is handled by truncate the last 4 characters for temporary use.
+
+        Args:
+            id (_type_): Deposition id, PDB ID, extended PDB ID, or EMDB ID, or any input text string as ID
+
+        Returns:
+            _type_: verfied or converted deposition id at the same site, or 'None' for invalid id input
+        """
+        id_to_check = id_to_check.strip()
+        if not id_to_check:
+            return None
+
+        logger.info("verify or convert id: %s through DA_INTERNAL DB", id_to_check)
+        db_da_internal = DaInternalDb()  # connect to DA_INTERNAL DB utility
+        id_to_check = id_to_check.upper()
+        if id_to_check.startswith("D_"):  # format of deposition id
+            dep_id = id_to_check
+            if db_da_internal.verifyDepId(dep_id):
+                logger.debug("%s is valid deposition id at this site", id_to_check)
+                return dep_id  # return the input id itself is vefified
+            else:
+                return None
+        elif id_to_check.startswith("EMD-"):  # format of EMDB ID
+            emdb_id = id_to_check
+            if db_da_internal.verifyEmdbId(emdb_id):
+                logger.debug("%s is valid EMDB ID, convert it to deposition id", id_to_check)
+                return db_da_internal.convertEmdbIdToDepId(emdb_id)  # EMDB->dep conversion
+            else:
+                return None
+        elif id_to_check.startswith("PDB_0000") and len(id_to_check) == 12:  # format of extended PDB ID
+            pdb_id = id_to_check[-4:]  # truncate the last 4 chars as temporary solution
+            if db_da_internal.verifyPdbId(pdb_id):
+                logger.debug("%s is valid extended PDB ID, convert it to deposition id", id_to_check)
+                return db_da_internal.convertPdbIdToDepId(pdb_id)  # PDB->dep conversion
+            else:
+                return None
+        elif len(id_to_check) == 4:  # format of PDB ID
+            pdb_id = id_to_check
+            if db_da_internal.verifyPdbId(pdb_id):
+                logger.debug("%s is valid PDB ID, convert it to deposition id", id_to_check)
+                return db_da_internal.convertPdbIdToDepId(pdb_id)  # PDB->dep conversion
+            else:
+                return None
+        else:  # wrong id input
+            return None
+
     def _propagateMsg(self, actionType):
         """
         :Helpers:
@@ -1229,6 +1286,7 @@ class MessagingWebAppWorker(object):
 
         """
         #
+        logger.info("start _propagateMsg with actionType = %s", actionType)
         #
         self.__getSession()
         # depId = self.__reqObj.getValue("entry_id") # getValue("identifier")
@@ -1278,17 +1336,29 @@ class MessagingWebAppWorker(object):
         #
         # Added by ZF
         #
-        statusApi = StatusDbApi(siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
+        # statusApi = StatusDbApi(siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
+
+        bOk = False  # initiate bOk in case of exit from loop below
         for depId in depIdLst:
-            self.__reqObj.setValue("identifier", depId)  # setting here for downstream processing
+            depId = depId.strip()
+            logger.debug("start processing %s", depId)
+            depId_2 = self._verifyOrConvertId(depId)  # CS 2024-08-30 verify dep id or convert PDB/EMDB ID to dep id for archiving
+            logger.debug("verified or converted id %s", depId_2)
+
+            if not depId_2:
+                logger.error("fail to verify or convert the input id %s", depId)  # skip unverified id
+                rtrnDict["success"][depId] = "false"
+                continue
+
+            self.__reqObj.setValue("identifier", depId_2)  # setting here for downstream processing
             #
-            # Added by ZF
+            # Added by ZF for GroupDep group message
             #
             groupId = ""
-            if depId.startswith("G_"):
-                groupId = depId
+            if depId_2.startswith("G_"):
+                groupId = depId_2
             else:
-                found_groupId = statusApi.getGroupId(depId)
+                found_groupId = self.statusApi.getGroupId(depId_2)
                 if found_groupId:
                     groupId = found_groupId
                 #
@@ -1299,7 +1369,8 @@ class MessagingWebAppWorker(object):
             msgObj = Message.fromReqObj(self.__reqObj, self.__verbose, self.__lfh)
             #
             if self.__verbose:
-                logger.info("dep_id is: %s", depId)
+                logger.info("original dep_id is: %s", depId)
+                logger.info("verified/converted dep_id is: %s", depId_2)
             #
             bOk, _bPdbxMdlFlUpdtd, _failedFileRefs = msgingIo.processMsg(msgObj)
             #

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/wwpdb.apps.msgmodule.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wwpdb.apps.msgmodule
-Version: 0.176.2
+Version: 0.177
 Summary: wwPDB messaging module
 Home-page: https://github.com/rcsb/py-wwpdb_apps_ann_tasks_v2
 Author: Ezra Peisach
@@ -15,8 +15,10 @@ Classifier: Programming Language :: Python :: 2.7
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.6
 Classifier: Programming Language :: Python :: 3.7
+Requires-Dist: oslo.concurrency
 Requires-Dist: wwpdb.io
 Requires-Dist: wwpdb.utils.config~=0.39
+Requires-Dist: wwpdb.utils.db
 Requires-Dist: wwpdb.utils.session
 Requires-Dist: wwpdb.utils.wf>=0.8
 Requires-Dist: mmcif

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/wwpdb.apps.msgmodule.egg-info/SOURCES.txt

@@ -22,6 +22,7 @@ wwpdb/apps/msgmodule/io/__init__.py
 wwpdb/apps/msgmodule/models/Message.py
 wwpdb/apps/msgmodule/models/__init__.py
 wwpdb/apps/msgmodule/util/AutoMessage.py
+wwpdb/apps/msgmodule/util/DaInternalDb.py
 wwpdb/apps/msgmodule/util/ExtractMessage.py
 wwpdb/apps/msgmodule/util/__init__.py
 wwpdb/apps/msgmodule/webapp/MessagingWebApp.py

{wwpdb_apps_msgmodule-0.176.2 → wwpdb_apps_msgmodule-0.177}/wwpdb.apps.msgmodule.egg-info/requires.txt

@@ -1,5 +1,7 @@
+oslo.concurrency
 wwpdb.io
 wwpdb.utils.config~=0.39
+wwpdb.utils.db
 wwpdb.utils.session
 wwpdb.utils.wf>=0.8
 mmcif