wwpdb.apps.msgmodule 0.177__tar.gz → 0.178__tar.gz

{wwpdb_apps_msgmodule-0.177 → wwpdb_apps_msgmodule-0.178}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: wwpdb.apps.msgmodule
-Version: 0.177
+Version: 0.178
 Summary: wwPDB messaging module
 Home-page: https://github.com/rcsb/py-wwpdb_apps_ann_tasks_v2
 Author: Ezra Peisach
@@ -31,5 +31,14 @@ Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"
 Provides-Extra: test
 Requires-Dist: coverage; extra == "test"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 See:  README.md

{wwpdb_apps_msgmodule-0.177 → wwpdb_apps_msgmodule-0.178}/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__ = "0.177"
+__version__ = "0.178"

{wwpdb_apps_msgmodule-0.177 → wwpdb_apps_msgmodule-0.178}/wwpdb/apps/msgmodule/util/DaInternalDb.py

@@ -2,6 +2,7 @@
 # Author:  Chenghua Shao
 # Date:    2024-08-30
 # Updates:
+# 2024-12-23    CS     Add support on extended PDB ID
 #
 # =============================================================================
 """
@@ -18,13 +19,13 @@ class DaInternalDb(object):
     """DA_INTERNAL DB class for data lookup
 
     Args:
-        object (_type_): object
+        object (obj): 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.
+            siteId (str, optional): SITE ID. Defaults to None that will use the SITE ID of the current server.
         """
         self.__mydb = None
         self.__siteId = siteId
@@ -42,7 +43,7 @@ class DaInternalDb(object):
             resource (str, optional): DB name. Defaults to "DA_INTERNAL".
 
         Returns:
-            _type_: True/False for DB connection
+            bool: True/False for DB connection
         """
         self.__mydb = MyConnectionBase(siteId=self.__siteId)
         self.__mydb.setResource(resourceName=resource)
@@ -65,10 +66,10 @@ class DaInternalDb(object):
         """Simplified query runner
 
         Args:
-            query (_type_): Full text of a query
+            query (str): Full text of a query
 
         Returns:
-            _type_: raw query results as tuple of tuples, e.g. ((1,2),(3,4))
+            tuple: raw query results as tuple of tuples, e.g. ((1,2),(3,4))
         """
         cur = self.__mydb.getCursor()
         cur.execute(query)
@@ -80,10 +81,10 @@ class DaInternalDb(object):
         """Verify if an id is deposition id
 
         Args:
-            dep_id (_type_): presumed dep id input
+            dep_id (str): presumed dep id input
 
         Returns:
-            _type_: True/False
+            bool: True/False
         """
         query = "select structure_id from rcsb_status where structure_id = '%s'" % dep_id
         rows = self.run(query)
@@ -96,10 +97,10 @@ class DaInternalDb(object):
         """Verify if an id is PDB ID
 
         Args:
-            pdb_id (_type_): presumed PDB id input
+            pdb_id (str): presumed PDB id input
 
         Returns:
-            _type_: True/False
+            bool: True/False
         """
         query = "select structure_id from rcsb_status where pdb_id = '%s'" % pdb_id
         rows = self.run(query)
@@ -108,14 +109,30 @@ class DaInternalDb(object):
         else:
             return False
 
+    def verifyExtendedPdbId(self, pdb_ext_id):
+        """Verify if an id is extended PDB ID
+
+        Args:
+            pdb_ext_id (str): presumed extended PDB id input
+
+        Returns:
+            bool: True/False
+        """
+        query = "select structure_id from database_2 where database_id = 'PDB' and pdbx_database_accession = '%s'" % pdb_ext_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
+            emdb_id (str): presumed EMDB ID input
 
         Returns:
-            _type_: True/False
+            bool: True/False
         """
         query = "select structure_id from database_2 where database_id = 'EMDB' and database_code = '%s'" % emdb_id
         rows = self.run(query)
@@ -128,10 +145,10 @@ class DaInternalDb(object):
         """Convert PDB ID to deposition id
 
         Args:
-            pdb_id (_type_): presumed PDB ID
+            pdb_id (str): presumed PDB ID
 
         Returns:
-            _type_: valid deposition id at this site, or None
+            str: 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)
@@ -140,14 +157,30 @@ class DaInternalDb(object):
         else:
             return None
 
+    def convertExtendedPdbIdToDepId(self, pdb_ext_id):
+        """Convert extended PDB ID to deposition id
+
+        Args:
+            pdb_id (str): presumed PDB ID
+
+        Returns:
+            str: valid deposition id at this site, or None
+        """
+        query = "select structure_id from database_2 where database_id = 'PDB' and pdbx_database_accession = '%s'" % pdb_ext_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
+            pdb_id (str): presumed EMDB ID
 
         Returns:
-            _type_: valid deposition id at this site, or None
+            str: 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)

{wwpdb_apps_msgmodule-0.177 → wwpdb_apps_msgmodule-0.178}/wwpdb/apps/msgmodule/webapp/MessagingWebApp.py

@@ -38,6 +38,7 @@
 # 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
+# 2024-12-23    CS     Add support on extended PDB ID for _verifyOrConvertId() to convert ID for archiving
 ##
 """
 wwPDB Messaging web request and response processing modules.
@@ -1250,28 +1251,32 @@ class MessagingWebAppWorker(object):
         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)
+                logger.debug("%s is valid deposition id at this site", dep_id)
                 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)
+                logger.debug("%s is valid EMDB ID, convert it to deposition id", emdb_id)
                 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
+        elif id_to_check.startswith("PDB_") 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
+            pdb_ext_id = id_to_check
+            if db_da_internal.verifyExtendedPdbId(pdb_ext_id):
+                logger.debug("%s is valid extended PDB ID, convert it to deposition id", pdb_ext_id)
+                return db_da_internal.convertExtendedPdbIdToDepId(pdb_ext_id)  # PDB extended->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)
+                logger.debug("%s is valid PDB ID, convert it to deposition id", pdb_id)
                 return db_da_internal.convertPdbIdToDepId(pdb_id)  # PDB->dep conversion
             else:
                 return None

{wwpdb_apps_msgmodule-0.177 → wwpdb_apps_msgmodule-0.178}/wwpdb.apps.msgmodule.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: wwpdb.apps.msgmodule
-Version: 0.177
+Version: 0.178
 Summary: wwPDB messaging module
 Home-page: https://github.com/rcsb/py-wwpdb_apps_ann_tasks_v2
 Author: Ezra Peisach
@@ -31,5 +31,14 @@ Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"
 Provides-Extra: test
 Requires-Dist: coverage; extra == "test"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 See:  README.md