Merge pull request #29 from rcsb/development-dwp

V0.88.0 - Add copy method to PdbxContainers for copying entire categories

HISTORY.txt

@@ -88,3 +88,5 @@
 23-Feb-2024    V0.86.0 - BinaryCIF writer properly tracks integer types to ensure
                          proper types passed through encoders.  Ensure compatibility with ciftools-java and Mol*.
  6-Apr-2024    V0.87.0 - Correct internal data of PdbxContainers when rename operation is used
+24-Apr-2024    V0.88.0 - Add copy method to PdbxContainers for copying entire categories;
+                         Update rename method to fail if new category name already exists (i.e., don't allow overwrite)

mmcif/__init__.py

@@ -2,6 +2,6 @@
 __author__ = "John Westbrook"
 __email__ = "john.westbrook@rcsb.org"
 __license__ = "Apache 2.0"
-__version__ = "0.87.0"
+__version__ = "0.88.0"
 
 __apiUrl__ = "https://mmcif.wwpdb.org"

mmcif/api/PdbxContainers.py

@@ -20,6 +20,8 @@
 #    4-Apr-2018   jdw adding internal __eq__ and __hash__ methods
 #    6-Aug-2018   jdw add setters/getters for container properties
 #    5-Feb-2019   jdw add merge method and logging
+#   24-Apr-2024   dwp add copy method; update rename method to fail if new category name already exists
+#                     (i.e., don't allow overwrite)
 ##
 """
 
@@ -46,6 +48,7 @@
 
 import logging
 import sys
+import copy
 
 __docformat__ = "google en"
 __author__ = "John Westbrook"
@@ -85,7 +88,7 @@ def attributePart(name):
             if i == -1:
                 return None
             else:
-                return name[i + 1 :]
+                return name[i + 1:]
         except Exception:
             return None
 
@@ -197,15 +200,63 @@ def printIt(self, fh=sys.stdout, pType="brief"):
                 self.__objCatalog[nm].dumpIt(fh)
 
     def rename(self, curName, newName):
-        """Change the name of an object in place -"""
+        """Change the name of an object in place
+        Will fail if newName already exists or curName doesn't exist.
+
+        Args:
+            curName (str): current category name
+            newName (str): new category name
+
+        Returns:
+            (bool): True for success or False otherwise
+        """
+
         try:
+            # first check if requested new category already exists
+            if newName in self.__objNameList:
+                logger.error("Category already exists, %r", newName)
+                return False
+            # also check if current category exists
+            if curName not in self.__objNameList:
+                logger.error("Category doesn't exist, %r", curName)
+                return False
             i = self.__objNameList.index(curName)
             self.__objNameList[i] = newName
             self.__objCatalog[newName] = self.__objCatalog[curName]
             self.__objCatalog[newName].setName(newName)
             del self.__objCatalog[curName]
             return True
-        except Exception:
+        except Exception as e:
+            logger.exception("Failing with %s", str(e))
+            return False
+
+    def copy(self, curName, newName):
+        """Copy the object to a new category name.
+        Will fail if newName already exists or curName doesn't exist.
+
+        Args:
+            curName (str): current category name
+            newName (str): new category name
+
+        Returns:
+            (bool): True for success or False otherwise
+        """
+        try:
+            # first check if requested new category already exists
+            if newName in self.__objNameList:
+                logger.error("Category already exists, %r", newName)
+                return False
+            # also check if current category exists
+            if curName not in self.__objNameList:
+                logger.error("Category doesn't exist, %r", curName)
+                return False
+            # now do the copy
+            obj = copy.deepcopy(self.__objCatalog[curName])
+            obj.setName(newName)
+            self.append(obj)
+            return True
+        except Exception as e:
+            logger.exception("Failing with %s", str(e))
             return False
 
     def remove(self, curName):

mmcif/tests/testPdbxContainers.py

@@ -102,9 +102,19 @@ def testRename(self):
         self.assertIsNone(blk.getObj(newName))
 
         # Now rename
-        # Test non existant
+        # Test non existent
+        logger.info("test non-existent")
         self.assertFalse(blk.rename("noname", "othernoname"))
 
+        # Test overwrite
+        logger.info("test overwrite")
+        # First create a new category
+        self.assertTrue(blk.copy(curName, "othernoname"))
+        # Next test overwriting that name
+        self.assertFalse(blk.rename(curName, "othernoname"))
+        # Now remove that new category
+        self.assertTrue(blk.remove("othernoname"))
+
         # Expect nothing changed
         self.assertEqual(blk.getObjNameList(), [curName])
         self.assertTrue(blk.exists(curName))
@@ -122,11 +132,38 @@ def testRename(self):
         self.assertIsNone(blk.getObj(curName))
         self.assertIsNotNone(blk.getObj(newName))
 
+    def testCopy(self):
+        """Tests copy method
+        """
+        blk = self.__createContainer()
+
+        curName = "pdbx_seqtool_mapping_ref"
+        newName = "newName"
+
+        # Test non-existent copy (should Fail)
+        self.assertFalse(blk.copy("noname", "othernoname"))
+
+        # Test actual copy
+        self.assertTrue(blk.copy(curName, newName))
+        self.assertTrue(blk.exists(curName))
+        self.assertTrue(blk.exists(newName))
+
+        # Test copy to already existent destination (should Fail)
+        self.assertFalse(blk.copy(curName, newName))
+
+        # Check that things look as expected
+        self.assertEqual(blk.getObjNameList(), [curName, newName])
+        self.assertTrue(blk.exists(curName))
+        self.assertTrue(blk.exists(newName))
+        self.assertIsNotNone(blk.getObj(curName))
+        self.assertIsNotNone(blk.getObj(newName))
+
 
 def containerSuite():
     suiteSelect = unittest.TestSuite()
     suiteSelect.addTest(PdbxContainersTests("testGeneral"))
     suiteSelect.addTest(PdbxContainersTests("testRename"))
+    suiteSelect.addTest(PdbxContainersTests("testCopy"))
     return suiteSelect