wwpdb.apps.ccmodule 0.26__tar.gz → 0.27__tar.gz

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wwpdb.apps.ccmodule
-Version: 0.26
+Version: 0.27
 Summary: wwPDB workflow engine utils
 Home-page: https://github.com/rcsb/py-wwpdb_apps_wf_engine_utils
 Author: Ezra Peisach

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/__init__.py

@@ -3,4 +3,4 @@ __docformat__ = "restructuredtext en"
 __author__ = "Ezra Peisach"
 __email__ = "ezra.peisach@rcsb.org"
 __license__ = "Apache 2.0"
-__version__ = "0.26"
+__version__ = "0.27"

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/chem/ChemCompAssign.py

@@ -166,9 +166,9 @@ class ChemCompAssign(object):
             self.__ccReportPath = os.path.join(self.__sessionPath, 'assign')
         elif context == 'deposition':
             self.__depId = self.__reqObj.getValue('identifier')
-            self.__depositPath = Path(PathInfo().getDepositPath(self.__depId)).parent
-            self.__modelDirPath = os.path.join(self.__depositPath, self.__depId)
-            self.__ccReportPath = os.path.join(self.__depositPath, self.__depId, self._CC_REPORT_DIR)
+            depositPath = Path(PathInfo().getDepositPath(self.__depId))
+            self.__modelDirPath = os.path.join(depositPath)
+            self.__ccReportPath = os.path.join(depositPath, self._CC_REPORT_DIR)
 
         self.normal = ['ALA', 'CYS', 'ASP', 'GLU', 'PHE', 'GLY', 'HIS', 'ILE',
                        'LYS', 'LEU', 'MET', 'ASN', 'PRO', 'GLN', 'ARG', 'SER',

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/chem/ChemCompAssignDepict.py

@@ -101,6 +101,7 @@ from wwpdb.apps.ccmodule.depict.ChemCompDepict import ChemCompDepict
 # from wwpdb.apps.ccmodule.chem.PdbxChemCompAssign import PdbxCategoryDefinition
 from wwpdb.apps.ccmodule.io.ChemCompAssignDataStore import ChemCompAssignDataStore
 from wwpdb.utils.config.ConfigInfo import ConfigInfo
+from wwpdb.utils.config.ConfigInfoApp import ConfigInfoAppCc
 from wwpdb.utils.oe_util.oedepict.OeDepict import OeDepict
 from wwpdb.utils.oe_util.build.OeBuildMol import OeBuildMol
 
@@ -123,6 +124,7 @@ class ChemCompAssignDepict(ChemCompDepict):
         self.__debug = True
         #
         self.__cI = ConfigInfo()
+        self.__cIAppCc = ConfigInfoAppCc(verbose=self.__verbose, log=self.__lfh)
         #
         # self.__cDict = PdbxCategoryDefinition._cDict
         #
@@ -382,6 +384,8 @@ class ChemCompAssignDepict(ChemCompDepict):
         #
         oL = []
         #
+        if self.__cIAppCc.get_extended_ccd_supp():
+            oL.append('<script>max_ccd_width = 5;</script>\n')
         oL.append('<div id="cc_entity_browser">\n<h4>Browse Chem Components by Entity Group</h4>\n<div id="pagi" class="noprint fltlft"></div>\n<br class="clearfloat" />\n')
         oL.append('<div id="cc_entity_browse_content">\n')
         i = 0
@@ -531,6 +535,12 @@ class ChemCompAssignDepict(ChemCompDepict):
         ##
         ############################################################
         #
+        # CCD ID width expansion
+        if self.__cIAppCc.get_extended_ccd_supp():
+            lclDict['max_ccd_width'] = '5'
+        else:
+            lclDict['max_ccd_width'] = '3'
+
         # ######## Rerun Search handling ############################
         ##
         lclDict['link_radius_dlta'] = p_ccAssgnDataStr.getGlblRerunSrchParam_lnkRadii(p_authAssignedGrp)
@@ -628,6 +638,11 @@ class ChemCompAssignDepict(ChemCompDepict):
         #
         #######################################################################################################################################################
         #######################################################################################################################################################
+        if self.__cIAppCc.get_extended_ccd_supp():
+            p_hlprDict['max_ccd_width'] = '5'
+        else:
+            p_hlprDict['max_ccd_width'] = '3'
+
         p_hlprDict['top_hit_ccid'] = topHitCcId
         p_hlprDict['2dpath_labld_w_hy_ref'] = os.path.join(self.rltvSessionPath, 'assign', instId, 'image', topHitCcId + '_Big.svg')
         # p_hlprDict['2dpath_labld_w_hy_ref'] = os.path.join(self.rltvSessionPath, 'assign', 'rfrnc_reports', topHitCcId, topHitCcId + '_D3L3.gif')

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/chem/ChemCompAssignDepictLite.py

@@ -124,10 +124,8 @@ class ChemCompAssignDepictLite(ChemCompDepict):
 
         self.__alternateTopHitMarkup = '''<input id="use_exact_mtch_id_%(auth_assgnd_grp)s_%(tophit_id)s" class="c_%(auth_assgnd_grp)s addrss_msmtch use_exact_mtch_id" type="radio" name="addrss_msmtch_chc" value="use_exact_mtch_id" %(use_exact_mtch_id_checked)s %(disabled)s /><label for="use_exact_mtch_id_%(auth_assgnd_grp)s_%(tophit_id)s">Use exact match ID of <span name="%(tophit_id)s" style="color: #F00;" class="strong tophit">%(tophit_id)s</span> (<a href="http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=%(tophit_id)s&operation=ccid" target="_blank">See Definition</a>) instead of originally proposed ID</label><br />'''  # noqa: E501
 
-        print("XXXX", self.__depId)
-        self.__depositPath = Path(PathInfo().getDepositPath(self.__depId)).parent
-        self.__ccReportPath = os.path.join(self.__depositPath, self.__depId, self._CC_REPORT_DIR)
-        # self.__depositAssignPath = os.path.join(self.__depositPath, self.__depId, self._CC_ASSIGN_DIR)
+        depositPath = Path(PathInfo().getDepositPath(self.__depId))
+        self.__ccReportPath = os.path.join(depositPath, self._CC_REPORT_DIR)
         self.__logger = self._setupLog(log)
 
     ################################################################################################################

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/reports/ChemCompReports.py

@@ -72,8 +72,8 @@ class ChemCompReport(object):
             self.__ccReportPath = os.path.join(self.__sessionPath, 'assign')
         elif context == 'deposition':
             self.__depId = self.__reqObj.getValue('identifier').upper()
-            self.__depositPath = Path(PathInfo().getDepositPath(self.__depId)).parent
-            self.__ccReportPath = os.path.join(self.__depositPath, self.__depId, 'cc_analysis')
+            depositPath = Path(PathInfo().getDepositPath(self.__depId))
+            self.__ccReportPath = os.path.join(depositPath, 'cc_analysis')
 
     def __getContext(self):
         filesource = self.__reqObj.getValue('filesource')

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/sketch/ChemCompSketch.py

@@ -21,6 +21,7 @@ import shutil
 from wwpdb.apps.ccmodule.utils.ChemCompConfig import ChemCompConfig
 from wwpdb.apps.ccmodule.io.ChemCompIo import ChemCompReader
 from wwpdb.apps.ccmodule.extract.ccOps import ccOps
+from wwpdb.io.locator.ChemRefPathInfo import ChemRefPathInfo
 
 
 class ChemCompSketch(object):
@@ -76,9 +77,10 @@ class ChemCompSketch(object):
     def __getFilePathFromId(self, ccId):
         """
         """
-        idUc = str(ccId).upper()
-        fileName = idUc + ".cif"
-        self.__ccFilePath = os.path.join(self.__ccConfig.getPath('chemCompCachePath'), idUc[0:1], idUc[0:3], fileName)
+        siteid = self.__reqObj.getValue("WWPDB_SITE_ID")
+        crpi = ChemRefPathInfo(siteid, verbose=self.__verbose, log=self.__lfh)
+
+        self.__ccFilePath = crpi.getFilePath(ccId, "CC")
         #
         if (not os.access(self.__ccFilePath, os.R_OK)):
             return False

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/utils/ChemCompConfig.py

@@ -59,7 +59,6 @@ class ChemCompConfig(object):
         # RPS 2011-11-29 --- use of above symbolic links for archBinPath and archDataPath being superseded by paths determined via calls to ConfigInfo
         self.__ccAppsBinPath = os.path.join(self.__cICommon.get_site_cc_apps_path(), "bin")
         self.__ccDictPath = self.__cIAppCc.get_site_cc_dict_path()
-        self.__ccCvsPath = self.__cIAppCc.get_site_cc_cvs_path()
         self.__oeLicenseFilePath = self.__cICommon.get_site_cc_oe_licence()
         self.__oeDirPath = self.__cICommon.get_site_cc_oe_dir()
 
@@ -68,7 +67,6 @@ class ChemCompConfig(object):
             self.__lfh.write("+ChemCompConfig.__init() --------------------------------------------------------------------------\n")
             self.__lfh.write("+ChemCompConfig.__init() ------ self.__ccAppsBinPath is: %s \n" % self.__ccAppsBinPath)
             self.__lfh.write("+ChemCompConfig.__init() ------ self.__ccDictPath is: %s \n" % self.__ccDictPath)
-            self.__lfh.write("+ChemCompConfig.__init() ------ self.__ccCvsPath is: %s \n" % self.__ccCvsPath)
             self.__lfh.write("+ChemCompConfig.__init() --------------------------------------------------------------------------\n")
         #
         # Place holders for working path info -
@@ -147,8 +145,8 @@ class ChemCompConfig(object):
         # elif (type == "sandboxPathV2"):
         #    return os.path.join("/data/components/ligand-dict-v1")
         #
-        elif (type == "sandboxPathV3" or type == "chemCompCachePath"):
-            return self.__ccCvsPath
+        # elif (type == "sandboxPathV3" or type == "chemCompCachePath"):
+        #    return self.__ccCvsPath
         elif (type == "fpPatternPath"):
             return self.__cICommon.get_cc_fp_patterns()
         elif (type == "serializedCcDictPath"):

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/utils/ChemCompDpUtility.py

@@ -57,9 +57,9 @@ class ChemCompDpUtility(object):
         siteId = str(self._reqObj.getValue("WWPDB_SITE_ID"))
 
         self._ccRefPathInfo = ChemRefPathInfo(siteId, verbose=self._verbose, log=self._lfh)
-        self._depositPath = Path(PathInfo().getDepositPath(self._depId)).parent
-        self._ccReportPath = os.path.join(self._depositPath, self._depId, self._CC_REPORT_DIR)
-        self._depositAssignPath = os.path.join(self._depositPath, self._depId, self._CC_ASSIGN_DIR)
+        depositPath = Path(PathInfo().getDepositPath(self._depId))
+        self._ccReportPath = os.path.join(depositPath, self._CC_REPORT_DIR)
+        self._depositAssignPath = os.path.join(depositPath, self._CC_ASSIGN_DIR)
         self._ligState = LigandAnalysisState(self._depId, self._verbose, self._lfh)
 
     def doAnalysis(self):
@@ -552,7 +552,8 @@ class ChemCompDpUtility(object):
                 self._logger.warning('---- WARNING ---- No path obtained for CC assign details export file, id %s', depId)
 
             # chem comp depositor progress file
-            pathDict['dpstrPrgrssFileFlPth'] = os.path.join(self._depositPath, depId, 'cc-dpstr-progress')
+            depositPath = Path(PathInfo().getDepositPath(depId))
+            pathDict['dpstrPrgrssFileFlPth'] = os.path.join(depositPath, 'cc-dpstr-progress')
             pathDict['dpstrPrgrssFileDirPth'] = os.path.split(pathDict['dpstrPrgrssFileFlPth'])[0]
 
             if (self._verbose):

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/utils/LigandAnalysisState.py

@@ -28,8 +28,8 @@ class LigandAnalysisState:
 
         self._cI = ConfigInfo()
         self._depId = depId
-        self._depositPath = Path(PathInfo().getDepositPath(self._depId)).parent
-        self._ccReportPath = os.path.join(self._depositPath, self._depId, 'cc_analysis')
+        depositPath = Path(PathInfo().getDepositPath(self._depId))
+        self._ccReportPath = os.path.join(depositPath, 'cc_analysis')
         self._ccStateFilePath = os.path.join(self._ccReportPath, self._CC_STATE_FILE)
 
         self._progress = 0

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/view/ChemCompViewDepict.py

@@ -56,8 +56,8 @@ class ChemCompViewDepict(ChemCompDepict):
         #
         checked = ''
         #
-        sPathRel = os.path.join(self.rltvSessionPath, ccId)
-        sPathAbslt = os.path.join(self.absltSessionPath, ccId)
+        sPathRel = os.path.join(self.rltvAssgnSessionPath, ccId)
+        sPathAbslt = os.path.join(self.absltAssgnSessionPath, ccId)
         #
         p_ccDict['sess_path_rel'] = sPathRel
         p_ccDict['jmol_code_base'] = self.jmolCodeBase

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/webapp/ChemCompWebApp.py

@@ -166,7 +166,7 @@ from wwpdb.apps.ccmodule.io.ChemCompDataExport import ChemCompDataExport
 from wwpdb.apps.ccmodule.io.ChemCompIo import ChemCompReader
 #
 from wwpdb.utils.config.ConfigInfo import ConfigInfo
-from wwpdb.utils.config.ConfigInfoApp import ConfigInfoAppCommon
+from wwpdb.utils.config.ConfigInfoApp import ConfigInfoAppCommon, ConfigInfoAppCc
 #
 from wwpdb.io.file.mmCIFUtil import mmCIFUtil
 #
@@ -298,6 +298,7 @@ class ChemCompWebAppWorker(object):
         self.__rltvSessionPath = None
         self.__siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
         self.__cI = ConfigInfo(self.__siteId)
+        self.__cIAppCc = ConfigInfoAppCc(self.__siteId, verbose=self.__verbose, log=self.__lfh)
         self.__modelFilePath = None
         #
         self.__pathInstncsVwTmplts = "templates/workflow_ui/instances_view"
@@ -623,6 +624,11 @@ class ChemCompWebAppWorker(object):
         myD['instance'] = wfInstId
         myD['pdbid'] = str(self.__reqObj.getValue("pdbid"))
         myD['annotator'] = str(self.__reqObj.getValue("annotator"))
+        # CCD ID width expansion
+        if self.__cIAppCc.get_extended_ccd_supp():
+            myD['max_ccd_width'] = '5'
+        else:
+            myD['max_ccd_width'] = '3'
         #
         myD['session_url_prefix'] = os.path.join(self.__rltvSessionPath, "assign", instanceId)
         myD['processing_site'] = self.__cI.get('SITE_NAME').upper()

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/webapp/ChemCompWebAppLite.py

@@ -248,9 +248,6 @@ class ChemCompWebAppLiteWorker(object):
         # self.__siteConfigDir = self.__cI.get('TOP_WWPDB_SITE_CONFIG_DIR')
         # self.__siteLoc = self.__cI.get('WWPDB_SITE_LOC')
         self.__pathInfo = PathInfo()
-        self.__depositPath = Path(self.__pathInfo.getDepositPath(self.__depId)).parent
-        # self.__depositAssignPath = os.path.join(self.__depositPath, self.__depId, 'assign')
-        # self.__ccReportPath = os.path.join(self.__depositPath, self.__depId, 'cc_analysis')  # should we add 'cc_analysis' in a variable in site-config?
         self.__logger = self._setupLog(log)
 
         #
@@ -380,7 +377,8 @@ class ChemCompWebAppLiteWorker(object):
         ligandId = self.__reqObj.getValue("ligid")
         filename = self.__reqObj.getValue("file")
 
-        ccReportPath = os.path.join(self.__depositPath, depId, "cc_analysis")
+        depositPath = Path(self.__pathInfo.getDepositPath(depId))
+        ccReportPath = os.path.join(depositPath, "cc_analysis")
         fileType = filename.split(".")[-1]
         filePath = None
 

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb.apps.ccmodule.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wwpdb.apps.ccmodule
-Version: 0.26
+Version: 0.27
 Summary: wwPDB workflow engine utils
 Home-page: https://github.com/rcsb/py-wwpdb_apps_wf_engine_utils
 Author: Ezra Peisach

{wwpdb.apps.ccmodule-0.26 → wwpdb.apps.ccmodule-0.27}/wwpdb.apps.ccmodule.egg-info/SOURCES.txt

@@ -18,9 +18,6 @@ wwpdb/apps/ccmodule/chem/PdbxChemCompAssign.py
 wwpdb/apps/ccmodule/chem/__init__.py
 wwpdb/apps/ccmodule/depict/ChemCompDepict.py
 wwpdb/apps/ccmodule/depict/__init__.py
-wwpdb/apps/ccmodule/edit/ChemCompTableEditor.py
-wwpdb/apps/ccmodule/edit/ChemCompTableEditorDepict.py
-wwpdb/apps/ccmodule/edit/__init__.py
 wwpdb/apps/ccmodule/extract/__init__.py
 wwpdb/apps/ccmodule/extract/ccOps.py
 wwpdb/apps/ccmodule/io/ChemCompAssignDataStore.py

wwpdb.apps.ccmodule-0.26/wwpdb/apps/ccmodule/edit/ChemCompTableEditor.py

@@ -1,384 +0,0 @@
-##
-# File:  ChemCompTableEditor.py
-# Date:  21-Aug-2010
-#
-# Updates:
-#  1-Sep-2010    jdw   New incremental storage of edits using ChemCompEditStore()
-#  2012-10-24    RPS    Updated to reflect reorganization of modules in pdbx packages#
-##
-"""
-Chemical component text edit functions.
-
-"""
-__docformat__ = "restructuredtext en"
-__author__ = "John Westbrook"
-__email__ = "jwest@rcsb.rutgers.edu"
-__license__ = "Creative Commons Attribution 3.0 Unported"
-__version__ = "V0.01"
-
-import os
-import sys
-import shutil
-import traceback
-from wwpdb.apps.ccmodule.utils.ChemCompConfig import ChemCompConfig
-from mmcif_utils.chemcomp.PdbxChemCompUtils import PdbxChemCompReader, PdbxChemCompUpdater
-#
-from wwpdb.apps.ccmodule.io.ChemCompEditStore import ChemCompEditStore, ChemCompEdit
-#
-# temporary -
-# from wwpdb.apps.ccmodule.io.ccIo                 import ccIo
-
-
-class ChemCompTableEditor(object):
-    """Chemical component table/text edit functions.
-
-    """
-    def __init__(self, reqObj, verbose=False, log=sys.stderr):
-        """Chemical component text edit functions -
-
-         :param `verbose`:  boolean flag to activate verbose logging.
-         :param `log`:      stream for logging.
-
-        """
-        self.__verbose = verbose
-        self.__lfh = log
-        # self.__debug = True
-        #
-        self.__reqObj = reqObj
-        #
-        self.__sObj = self.__reqObj.newSessionObj()
-        self.__sessionPath = self.__sObj.getPath()
-        self.__sessionRelativePath = self.__sObj.getRelativePath()
-        self.__sessionId = self.__sObj.getId()
-        #
-        self.__ccConfig = ChemCompConfig(self.__reqObj, verbose=self.__verbose, log=self.__lfh)
-        #
-        self.__ccId = None
-        self.__ccFilePath = None
-        self.__ccFileFormat = 'cif'
-        #
-        #
-
-    def setCcId(self, ccId):
-        """Set an existing chemical component identifier in archive collection as
-           the edit target
-        """
-        self.__ccId = str(ccId.upper())
-        return self.__getFilePathFromId(self.__ccId)
-
-    def setFilePath(self, ccFilePath, ccFileFormat='cif', ccId=None):
-        self.__ccFilePath = ccFilePath
-        self.__ccFileFormat = ccFileFormat
-        if not os.access(self.__ccFilePath, os.R_OK):
-            return False
-        if ccId is not None:
-            self.__ccId = str(ccId).upper()
-        #
-        return True
-
-    def getFilePath(self):
-        return self.__ccFilePath
-
-    def __getFilePathFromId(self, ccId):
-        """
-        """
-        idUc = str(ccId).upper()
-        fileName = idUc + ".cif"
-        self.__ccFilePath = os.path.join(self.__ccConfig.getPath('chemCompCachePath'), idUc[0:1], idUc[0:3], fileName)
-        #
-        if not os.access(self.__ccFilePath, os.R_OK):
-            return False
-        self.__ccFileFormat = 'cif'
-        return True
-
-    def doUndo(self):
-        """  Process an undo edit request.
-        """
-        rD = {}
-        #
-        # id = self.__reqObj.getValue('id')
-        blockId = self.__reqObj.getValue('blockId')
-        #
-        # edit number controlled from edit store -
-        editToUndo = self.__reqObj.getValue('editOpNumber')
-        #
-        if self.__verbose:
-            self.__lfh.write("+ChemCompEdit.doUndo() - Starting doUndo() \n")
-            self.__lfh.write("+ChemCompEdit.doUndo() - session id    %s\n" % self.__sessionId)
-            self.__lfh.write("+ChemCompEdit.doUndo() - block id      %s\n" % blockId)
-            self.__lfh.write("+ChemCompEdit.doUndo() - edit to undo  %r\n" % editToUndo)
-            self.__lfh.flush()
-
-        #
-        es = ChemCompEditStore(self.__reqObj, verbose=self.__verbose, log=self.__lfh)
-        editOpLast = es.getLastOpNumber()
-        #
-        if self.__verbose:
-            self.__lfh.write("+ChemCompEdit.doUndo() - last stored edit operation %d\n" % editOpLast)
-        #
-        edNo = int(editToUndo)
-        edList = es.get(edNo)
-        undoList = []
-        for ed in edList:
-            if (ed.getEditType() == "replace-value"):
-                targetId = "#" + ed.getTargetId()
-                priorValue = ed.getValuePrevious()
-                undoList.append({'id' : targetId, 'value' : priorValue})
-            else:
-                ed.printIt(self.__lfh)
-
-        es.remove(edNo)
-        #
-        ok = True
-        if not ok:
-            rD['errortext'] = 'edit failed during update'
-            rD['errorflag'] = True
-            rD['value'] = None
-            rD['editOpNumber'] = edNo - 1
-        else:
-            rD['editOpNumber'] = edNo - 1
-            rD['id'] = None
-            rD['value'] = None
-            rD['valuelist'] = undoList
-
-        #
-        return rD
-
-    def doItemValueUpdate(self):
-        """  Process an item value edit.update request.
-        """
-        rD = {}
-        #
-        id = self.__reqObj.getValue('id')  # pylint: disable=redefined-builtin
-        blockId = self.__reqObj.getValue('blockId')
-        value = self.__reqObj.getValue('value')
-        priorValue = self.__reqObj.getValue('priorValue')
-        localPath = self.__reqObj.getValue('localPath')
-        targetRowId = self.__reqObj.getValue('targetRowId')
-        #
-        # edit number controlled from edit store -
-        editNumberReported = self.__reqObj.getValue('editOpNumber')
-        #
-        if self.__verbose:
-            self.__lfh.write("+ChemCompEdit.doItemValueUpdate() - Starting doItemValueUpdate() \n")
-            self.__lfh.write("+ChemCompEdit.doItemValueUpdate() - session id    %s\n" % self.__sessionId)
-            self.__lfh.write("+ChemCompEdit.doItemValueUpdate() - local path    %s\n" % localPath)
-            self.__lfh.write("+ChemCompEdit.doItemValueUpdate() - id            %s\n" % id)
-            self.__lfh.write("+ChemCompEdit.doItemValueUpdate() - block id      %s\n" % blockId)
-            self.__lfh.write("+ChemCompEdit.doItemValueUpdate() - value         %s\n" % value)
-            self.__lfh.write("+ChemCompEdit.doItemValueUpdate() - prior value   %s\n" % priorValue)
-            self.__lfh.write("+ChemCompEdit.doItemValueUpdate() - target row id %s\n" % targetRowId)
-            self.__lfh.write("+ChemCompEdit.doItemValueUpdate() - editNumber    %r\n" % editNumberReported)
-            self.__lfh.flush()
-
-        (catName, attributeName, _sRow, _insertCode, _opNum) = id.split(':')
-        # iRow = int(sRow)
-        itemName = '_' + catName + '.' + attributeName
-        #
-        #
-        es = ChemCompEditStore(self.__reqObj, verbose=self.__verbose, log=self.__lfh)
-        #
-        editOpLast = es.getLastOpNumber()
-        editOpNext = int(editOpLast) + 1
-
-        ccEd = ChemCompEdit(self.__verbose, self.__lfh)
-        #
-        ccEd.setTargetId(id)
-        ccEd.setBlockId(blockId)
-        ccEd.setTargetRowId(targetRowId)
-        ccEd.setEditType("replace-value")
-        ccEd.setEditOpNumber(editOpNext)
-        #
-        ccEd.setTargetItemName(itemName)
-        ccEd.setValueNew(value)
-        ccEd.setValuePrevious(priorValue)
-
-        ok = es.storeEdit(ccEd)
-        if not ok:
-            rD['errortext'] = 'edit failed during update'
-            rD['errorflag'] = True
-            rD['value'] = priorValue
-            rD['editOpNumber'] = editNumberReported
-        else:
-            rD['editOpNumber'] = editOpNext
-            rD['value'] = value
-            rD['valuelist'] = [{'id': id, 'value': value}, {'id': id, 'value': value}]
-
-        #
-        return rD
-
-    # def __getRowDefault(self, catName):
-    #     """ Provide a
-    #     """
-    #     # rD = {}
-    #     pass
-
-    def doRowUpdate(self):
-        """  Process a row edit update request -
-        """
-        rD = {}
-        id = self.__reqObj.getValue('id')  # pylint: disable=redefined-builtin
-        value = self.__reqObj.getValue('value')
-        blockId = self.__reqObj.getValue('blockId')
-        priorValue = self.__reqObj.getValue('priorValue')
-        localPath = self.__reqObj.getValue('localPath')
-        targetRowId = self.__reqObj.getValue('targetRowId')
-        editNumberReported = self.__reqObj.getValue('editOpNumber')
-        #
-        if self.__verbose:
-            self.__lfh.write("+ChemCompEdit.doRowUpdate() - Starting doUpdate() \n")
-            self.__lfh.write("+ChemCompEdit.doRowUpdate() - session id    %s\n" % self.__sessionId)
-            self.__lfh.write("+ChemCompEdit.doRowUpdate() - local path    %s\n" % localPath)
-            self.__lfh.write("+ChemCompEdit.doRowUpdate() - id            %s\n" % id)
-            self.__lfh.write("+ChemCompEdit.doRowUpdate() - block id      %s\n" % blockId)
-            self.__lfh.write("+ChemCompEdit.doRowUpdate() - value         %s\n" % value)
-            self.__lfh.write("+ChemCompEdit.doRowUpdate() - prior value   %s\n" % priorValue)
-            self.__lfh.write("+ChemCompEdit.doRowUpdate() - target row id %s\n" % targetRowId)
-            self.__lfh.write("+ChemCompEdit.doRowUpdate() - editNumber    %r\n" % editNumberReported)
-            self.__lfh.flush()
-
-        try:
-            rD['editOpNumber'] = int(editOpNumber) + 1  # noqa: F821  XXXX This might be editOpeNumberReported - what are implications?  pylint: disable=undefined-variable
-        except:  # noqa: E722 pylint: disable=bare-except
-            rD['editOpNumber'] = 1
-
-        rD['value'] = '+/-'
-        rD['op'] = value
-
-        (catName, opName, sRow, insertCode, sOpNum) = id.split(':')
-        iRow = int(sRow)
-        opNum = int(sOpNum)
-
-        rD['id'] = '#%s:%s:%d:%s:%d' % (catName, opName, iRow, insertCode, opNum)
-
-        if True:  # pylint: disable=using-constant-test
-            return rD
-
-        ccU = PdbxChemCompUpdater(verbose=self.__verbose, log=self.__lfh)
-        ok = ccU.readComp(localPath, compId=None)
-        if not ok:
-            rD['errortext'] = 'update file not found'
-            rD['errorflag'] = True
-
-        ok = ccU.updateItem(itemName, value, iRow)  # noqa: F821  XXXX This code clearly not used as cannot work pylint: disable=undefined-variable
-        if not ok:
-            rD['errortext'] = 'item update failed'
-            rD['errorflag'] = True
-
-        ok = ccU.write()
-        if not ok:
-            rD['errortext'] = 'write failed during update'
-            rD['errorflag'] = True
-
-        #
-        return rD
-
-    def doEdit(self):
-        """ Return content to launch the chemical component editor -
-        """
-        #
-        oD = {}
-        oD['dataDict'] = {}
-        filePath = self.__ccFilePath
-        fileFormat = self.__ccFileFormat
-        blockId = self.__ccId
-        #
-        editOpNumber = 0
-        if self.__verbose:
-            self.__lfh.write("+ChemCompEdit.doEdit() - Starting doEdit() \n")
-            self.__lfh.write("+ChemCompEdit.doEdit() - file path    %s\n" % filePath)
-            self.__lfh.write("+ChemCompEdit.doEdit() - file format  %s\n" % fileFormat)
-            self.__lfh.write("+ChemCompEdit.doEdit() - block Id     %s\n" % blockId)
-            self.__lfh.flush()
-        #
-        #
-        # make a local copy of the file (if required)
-        #
-        (_pth, fileName) = os.path.split(filePath)
-        dirPath = os.path.join(self.__sessionPath, 'edit')
-        localPath = os.path.join(dirPath, fileName)
-        localRelativePath = os.path.join(self.__sessionRelativePath, 'edit', fileName)
-        if filePath != localPath:
-            if not os.access(dirPath, os.F_OK):
-                os.makedirs(dirPath)
-            shutil.copyfile(filePath, localPath)
-            #
-            if self.__verbose:
-                self.__lfh.write("+ChemCompEdit.doEdit() - Copied input file %s to edit session path %s \n"
-                                 % (filePath, localPath))
-                self.__lfh.flush()
-        #
-        # Path context --
-
-        oD['filePath'] = filePath
-        oD['localPath'] = localPath
-        oD['localRelativePath'] = localRelativePath
-        oD['sessionId'] = self.__sessionId
-        oD['editOpNumber'] = editOpNumber
-        #
-        try:
-            ccf = PdbxChemCompReader(verbose=self.__verbose, log=self.__lfh)
-            ccf.setFilePath(localPath, compId=blockId)
-            ccf.getComp()
-            oD['blockId'] = ccf.getBlockId()
-            for catName in ['chem_comp', 'chem_comp_atom', 'chem_comp_bond']:
-                oD['dataDict'][catName] = ccf.getChemCompCategory(catName=catName)
-        except:  # noqa: E722 pylint: disable=bare-except
-            if (self.__verbose):
-                self.__lfh.write("+ChemCompEdit.doEdit() - edit preparation failed for:  %s\n" % fileName)
-                traceback.print_exc(file=self.__lfh)
-                self.__lfh.flush()
-            return oD
-
-        return oD
-
-    def doLiveUpdate(self):
-        """  Process an edit update request.
-        """
-        rD = {}
-        id = self.__reqObj.getValue('id')  # pylint: disable=redefined-builtin
-        value = self.__reqObj.getValue('value')
-        priorValue = self.__reqObj.getValue('priorValue')
-        localPath = self.__reqObj.getValue('localPath')
-        editOpNumber = self.__reqObj.getValue('editOpNumber')
-        if self.__verbose:
-            self.__lfh.write("+ChemCompEdit.doUpdate() - Starting doUpdate() \n")
-            self.__lfh.write("+ChemCompEdit.doUpdate() - local path    %s\n" % localPath)
-            self.__lfh.write("+ChemCompEdit.doUpdate() - id            %s\n" % id)
-            self.__lfh.write("+ChemCompEdit.doUpdate() - value         %s\n" % value)
-            self.__lfh.write("+ChemCompEdit.doUpdate() - prior value   %s\n" % priorValue)
-            self.__lfh.write("+ChemCompEdit.doUpdate() - editOpNumber  %r\n" % editOpNumber)
-            self.__lfh.flush()
-        try:
-            rD['editOpNumber'] = int(editOpNumber) + 1
-        except:  # noqa: E722 pylint: disable=bare-except
-            rD['editOpNumber'] = 1
-
-        rD['value'] = value
-        rD['valuelist'] = [{'id': id, 'value': value}, {'id': id, 'value': value}]
-        (catName, attributeName, sRow, _insertCode, _opNum) = id.split(':')
-        iRow = int(sRow)
-        itemName = '_' + catName + '.' + attributeName
-
-        ccU = PdbxChemCompUpdater(verbose=self.__verbose, log=self.__lfh)
-        ok = ccU.readComp(localPath, compId=None)
-        if not ok:
-            rD['errortext'] = 'update file not found'
-            rD['errorflag'] = True
-
-        ok = ccU.updateItem(itemName, value, iRow)
-        if not ok:
-            rD['errortext'] = 'item update failed'
-            rD['errorflag'] = True
-
-        ok = ccU.write()
-        if not ok:
-            rD['errortext'] = 'write failed during update'
-            rD['errorflag'] = True
-
-        #
-        return rD
-
-
-if __name__ == '__main__':
-    pass