wwpdb.apps.ccmodule 0.25.dev1__tar.gz → 0.27__tar.gz

{wwpdb.apps.ccmodule-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wwpdb.apps.ccmodule
-Version: 0.25.dev1
+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-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/setup.py

@@ -46,12 +46,12 @@ setup(
     },
     #
     # Also depends on 'openeye.oechem' but cannot install by pypi
-    install_requires=['mmcif', 'mmcif.utils >= 0.13', 'wwpdb.utils.config ~= 0.24',
+    install_requires=['mmcif', 'mmcif.utils >= 0.13', 'wwpdb.utils.config ~= 0.34',
                       'wwpdb.utils.dp >= 0.11', 'rcsb.utils.multiproc',
                       'wwpdb.utils.wf',
                       'wwpdb.utils.session >= 0.2',
                       'mysqlclient',
-                      "wwpdb.io >= 0.16.dev1"
+                      "wwpdb.io ~= 0.27"
                       ],
     packages=find_packages(exclude=['wwpdb.apps.tests_ccmodule']),
     package_data={

{wwpdb.apps.ccmodule-0.25.dev1 → 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__ = "0.25.dev1"
+__version__ = "0.27"

{wwpdb.apps.ccmodule-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/chem/ChemCompAnnotate.py

@@ -20,6 +20,7 @@ import shutil
 
 
 from wwpdb.apps.ccmodule.utils.ChemCompConfig import ChemCompConfig
+from wwpdb.io.locator.ChemRefPathInfo import ChemRefPathInfo
 
 
 class ChemCompAnnotate(object):
@@ -77,8 +78,9 @@ class ChemCompAnnotate(object):
         """
         """
         idUc = str(ccId).upper()
-        fileName = idUc + ".cif"
-        self.__definitionFilePath = os.path.join(self.__ccConfig.getPath('chemCompCachePath'), idUc[0:1], idUc[0:3], fileName)
+        crpi = ChemRefPathInfo(verbose=self.__verbose, log=self.__lfh)
+
+        self.__definitionFilePath = crpi.getFilePath(idUc, "CC")
         #
         if (not os.access(self.__definitionFilePath, os.R_OK)):
             return False

{wwpdb.apps.ccmodule-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/chem/ChemCompAssign.py

@@ -104,10 +104,10 @@ from wwpdb.apps.ccmodule.io.ChemCompDataImport import ChemCompDataImport
 from wwpdb.apps.ccmodule.io.ChemCompDataExport import ChemCompDataExport
 from wwpdb.apps.ccmodule.io.ChemCompIo import ChemCompReader
 from wwpdb.apps.ccmodule.io.ChemCompAssignDataStore import ChemCompAssignDataStore
-from wwpdb.apps.ccmodule.utils.ChemCompConfig import ChemCompConfig
 from mmcif.io.PdbxReader import PdbxReader
 from pathlib import Path
 from wwpdb.io.locator.PathInfo import PathInfo
+from wwpdb.io.locator.ChemRefPathInfo import ChemRefPathInfo
 from mmcif.io.IoAdapterCore import IoAdapterCore
 
 
@@ -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',
@@ -804,9 +804,9 @@ class ChemCompAssign(object):
             self.__lfh.write("+%s.%s() starting\n" % (self.__class__.__name__, inspect.currentframe().f_code.co_name))
         #
         rtrnCode = -1
-        ccConfig = ChemCompConfig(self.__reqObj, verbose=self.__verbose, log=self.__lfh)
-        pathPrefix = ccConfig.getPath('chemCompCachePath')
-        validationPth = os.path.join(pathPrefix, ccId[:1], ccId, ccId + '.cif')
+        crpi = ChemRefPathInfo(self.__cI.get("SITE_PREFIX"), verbose=self.__verbose, log=self.__lfh)
+        validationPth = crpi.getFilePath(ccId, "CC")
+
         #
         if os.access(validationPth, os.R_OK):
             rtrnCode = 0

{wwpdb.apps.ccmodule-0.25.dev1 → 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-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/chem/ChemCompAssignDepictLite.py

@@ -62,6 +62,7 @@ from wwpdb.apps.ccmodule.chem.ChemCompAssign import ChemCompAssign
 # 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 pathlib import Path
 from wwpdb.io.locator.PathInfo import PathInfo
 
@@ -87,7 +88,7 @@ class ChemCompAssignDepictLite(ChemCompDepict):
         self.__lfh = log
         self.__debug = False
         self.__reqObj = p_reqObj
-        self.__depId = "D_0" if self.__reqObj.getValue("identifier") in [None, 'TMP_ID'] else str(self.__reqObj.getValue("identifier")).upper()
+        self.__depId = "D_0" if self.__reqObj.getValue("identifier") in [None, "", 'TMP_ID'] else str(self.__reqObj.getValue("identifier")).upper()
         #
         # self.__cDict = PdbxCategoryDefinition._cDict
         #
@@ -115,15 +116,16 @@ class ChemCompAssignDepictLite(ChemCompDepict):
         #
         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.__deployPath = self.__cI.get('SITE_DEPLOY_PATH')
         self.__siteSrvcUrlPathPrefix = self.__cI.get('SITE_SERVICE_URL_PATH_PREFIX', '')
         self.__workingRltvAssgnSessionPath = ''
 
         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
 
-        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)
 
     ################################################################################################################
@@ -604,6 +606,7 @@ class ChemCompAssignDepictLite(ChemCompDepict):
         lclDict['none_of_abv_checked'] = ''
 
         lclDict['alt_ccid'] = ''
+        lclDict['alt_ccid_width'] = '3'
         lclDict['dscrptr_type'] = ''
         lclDict['dscrptr_str'] = ''
         lclDict['inchi_selected'] = ''
@@ -626,6 +629,9 @@ class ChemCompAssignDepictLite(ChemCompDepict):
         ligFrmla = p_ccAssgnDataStr.getDpstrCcFrmla(p_authAssignedGrp) if p_ccAssgnDataStr.getDpstrCcFrmla(p_authAssignedGrp) != '?' else ""
         ligComments = p_ccAssgnDataStr.getDpstrComments(p_authAssignedGrp) if p_ccAssgnDataStr.getDpstrComments(p_authAssignedGrp) != '?' else ""
 
+        if self.__cIAppCc.get_extended_ccd_supp():
+            lclDict['alt_ccid_width'] = '5'
+
         if p_authAssignedGrp in p_hlprDict['hndle_msmtch_tophit_id_list'] and len(p_hlprDict['hndle_msmtch_tophit_id_list'][p_authAssignedGrp]) > 0:
             lclDict['dsply_addrss_msmtch_opts'] = ''
         else:

{wwpdb.apps.ccmodule-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/reports/ChemCompAlignImageGenerator.py

@@ -24,7 +24,6 @@ import os
 import sys
 
 from wwpdb.utils.config.ConfigInfo import ConfigInfo
-from wwpdb.utils.config.ConfigInfoApp import ConfigInfoAppCommon
 from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility
 from wwpdb.io.locator.ChemRefPathInfo import ChemRefPathInfo
 
@@ -44,10 +43,8 @@ class ChemCompAlignImageGenerator(object):
 
         self.__siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
         self.__cI = ConfigInfo(self.__siteId)
-        self.__cICommon = ConfigInfoAppCommon(self.__siteId)
         #
-        self.__ccRefPathInfo = ChemRefPathInfo(configObj=self.__cI, configCommonObj=self.__cICommon,
-                                               verbose=self.__verbose, log=self.__lfh)
+        self.__ccRefPathInfo = ChemRefPathInfo(self.__siteId, verbose=self.__verbose, log=self.__lfh)
 
     def generateImages(self, instId=None, instFile=None, hitList=None):
         if (not instId) or (not instFile):

{wwpdb.apps.ccmodule-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/reports/ChemCompReports.py

@@ -24,9 +24,9 @@ import sys
 import shutil
 
 from wwpdb.apps.ccmodule.utils.ChemCompConfig import ChemCompConfig
-# from wwpdb.utils.config.ConfigInfo import ConfigInfo
 from pathlib import Path
 from wwpdb.io.locator.PathInfo import PathInfo
+from wwpdb.io.locator.ChemRefPathInfo import ChemRefPathInfo
 
 
 class ChemCompReport(object):
@@ -60,8 +60,9 @@ class ChemCompReport(object):
         self.__reportFileRelativePath = None
         self.__definitionId = None
         self.__definitionFilePath = None
-        # self.__siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
+        self.__siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
         # self.__cI = ConfigInfo(self.__siteId)
+        self.__crpi = ChemRefPathInfo(self.__siteId, verbose=verbose, log=log)
 
         context = self.__getContext()
         if context == 'standalone':
@@ -71,8 +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')
@@ -113,8 +114,7 @@ class ChemCompReport(object):
         """
         """
         idUc = str(ccId).upper()
-        fileName = idUc + ".cif"
-        self.__definitionFilePath = os.path.join(self.__ccConfig.getPath('chemCompCachePath'), idUc[0:1], idUc[0:3], fileName)
+        self.__definitionFilePath = self.__crpi.getFilePath(idUc, "CC")
         #
         if (not os.access(self.__definitionFilePath, os.R_OK)):
             return False
@@ -273,6 +273,8 @@ class ChemCompCheckReport(object):
         self.__sessionRelativePath = self.__sObj.getRelativePath()
         #
         self.__ccConfig = ChemCompConfig(reqObj, verbose=self.__verbose, log=self.__lfh)
+        siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
+        self.__crpi = ChemRefPathInfo(siteId, verbose=verbose, log=log)
 
         #
         self.__reportFilePath = None
@@ -299,8 +301,7 @@ class ChemCompCheckReport(object):
         """
         """
         idUc = str(ccId).upper()
-        fileName = idUc + ".cif"
-        self.__definitionFilePath = os.path.join(self.__ccConfig.getPath('chemCompCachePath'), idUc[0:1], idUc[0:3], fileName)
+        self.__definitionFilePath = self.__crpi.getFilePath(idUc, "CC")
         #
         if (not os.access(self.__definitionFilePath, os.R_OK)):
             return False

{wwpdb.apps.ccmodule-0.25.dev1 → 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-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/utils/ChemCompConfig.py

@@ -20,7 +20,7 @@ Maintain configuration and path information for chemical component module applic
 import sys
 import os
 import os.path
-from wwpdb.utils.config.ConfigInfoApp import ConfigInfoAppCommon
+from wwpdb.utils.config.ConfigInfoApp import ConfigInfoAppCommon, ConfigInfoAppCc
 
 
 class ChemCompConfig(object):
@@ -48,6 +48,7 @@ class ChemCompConfig(object):
         #
         self.__siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
         self.__cICommon = ConfigInfoAppCommon(self.__siteId)
+        self.__cIAppCc = ConfigInfoAppCc(self.__siteId, verbose=verbose, log=log)
         #
         # derived from the top path by convention
         #
@@ -57,8 +58,7 @@ 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.__cICommon.get_site_cc_dict_path()
-        self.__ccCvsPath = self.__cICommon.get_site_cc_cvs_path()
+        self.__ccDictPath = self.__cIAppCc.get_site_cc_dict_path()
         self.__oeLicenseFilePath = self.__cICommon.get_site_cc_oe_licence()
         self.__oeDirPath = self.__cICommon.get_site_cc_oe_dir()
 
@@ -67,7 +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 -
@@ -146,8 +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-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/utils/ChemCompDpUtility.py

@@ -53,11 +53,13 @@ class ChemCompDpUtility(object):
 
         # setting up chem comp config
         self._ccConfig = ChemCompConfig(self._reqObj, self._verbose, self._lfh)
-        self._ccRefPathInfo = ChemRefPathInfo(configObj=self._cI, configCommonObj=self._cICommon,
-                                              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)
+
+        siteId = str(self._reqObj.getValue("WWPDB_SITE_ID"))
+
+        self._ccRefPathInfo = ChemRefPathInfo(siteId, verbose=self._verbose, log=self._lfh)
+        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):
@@ -254,8 +256,7 @@ class ChemCompDpUtility(object):
             IOError: if we were not able to read the ligand ".cif" file from
                 the ligand dict
         """
-        ccDictPrefix = self._ccConfig.getPath('chemCompCachePath')
-        chemCompCifPath = os.path.join(ccDictPrefix, topHitCcId[:1], topHitCcId, topHitCcId + '.cif')
+        chemCompCifPath = self._ccRefPathInfo.getFilePath(topHitCcId)
         refImageOutputPath = os.path.join(self._ccReportPath, topHitCcId + '.svg')
 
         if os.access(chemCompCifPath, os.R_OK):
@@ -275,8 +276,7 @@ class ChemCompDpUtility(object):
         Returns:
             bool: True if the ligand has an entry in the dictionary, False otherwise
         """
-        ccDictPrefix = self._ccConfig.getPath('chemCompCachePath')
-        ligandEntryPath = os.path.join(ccDictPrefix, ccid[:1], ccid, ccid + '.cif')
+        ligandEntryPath = self._ccRefPathInfo.getFilePath(ccid)
 
         if not os.access(ligandEntryPath, os.R_OK):
             self._logger.warning('Ligand ID %s has no corresponding dict ref file at %s', ccid, ligandEntryPath)
@@ -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-0.25.dev1 → 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-0.25.dev1 → 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-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/webapp/ChemCompWebApp.py

@@ -159,7 +159,6 @@ from wwpdb.apps.ccmodule.sketch.ChemCompSketch import ChemCompSketch
 from wwpdb.apps.ccmodule.sketch.ChemCompSketchDepict import ChemCompSketchDepict
 #
 from wwpdb.utils.wf.dbapi.WfTracking import WfTracking
-from wwpdb.apps.ccmodule.utils.ChemCompConfig import ChemCompConfig
 #
 from wwpdb.apps.ccmodule.io.ChemCompAssignDataStore import ChemCompAssignDataStore
 from wwpdb.apps.ccmodule.io.ChemCompDataImport import ChemCompDataImport
@@ -167,7 +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
 #
@@ -175,6 +174,7 @@ from wwpdb.utils.oe_util.oedepict.OeDepict import OeDepict
 from wwpdb.utils.oe_util.build.OeBuildMol import OeBuildMol
 #
 from wwpdb.io.locator.PathInfo import PathInfo
+from wwpdb.io.locator.ChemRefPathInfo import ChemRefPathInfo
 from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility
 
 
@@ -298,7 +298,7 @@ class ChemCompWebAppWorker(object):
         self.__rltvSessionPath = None
         self.__siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
         self.__cI = ConfigInfo(self.__siteId)
-        self.__ccConfig = ChemCompConfig(reqObj, verbose=self.__verbose, log=self.__lfh)
+        self.__cIAppCc = ConfigInfoAppCc(self.__siteId, verbose=self.__verbose, log=self.__lfh)
         self.__modelFilePath = None
         #
         self.__pathInstncsVwTmplts = "templates/workflow_ui/instances_view"
@@ -624,6 +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()
@@ -1582,8 +1587,8 @@ class ChemCompWebAppWorker(object):
         self.__reqObj.setReturnFormat(return_format="json")
         rC = ResponseContent(reqObj=self.__reqObj, verbose=self.__verbose, log=self.__lfh)
         #
-        pathPrefix = self.__ccConfig.getPath('chemCompCachePath')
-        validationPth = os.path.join(pathPrefix, ccId[:1], ccId, ccId + '.cif')
+        crpi = ChemRefPathInfo(siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
+        validationPth = crpi.getFilePath(ccId, "CC")
         if (self.__verbose):
             self.__lfh.write("+ChemCompWebAppWorker._ccAssign_validateCcId() ---- validating CC ID %s against path: %s\n" % (ccId, validationPth))
         if not os.access(validationPth, os.R_OK):

{wwpdb.apps.ccmodule-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb/apps/ccmodule/webapp/ChemCompWebAppLite.py

@@ -106,7 +106,6 @@ except Exception as e:
 # from wwpdb.apps.ccmodule.search.ChemCompSearchDbDepict import ChemCompSearchDbDepict
 #
 # from wwpdb.utils.wf.dbapi.WfTracking import WfTracking
-from wwpdb.apps.ccmodule.utils.ChemCompConfig import ChemCompConfig
 #
 from wwpdb.apps.ccmodule.io.ChemCompAssignDataStore import ChemCompAssignDataStore
 from wwpdb.apps.ccmodule.io.ChemCompDataExport import ChemCompDataExport
@@ -119,6 +118,7 @@ from wwpdb.io.file.mmCIFUtil import mmCIFUtil
 from wwpdb.utils.wf.dbapi.WfDbApi import WfDbApi
 from wwpdb.utils.wf.dbapi.WFEtime import getTimeNow
 from wwpdb.io.locator.PathInfo import PathInfo
+from wwpdb.io.locator.ChemRefPathInfo import ChemRefPathInfo
 
 
 class ChemCompWebAppLite(object):
@@ -247,11 +247,7 @@ class ChemCompWebAppLiteWorker(object):
         self.__siteSrvcUrlPathPrefix = self.__cI.get('SITE_SERVICE_URL_PATH_PREFIX', '')
         # self.__siteConfigDir = self.__cI.get('TOP_WWPDB_SITE_CONFIG_DIR')
         # self.__siteLoc = self.__cI.get('WWPDB_SITE_LOC')
-        self.__ccConfig = ChemCompConfig(reqObj, verbose=self.__verbose, log=self.__lfh)
         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)
 
         #
@@ -381,7 +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
 
@@ -1134,8 +1131,9 @@ class ChemCompWebAppLiteWorker(object):
         self.__reqObj.setReturnFormat(return_format="json")
         rC = ResponseContent(reqObj=self.__reqObj, verbose=self.__verbose, log=self.__lfh)
         #
-        pathPrefix = self.__ccConfig.getPath('chemCompCachePath')
-        validationPth = os.path.join(pathPrefix, ccId[:1], ccId, ccId + '.cif')
+
+        crpi = ChemRefPathInfo(self.__siteId, verbose=self.__verbose, log=self.__lfh)
+        validationPth = crpi.getFilePath(ccId, "CC")
         if (self.__verbose):
             self.__lfh.write("+%s.%s() ---- validating CC ID %s against path: %s\n" % (self.__class__.__name__, inspect.currentframe().f_code.co_name, ccId, validationPth))
         if not os.access(validationPth, os.R_OK):

{wwpdb.apps.ccmodule-0.25.dev1 → 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: 0.25.dev1
+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-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb.apps.ccmodule.egg-info/SOURCES.txt

@@ -10,8 +10,6 @@ wwpdb.apps.ccmodule.egg-info/requires.txt
 wwpdb.apps.ccmodule.egg-info/top_level.txt
 wwpdb/apps/__init__.py
 wwpdb/apps/ccmodule/__init__.py
-wwpdb/apps/ccmodule/admin/ChemCompAdmin.py
-wwpdb/apps/ccmodule/admin/__init__.py
 wwpdb/apps/ccmodule/chem/ChemCompAnnotate.py
 wwpdb/apps/ccmodule/chem/ChemCompAssign.py
 wwpdb/apps/ccmodule/chem/ChemCompAssignDepict.py
@@ -20,9 +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
@@ -30,7 +25,6 @@ wwpdb/apps/ccmodule/io/ChemCompDataExport.py
 wwpdb/apps/ccmodule/io/ChemCompDataImport.py
 wwpdb/apps/ccmodule/io/ChemCompEditStore.py
 wwpdb/apps/ccmodule/io/ChemCompIo.py
-wwpdb/apps/ccmodule/io/PdbxChemComp.py
 wwpdb/apps/ccmodule/io/__init__.py
 wwpdb/apps/ccmodule/reports/ChemCompAlignImageGenerator.py
 wwpdb/apps/ccmodule/reports/ChemCompAlignImages.py

{wwpdb.apps.ccmodule-0.25.dev1 → wwpdb.apps.ccmodule-0.27}/wwpdb.apps.ccmodule.egg-info/requires.txt

@@ -1,12 +1,12 @@
 mmcif
 mmcif.utils>=0.13
-wwpdb.utils.config~=0.24
+wwpdb.utils.config~=0.34
 wwpdb.utils.dp>=0.11
 rcsb.utils.multiproc
 wwpdb.utils.wf
 wwpdb.utils.session>=0.2
 mysqlclient
-wwpdb.io>=0.16.dev1
+wwpdb.io~=0.27
 
 [consumer]
 wwpdb.utils.oe_util>=0.2