display the assembly provenance tag

wwpdb/apps/ann_tasks_v2/__init__.py

@@ -2,4 +2,4 @@
 __author__ = "Ezra Peisach"
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"
-__version__ = "0.41.1"
+__version__ = "0.41.2"

wwpdb/apps/ann_tasks_v2/assembly/AssemblyInput.py

@@ -347,6 +347,8 @@ def makeSymopInfoTable(self, entryId="1ABC", entryFileName=None):
             #
         #
         symopFile = os.path.join(self.__sessionPath, entryId + "-symop-info.txt")
+        if os.access(symopFile, os.R_OK):
+            os.remove(symopFile)
         #
         try:
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)

wwpdb/apps/ann_tasks_v2/assembly/AssemblySelect.py

@@ -96,11 +96,16 @@ def run(self, entryId, inpFile, sessionName, maxAssems=50):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             reportPath = os.path.join(self.__sessionPath, entryId + "_assembly-report_P1.xml")
             logPath = os.path.join(self.__sessionPath, entryId + "-assembly-report.log")
+            for filePath in ( reportPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
             if self.__assemblyArgs is not None and len(self.__assemblyArgs) > 0:
                 dp.addInput(name="pisa_assembly_arguments", value=self.__assemblyArgs)
+            #
             dp.addInput(name="pisa_session_name", value=sessionName)
             dp.op("pisa-analysis")
             dp.expLog(logPath)
@@ -127,7 +132,10 @@ def run(self, entryId, inpFile, sessionName, maxAssems=50):
                     dp.exp(assemModelFileName)
                     if self.__verbose:
                         self.__lfh.write("+AssemblySelect.run - creating assembly model %r file %s\n" % (assemblyUid, assemModelFileName))
-                # dp.cleanup()
+                    #
+                #
+            #
+            # dp.cleanup()
             return True
         except:  # noqa: E722 pylint: disable=bare-except
             if self.__verbose:
@@ -273,6 +281,11 @@ def updateModelFile(self, entryId, inpFile, assignPath, updateInput=True):
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
             logPath = os.path.join(self.__sessionPath, entryId + "_assembly-merge.log")
             reportPath = os.path.join(self.__sessionPath, entryId + "_assembly-report_P1.xml")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
+            #
             if self.__verbose:
                 self.__lfh.write("+AssemblySelect.updateModelFile() input  path %s\n" % inpPath)
                 self.__lfh.write("+AssemblySelect.updateModelFile() return path %s\n" % retPath)
@@ -288,14 +301,14 @@ def updateModelFile(self, entryId, inpFile, assignPath, updateInput=True):
             #
             dp.op("pisa-assembly-merge-cif")
             dp.exp(retPath)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
+            #
             dp.expLog(logPath)
             #
             #  Added generation of assembly files to the model update.
             if os.access(retPath, os.R_OK):
                 self.generateAssemblies(entryId, modelFilePath=retPath)
-
             #
             # dp.cleanup()
             return True
@@ -314,6 +327,10 @@ def autoAssignDefaultAssembly(self, entryId, inpFile):
             logPath = os.path.join(self.__sessionPath, entryId + "_assembly-merge.log")
             assignPath = os.path.join(self.__sessionPath, entryId + "_assembly-assign_P1.cif")
             reportPath = os.path.join(self.__sessionPath, entryId + "_assembly-report_P1.xml")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -339,7 +356,6 @@ def autoAssignDefaultAssembly(self, entryId, inpFile):
             #  Added generation of assembly files to the model update.
             if os.access(retPath, os.R_OK):
                 self.generateAssemblies(entryId, modelFilePath=retPath)
-
             #
             # dp.cleanup()
             return True
@@ -539,6 +555,10 @@ def runPdb(self, entryId, inpFile, sessionName):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             reportPath = os.path.join(self.__sessionPath, entryId + "_assembly-report_P1.xml")
             logPath = os.path.join(self.__sessionPath, entryId + "_assembly-report.log")
+            for filePath in ( reportPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)

wwpdb/apps/ann_tasks_v2/check/ExtraCheck.py

@@ -42,7 +42,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         #
         self.__exportPath = None
         self.__checkArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         self.__reportFileSize = 0
         self.__reportPath = None
         #

wwpdb/apps/ann_tasks_v2/check/FormatCheck.py

@@ -42,7 +42,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
 
         self.__exportPath = None
         self.__checkArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         self.__reportFileSize = 0
         self.__reportPath = None
 

wwpdb/apps/ann_tasks_v2/check/GeometryCalc.py

@@ -49,7 +49,7 @@ def __setup(self):
         self.__siteId = self.__reqObj.getValue("WWPDB_SITE_ID")
         self.__sObj = self.__reqObj.getSessionObj()
         self.__sessionPath = self.__sObj.getPath()
-        self.__cleanup = False
+        self.__cleanup = True
 
     def setArguments(self, checkArgs):
         self.__checkArgs = checkArgs
@@ -76,15 +76,20 @@ def run(self, entryId, inpFile, updateInput=True):
             dp.exp(retPath)
             self.addDownloadPath(retPath)
             self.addDownloadPath(logPath)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
             #
             if self.__verbose:
                 self.__lfh.write("+%s.%s geometry calc completed for entryId %s file %s\n" % (self.__class__.__name__, inspect.currentframe().f_code.co_name, entryId, inpFile))
 
             if self.__cleanup:
                 dp.cleanup()
-            return True
+            #
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             if self.__verbose:
                 self.__lfh.write("+%s.%s geometry calc failed for entryId %s file %s\n" % (self.__class__.__name__, inspect.currentframe().f_code.co_name, entryId, inpFile))

wwpdb/apps/ann_tasks_v2/check/GeometryCheck.py

@@ -44,7 +44,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__checkArgs = None
         self.__reportFileSize = 0
         self.__reportPath = None
-        self.__cleanup = False
+        self.__cleanup = True
 
         self.__setup()
 

wwpdb/apps/ann_tasks_v2/correspnd/CorresPNDTemplate.py

@@ -86,6 +86,10 @@ def __runGetCorresInfo(self):
         try:
             resultfile = os.path.join(self.__sessionPath, "corres_1.cif")
             logfilename = os.path.join(self.__sessionPath, "corres_1.log")
+            for filePath in ( resultfile, logfilename ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryFile))

wwpdb/apps/ann_tasks_v2/editCoord/CSEditorForm.py

@@ -63,11 +63,18 @@ def get(self):
     def __runScript(self):
         """ """
         try:
+            retPath = os.path.join(self.__sessionPath, self.__entryId + "_cs_html.txt")
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_cs_summary.log")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
+            #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryFile))
             dp.op("annot-depict-chemical-shift")
-            dp.exp(os.path.join(self.__sessionPath, self.__entryId + "_cs_html.txt"))
-            dp.expLog(os.path.join(self.__sessionPath, self.__entryId + "_cs_summary.log"))
+            dp.exp(retPath)
+            dp.expLog(logPath)
             dp.cleanup()
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)

wwpdb/apps/ann_tasks_v2/editCoord/CSEditorUpdate.py

@@ -103,12 +103,16 @@ def __writeSelectInfo(self, cmap):
     def __runUpdateScript(self):
         """ """
         try:
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_cs_update.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryFile))
             dp.addInput(name="assign", value=os.path.join(self.__sessionPath, self.__entryId + "_cs_select.cif"))
             dp.op("annot-edit-chemical-shift")
             dp.exp(os.path.join(self.__sessionPath, self.__entryFile))
-            dp.expLog(os.path.join(self.__sessionPath, self.__entryId + "_cs_update.log"))
+            dp.expLog(logPath)
             dp.cleanup()
             #
             return self.__readLogFile("_cs_update.log", "Update failed!")

wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorForm_v2.py

@@ -157,8 +157,14 @@ def __runScript(self):
             jsonPath = os.path.join(self.__jsonPath, self.__entryId + ".json")
             textPath = os.path.join(self.__sessionPath, self.__entryId + "_chainids.txt")
             indxPath = os.path.join(self.__sessionPath, self.__entryId + "_index.cif")
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_summary.log")
+            for filePath in ( jsonPath, textPath, indxPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
+            #
             dp.expList(dstPathList=[jsonPath, textPath, indxPath])
-            dp.expLog(os.path.join(self.__sessionPath, self.__entryId + "_summary.log"))
+            dp.expLog(logPath)
             dp.cleanup()
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)

wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorUpdate.py

@@ -114,11 +114,15 @@ def __writeSelectInfo(self, smap):
     def __runCheckScript(self):
         """ """
         try:
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_check.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryId + "_index.cif"))
             dp.addInput(name="select", value=os.path.join(self.__sessionPath, self.__entryId + "_select.cif"))
             dp.op("annot-check-select-number")
-            dp.expLog(dstPath=os.path.join(self.__sessionPath, self.__entryId + "_check.log"), appendMode=False)
+            dp.expLog(dstPath=logPath, appendMode=False)
             dp.cleanup()
             #
             return self.__readLogFile("_check.log", "Run numbering checking failed")
@@ -131,12 +135,16 @@ def __runCheckScript(self):
     def __runUpdateScript(self):
         """ """
         try:
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_update.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryFile))
             dp.addInput(name="assign", value=os.path.join(self.__sessionPath, self.__entryId + "_select.cif"))
             dp.op("annot-update-molecule")
             dp.exp(os.path.join(self.__sessionPath, self.__entryFile))
-            dp.expLog(dstPath=os.path.join(self.__sessionPath, self.__entryId + "_update.log"), appendMode=False)
+            dp.expLog(dstPath=logPath, appendMode=False)
             dp.cleanup()
             #
             return self.__readLogFile("_update.log", "Update failed!")

wwpdb/apps/ann_tasks_v2/em3d/EmAutoFix.py

@@ -31,7 +31,7 @@ def __init__(self, sessionPath, siteId=None, verbose=True, log=sys.stderr):
         self.__lfh = log
         self.__siteId = siteId
         self.__sessionPath = sessionPath
-        self.__cleanup = False
+        self.__cleanup = True
         self.__pI = PathInfo(sessionPath=sessionPath, verbose=self.__verbose, log=self.__lfh)
         self.__mD = {"primary map": "em-volume", "mask": "em-mask-volume", "additional map": "em-additional-volume", "half map": "em-half-volume", "map header": "em-volume-header"}
 
@@ -53,6 +53,11 @@ def __getEmdDbCode(blockobj):
     def __mapfix(self, depsetid, emdbid, volin, volout, voxel):
         resultPath = os.path.join(self.__sessionPath, depsetid + "_mapfix-header-report_P1.json")
         logPath = os.path.join(self.__sessionPath, depsetid + "_mapfix-report_P1.txt")
+        for filePath in ( resultPath, logPath ):
+            if os.access(filePath, os.R_OK):
+                os.remove(filePath)
+            #
+        #
         dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
         dp.setDebugMode(flag=True)
         dp.addInput(name="input_map_file_path", value=volin, type="file")
@@ -65,7 +70,7 @@ def __mapfix(self, depsetid, emdbid, volin, volout, voxel):
 
         if self.__cleanup:
             dp.cleanup()
-
+        #
         return resultPath
 
     def autoFixMapLabels(self, datasetid, modelin, modelout, vollocation="archive"):

wwpdb/apps/ann_tasks_v2/em3d/EmEditUtils.py

@@ -47,7 +47,7 @@ def __setup(self):
         self.__sessionId = self.__sObj.getId()
         self.__sessionPath = self.__sObj.getPath()
         self.__pI = PathInfo(siteId=self.__siteId, sessionPath=self.__sessionPath, verbose=self.__verbose, log=self.__lfh)
-        self.__cleanup = False
+        self.__cleanup = True
 
         self.__headerKeyList = [
             ("Map title", "label", True),
@@ -107,6 +107,10 @@ def getMapHeader(self, entryId, mapFilePath):
         try:
             resultPath = os.path.join(self.__sessionPath, entryId + "_mapfix-header-report_P1.json")
             logPath = os.path.join(self.__sessionPath, entryId + "_mapfix-report_P1.txt")
+            for filePath in ( resultPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.setDebugMode(flag=True)
@@ -289,6 +293,10 @@ def updateMapHeader(self, entryId, inputMapFileName, outputMapFilePath=None):
 
             resultPath = os.path.join(self.__sessionPath, entryId + "_mapfix-header-report_P1.json")
             logPath = os.path.join(self.__sessionPath, entryId + "_mapfix-report_P1.txt")
+            for filePath in ( resultPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.setDebugMode(flag=True)

wwpdb/apps/ann_tasks_v2/link/Link.py

@@ -60,14 +60,16 @@ def run(self, entryId, inpFile, updateInput=True):
             pI = PathInfo(siteId=self.__siteId, sessionPath=self.__sessionPath, verbose=self.__verbose, log=self.__lfh)
             csvFile = pI.getFileName(entryId, contentType="pcm-missing-data", formatType="csv", versionId="none", partNumber="1")
             csvPath = os.path.join(self.__sessionPath, csvFile)
-            if os.access(csvPath, os.F_OK):
-                os.remove(csvPath)
             #
             inpPath = os.path.join(self.__sessionPath, inpFile)
             logPath1 = os.path.join(self.__sessionPath, entryId + "-link-anal.log")
             logPath2 = os.path.join(self.__sessionPath, entryId + "-cispeptide-anal.log")
             retPath1 = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
             retPath2 = os.path.join(self.__sessionPath, entryId + "_model-updated_P2.cif")
+            for filePath in ( csvPath, retPath1, retPath2, logPath1, logPath2 ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)

wwpdb/apps/ann_tasks_v2/mapcalc/BisoFullCalc.py

@@ -37,7 +37,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__lfh = log
         self.__reqObj = reqObj
         self.__dccArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         #
         self.__setup()
 
@@ -67,6 +67,10 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True)
             #
             logPath = os.path.join(self.__sessionPath, entryId + "_biso-full-calc.log")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -79,15 +83,20 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True)
             dp.expLog(logPath)
             dp.exp(retPath)
 
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
             #
             if self.__verbose:
                 self.__lfh.write("+BisoFullCalc.run-  completed for entryId %s file %s\n" % (entryId, inpPath))
 
             if self.__cleanup:
                 dp.cleanup()
-            return True
+            #
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             if self.__verbose:
                 self.__lfh.write("+BisoFullCalc.run-  failed with exception for entryId %s file %s\n" % (entryId, inpPath))

wwpdb/apps/ann_tasks_v2/mapcalc/DccCalc.py

@@ -37,7 +37,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__lfh = log
         self.__reqObj = reqObj
         self.__dccArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         self.__exportPath = None
         self.__reportPath = None
         #