Merge pull request #29 from wwPDB/DAOTHER-9171

Create the "PCM/PTM" tab in AnnMod

wwpdb/apps/ann_tasks_v2/pcm/PcmCCDEditorForm.py

@@ -10,10 +10,7 @@
 import traceback
 
 from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility
-
-# Set the default logger handler level to INFO -- this should not be set here - but at hight level
-# logging.getLogger().setLevel(logging.INFO)
-
+from wwpdb.io.locator.PathInfo import PathInfo
 
 class PcmCCDEditorForm(object):
     """
@@ -35,9 +32,12 @@ def __setup(self):
         self.__sessionPath = self.__sObj.getPath()
         self.__entryId = self.__reqObj.getValue("entryid")
         self.__identifier = self.__reqObj.getValue("display_identifier")
-        self.__csvPath = os.path.join(self.__sessionPath, self.__entryId + "_ccd_no_pcm_ann.csv")
         self.__entryFile = None
         #
+        self.__pI = PathInfo(siteId=self.__siteId, sessionPath=self.__sessionPath, verbose=self.__verbose, log=self.__lfh)
+        self.__csvFile = self.__pI.getFileName(self.__entryId, contentType="pcm-missing-data", formatType="csv", versionId="none", partNumber="1")
+        self.__csvPath = os.path.join(self.__sessionPath, self.__csvFile)
+        #
         self.__tableTemplate = '<table id="table_%s" class="table table-condensed table-bordered table-striped">\n'
         self.__tdTagTemplate = '<td style="border-style:none">%s</td>\n'
         self.__editableTemplate = '<b class="%s" id="%s" style="display:inline">%s</b>'
@@ -69,21 +69,22 @@ def run(self):
     def __runPcmCcdCheck(self):
         """Run PCM script to check missing annotation"""
         self.__entryFile = self.__reqObj.getValue("entryfilename")
-        entry_file_path = os.path.join(self.__sessionPath, self.__entryFile)
+        inpPdbxPath = os.path.join(self.__sessionPath, self.__entryFile)
 
-        if not os.access(entry_file_path, os.F_OK):
-            logging.error("Missing entry file %s", entry_file_path)
+        if not os.access(inpPdbxPath, os.F_OK):
+            logging.error("Missing entry file %s", inpPdbxPath)
             return
         #
         logging.info("Processing entry file %s", self.__entryFile)
-
+        #
+        if os.access(self.__csvPath, os.F_OK):
+            os.remove(self.__csvPath)
+        #
         try:
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
-            dp.imp(entry_file_path)
-            dp.addInput(name="id", value=self.__entryId)
+            dp.imp(inpPdbxPath)
             dp.op("annot-pcm-check-ccd-ann")
-            dp.exp(dstPath=self.__csvPath)
-            dp.expLog(os.path.join(self.__sessionPath, self.__entryId + "_ccd_no_pcm_ann.log"))
+            dp.expList(dstPathList=[inpPdbxPath, self.__csvPath])
             dp.cleanup()
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
@@ -109,9 +110,17 @@ def __buildCCDFormHtml(self):
         if not os.access(self.__csvPath, os.F_OK):
             myD = {}
             myD["statuscode"] = "failed"
-            myD["statustext"] = "Failed to build form for %s" % self.__entryId
+            myD["statustext"] = "Failed to build form for %s. Couldn't find output csv file" % self.__entryId
             return myD
 
+        with open(self.__csvPath, 'r') as fp:
+            content = "PTM annotation is successfully updated. No missing pcm data found."
+            if content in fp.read():
+                myD = {}
+                myD["statuscode"] = "ok"
+                myD["htmlcontent"] = content
+                return myD
+
         htmlcontent = self.__tableTemplate % self.__identifier
         htmlcontent += (
             "<tr>\n<th>Comp Id</th>\n<th>Modified Residue Id</th>\n<th>Type</th>\n<th>Category</th>\n<th>Position</th>\n<th>Polypeptide Position</th>\n<th>Comp Id Linking Atom</th>\n<th>Modified Residue Id Linking Atom</th>\n<th>First Instance Model Db Code</th>\n<th>ChemRefUI Link</th>\n</tr>\n"  # noqa: E501
@@ -152,4 +161,4 @@ def __buildCCDFormHtml(self):
         myD = {}
         myD["statuscode"] = "ok"
         myD["htmlcontent"] = htmlcontent
-        return myD
+        return myD