def test_WhyNot(self): cingDirTmpTest = os.path.join(cingDirTmp, getCallerName()) mkdirs(cingDirTmpTest) self.failIf(os.chdir(cingDirTmpTest), msg="Failed to change to test directory for files: " + cingDirTmpTest) whyNot = WhyNot() for entryId in ['1brv', '9pcy']: whyNotEntry = WhyNotEntry(entryId) whyNot[entryId] = whyNotEntry if entryId not in ['1brv']: whyNotEntry.comment = NOT_NMR_ENTRY whyNotEntry.exists = False continue whyNotEntry.comment = FAILED_TO_BE_VALIDATED_CING whyNotStr = '%s' % whyNot nTdebug("whyNotStr: [" + whyNotStr + "]") writeTextToFile("NRG-CING.txt", whyNotStr)
def doWriteWhyNot(self): "Write the WHYNOT files" if self.writeWhyNot: nTdebug("Create WHY_NOT list") else: nTmessage("Skipping create WHY_NOT list") return whyNot = WhyNot() # Loop for speeding up the checks. Most are not nmr. for entryId in self.entry_list_pdb: whyNotEntry = WhyNotEntry(entryId) whyNot[entryId] = whyNotEntry whyNotEntry.comment = '' whyNotEntry.exists = False for entryId in self.entry_list_pdb: whyNotEntry = whyNot[entryId] whyNotEntry.exists = True # if entryId not in self.entry_list_nrg: # whyNotEntry.comment = NO_EXPERIMENTAL_DATA # whyNotEntry.exists = False # continue # if entryId not in self.entry_list_nrg_docr: # whyNotEntry.comment = FAILED_TO_BE_CONVERTED_NRG # whyNotEntry.exists = False # continue if entryId not in self.entry_list_tried: whyNotEntry.comment = TO_BE_VALIDATED_BY_CING whyNotEntry.exists = False continue if entryId not in self.entry_list_done: whyNotEntry.comment = FAILED_TO_BE_VALIDATED_CING whyNotEntry.exists = False continue # whyNotEntry.comment = PRESENT_IN_CING # Entries that are present in the database do not need a comment del (whyNot[entryId]) # end loop over entries whyNotStr = '%s' % whyNot # nTdebug("whyNotStr truncated to 1000 chars: [" + whyNotStr[0:1000] + "]") whyNotFileName = "PDB-CING.txt" writeTextToFile(whyNotFileName, whyNotStr) why_not_db_comments_file = os.path.join(self.why_not_db_comments_dir, self.why_not_db_comments_file) nTdebug("Copying to: " + why_not_db_comments_file) shutil.copy(whyNotFileName, why_not_db_comments_file) if self.writeTheManyFiles: for entryId in self.entry_list_done: # For many files like: /usr/data/raw/nmr-cing/ d3/1d3z/1d3z.exist char23 = entryId[1:3] subDir = os.path.join(self.why_not_db_raw_dir, char23, entryId) if not os.path.exists(subDir): os.makedirs(subDir) fileName = os.path.join(subDir, entryId + ".exist") if not os.path.exists(fileName): # nTdebug("Creating: " + fileName) fp = open(fileName, 'w') # fprintf(fp, ' ') fp.close()
def doWriteWhyNot(self): "Write the WHYNOT files" if self.writeWhyNot: nTdebug("Create WHY_NOT list") else: nTmessage("Skipping create WHY_NOT list") return whyNot = WhyNot() # Loop for speeding up the checks. Most are not nmr. for entryId in self.entry_list_pdb: whyNotEntry = WhyNotEntry(entryId) whyNot[entryId] = whyNotEntry whyNotEntry.comment = '' whyNotEntry.exists = False for entryId in self.entry_list_pdb: whyNotEntry = whyNot[entryId] whyNotEntry.exists = True # if entryId not in self.entry_list_nrg: # whyNotEntry.comment = NO_EXPERIMENTAL_DATA # whyNotEntry.exists = False # continue # if entryId not in self.entry_list_nrg_docr: # whyNotEntry.comment = FAILED_TO_BE_CONVERTED_NRG # whyNotEntry.exists = False # continue if entryId not in self.entry_list_tried: whyNotEntry.comment = TO_BE_VALIDATED_BY_CING whyNotEntry.exists = False continue if entryId not in self.entry_list_done: whyNotEntry.comment = FAILED_TO_BE_VALIDATED_CING whyNotEntry.exists = False continue # whyNotEntry.comment = PRESENT_IN_CING # Entries that are present in the database do not need a comment del(whyNot[entryId]) # end loop over entries whyNotStr = '%s' % whyNot # nTdebug("whyNotStr truncated to 1000 chars: [" + whyNotStr[0:1000] + "]") whyNotFileName = "PDB-CING.txt" writeTextToFile(whyNotFileName, whyNotStr) why_not_db_comments_file = os.path.join(self.why_not_db_comments_dir, self.why_not_db_comments_file) nTdebug("Copying to: " + why_not_db_comments_file) shutil.copy(whyNotFileName, why_not_db_comments_file) if self.writeTheManyFiles: for entryId in self.entry_list_done: # For many files like: /usr/data/raw/nmr-cing/ d3/1d3z/1d3z.exist char23 = entryId[1:3] subDir = os.path.join(self.why_not_db_raw_dir, char23, entryId) if not os.path.exists(subDir): os.makedirs(subDir) fileName = os.path.join(subDir, entryId + ".exist") if not os.path.exists(fileName): # nTdebug("Creating: " + fileName) fp = open(fileName, 'w') # fprintf(fp, ' ') fp.close()