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()
