def expList(self, dstPathList=None):
if dstPathList is None:
dstPathList = []
if self.__op in [
"annot-wwpdb-validate-all", "annot-wwpdb-validate-all-v2"
]:
return super(ValidationWrapper, self).expList(dstPathList)
logger.debug("Intercepting expList")
# Op should be annot-wwpdb-validate-all-sf - so we will "pull" and interpret
# Handle the first arguments
# ofpdf,ofxml,offullpdf,ofpng,ofsvg,ofmtz
basedst = dstPathList[0:7]
outfosf = dstPathList[7]
out2fosf = dstPathList[8]
mtzfile = os.path.join(self.getWorkingDir(), "mapcoef.mtz")
basedst.append(mtzfile)
ret = super(ValidationWrapper, self).expList(basedst)
logger.debug("expList ret is %s", ret)
# Need to "produce files" for last arguments if possible
if not os.path.exists(mtzfile):
return False
pdbid = self.__getPDBId()
logger.info("pdbID %s", pdbid)
if not pdbid:
pdbid = "xxxx"
psm = PdbxSFMapCoefficients(siteid=self.__siteId,
tmppath=self._tmppath)
ret = psm.read_mtz_sf(mtzfile)
logger.debug("read_mtz_sf ret %s", ret)
if ret:
# Ensure map coefficients produced in conversion - returns True if present
ret = psm.has_map_coeff()
logger.debug("Check for map coeffcients returns %s", ret)
scrpath = self.getWorkingDir()
fotemp = os.path.join(scrpath, "fotemp.cif")
twofotemp = os.path.join(scrpath, "twofotemp.cif")
if ret:
ret = psm.write_mmcif_coef(fopathout=fotemp,
twofopathout=twofotemp,
entry_id=pdbid.lower())
df = DataFile(fotemp)
if df.srcFileExists():
df.copy(outfosf)
df = DataFile(twofotemp)
if df.srcFileExists():
df.copy(out2fosf)
logger.debug("Returning %s", ret)
return ret
def testFileEMail(self): # pragma: no cover
self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
fPath = os.path.join(self.__testFilePath, self.__testFile)
f1 = DataFile(fPath)
f1.eMail("*****@*****.**", "*****@*****.**", "IGNORE THIS TEST MESSAGE")
except: # noqa: E722
traceback.print_exc(file=sys.stdout)
self.fail()
def testPrintInfo(self):
""""""
self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
fPath = os.path.join(self.__testFilePath, self.__testFile)
f1 = DataFile(fPath)
f1.pr(self.lfh)
except: # noqa: E722 # pragma: no cover
traceback.print_exc(file=sys.stdout)
self.fail()
def testSymlink(self):
"""Tests symlink creation """
self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
# Test non existant case
f1path = os.path.join(TESTOUTPUT, "linkorigin.tst")
f2path = os.path.join(TESTOUTPUT, "symlinkdst.tst")
for f in [f1path, f2path]:
if os.path.exists(f):
os.remove(f)
with open(f1path, "w") as f:
pass
d1 = DataFile(f1path)
d1.symLink(f2path)
def testCreateHistory(self):
"""Read existing entry and create initial status records as required -"""
startTime = time.time()
self.__lfh.write("\n\n========================================================================================================\n")
self.__lfh.write("Starting StatusHistoryTests testCreateHistory at %s\n" % time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
try:
# Read model file and return status dictionary -
ei = PdbxEntryInfoIo(verbose=self.__verbose, log=self.__lfh)
ei.setFilePath(filePath=self.__testFile2)
sD = ei.getInfoD(contextType="history")
(
_entryId,
_pdbId,
statusCode,
_authReleaseCode,
annotatorInitials,
initialDepositionDate,
beginProcessingDate,
authorApprovalDate,
releaseDate,
) = ei.getCurrentStatusDetails()
self.__lfh.write("+StatusHistoryTests.testReadWriteHistory() status dictionary %r\n" % sD.items())
#
# Get the modification date for the model file -
df = DataFile(fPath=self.__testFile2)
currentModelTimeStamp = df.srcModTimeStamp()
self.__lfh.write("+StatusHistoryTests.testCreateHistory() model file modification time %r\n" % currentModelTimeStamp)
#
#
sH = StatusHistory(siteId=self.__siteId, fileSource="archive", sessionPath=self.__sessionPath, verbose=self.__verbose, log=self.__lfh)
numHist = sH.setEntryId(entryId=sD["entry_id"], pdbId=sD["pdb_id"])
self.__lfh.write("Status history count %r\n" % numHist)
#
# New status history? The first record of a new file will mark the PROC->AUTH transition with at one
# additional record depending on the current status state.
#
if (numHist < 1) and (statusCode not in ["PROC"]):
sH.add(
statusCodeBegin="PROC",
dateBegin=initialDepositionDate,
statusCodeEnd="AUTH",
dateEnd=beginProcessingDate,
annotator=annotatorInitials,
details="Automated entry",
)
if statusCode in ["REL"]:
sH.add(
statusCodeBegin="AUTH", dateBegin=beginProcessingDate, statusCodeEnd=statusCode, dateEnd=releaseDate, annotator=annotatorInitials, details="Automated entry"
)
elif statusCode in ["HOLD", "HPUB"]:
sH.add(
statusCodeBegin="AUTH",
dateBegin=beginProcessingDate,
statusCodeEnd=statusCode,
dateEnd=authorApprovalDate,
annotator=annotatorInitials,
details="Automated entry",
)
elif statusCode in ["AUCO", "REPL"]:
sH.add(
statusCodeBegin="AUTH",
dateBegin=beginProcessingDate,
statusCodeEnd=statusCode,
dateEnd=currentModelTimeStamp,
annotator=annotatorInitials,
details="Automated entry",
)
else:
pass
#
(lastStatus, lastDate) = sH.getLastStatusAndDate()
self.__lfh.write("+StatusHistoryTests.testCreateHistory() last values %r %r\n" % (lastStatus, lastDate))
#
# Save the current status history file --
ok = sH.store(entryId=sD["entry_id"])
#
#
# Recover the contents of the current history file -
#
sH = StatusHistory(siteId=self.__siteId, fileSource="archive", sessionPath=self.__sessionPath, verbose=self.__verbose, log=self.__lfh)
ok = sH.setEntryId(entryId=sD["entry_id"], pdbId=sD["pdb_id"])
self.__lfh.write("Status is %r\n" % ok)
dList = sH.get()
for ii, d in enumerate(dList):
self.__lfh.write("Row %r : %r\n" % (ii, d.items()))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
endTime = time.time()
self.__lfh.write("\nCompleted StatusHistoryTests testCreateHistory at %s (%.2f seconds)\n" % (time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - startTime))
def testInstantiate(self):
_vc = DataFile()
_vc = mmCIFUtil() # noqa: F841
def testCopyTimeModeToday(self):
self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
fPath = os.path.join(self.__testFilePath, self.__testFile)
f1 = DataFile(fPath)
f1.pr(self.lfh)
#
f1.timeMode("today")
for fn in self.__outFileList:
fp = os.path.join(self.__outPath, fn)
f1.copy(fp)
f1.pr(self.lfh)
self.lfh.write("Files are the same = %s\n" % str(f1.compare()))
self.lfh.write("Source newer than %s\n" % f1.newerThan(fp))
f2 = DataFile(fp)
if f2.srcFileExists():
f2.remove()
except: # noqa: E722 # pragma: no cover
traceback.print_exc(file=sys.stdout)
self.fail()
def testMove(self):
"""Tests moving file -- and timemodes"""
self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
f1path = os.path.join(TESTOUTPUT, "startfile.tst")
f2path = os.path.join(TESTOUTPUT, "movedest.tst")
f3path = os.path.join(TESTOUTPUT, "appendest.tst")
if os.path.exists(f3path):
os.remove(f3path)
f1 = DataFile(os.path.join(TESTOUTPUT, "nonexistant"))
self.assertEqual(f1.srcFileSize(), 0)
# For test coverage
f1.src(f1path)
f3len = 0
for tmode in ["preserve", "today", "yesterday", "tomorrow", "lastweek"]:
for f in [f1path, f2path]:
if os.path.exists(f):
os.remove(f)
with open(f1path, "w") as f:
f.write(tmode)
pass
d1 = DataFile(f1path)
d1.timeMode(tmode)
self.assertTrue(d1.setSrcFileMode(0o644))
self.assertEqual(d1.srcFileSize(), len(tmode))
# Pre copy - no dst set
self.assertEqual(d1.dstFileSize(), 0)
# Test append
d1.append(f3path)
f3len += len(tmode)
d3 = DataFile(f3path)
self.assertEqual(d3.srcFileSize(), f3len)
d1.move(f2path)
self.assertTrue(d1.setDstFileMode(0o644))
self.assertEqual(d1.dstFileSize(), len(tmode))
def testTimes(self):
"""Tests accessing times"""
self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
fList = [self.__testFile, self.__testFileGzip, self.__testFileZlib, self.__testFileBzip]
for fn in fList:
fPath = os.path.join(self.__testFilePath, fn)
f1 = DataFile(fPath)
self.assertIsNotNone(f1.srcModTimeStamp())
# Test non existant case
f1 = DataFile(os.path.join(TESTOUTPUT, "nonexistant"))
self.assertIsNone(f1.srcModTimeStamp())
# newerThan testing
f1path = os.path.join(TESTOUTPUT, "file1.tst")
f2path = os.path.join(TESTOUTPUT, "file2.tst")
for f in [f1path, f2path]:
if os.path.exists(f):
os.remove(f)
# touch file
with open(f, "w") as f:
pass
# So timestamp not same
time.sleep(1.2)
d1 = DataFile(f1path)
self.assertIsNone(d1.newerThan(None))
self.assertIsNone(d1.newerThan(os.path.join(TESTOUTPUT, "nonexistant")))
self.assertFalse(d1.newerThan(f2path))
d2 = DataFile(f2path)
self.assertTrue(d2.newerThan(f1path))
# Compare same times
self.assertFalse(d1.newerThan(f1path))
# f1 is still nonexistant
self.assertIsNone(f1.newerThan(f2path))
def testSymbolicLinks(self):
self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
fList = [self.__testFile, self.__testFileGzip, self.__testFileZlib, self.__testFileBzip]
for fn in fList:
fPath = os.path.join(self.__testFilePath, fn)
f1 = DataFile(fPath)
fp = os.path.join(self.__outPath, fn)
f1.symLinkRelative(fp)
f1.pr()
self.lfh.write("Files are the same = %s\n" % str(f1.compare()))
self.lfh.write("Source newer than %s\n" % str(f1.newerThan(fp)))
f2 = DataFile(fp)
if f2.srcFileExists():
f2.remove()
except: # noqa: E722 # pragma: no cover
traceback.print_exc(file=sys.stdout)
self.fail()