def annotateEntry(entryCodeNew, *extraArgList):
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = []
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTerror("Got arguments: " + repr(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" % (
expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# entryCode, city = entryCodePlusCity.split('_')
# Adjust the parameters below
isInteractive = False
sourceIsOrgProject = True
checkOrgProject = False
replaceCoordinates = True # From all *.pdb files in inputDir.
replaceRestraints = True
doSwapCheck = True
doSaveProject = True
doExport = True
minimalPrompts = True
verbose = True
if isInteractive:
allowPopups = True
minimalPrompts = False
# verbose = True
else:
allowPopups = False
# minimalPrompts = True
# verbose = False
print 'allowPopups ', allowPopups
print 'isInteractive ', isInteractive
print 'minimalPrompts ', minimalPrompts
print 'verbose ', verbose
print 'sourceIsOrgProject (or new CCPN file) ', sourceIsOrgProject
print 'checkOrgProject ', checkOrgProject
print 'replaceCoordinates ', replaceCoordinates
print 'replaceRestraints ', replaceRestraints
print 'doSwapCheck ', doSwapCheck
print 'doSaveProject ', doSaveProject
print 'doExport ', doExport
guiRoot = None
if allowPopups:
guiRoot = Tkinter.Tk()
entryCode,city = mapEntrycodeNew2EntrycodeAndCity[entryCodeNew]
ch23 = entryCode[1:3]
entryCodeOrg = entryCode + 'Org'
dataOrgEntryDir = os.path.join(dataDir, ch23, entryCodeOrg)
ccpnFile = os.path.join(dataOrgEntryDir, entryCodeOrg + ".tgz")
# entryCodeNew = entryCode + city
programId = getDeepByKeys(programHoH, entryCode, city)
if not (city == 'Test' or programId):
# nTdebug("Skipping %s" % entryCodeNew)
nTerror("Neither City is 'Test' or programId given")
return
else:
nTdebug("Looking at %s" % entryCodeNew)
# continue # TODO disable premature stop.
dataDividedXDir = os.path.join(dataDir, ch23)
entryDir = os.path.join(dataDividedXDir, entryCodeNew)
inputAuthorDir = os.path.join(entryDir, 'Author')
outputNijmegenDir = os.path.join(entryDir, 'Nijmegen')
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
presets = getDeepByKeysOrDefault(presetDict, {}, entryCodeNew)
if presets:
nTmessage("In annotateLoop using preset values...")
# end if
if sourceIsOrgProject:
if os.path.exists(entryCodeOrg):
nTmessage("Removing previous Org directory: %s" % entryCodeOrg)
rmtree(entryCodeOrg)
do_cmd("tar -xzf " + ccpnFile)
if os.path.exists(entryCodeNew):
nTmessage("Removing previous directory: %s" % entryCodeNew)
rmtree(entryCodeNew)
copytree(entryCodeOrg, entryCodeNew)
if checkOrgProject:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entryCodeOrg, status='new')
if not project.initCcpn(ccpnFolder=ccpnFile, modelCount=1):
nTerror("Failed check of original project")
return
project.removeFromDisk()
project.close(save=False)
ccpnProject = loadProject(entryCodeNew)
if not ccpnProject:
nTerror("Failed to read project: %s" % entryCodeNew)
return
# nmrProject = ccpnProject.currentNmrProject
# ccpnMolSystem = ccpnProject.findFirstMolSystem()
# nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if replaceCoordinates or replaceRestraints:
if programId == CYANA:
importCyanaCoorAndRes(ccpnProject, inputAuthorDir, guiRoot,
replaceCoordinates=replaceCoordinates, replaceRestraints=replaceRestraints,
allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **presets)
elif programId == XPLOR:
importXplorCoorAndRes(ccpnProject, inputAuthorDir, guiRoot,
replaceCoordinates=replaceCoordinates, replaceRestraints=replaceRestraints,
allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **presets)
elif programId == PDB:
importPseudoPdb(ccpnProject, inputAuthorDir, guiRoot,
allowPopups=allowPopups, minimalPrompts=minimalPrompts, verbose=verbose, **presets)
else:
nTerror("Failed to doImportCoordinatesAndRestraints because action for program Id not coded for: %s" % programId)
nTerror("Skipping entry")
return
if doSwapCheck:
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore()
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
numSwapCheckRuns = 3
if nmrConstraintStore:
if structureEnsemble:
swapCheck(nmrConstraintStore, structureEnsemble, numSwapCheckRuns)
else:
nTmessage("Failed to find structureEnsemble; skipping swapCheck")
else:
nTmessage("Failed to find nmrConstraintStore; skipping swapCheck")
# constraintsHandler.swapCheck(nmrConstraintStore, structureEnsemble, numSwapCheckRuns)
if doSaveProject:
# nTmessage('Checking validity and saving to new path')
nTmessage('Saving to new path: %s' % entryCodeNew)
# checkValid=True,
saveProject(ccpnProject, newPath=entryCodeNew, removeExisting=True)
if doExport:
tarPath = os.path.join(entryDir, entryCodeNew + ".tgz")
if os.path.exists(tarPath):
nTmessage("Overwriting: " + tarPath)
myTar = tarfile.open(tarPath, mode='w:gz') # overwrites
myTar.add(entryCodeNew)
myTar.close()
if guiRoot:
guiRoot.destroy()
def annotateEntry(entry_code, bmrb_id, *extraArgList):
'Return True on error'
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = []
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTerror("Got arguments: " + repr(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" %
(expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# entry_code, city = entryCodePlusCity.split('_')
# Adjust the parameters below
isInteractive = False
checkOrgProject = False
doSwapCheck = False
doSaveProject = True
doExport = True
minimalPrompts = True
verbose = True
allowPopups = False
if isInteractive:
allowPopups = True
minimalPrompts = False
# verbose = True
else:
pass
# minimalPrompts = True
# verbose = False
print 'entry_code ', entry_code
print 'bmrb_id ', bmrb_id
print 'allowPopups ', allowPopups
print 'isInteractive ', isInteractive
print 'minimalPrompts ', minimalPrompts
print 'verbose ', verbose
print 'checkOrgProject ', checkOrgProject
print 'doSwapCheck ', doSwapCheck
print 'doSaveProject ', doSaveProject
print 'doExport ', doExport
guiRoot = None
if allowPopups:
guiRoot = Tkinter.Tk()
ch23 = entry_code[1:3]
dataOrgEntryDir = os.path.join(results_dir, 'recoordSync', entry_code)
ccpnFile = os.path.join(dataOrgEntryDir, entry_code + ".tgz")
if not os.path.exists(ccpnFile):
nTerror("Input file not found: %s" % ccpnFile)
return True
nTdebug("Looking at %s" % entry_code)
# continue # TODO disable premature stop.
bmrb_code = 'bmr' + bmrb_id
digits12 = "%02d" % (bmrb_id % 100)
inputStarDir = os.path.join(bmrbDir, digits12)
if not os.path.exists(inputStarDir):
nTerror("Input star dir not found: %s" % inputStarDir)
return True
inputStarFile = os.path.join(inputStarDir, '%s.str' % bmrb_code)
if not os.path.exists(inputStarFile):
nTerror("inputStarFile not found: %s" % inputStarFile)
return True
dataDividedXDir = os.path.join(nrgPlusDir, ch23)
entryDir = os.path.join(dataDividedXDir, entry_code)
outputNijmegenDir = os.path.join(entryDir, 'Nijmegen')
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
presets = getDeepByKeysOrDefault(presetDict, {}, bmrb_code)
if presets:
nTmessage("In annotateLoop using preset values...")
nTdebug(str(presets))
if os.path.exists(entry_code):
nTmessage("Removing previous directory: %s" % entry_code)
rmtree(entry_code)
do_cmd("tar -xzf " + ccpnFile)
if os.path.exists('linkNmrStarData'):
nTmessage("Renaming standard directory linkNmrStarData to entry: %s" %
entry_code)
os.rename('linkNmrStarData', entry_code)
if checkOrgProject:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entry_code, status='new')
if not project.initCcpn(ccpnFolder=ccpnFile, modelCount=1):
nTerror("Failed check of original project")
return True
project.removeFromDisk()
project.close(save=False)
ccpnProject = loadProject(entry_code)
if not ccpnProject:
nTerror("Failed to read project: %s" % entry_code)
return True
# nmrProject = ccpnProject.currentNmrProject
# ccpnMolSystem = ccpnProject.findFirstMolSystem()
# nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
importStarChemicalShifts(ccpnProject,
inputStarDir,
guiRoot,
allowPopups=allowPopups,
minimalPrompts=minimalPrompts,
verbose=verbose,
**presets)
if doSwapCheck:
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore()
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
numSwapCheckRuns = 3
if nmrConstraintStore:
if structureEnsemble:
swapCheck(nmrConstraintStore, structureEnsemble,
numSwapCheckRuns)
else:
nTmessage(
"Failed to find structureEnsemble; skipping swapCheck")
else:
nTmessage("Failed to find nmrConstraintStore; skipping swapCheck")
# constraintsHandler.swapCheck(nmrConstraintStore, structureEnsemble, numSwapCheckRuns)
if doSaveProject:
# nTmessage('Checking validity and saving to new path')
nTmessage('Saving to new path')
# checkValid=True,
saveProject(ccpnProject, newPath=entry_code, removeExisting=True)
if doExport:
tarPath = os.path.join(entryDir, entry_code + ".tgz")
if os.path.exists(tarPath):
nTmessage("Overwriting: " + tarPath)
myTar = tarfile.open(tarPath, mode='w:gz') # overwrites
myTar.add(entry_code)
myTar.close()
if guiRoot:
guiRoot.destroy()
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = False # default: False
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doQueeny = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
# NB leave this set to True or modify code below.
removeCcpnDirectory = 1 # perhaps not so in the future.
modelCount = None # default setting is None
# ranges = None
if fastestTest:
modelCount = 2 # if this is more and there is only one model present it leads to an error message.
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doQueeny = False
doTalos = False
forceRedo = True
forceRetrieveInput = True
nTmessage(header)
nTmessage(getStartMessage())
# Sync below code with nrgCing#createToposTokens
expectedArgumentList = """
verbosity inputDir outputDir
pdbConvention restraintsConvention archiveType projectType
storeCING2db ranges filterTopViolations filterVasco
singleCoreOperation
""".split()
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTmessage("consider updating code to include all sequential parameters: %s" % str(expectedArgumentList))
if len(extraArgList) > expectedNumberOfArguments:
nTerror("Got arguments: " + str(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" % (
expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# end if
# end if
entryCodeChar2and3 = entryId[1:3]
cing.verbosity = int( extraArgList[IDX_VERBOSITY] )
inputDir = extraArgList[IDX_INPUT]
outputDir = os.path.join(extraArgList[IDX_OUTPUT], DATA_STR, entryCodeChar2and3, entryId)
pdbConvention = extraArgList[IDX_PDB] #@UnusedVariable
restraintsConvention = extraArgList[IDX_RESTRAINTS]
archiveType = extraArgList[IDX_ARCHIVE] # Only used for deriving the input location not the output.
projectType = extraArgList[IDX_PROJECT_TYPE]
storeCING2db = stringMeansBooleanTrue( getDeepByKeysOrAttributes(extraArgList, IDX_STORE_DB))
ranges = getDeepByKeysOrAttributes(extraArgList, IDX_RANGES)
filterTopViolations = getDeepByKeysOrAttributes(extraArgList, IDX_FILTER_TOP)
if filterTopViolations:
filterTopViolations = int(filterTopViolations) # change '0' to 0
filterVasco = getDeepByKeysOrAttributes(extraArgList, IDX_FILTER_VASCO)
if filterVasco:
filterVasco = int(filterVasco)
else:
filterVasco = 1 # Default should be True
# end if
singleCoreOperation = getDeepByKeysOrAttributes(extraArgList, IDX_SINGLE_CORE_OPERATION )
if singleCoreOperation:
singleCoreOperation = int(singleCoreOperation)
else:
singleCoreOperation = 0 # Default should be True
# end if
if archiveType == ARCHIVE_TYPE_FLAT:
pass # default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
isRemoteOutputDir = False
if '@' in outputDir:
isRemoteOutputDir = True
# end if
# vc = vCing('.') # argument is a fake master_ssh_url not needed here.
archive_id = getArchiveIdFromDirectoryName( outputDir )
nTdebug("Using program arguments:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
nTdebug("filterTopViolations: %s" % filterTopViolations)
nTdebug("filterVasco: %s" % filterVasco)
nTdebug("singleCoreOperation: %s" % singleCoreOperation)
nTdebug("")
nTdebug("Using derived settings:")
nTdebug("modelCount: %s" % modelCount)
nTdebug("isRemoteOutputDir: %s" % isRemoteOutputDir)
nTdebug("archive_id: %s" % archive_id)
# For NMR_REDO required as most efficient.
if singleCoreOperation:
setToSingleCoreOperation()
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if forceRedo:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
if isRemoteOutputDir:
os.chdir(cingDirTmp)
else:
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
formatFileName = '%s.tgz'
if projectType == PROJECT_TYPE_CING:
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
allowedInputProtocolList = 'http file ssh'.split()
inputProtocal = string.split( inputDir, ':' )[0]
if inputProtocal in allowedInputProtocolList:
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if forceRetrieveInput:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId, inputDir, archiveType=archiveType, formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
else:
nTdebug("Entry not retrieved which might be normal in some situations.")
# end if.
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
# fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
# shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
pdbFilePath = entryId + ".pdb"
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC, nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# end if
if ranges is not None:
project.molecule.setRanges(ranges)
# end if
if archive_id:
project.molecule.setArchiveId(archive_id)
# end if
project.molecule.superpose(ranges=ranges)
if filterTopViolations and not project.filterHighRestraintViol():
nTerror("Failed to filterHighRestraintViol")
####> MAIN UTILITY HERE
if 0: # DEFAULT 0
project.save()
if project.validate(htmlOnly=htmlOnly, ranges=ranges, doProcheck=doProcheck, doWhatif=doWhatif,
doWattos=doWattos, doQueeny = doQueeny, doTalos=doTalos, filterVasco = filterVasco ):
nTerror("Failed to validate project read")
return True
# end if filterVasco
# Write a single PDB file containing all models
# according to IUPAC conventions
project.export2PDB()
project.save()
if storeCING2db and archive_id:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
# archive_id = ARCHIVE_DEV_NRG_ID
# if isProduction:
# archive_id = ARCHIVE_NRG_ID
try:
if doStoreCING2db( entryId, archive_id, project=project):
nTerror("Failed to store CING project's data to DB but continuing.")
except:
nTtracebackError()
nTerror("Failed to store CING project's data due to above traceback error.")
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
os.unlink(fileNameTgz) # temporary ccpn tgz
if removeCcpnDirectory:
rmdir(entryId) # ccpn dir may contain vasco info.
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
nTdebug("cmd: %s" % cmd)
# do_cmd(cmd)
status, result = commands.getstatusoutput(cmd)
if status:
nTerror("Failed to tar status: %s with result %s" % (status, result))
return True
if isRemoteOutputDir:
if putFileBySsh(tgzFileNameCing, outputDir, ntriesMax = 2):
nTerror("Failed to send File By Scp status: %s with result %s" % (status, result))
nTerror("Maintaining results.")
return True
# end if
nTmessage("Removing tgz result: %s" % tgzFileNameCing)
os.remove(tgzFileNameCing)
nTmessage("Removing cing dir itself: %s" % directoryNameCing)
rmdir(directoryNameCing)
else: # do NOT remove local copy
pass
job = job_list[id]
_do_cmd, cmdTuple = job
cmd = cmdTuple[0]
nTerror("In runSlave Failed forked: %s" % cmd)
# end for
# end def
# end class
if __name__ == "__main__":
cing.verbosity = verbosityDebug
nTmessage(header)
nTmessage(getStartMessage())
vc = Vcing(cmdDict=cmdDict)
nTmessage("Starting with %r" % vc)
destination = sys.argv[1]
startArgListOther = 2
argListOther = []
if len(sys.argv) > startArgListOther:
argListOther = sys.argv[startArgListOther:]
# end if
nTmessage('\nGoing to destination: %s with(out) arguments %s' %
(destination, str(argListOther)))
try:
if destination == 'runSlaveThread':
if vc.runSlaveThread():
def annotateEntry(entry_code, bmrb_id, *extraArgList):
'Return True on error'
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = []
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTerror("Got arguments: " + repr(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" % (
expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# entry_code, city = entryCodePlusCity.split('_')
# Adjust the parameters below
isInteractive = False
checkOrgProject = False
doSwapCheck = False
doSaveProject = True
doExport = True
minimalPrompts = True
verbose = True
allowPopups = False
if isInteractive:
allowPopups = True
minimalPrompts = False
# verbose = True
else:
pass
# minimalPrompts = True
# verbose = False
print 'entry_code ', entry_code
print 'bmrb_id ', bmrb_id
print 'allowPopups ', allowPopups
print 'isInteractive ', isInteractive
print 'minimalPrompts ', minimalPrompts
print 'verbose ', verbose
print 'checkOrgProject ', checkOrgProject
print 'doSwapCheck ', doSwapCheck
print 'doSaveProject ', doSaveProject
print 'doExport ', doExport
guiRoot = None
if allowPopups:
guiRoot = Tkinter.Tk()
ch23 = entry_code[1:3]
dataOrgEntryDir = os.path.join(results_dir, 'recoordSync', entry_code)
ccpnFile = os.path.join(dataOrgEntryDir, entry_code + ".tgz")
if not os.path.exists(ccpnFile):
nTerror("Input file not found: %s" % ccpnFile)
return True
nTdebug("Looking at %s" % entry_code)
# continue # TODO disable premature stop.
bmrb_code = 'bmr'+bmrb_id
digits12 ="%02d" % ( bmrb_id % 100 )
inputStarDir = os.path.join(bmrbDir, digits12)
if not os.path.exists(inputStarDir):
nTerror("Input star dir not found: %s" % inputStarDir)
return True
inputStarFile = os.path.join(inputStarDir, '%s.str'%bmrb_code)
if not os.path.exists(inputStarFile):
nTerror("inputStarFile not found: %s" % inputStarFile)
return True
dataDividedXDir = os.path.join(nrgPlusDir, ch23)
entryDir = os.path.join(dataDividedXDir, entry_code)
outputNijmegenDir = os.path.join(entryDir, 'Nijmegen')
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
presets = getDeepByKeysOrDefault(presetDict, {}, bmrb_code)
if presets:
nTmessage("In annotateLoop using preset values...")
nTdebug(str(presets))
if os.path.exists(entry_code):
nTmessage("Removing previous directory: %s" % entry_code)
rmtree(entry_code)
do_cmd("tar -xzf " + ccpnFile)
if os.path.exists('linkNmrStarData'):
nTmessage("Renaming standard directory linkNmrStarData to entry: %s" % entry_code)
os.rename('linkNmrStarData', entry_code)
if checkOrgProject:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entry_code, status='new')
if not project.initCcpn(ccpnFolder=ccpnFile, modelCount=1):
nTerror("Failed check of original project")
return True
project.removeFromDisk()
project.close(save=False)
ccpnProject = loadProject(entry_code)
if not ccpnProject:
nTerror("Failed to read project: %s" % entry_code)
return True
# nmrProject = ccpnProject.currentNmrProject
# ccpnMolSystem = ccpnProject.findFirstMolSystem()
# nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
importStarChemicalShifts(ccpnProject, inputStarDir, guiRoot, allowPopups=allowPopups, minimalPrompts=minimalPrompts,
verbose=verbose, **presets)
if doSwapCheck:
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore()
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
numSwapCheckRuns = 3
if nmrConstraintStore:
if structureEnsemble:
swapCheck(nmrConstraintStore, structureEnsemble, numSwapCheckRuns)
else:
nTmessage("Failed to find structureEnsemble; skipping swapCheck")
else:
nTmessage("Failed to find nmrConstraintStore; skipping swapCheck")
# constraintsHandler.swapCheck(nmrConstraintStore, structureEnsemble, numSwapCheckRuns)
if doSaveProject:
# nTmessage('Checking validity and saving to new path')
nTmessage('Saving to new path')
# checkValid=True,
saveProject(ccpnProject, newPath=entry_code, removeExisting=True)
if doExport:
tarPath = os.path.join(entryDir, entry_code + ".tgz")
if os.path.exists(tarPath):
nTmessage("Overwriting: " + tarPath)
myTar = tarfile.open(tarPath, mode='w:gz') # overwrites
myTar.add(entry_code)
myTar.close()
if guiRoot:
guiRoot.destroy()
#!/usr/bin/env python
# Execute like:
# $CINGROOT/python/cing/Scripts/vCing/test/cingByVCtest.py a b
from cing import header
from cing.Libs.NTutils import * #@UnusedWildImport
from cing.main import getStartMessage
from cing.main import getStopMessage
if __name__ == "__main__":
cing.verbosity = verbosityDebug
nTmessage(header)
nTmessage(getStartMessage())
nTmessage("Starting program: %s" % sys.argv[0])
nTdebug("Argument retrieved: %s" % str(sys.argv[1:] ))
nTmessage(getStopMessage(cing.starttime))
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = False # default: False
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doQueeny = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
# NB leave this set to True or modify code below.
removeCcpnDirectory = 1 # perhaps not so in the future.
modelCount = None # default setting is None
# ranges = None
if fastestTest:
modelCount = 2 # if this is more and there is only one model present it leads to an error message.
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doQueeny = False
doTalos = False
forceRedo = True
forceRetrieveInput = True
nTmessage(header)
nTmessage(getStartMessage())
# Sync below code with nrgCing#createToposTokens
expectedArgumentList = """
verbosity inputDir outputDir
pdbConvention restraintsConvention archiveType projectType
storeCING2db ranges filterTopViolations filterVasco
singleCoreOperation
""".split()
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTmessage(
"consider updating code to include all sequential parameters: %s" %
str(expectedArgumentList))
if len(extraArgList) > expectedNumberOfArguments:
nTerror("Got arguments: " + str(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" %
(expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
# end if
# end if
entryCodeChar2and3 = entryId[1:3]
cing.verbosity = int(extraArgList[IDX_VERBOSITY])
inputDir = extraArgList[IDX_INPUT]
outputDir = os.path.join(extraArgList[IDX_OUTPUT], DATA_STR,
entryCodeChar2and3, entryId)
pdbConvention = extraArgList[IDX_PDB] #@UnusedVariable
restraintsConvention = extraArgList[IDX_RESTRAINTS]
archiveType = extraArgList[
IDX_ARCHIVE] # Only used for deriving the input location not the output.
projectType = extraArgList[IDX_PROJECT_TYPE]
storeCING2db = stringMeansBooleanTrue(
getDeepByKeysOrAttributes(extraArgList, IDX_STORE_DB))
ranges = getDeepByKeysOrAttributes(extraArgList, IDX_RANGES)
filterTopViolations = getDeepByKeysOrAttributes(extraArgList,
IDX_FILTER_TOP)
if filterTopViolations:
filterTopViolations = int(filterTopViolations) # change '0' to 0
filterVasco = getDeepByKeysOrAttributes(extraArgList, IDX_FILTER_VASCO)
if filterVasco:
filterVasco = int(filterVasco)
else:
filterVasco = 1 # Default should be True
# end if
singleCoreOperation = getDeepByKeysOrAttributes(extraArgList,
IDX_SINGLE_CORE_OPERATION)
if singleCoreOperation:
singleCoreOperation = int(singleCoreOperation)
else:
singleCoreOperation = 0 # Default should be True
# end if
if archiveType == ARCHIVE_TYPE_FLAT:
pass # default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
isRemoteOutputDir = False
if '@' in outputDir:
isRemoteOutputDir = True
# end if
# vc = vCing('.') # argument is a fake master_ssh_url not needed here.
archive_id = getArchiveIdFromDirectoryName(outputDir)
nTdebug("Using program arguments:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
nTdebug("filterTopViolations: %s" % filterTopViolations)
nTdebug("filterVasco: %s" % filterVasco)
nTdebug("singleCoreOperation: %s" % singleCoreOperation)
nTdebug("")
nTdebug("Using derived settings:")
nTdebug("modelCount: %s" % modelCount)
nTdebug("isRemoteOutputDir: %s" % isRemoteOutputDir)
nTdebug("archive_id: %s" % archive_id)
# For NMR_REDO required as most efficient.
if singleCoreOperation:
setToSingleCoreOperation()
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if forceRedo:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
if isRemoteOutputDir:
os.chdir(cingDirTmp)
else:
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
formatFileName = '%s.tgz'
if projectType == PROJECT_TYPE_CING:
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
allowedInputProtocolList = 'http file ssh'.split()
inputProtocal = string.split(inputDir, ':')[0]
if inputProtocal in allowedInputProtocolList:
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if forceRetrieveInput:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId,
inputDir,
archiveType=archiveType,
formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
else:
nTdebug(
"Entry not retrieved which might be normal in some situations.")
# end if.
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
# fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
# shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
pdbFilePath = entryId + ".pdb"
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath,
convention=IUPAC,
nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# end if
if ranges is not None:
project.molecule.setRanges(ranges)
# end if
if archive_id:
project.molecule.setArchiveId(archive_id)
# end if
project.molecule.superpose(ranges=ranges)
if filterTopViolations and not project.filterHighRestraintViol():
nTerror("Failed to filterHighRestraintViol")
####> MAIN UTILITY HERE
if 0: # DEFAULT 0
project.save()
if project.validate(htmlOnly=htmlOnly,
ranges=ranges,
doProcheck=doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
doQueeny=doQueeny,
doTalos=doTalos,
filterVasco=filterVasco):
nTerror("Failed to validate project read")
return True
# end if filterVasco
# Write a single PDB file containing all models
# according to IUPAC conventions
project.export2PDB()
project.save()
if storeCING2db and archive_id:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
# archive_id = ARCHIVE_DEV_NRG_ID
# if isProduction:
# archive_id = ARCHIVE_NRG_ID
try:
if doStoreCING2db(entryId, archive_id, project=project):
nTerror(
"Failed to store CING project's data to DB but continuing."
)
except:
nTtracebackError()
nTerror(
"Failed to store CING project's data due to above traceback error."
)
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
os.unlink(fileNameTgz) # temporary ccpn tgz
if removeCcpnDirectory:
rmdir(entryId) # ccpn dir may contain vasco info.
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
nTdebug("cmd: %s" % cmd)
# do_cmd(cmd)
status, result = commands.getstatusoutput(cmd)
if status:
nTerror("Failed to tar status: %s with result %s" %
(status, result))
return True
if isRemoteOutputDir:
if putFileBySsh(tgzFileNameCing, outputDir, ntriesMax=2):
nTerror(
"Failed to send File By Scp status: %s with result %s" %
(status, result))
nTerror("Maintaining results.")
return True
# end if
nTmessage("Removing tgz result: %s" % tgzFileNameCing)
os.remove(tgzFileNameCing)
nTmessage("Removing cing dir itself: %s" % directoryNameCing)
rmdir(directoryNameCing)
else: # do NOT remove local copy
pass
from cing.main import getStartMessage
try:
import yasaramodule as yasara #@UnresolvedImport
except:
pass
# nTdebug("Yasara is not available for interactive work in CING; no problem have a homebrew")
MolmolColorDict = dict(green = '0 1 0', orange = '1 0.647 0', red = '1 0 0')
loadTestingFile = True
originatingProgramDeclaration = """Created by:
%s
%s""" % (header, getStartMessage())
originatingProgramDeclaration = toPoundedComment(originatingProgramDeclaration)
molmolMacroFileHeader = """# Execute by issuing command (without pound sign):
# molmol -f THIS_FILE_NAME
""" + originatingProgramDeclaration
pyMolMacroFileHeader = """# Execute by issuing command (without pound sign):
# pymol THIS_FILE_NAME
""" + originatingProgramDeclaration
yasaraMacroFileHeader = """# Execute by issuing command (without pound sign):
# Inside YASARA having the molecule in the soup.
# E.g. sequence:
# Read the PDB file.
# LoadPDB /home/i/2kq3/2kq3.pdb
from cing.main import getStartMessage
try:
import yasaramodule as yasara #@UnresolvedImport
except:
pass
# nTdebug("Yasara is not available for interactive work in CING; no problem have a homebrew")
MolmolColorDict = dict(green = '0 1 0', orange = '1 0.647 0', red = '1 0 0')
loadTestingFile = True
originatingProgramDeclaration = """Created by:
%s
%s""" % (header, getStartMessage())
originatingProgramDeclaration = toPoundedComment(originatingProgramDeclaration)
molmolMacroFileHeader = """# Execute by issuing command (without pound sign):
# molmol -f THIS_FILE_NAME
""" + originatingProgramDeclaration
pyMolMacroFileHeader = """# Execute by issuing command (without pound sign):
# pymol THIS_FILE_NAME
""" + originatingProgramDeclaration
yasaraMacroFileHeader = """# Execute by issuing command (without pound sign):
# Inside YASARA having the molecule in the soup.
# E.g. sequence:
# Read the PDB file.
# LoadPDB /home/i/2kq3/2kq3.pdb
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = True # default: False
# ranges=AUTO_STR # default is None retrieved from DBMS csv files.
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
modelCount = None # default setting is None
if fastestTest:
modelCount = 3
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
force_redo = True
force_retrieve_input = True
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = [ 'inputDir', 'outputDir', 'pdbConvention', 'restraintsConvention', 'archiveType','projectType','storeCING2db']
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTerror("Got arguments: " + repr(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" % (
expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
entryCodeChar2and3 = entryId[1:3]
inputDir = extraArgList[0]
outputDir = os.path.join(extraArgList[1], DATA_STR, entryCodeChar2and3, entryId)
pdbConvention = extraArgList[2] #@UnusedVariable
restraintsConvention = extraArgList[3]
archiveType = extraArgList[4]
projectType = extraArgList[5]
storeCING2db = False
if len(extraArgList) >= expectedNumberOfArguments:
storeCING2db = extraArgList[6]
if archiveType == ARCHIVE_TYPE_FLAT:
pass
# default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
ranges = None
# targetId = getTargetForFullEntryName(entryId)
# if not targetId:
# nTerror("Failed to getTargetForFullEntryName for entryId: %s" % entryId)
# return True
# ranges = getRangesForTarget(targetId)
# if ranges == None:
# nTerror("Failed to getRangesForTarget for targetId: %s" % targetId)
# return True
nTdebug("Using:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("modelCount: %s" % modelCount)
nTdebug("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if force_redo:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
# extension = '.tgz'
formatFileName = '%s.tgz'
# fileNameTgz = entryId + '.tgz'
if projectType == PROJECT_TYPE_CING:
# fileNameTgz = entryId + '.cing.tgz'
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
# if true will do retrieveTgzFromUrl.
if inputDir.startswith("http") or inputDir.startswith("file"):
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if force_retrieve_input:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId, inputDir, archiveType=archiveType, formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
# end if.
# retrieveTgzFromUrl(entryId, inputDir)
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
# pdbFileFormats = [ entryId + ".pdb", "pdb" + entryId + ".ent.gz" ]
# for pdbFileName in pdbFileFormats:
# pdbFileName = "pdb" + entryId + ".ent.gz"
# # pdbFilePath = os.path.join( inputDir, pdbFileName)
# pdbFilePath = os.path.join(inputDir, pdbFileName)
# if os.path.exists(pdbFilePath):
# break
# tmpPdbFile = None
# if pdbFileName.endswith('.gz'):
pdbFilePath = entryId + ".pdb"
# tmpPdbFile = pdbFilePath
# if os.path.exists(pdbFilePath):
# os.unlink(pdbFilePath)
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC, nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# if inputDirOrg == inputDirCASD_NMR:
# if True: # Default is False for this is specific to CASD-NMR
# nTmessage("Renaming molecule name to entry id: %s" % entryId)
# project.molecule.name = entryId # insufficient since all data is already initialized to disk.
# project.updateProject()
# project.molecule.rename( entryId )
# project.save()
# project.molecule.ranges = ranges # JFD: this doesn't seem to be set there exactly.
project.molecule.superpose(ranges=ranges)
if True:
if project.validate(htmlOnly=htmlOnly, ranges=ranges, doProcheck=doProcheck, doWhatif=doWhatif,
doWattos=doWattos, doTalos=doTalos):
nTerror("Failed to validate project read")
return True
if storeCING2db:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
try:
if doStoreCING2db( entryId, ARCHIVE_CASP_ID, project=project):
nTerror("Failed to store CING project's data to DB but continuing.")
except:
nTtracebackError()
nTerror("Failed to store CING project's data due to above traceback error.")
project.save()
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
# os.unlink(fileNameTgz) # temporary ccpn tgz
rmdir(entryId) # temporary ccpn dir
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
do_cmd(cmd)
def main(entryId, *extraArgList):
"""inputDir may be a directory or a url. A url needs to start with http://.
"""
fastestTest = True # default: False
# ranges=AUTO_STR # default is None retrieved from DBMS csv files.
htmlOnly = False # default: False but enable it for faster runs without some actual data.
doWhatif = True # disables whatif actual run
doProcheck = True
doWattos = True
doTalos = True
tgzCing = True # default: True # Create a tgz for the cing project. In case of a CING project input it will be overwritten.
modelCount = None # default setting is None
if fastestTest:
modelCount = 3
htmlOnly = True
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
force_redo = True
force_retrieve_input = True
nTmessage(header)
nTmessage(getStartMessage())
expectedArgumentList = [
'inputDir', 'outputDir', 'pdbConvention', 'restraintsConvention',
'archiveType', 'projectType', 'storeCING2db'
]
expectedNumberOfArguments = len(expectedArgumentList)
if len(extraArgList) != expectedNumberOfArguments:
nTerror("Got arguments: " + repr(extraArgList))
nTerror("Failed to get expected number of arguments: %d got %d" %
(expectedNumberOfArguments, len(extraArgList)))
nTerror("Expected arguments: %s" % expectedArgumentList)
return True
entryCodeChar2and3 = entryId[1:3]
inputDir = extraArgList[0]
outputDir = os.path.join(extraArgList[1], DATA_STR, entryCodeChar2and3,
entryId)
pdbConvention = extraArgList[2] #@UnusedVariable
restraintsConvention = extraArgList[3]
archiveType = extraArgList[4]
projectType = extraArgList[5]
storeCING2db = False
if len(extraArgList) >= expectedNumberOfArguments:
storeCING2db = extraArgList[6]
if archiveType == ARCHIVE_TYPE_FLAT:
pass
# default
elif archiveType == ARCHIVE_TYPE_BY_ENTRY:
inputDir = os.path.join(inputDir, entryId)
elif archiveType == ARCHIVE_TYPE_BY_CH23:
inputDir = os.path.join(inputDir, entryCodeChar2and3)
elif archiveType == ARCHIVE_TYPE_BY_CH23_BY_ENTRY:
inputDir = os.path.join(inputDir, entryCodeChar2and3, entryId)
ranges = None
# targetId = getTargetForFullEntryName(entryId)
# if not targetId:
# nTerror("Failed to getTargetForFullEntryName for entryId: %s" % entryId)
# return True
# ranges = getRangesForTarget(targetId)
# if ranges == None:
# nTerror("Failed to getRangesForTarget for targetId: %s" % targetId)
# return True
nTdebug("Using:")
nTdebug("inputDir: %s" % inputDir)
nTdebug("outputDir: %s" % outputDir)
nTdebug("pdbConvention: %s" % pdbConvention)
nTdebug("restraintsConvention: %s" % restraintsConvention)
nTdebug("archiveType: %s" % archiveType)
nTdebug("projectType: %s" % projectType)
nTdebug("modelCount: %s" % modelCount)
nTdebug("storeCING2db: %s" % storeCING2db)
nTdebug("ranges: %s" % ranges)
# presume the directory still needs to be created.
cingEntryDir = entryId + ".cing"
if os.path.isdir(cingEntryDir):
if force_redo:
nTmessage("Enforcing a redo")
rmtree(cingEntryDir)
else:
mainIndexFile = os.path.join(cingEntryDir, "index.html")
isDone = os.path.isfile(mainIndexFile)
if isDone:
nTmessage("SKIPPING ENTRY ALREADY DONE")
return
nTmessage("REDOING BECAUSE VALIDATION CONSIDERED NOT DONE.")
rmtree(cingEntryDir)
# end if.
# end if.
os.chdir(outputDir)
project = Project(entryId)
if project.removeFromDisk():
nTerror("Failed to remove existing project (if present)")
return True
# end if.
# extension = '.tgz'
formatFileName = '%s.tgz'
# fileNameTgz = entryId + '.tgz'
if projectType == PROJECT_TYPE_CING:
# fileNameTgz = entryId + '.cing.tgz'
formatFileName = '%s.cing.tgz'
elif projectType == PROJECT_TYPE_PDB:
formatFileName = 'pdb%s.ent.gz'
fileNameTgz = formatFileName % entryId
# nTdebug("fileNameTgz: %s" % fileNameTgz)
# if true will do retrieveTgzFromUrl.
if inputDir.startswith("http") or inputDir.startswith("file"):
stillToRetrieve = False
if os.path.exists(fileNameTgz):
if force_retrieve_input:
os.unlink(fileNameTgz)
stillToRetrieve = True
# end if
else:
stillToRetrieve = True
# end if
if stillToRetrieve:
retrieveTgzFromUrl(entryId,
inputDir,
archiveType=archiveType,
formatFileName=formatFileName)
# end if
if not os.path.exists(fileNameTgz):
nTerror("Tgz should already have been present skipping entry")
return
# end if
# end if.
# retrieveTgzFromUrl(entryId, inputDir)
if projectType == PROJECT_TYPE_CING:
# Needs to be copied because the open method doesn't take a directory argument..
fullFileNameTgz = os.path.join(inputDir, fileNameTgz)
shutil.copy(fullFileNameTgz, '.')
project = Project.open(entryId, status='old')
if not project:
nTerror("Failed to init old project")
return True
elif projectType == PROJECT_TYPE_CCPN:
project = Project.open(entryId, status='new')
if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
nTerror("Failed to init project from ccpn")
return True
elif projectType == PROJECT_TYPE_PDB:
project = Project.open(entryId, status='new')
# pdbFileFormats = [ entryId + ".pdb", "pdb" + entryId + ".ent.gz" ]
# for pdbFileName in pdbFileFormats:
# pdbFileName = "pdb" + entryId + ".ent.gz"
# # pdbFilePath = os.path.join( inputDir, pdbFileName)
# pdbFilePath = os.path.join(inputDir, pdbFileName)
# if os.path.exists(pdbFilePath):
# break
# tmpPdbFile = None
# if pdbFileName.endswith('.gz'):
pdbFilePath = entryId + ".pdb"
# tmpPdbFile = pdbFilePath
# if os.path.exists(pdbFilePath):
# os.unlink(pdbFilePath)
gunzip(fileNameTgz, outputFileName=pdbFilePath, removeOriginal=True)
project.initPDB(pdbFile=pdbFilePath,
convention=IUPAC,
nmodels=modelCount)
# if tmpPdbFile:
if True:
nTdebug("Removing tmp: %s" % pdbFilePath)
os.unlink(pdbFilePath)
# if inputDirOrg == inputDirCASD_NMR:
# if True: # Default is False for this is specific to CASD-NMR
# nTmessage("Renaming molecule name to entry id: %s" % entryId)
# project.molecule.name = entryId # insufficient since all data is already initialized to disk.
# project.updateProject()
# project.molecule.rename( entryId )
# project.save()
# project.molecule.ranges = ranges # JFD: this doesn't seem to be set there exactly.
project.molecule.superpose(ranges=ranges)
if True:
if project.validate(htmlOnly=htmlOnly,
ranges=ranges,
doProcheck=doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
doTalos=doTalos):
nTerror("Failed to validate project read")
return True
if storeCING2db:
# Does require:
#from cing.PluginCode.sqlAlchemy import csqlAlchemy
# and should never crash run.
try:
if doStoreCING2db(entryId, ARCHIVE_CASP_ID, project=project):
nTerror(
"Failed to store CING project's data to DB but continuing."
)
except:
nTtracebackError()
nTerror(
"Failed to store CING project's data due to above traceback error."
)
project.save()
if projectType == PROJECT_TYPE_CCPN:
# fileNameTgz = entryId + '.tgz'
# os.unlink(fileNameTgz) # temporary ccpn tgz
rmdir(entryId) # temporary ccpn dir
if tgzCing:
directoryNameCing = entryId + ".cing"
tgzFileNameCing = directoryNameCing + ".tgz"
if os.path.exists(tgzFileNameCing):
nTwarning("Overwriting: " + tgzFileNameCing)
cmd = "tar -czf %s %s" % (tgzFileNameCing, directoryNameCing)
do_cmd(cmd)
