def convert(projectName, inputDir, projectNameNew):
"Testing doc strings"
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage( 'found ccpnMolSystem: %s' % ccpnMolSystem )
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("Removing first found structureEnsemble -A-")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = ccpnProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose = 1)
globPattern = inputDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern,fileList))
format.readCoordinates(fileList, strucGen = structureGeneration, minimalPrompts = 1, linkAtoms = 0)
nTmessage( 'saving to new path if all checks are valid' )
# the newPath basename will be taken according to ccpn code doc.
ccpnPathNew = os.path.join(inputDir, projectNameNew)
saveProject(ccpnProject, checkValid=True, newPath=ccpnPathNew, removeExisting=True)
def runSpecific(self):
""" Returns True on error """
entryCodeChar2and3 = self.idCode[1:3]
projectDirectory = os.path.join(dir_S, entryCodeChar2and3, self.idCode)
os.chdir(projectDirectory)
curDir = os.getcwd() #@UnusedVariable
nTdebug("curDir: %s" % curDir)
# ccpnDir = self.baseName #@UnusedVariable
# Read the existing CCPN project, set up format object dict
self.loadProject()
self.createFormatObjects()
self.entry = self.ccpnProject.findFirstNmrEntryStore().findFirstEntry()
self.molSystem = self.ccpnProject.findFirstMolSystem()
self.nmrProject = self.ccpnProject.findFirstNmrProject()
self.strucGen = self.nmrProject.findFirstStructureGeneration()
bmrbCodesLength = len(self.bmrbCodes)
if not bmrbCodesLength:
nTerror("Not a single BMRB entry presented.")
return
if bmrbCodesLength > 1:
nTwarning("Currently NRG-CING only loads a single BMRB entry's CS. Skipping others.")
# Read the BMRB NMR-STAR file (only chem shift data)
# for bmrbCode in self.bmrbCodes:
bmrbFile = self.bmrbCodes[0]
bmrbCode = bmrbFile.split('_')[0]
self.initShiftPresets(bmrbCode)
# bmrbNmrStarFile = os.path.join(bmrbArchiveDataDir, self.bmrbFileFormat % bmrbCode)
# bmrb_id = int(bmrbCode[3:])
# digits12 = "%02d" % (bmrb_id % 100)
# inputStarDir = os.path.join(bmrbDir, digits12)
# inputStarDir = os.path.join(bmrbDir, bmrbCode)
# if not os.path.exists(bmrbFile):
# nTerror("Input star dir not found: %s" % bmrbFile)
# return True
inputStarFile = bmrbFile
if not os.path.exists(inputStarFile):
nTerror("inputStarFile not found: %s" % inputStarFile)
return True
nTdebug("Start readNmrStarFile")
self.readNmrStarFile(inputStarFile, components=['measurements'])
# Try to autoset mapping...
nTdebug("Start setBmrbNmrStarMapping")
self.setBmrbNmrStarMapping(inputStarFile)
# Run linkResonances, using custom keywds set above
nTdebug("Start runLinkResonances")
self.runLinkResonances(resonanceType='nmr')
# Save project in new location
newPath = self.baseName
nTmessage('Saving to new path: %s in cwd: %s' % (newPath, os.getcwd()))
saveProject(self.ccpnProject, removeExisting=True, newPath=newPath, newProjectName=self.baseName)
ccpnTgzFile = "%s.tgz" % self.idCode
cmd = "tar -czf %s %s" % (ccpnTgzFile, newPath)
if do_cmd(cmd):
nTerror("Failed tar")
return None
nTmessage("Saved ccpn project to tgz: %s" % ccpnTgzFile)
def saveFile(self):
if not self.project:
return False
try:
saveProject(self.project, createFallback=True)
print 'successfully saved project'
return True
except IOError, e:
showError('Saving file', str(e), parent=self)
return False
def _packageProject(memopsRoot):
"""Create a tar gzipped CCPN project from a MemopsRoot object"""
from memops.general.Io import saveProject, packageProject
repository = memopsRoot.findFirstRepository(name='userData')
if not repository:
return
projectPath = repository.url.path
parentDir, projectDir = os.path.split(projectPath)
writeable = os.access(parentDir, os.W_OK)
if not writeable:
msg = 'Directory %s does not have write access required to write temporary file.'
showWarning('Warning', msg % parentDir)
return
currentProjName = memopsRoot.name
newProjName = '__%s' % currentProjName
newProjDir = os.path.join(parentDir, newProjName)
while os.path.exists(newProjDir):
msg = 'Filename %s exists. Overwrite?' % newProjDir
if showYesNo('Query', msg):
break
newProjName = '_' + newProjName
newProjDir = os.path.join(parentDir, newProjName)
try:
saveProject(memopsRoot, newPath=newProjDir, removeExisting=True, revertToOriginal=True)
packageProject(memopsRoot, filePrefix=newProjDir, userPath=newProjDir)
finally:
# reset project name
# need to use override since name is frozen
# wb104: 6 Feb 2014: should not need to do below any more because added revertToOriginal and userPath above
#memopsRoot.override = True
#memopsRoot.name = currentProjName
#memopsRoot.override = False
pass
return newProjDir + '.tgz'
def convert(projectName, inputDir, projectNameNew):
"Testing doc strings"
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
ccpnPath = os.path.join(inputDir, projectName)
ccpnProject = loadProject(ccpnPath)
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("Removing first found structureEnsemble -A-")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = ccpnProject.newStructureGeneration()
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose=1)
globPattern = inputDir + '/*.pdb'
fileList = glob(globPattern)
nTdebug("From %s will read files: %s" % (globPattern, fileList))
format.readCoordinates(fileList,
strucGen=structureGeneration,
minimalPrompts=1,
linkAtoms=0)
nTmessage('saving to new path if all checks are valid')
# the newPath basename will be taken according to ccpn code doc.
ccpnPathNew = os.path.join(inputDir, projectNameNew)
saveProject(ccpnProject,
checkValid=True,
newPath=ccpnPathNew,
removeExisting=True)
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 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 test_ccpn(self):
# cing.verbosity = verbosityDebug
# if you have a local copy you can use it; make sure to adjust the path setting below.
fastestTest = True # DEFAULT: True. Not passed to the validate routine in order to customize checks for speed.
modelCount = 99 # DEFAULT: 99
redoFromCingProject = False # DEFAULT: False
htmlOnly = False # DEFAULT: False # default is False but enable it for faster runs without some actual data.
doWhatif = True # DEFAULT: True # disables whatif actual run
doProcheck = True # DEFAULT: True
doWattos = True # DEFAULT: True
doQueeny = True # DEFAULT: True
doTalos = True # DEFAULT: True
filterVasco = True # DEFAULT: True
filterTopViolations = True # DEFAULT: True
useNrgArchive = False # DEFAULT: False
ranges = CV_STR # DEFAULT: CV_STR
# ranges='173-177'
# ranges='6-13,29-45' # 1bus
doSwapCheck = False
doRestoreCheck = False
doStoreCheck = False # DEFAULT: False Requires sqlAlchemy
doSave = not redoFromCingProject # DEFAULT: False Requires sqlAlchemy
if fastestTest:
modelCount = 2 # DEFAULT 2
# redoFromCingProject = False
htmlOnly = True # DEFAULT: True
doWhatif = False # DEFAULT: False
doProcheck = False # DEFAULT: False
doWattos = False # DEFAULT: False
doQueeny = False # DEFAULT: False
doTalos = False # DEFAULT: False
filterVasco = False # DEFAULT: False
doRestoreCheck = False # DEFAULT: False
doStoreCheck = False # DEFAULT: False
if redoFromCingProject:
useNrgArchive = False
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for i, entryId in enumerate(AllChecks.entryList):
if i:
nTmessage('\n\n')
if redoFromCingProject:
project = Project.open(entryId, status='old')
else:
project = Project.open(entryId, status='new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if useNrgArchive: # default is False
# inputArchiveDir = os.path.join('/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
# Mounted from nmr.cmbi.ru.nl
# inputArchiveDir = os.path.join('/Volumes/tria1/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
inputArchiveDir = os.path.join(
'/Users/jd/ccpn_tmp/data/recoord', entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
ccpnFile = os.path.join(inputArchiveDir,
entryId + ".tar.gz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
if doSwapCheck: # Need to start with ccpn without loading into CING api yet.
if os.path.exists(entryId):
nTmessage("Removing previous directory: %s" % entryId)
rmtree(entryId)
do_cmd("tar -xzf " +
ccpnFile) # will extract to local dir.
if os.path.exists('linkNmrStarData'):
nTmessage(
"Renaming standard directory linkNmrStarData to entry: %s"
% entryId)
os.rename('linkNmrStarData', entryId)
ccpnProject = loadProject(entryId)
if not ccpnProject:
self.fail("Failed to read project: %s" % entryId)
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore(
)
structureEnsemble = ccpnProject.findFirstStructureEnsemble(
)
numSwapCheckRuns = 2
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)
nTmessage('Saving to new path')
# checkValid=True,
saveProject(ccpnProject,
newPath=entryId,
removeExisting=True)
ccpnFile = entryId # set to local dir now.
# end if doSwapCheck
self.assertTrue(
project.initCcpn(ccpnFolder=ccpnFile,
modelCount=modelCount))
# if doSave:
# self.assertTrue(project.save())
if False:
ranges = "173-183"
# residueOfInterest = range(171,174)
# for residue in project.molecule.A.allResidues():
# if residue.resNum not in residueOfInterest:
# # nTmessage("Removing residue of no interest")
# project.molecule.A.removeResidue(residue)
if False:
ccpnProject = project.ccpn
printSequenceFromCcpnProject(ccpnProject)
if True:
self.assertFalse(project.molecule.setRanges(ranges))
nTdebug('In test_ccpn.py: ranges: %s' %
str(project.molecule.ranges))
project.molecule.rangesToMmCifRanges(ranges)
if True:
self.assertFalse(
project.validate(
htmlOnly=htmlOnly,
ranges=ranges,
# fastestTest=fastestTest, # disabled
doProcheck=doProcheck,
doWhatif=doWhatif,
doWattos=doWattos,
doQueeny=doQueeny,
doTalos=doTalos,
filterVasco=filterVasco,
filterTopViolations=filterTopViolations))
if doWattos and False:
mol = project.molecule
completenessMol = mol.getDeepByKeys(
WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("completenessMol: %s" % completenessMol)
for res in mol.allResidues():
completenessRes = res.getDeepByKeys(
WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("%s: %s" % (res, completenessRes))
# end for
# end if
color = project.molecule.getRogColor()
nTdebug("The color of this molecule is: %s" % color)
self.assertFalse(color == COLOR_RED) # ;-)
# end if
# self.assertTrue(project.exportValidation2ccpn())
# self.assertFalse(project.removeCcpnReferences())
# Do not leave the old CCPN directory laying around since it might get added to by another test.
# if os.path.exists(entryId):
# self.assertFalse(shutil.rmtree(entryId))
if False:
self.assertTrue(project.save())
self.assertTrue(project.saveCcpn(entryId))
if doRestoreCheck:
del project
project = Project.open(entryId, status='old')
self.assertTrue(project,
'Failed reopening project: ' + entryId)
if doStoreCheck:
# # Does require below import which is used here to trigger import warning in case it's not installed.
# pylint: disable=W0612
from cing.PluginCode.sqlAlchemy import CsqlAlchemy #@UnusedImport # pylint: disable=W0404
if doStoreCING2db(entryId, ARCHIVE_NRG_ID, project=project):
nTerror(
"Failed to store CING project's data to DB but continuing."
)
if doSave:
self.assertTrue(project.save())
def makeCcpnProjectTgz(self, baseNameSuffix="", outputDir=None):
#
# Set up
#
userData = self.ccpnProject.findFirstRepository(name='userData')
ccpnProjectDir = userData.url.path
if not outputDir:
outputDir = ccpnProjectDir
tarFileBaseName = os.path.join(outputDir + baseNameSuffix)
tarFileName = "%s.tar" % tarFileBaseName
tgzFileName = "%s.tgz" % tarFileBaseName
#
# Re-save before tarring, in case of changes
#
if baseNameSuffix:
saveProject(self.ccpnProject,
newPath=tarFileBaseName,
removeExisting=True)
ccpnProjectDir = userData.url.path
else:
self.ccpnProject.saveModified()
# TJS: Use Wayne's packageProject, which only packages uses .xml files
packageProject(self.ccpnProject, tarFileBaseName)
"""
#
# Now go to directory containing CCPN project to make .tar file, do not want full path for project!
#
curDir = os.getcwd()
(mainCcpnDir,projectNameDir) = os.path.split(ccpnProjectDir)
os.chdir(mainCcpnDir)
tar = tarfile.open(tarFileName, "w")
tar.add(projectNameDir)
tar.close()
os.chdir(curDir)
#
# Now make .tgz, remove .tar file
#
inFile = open(tarFileName,'rb')
outFile = gzip.open(tgzFileName,'wb')
outFile.writelines(inFile)
outFile.close()
inFile.close()
os.remove(tarFileName)
"""
print " Created .tgz archive %s for CCPN project %s." % (
tgzFileName, self.ccpnProject.name)
return tgzFileName
def fcProcessEntry( entry_code, ccpnTgzFile, outputCcpnTgzFile, functionToRun='swapCheck'):
"""
E.g.
entry_code 1brv
ccpnTgzFile /NRG-CING/prep/S/br/1brv/1brv.tgz Full path
outputCcpnTgzFile 1brv_assign.tgz but inside the project will still be keyed and named 1brv.
Return True on error
Can be extended later on to run a different function.
Will run in cwd.
"""
# Adjust the parameters below
isInteractive = False
doSwapCheck = True
doSaveProject = True
doExport = True
minimalPrompts = True
verbose = True
allowPopups = False
if isInteractive:
allowPopups = True
minimalPrompts = False
print 'entry_code ', entry_code
# print 'bmrb_id ', bmrb_id
print 'allowPopups ', allowPopups
print 'isInteractive ', isInteractive
print 'minimalPrompts ', minimalPrompts
print 'verbose ', verbose
print 'doSwapCheck ', doSwapCheck
print 'doSaveProject ', doSaveProject
print 'doExport ', doExport
guiRoot = None
if allowPopups:
guiRoot = Tkinter.Tk()
if not os.path.exists(ccpnTgzFile):
nTerror("Input file not found: %s" % ccpnTgzFile)
return True
nTdebug("Looking at %s" % entry_code)
if os.path.exists(entry_code):
nTmessage("Removing previous directory: %s" % entry_code)
rmtree(entry_code)
do_cmd("tar -xzf " + ccpnTgzFile) # will unpack to cwd.
if os.path.exists('linkNmrStarData'):
nTmessage("Renaming standard directory linkNmrStarData to entry: %s" % entry_code)
os.rename('linkNmrStarData', entry_code)
ccpnProject = loadProject(entry_code)
if not ccpnProject:
nTerror("Failed to read project: %s" % entry_code)
return True
if doSwapCheck:
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore()
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if nmrConstraintStore:
if structureEnsemble:
swapCheck(nmrConstraintStore, structureEnsemble)
else:
nTmessage("Failed to find structureEnsemble; skipping swapCheck")
else:
nTmessage("Failed to find nmrConstraintStore; skipping swapCheck")
# constraintsHandler.swapCheck(nmrConstraintStore, structureEnsemble, numSwapCheckRuns)
# end if doSwapCheck
if doSaveProject:
nTmessage('Saving to new path: %s' % entry_code)
saveProject(ccpnProject, newPath=entry_code, removeExisting=True)
if doExport:
if os.path.exists(outputCcpnTgzFile):
nTmessage("Overwriting: " + outputCcpnTgzFile)
myTar = tarfile.open(outputCcpnTgzFile, mode='w:gz') # overwrites
myTar.add(entry_code)
myTar.close()
if guiRoot:
guiRoot.destroy()
def runSpecific(self):
""" Returns True on error """
# Read the existing CCPN project, set up format object dict
self.loadProject()
self.createFormatObjects()
self.entry = self.ccpnProject.findFirstNmrEntryStore().findFirstEntry()
self.molSystem = self.ccpnProject.findFirstMolSystem()
self.nmrProject = self.ccpnProject.findFirstNmrProject()
self.strucGen = self.nmrProject.findFirstStructureGeneration()
bmrbCodesLength = len(self.bmrbCodes)
if not bmrbCodesLength:
print("Not a single BMRB entry presented.")
return
if bmrbCodesLength > 1:
print(
"Currently NRG-CING only loads a single BMRB entry's CS. Skipping others."
)
# Read the BMRB NMR-STAR file (only chem shift data)
bmrbCode = self.bmrbCodes[0]
self.initShiftPresets(bmrbCode)
inputStarDir = os.path.join(self.bmrbDir, bmrbCode)
if not os.path.exists(inputStarDir):
print("Input star dir not found: %s" % inputStarDir)
return True
inputStarFile = os.path.join(inputStarDir,
self.bmrbFileFormat % bmrbCode[3:])
if not os.path.exists(inputStarFile):
print("inputStarFile not found: %s" % inputStarFile)
return True
print("Start readNmrStarFile")
self.readNmrStarFile(inputStarFile, components=['measurements'])
# Try to autoset mapping...
print("Start setBmrbNmrStarMapping")
self.setBmrbNmrStarMapping(inputStarFile)
# Run linkResonances, using custom keywds set above
print("Start runLinkResonances")
self.runLinkResonances(resonanceType='nmr')
# Save project in new location
finalProjectDirectory = os.path.join(self.finalProjectMainDir,
self.idCode)
if not os.path.exists(finalProjectDirectory):
os.mkdir(finalProjectDirectory)
print('Saving to new path: %s in cwd: %s' %
(finalProjectDirectory, os.getcwd()))
saveProject(self.ccpnProject,
removeExisting=True,
newPath=finalProjectDirectory,
newProjectName=self.baseName)
# Create .tgz of new project - can do this a bit nicer, quick hack
curDir = os.getcwd()
os.chdir(self.finalProjectMainDir)
tar = tarfile.open("{}.tgz".format(self.baseName), 'w:gz')
print self.baseName
tar.add(self.baseName)
tar.close()
os.chdir(curDir)
# Clean up non-archived CCPN projects to save disk space
shutil.rmtree(self.ccpnProjectDir)
shutil.rmtree(finalProjectDirectory)
def replaceCoordinates():
cityList = [ 'Cheshire', 'Frankfurt', 'Lyon', 'Paris', 'Piscataway', 'Seattle', 'Utrecht' ]
maxCities = 1
maxEntries = 1
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
dataOrgDir = os.path.join(baseDir,DATA_STR)
dataDividedDir = os.path.join(baseDir,DATA_STR)
# _scriptName = sys.argv[0]
# parameters for doScriptOnEntryList
startDir = '/Library/WebServer/Documents/' + CASD_NMR_BASE_NAME
entryListFileName = os.path.join(startDir, 'list', 'entry_list_todo.csv')
entryList = readLinesFromFile(entryListFileName) #@UnusedVariable
entryList = ['ET109Aox']
for entryCode in entryList[0:maxEntries]:
ch23 = entryCode[1:3]
dataOrgEntryDir = os.path.join( dataOrgDir, entryCode )
ccpnFile = os.path.join(dataOrgEntryDir, entryCode+".tgz")
for city in cityList[0:maxCities]:
entryCodeNew = entryCode + city
dataDividedXDir = os.path.join(dataDividedDir, ch23)
inputAuthorDir = os.path.join(dataDividedXDir, entryCodeNew, 'Author')
outputNijmegenDir = os.path.join(dataDividedXDir, entryCodeNew, 'Nijmegen')
globPattern = inputAuthorDir + '/*.pdb'
pdbFileList = glob(globPattern)
if not pdbFileList:
nTmessage("Skipping because there is no PDB file in: " + os.getcwd())
continue
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
if False:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entryCode, status = 'new')
project.initCcpn(ccpnFolder = ccpnFile, modelCount=1)
project.removeFromDisk()
project.close(save=False)
if True:
ccpnProject = loadProject(entryCode)
nmrProject = ccpnProject.currentNmrProject
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage( 'found ccpnMolSystem: %s' % ccpnMolSystem )
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
if structureEnsemble:
nTmessage("Removing first found structureEnsemble")
structureEnsemble.delete()
else:
nTwarning("No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = nmrProject.newStructureGeneration()
fileList = None
nTdebug("From %s will read files: %s" % (globPattern,fileList))
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose = 1)
format.readCoordinates(fileList, strucGen = structureGeneration, minimalPrompts = 1, linkAtoms = 0)
nTmessage( 'saving to new path if all checks are valid' )
# the newPath basename will be taken according to ccpn code doc.
saveProject(ccpnProject, checkValid=True, newPath=entryCodeNew, removeExisting=True)
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 replaceCoordinates():
cityList = [
'Cheshire', 'Frankfurt', 'Lyon', 'Paris', 'Piscataway', 'Seattle',
'Utrecht'
]
maxCities = 1
maxEntries = 1
# Adjust the parameters below!
removeOriginalStructureEnsemble = True
addStructureEnsemble = True # From all *.pdb files in inputDir.
dataOrgDir = os.path.join(baseDir, DATA_STR)
dataDividedDir = os.path.join(baseDir, DATA_STR)
# _scriptName = sys.argv[0]
# parameters for doScriptOnEntryList
startDir = '/Library/WebServer/Documents/' + CASD_NMR_BASE_NAME
entryListFileName = os.path.join(startDir, 'list', 'entry_list_todo.csv')
entryList = readLinesFromFile(entryListFileName) #@UnusedVariable
entryList = ['ET109Aox']
for entryCode in entryList[0:maxEntries]:
ch23 = entryCode[1:3]
dataOrgEntryDir = os.path.join(dataOrgDir, entryCode)
ccpnFile = os.path.join(dataOrgEntryDir, entryCode + ".tgz")
for city in cityList[0:maxCities]:
entryCodeNew = entryCode + city
dataDividedXDir = os.path.join(dataDividedDir, ch23)
inputAuthorDir = os.path.join(dataDividedXDir, entryCodeNew,
'Author')
outputNijmegenDir = os.path.join(dataDividedXDir, entryCodeNew,
'Nijmegen')
globPattern = inputAuthorDir + '/*.pdb'
pdbFileList = glob(globPattern)
if not pdbFileList:
nTmessage("Skipping because there is no PDB file in: " +
os.getcwd())
continue
if not os.path.exists(inputAuthorDir):
mkdirs(inputAuthorDir)
if not os.path.exists(outputNijmegenDir):
mkdirs(outputNijmegenDir)
os.chdir(outputNijmegenDir)
if False:
# By reading the ccpn tgz into cing it is also untarred/tested.
project = Project.open(entryCode, status='new')
project.initCcpn(ccpnFolder=ccpnFile, modelCount=1)
project.removeFromDisk()
project.close(save=False)
if True:
ccpnProject = loadProject(entryCode)
nmrProject = ccpnProject.currentNmrProject
ccpnMolSystem = ccpnProject.findFirstMolSystem()
nTmessage('found ccpnMolSystem: %s' % ccpnMolSystem)
# print 'status: %s' % ccpnMolSystem.setCode(projectName) # impossible; reported to ccpn team.
if removeOriginalStructureEnsemble:
structureEnsemble = ccpnProject.findFirstStructureEnsemble(
)
if structureEnsemble:
nTmessage("Removing first found structureEnsemble")
structureEnsemble.delete()
else:
nTwarning(
"No structureEnsemble found; can't remove it.")
if addStructureEnsemble:
structureGeneration = nmrProject.newStructureGeneration()
fileList = None
nTdebug("From %s will read files: %s" %
(globPattern, fileList))
guiRoot = Tkinter.Tk()
format = PseudoPdbFormat(ccpnProject, guiRoot, verbose=1)
format.readCoordinates(fileList,
strucGen=structureGeneration,
minimalPrompts=1,
linkAtoms=0)
nTmessage('saving to new path if all checks are valid')
# the newPath basename will be taken according to ccpn code doc.
saveProject(ccpnProject,
checkValid=True,
newPath=entryCodeNew,
removeExisting=True)
def runSpecific(self):
""" Returns True on error """
# Read the existing CCPN project, set up format object dict
self.loadProject()
self.createFormatObjects()
self.entry = self.ccpnProject.findFirstNmrEntryStore().findFirstEntry()
self.molSystem = self.ccpnProject.findFirstMolSystem()
self.nmrProject = self.ccpnProject.findFirstNmrProject()
self.strucGen = self.nmrProject.findFirstStructureGeneration()
bmrbCodesLength = len(self.bmrbCodes)
if not bmrbCodesLength:
print("Not a single BMRB entry presented.")
return
if bmrbCodesLength > 1:
print("Currently NRG-CING only loads a single BMRB entry's CS. Skipping others.")
# Read the BMRB NMR-STAR file (only chem shift data)
bmrbCode = self.bmrbCodes[0]
self.initShiftPresets(bmrbCode)
inputStarDir = os.path.join(self.bmrbDir, bmrbCode)
if not os.path.exists(inputStarDir):
print("Input star dir not found: %s" % inputStarDir)
return True
inputStarFile = os.path.join(inputStarDir, self.bmrbFileFormat % bmrbCode[3:])
if not os.path.exists(inputStarFile):
print("inputStarFile not found: %s" % inputStarFile)
return True
print("Start readNmrStarFile")
self.readNmrStarFile(inputStarFile, components=['measurements'])
# Try to autoset mapping...
print("Start setBmrbNmrStarMapping")
self.setBmrbNmrStarMapping(inputStarFile)
# Run linkResonances, using custom keywds set above
print("Start runLinkResonances")
self.runLinkResonances(resonanceType='nmr')
# Save project in new location
finalProjectDirectory = os.path.join(self.finalProjectMainDir,self.idCode)
if not os.path.exists(finalProjectDirectory):
os.mkdir(finalProjectDirectory)
print('Saving to new path: %s in cwd: %s' % (finalProjectDirectory, os.getcwd()))
saveProject(self.ccpnProject, removeExisting=True, newPath=finalProjectDirectory, newProjectName=self.baseName)
# Create .tgz of new project - can do this a bit nicer, quick hack
curDir = os.getcwd()
os.chdir(self.finalProjectMainDir)
tar = tarfile.open("{}.tgz".format(self.baseName),'w:gz')
print self.baseName
tar.add(self.baseName)
tar.close()
os.chdir(curDir)
# Clean up non-archived CCPN projects to save disk space
shutil.rmtree(self.ccpnProjectDir)
shutil.rmtree(finalProjectDirectory)
def test_ccpn(self):
# cing.verbosity = verbosityDebug
# if you have a local copy you can use it; make sure to adjust the path setting below.
fastestTest = True # DEFAULT: True. Not passed to the validate routine in order to customize checks for speed.
modelCount=99 # DEFAULT: 99
redoFromCingProject = False # DEFAULT: False
htmlOnly = False # DEFAULT: False # default is False but enable it for faster runs without some actual data.
doWhatif = True # DEFAULT: True # disables whatif actual run
doProcheck = True # DEFAULT: True
doWattos = True # DEFAULT: True
doQueeny = True # DEFAULT: True
doTalos = True # DEFAULT: True
filterVasco = True # DEFAULT: True
filterTopViolations = True # DEFAULT: True
useNrgArchive = False # DEFAULT: False
ranges = CV_STR # DEFAULT: CV_STR
# ranges='173-177'
# ranges='6-13,29-45' # 1bus
doSwapCheck = False
doRestoreCheck = False
doStoreCheck = False # DEFAULT: False Requires sqlAlchemy
doSave = not redoFromCingProject # DEFAULT: False Requires sqlAlchemy
if fastestTest:
modelCount=2 # DEFAULT 2
# redoFromCingProject = False
htmlOnly = True # DEFAULT: True
doWhatif = False # DEFAULT: False
doProcheck = False # DEFAULT: False
doWattos = False # DEFAULT: False
doQueeny = False # DEFAULT: False
doTalos = False # DEFAULT: False
filterVasco = False # DEFAULT: False
doRestoreCheck = False # DEFAULT: False
doStoreCheck = False # DEFAULT: False
if redoFromCingProject:
useNrgArchive = False
doWhatif = False
doProcheck = False
doWattos = False
doTalos = False
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for i,entryId in enumerate(AllChecks.entryList):
if i:
nTmessage('\n\n')
if redoFromCingProject:
project = Project.open(entryId, status = 'old')
else:
project = Project.open(entryId, status = 'new')
self.assertTrue(project, 'Failed opening project: ' + entryId)
if useNrgArchive: # default is False
# inputArchiveDir = os.path.join('/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
# Mounted from nmr.cmbi.ru.nl
# inputArchiveDir = os.path.join('/Volumes/tria1/Library/WebServer/Documents/NRG-CING/recoordSync', entryId)
inputArchiveDir = os.path.join('/Users/jd/ccpn_tmp/data/recoord', entryId)
else:
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tar.gz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
if doSwapCheck: # Need to start with ccpn without loading into CING api yet.
if os.path.exists(entryId):
nTmessage("Removing previous directory: %s" % entryId)
rmtree(entryId)
do_cmd("tar -xzf " + ccpnFile) # will extract to local dir.
if os.path.exists('linkNmrStarData'):
nTmessage("Renaming standard directory linkNmrStarData to entry: %s" % entryId)
os.rename('linkNmrStarData', entryId)
ccpnProject = loadProject(entryId)
if not ccpnProject:
self.fail("Failed to read project: %s" % entryId)
# constraintsHandler = ConstraintsHandler()
nmrConstraintStore = ccpnProject.findFirstNmrConstraintStore()
structureEnsemble = ccpnProject.findFirstStructureEnsemble()
numSwapCheckRuns = 2
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)
nTmessage('Saving to new path')
# checkValid=True,
saveProject(ccpnProject, newPath=entryId, removeExisting=True)
ccpnFile = entryId # set to local dir now.
# end if doSwapCheck
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile, modelCount=modelCount))
# if doSave:
# self.assertTrue(project.save())
if False:
ranges = "173-183"
# residueOfInterest = range(171,174)
# for residue in project.molecule.A.allResidues():
# if residue.resNum not in residueOfInterest:
# # nTmessage("Removing residue of no interest")
# project.molecule.A.removeResidue(residue)
if False:
ccpnProject = project.ccpn
printSequenceFromCcpnProject(ccpnProject)
if True:
self.assertFalse(project.molecule.setRanges(ranges))
nTdebug('In test_ccpn.py: ranges: %s' % str(project.molecule.ranges))
project.molecule.rangesToMmCifRanges(ranges)
if True:
self.assertFalse(project.validate(htmlOnly = htmlOnly,
ranges=ranges,
# fastestTest=fastestTest, # disabled
doProcheck = doProcheck,
doWhatif = doWhatif,
doWattos=doWattos,
doQueeny = doQueeny,
doTalos=doTalos,
filterVasco=filterVasco,
filterTopViolations = filterTopViolations
))
if doWattos and False:
mol = project.molecule
completenessMol = mol.getDeepByKeys( WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("completenessMol: %s" % completenessMol)
for res in mol.allResidues():
completenessRes = res.getDeepByKeys( WATTOS_STR, COMPLCHK_STR, VALUE_LIST_STR)
nTdebug("%s: %s" % (res, completenessRes))
# end for
# end if
color = project.molecule.getRogColor()
nTdebug("The color of this molecule is: %s" % color)
self.assertFalse( color == COLOR_RED ) # ;-)
# end if
# self.assertTrue(project.exportValidation2ccpn())
# self.assertFalse(project.removeCcpnReferences())
# Do not leave the old CCPN directory laying around since it might get added to by another test.
# if os.path.exists(entryId):
# self.assertFalse(shutil.rmtree(entryId))
if False:
self.assertTrue(project.save())
self.assertTrue(project.saveCcpn(entryId))
if doRestoreCheck:
del project
project = Project.open(entryId, status = 'old')
self.assertTrue(project, 'Failed reopening project: ' + entryId)
if doStoreCheck:
# # Does require below import which is used here to trigger import warning in case it's not installed.
# pylint: disable=W0612
from cing.PluginCode.sqlAlchemy import CsqlAlchemy #@UnusedImport # pylint: disable=W0404
if doStoreCING2db( entryId, ARCHIVE_NRG_ID, project=project):
nTerror("Failed to store CING project's data to DB but continuing.")
if doSave:
self.assertTrue(project.save())