def getChemCompCoordXmlFile(repository,
chemCompCoordPath,
sourceName,
molType,
ccpCode,
showError=None,
copyFile=True):
"""
Fetch chemCompCoord 'sourceName', 'molType', 'ccpCode' to local repository 'repository'
from repository defined by chemCompPath
showError is an error display function, passed in were appropriate for GUI
contexts
Returns name of copied file, or None if unsuccessful
"""
fileSearchString = "%s+%s+%s+*.xml" % (getCcpFileString(sourceName),
molType, getCcpFileString(ccpCode))
fileSearchPath = getChemCompCoordArchiveXmlFilePath(
chemCompCoordPath, sourceName, molType, ccpCode)
className = 'ChemCompCoord'
identifier = '%s.%s.%s' % (sourceName, molType, ccpCode)
return getChemCompOrCoordXmlFile(repository, fileSearchString,
fileSearchPath, className, identifier,
showError, copyFile)
def getNewChemCompOrCoordFilePath(chemCompOrCoord, mode = 'test'):
"""
Gets a new file path for the XML file for a chemComp(Coord) object.
mode If 'test' will use test/
If 'archive' will use archive/
If 'obsolete' will use obsolete/
"""
molType = chemCompOrCoord.molType
ccpCode = chemCompOrCoord.ccpCode
guid = chemCompOrCoord.guid
xmlFileName = "%s+%s+%s.xml" % (molType,getCcpFileString(ccpCode),guid)
if mode == 'obsolete':
xmlFileName += ".%s" % time.strftime("%Y_%m_%d_%H_%M_%S")
if chemCompOrCoord.className == 'ChemCompCoord':
xmlFileName = "%s+%s" % (chemCompOrCoord.sourceName,xmlFileName)
if mode == 'test':
dataDir = testChemCompCoordDataDir
elif mode == 'obsolete':
dataDir = obsoleteChemCompCoordDataDir
elif mode == 'archive':
dataDir = editChemCompCoordDataDir
elif mode == 'archiveLink':
dataDir = editLinkedChemCompCoordDataDir
xmlFileDir = getChemCompCoordArchiveXmlFilePath(dataDir,chemCompOrCoord.sourceName,molType,ccpCode)
else:
if mode == 'test':
dataDir = testChemCompDataDir
elif mode == 'obsolete':
dataDir = obsoleteChemCompDataDir
elif mode == 'archive':
dataDir = editChemCompDataDir
elif mode == 'archiveLink':
dataDir = editLinkedChemCompDataDir
xmlFileDir = getChemCompArchiveXmlFilePath(dataDir,molType,ccpCode)
# Create if doesn't exist yet!!!
if not os.path.exists(xmlFileDir):
os.makedirs(xmlFileDir)
xmlFilePath = os.path.join(xmlFileDir,xmlFileName)
return xmlFilePath
def getChemCompCoordFilePath(archiveDataDir,sourceName,molType,ccpCode):
fileSearchString = "%s+%s+%s+*.xml" % (sourceName,molType,getCcpFileString(ccpCode))
searchPath = getChemCompCoordArchiveXmlFilePath(archiveDataDir,sourceName,molType,ccpCode)
xmlFileNameMatches = glob.glob(os.path.join(searchPath,fileSearchString))
xmlFileName = None
if xmlFileNameMatches:
xmlFileName = xmlFileNameMatches[-1]
return xmlFileName
def getTopObjectFile(topObject):
"""Get topObject file name (not path)
where topObject can be of class MemopsRoot or TopObject
"""
from memops.general.Io import getCcpFileString
if topObject.root is topObject:
# This is MemopsRoot
result = topObject.name + fileSuffix
else:
ll = [getCcpFileString(str(x)) for x in topObject.getFullKey()]
ll.append(topObject.guid + fileSuffix)
result = separatorFileNameChar.join(ll)
return result[-254:]
def saveTemporaryChemCompOrCoord(chemCompOrCoord,testMode = True, isFresh = False):
"""
Saves the XML for a chemComp(Coord) object to a temporary directory.
testMode If False, will use archive/, otherwise will use test/ for existingFilePath.
isFresh If False, will remove tag that indicates chemComp(Coord) generated from scratch
If True, will set the tag.
"""
#
# Set/remove tag that indicates whether chemComp is newly generated or not
#
if isFresh:
tagAsFresh(chemCompOrCoord)
else:
removeFreshTag(chemCompOrCoord)
if chemCompOrCoord.className == 'ChemCompCoord':
className = 'ChemCompCoord'
else:
className = 'ChemComp'
tempRepositoryName = 'temporaryChemComp'
tempRepository = chemCompOrCoord.root.findFirstRepository(name = tempRepositoryName)
if not tempRepository:
tempRepository = chemCompOrCoord.root.newRepository(name= tempRepositoryName,
url=Implementation.Url(path=tempChemCompDir))
curStdOut = sys.stdout
textPipe = TextPipe([])
sys.stdout = textPipe
chemCompOrCoord.saveTo(tempRepository)
sys.stdout = curStdOut
#sys.stdout = sys.__stdout__
print
print " *** CCPN save output ***"
for text in textPipe.textArea:
if text.strip():
print " %s" % text.strip()
print
# This was failing horribly in large runs, now fixed (Wim 2010/03/08)
filePath = glob.glob(os.path.join(tempRepository.url.path,'ccp','molecule',className,"*%s*%s*.xml" % (chemCompOrCoord.molType,getCcpFileString(chemCompOrCoord.ccpCode))))[0]
(localPath,localFileName) = os.path.split(filePath)
existingFilePath = findChemCompOrCoordFilePath(chemCompOrCoord, testMode = testMode)
return (filePath,existingFilePath)
def getChemComp(project,
molType,
ccpCode,
download=True,
showError=None,
partialLoad=False,
chemCompArchiveDir=None,
copyFile=True):
""" get ChemComp corresponding to molType,ccpCode,
looking 1) in memory, 2) in Repositories on lookup path,
3) in chemCompArchiveDir directory, 4) downloading from msd ChemComp server.
For 3) and 4) save new ChemComp in first Repository on PAckageLocator lookup path
Do 4) only if download==True
showError is an optional GUI error handler that can be passed in.
partialLoad controls if only the TopObject (default) or the entire file is loaded
copyFile can be set to False to avoid copying file from central archive (good for testing)
Optimised to avoid mass reading.
"""
# First get it if already loaded
chemComp = project.getByNavigation(('chemComps', (molType, ccpCode)))
if chemComp is None:
# try to load it from an existing repository - avoiding mass loading
packageName = 'ccp.molecule.ChemComp'
chemCompFileSearchString = "%s+%s+*.xml" % (molType,
getCcpFileString(ccpCode))
chemCompXmlFile = findCcpXmlFile(project, packageName,
chemCompFileSearchString)
if chemCompXmlFile:
chemComp = XmlIO.loadFromFile(project,
chemCompXmlFile,
partialLoad=partialLoad)
if chemComp is None:
# try to get it from chemCompArchiveDir directory, if any, or to download it.
# Use custom directory if it was passed in!!!!
if not chemCompArchiveDir:
chemCompPath = getChemCompArchiveDataDir()
else:
chemCompPath = chemCompArchiveDir
ccLocator = (
project.findFirstPackageLocator(targetName=packageName)
or project.findFirstPackageLocator(targetName='any'))
repository = ccLocator.findFirstRepository()
fileFound = getChemCompXmlFile(repository,
chemCompPath,
molType,
ccpCode,
showError=showError,
copyFile=copyFile)
if not fileFound and download:
fileFound = downloadChemCompXmlFile(repository,
molType,
ccpCode,
showError=showError)
if fileFound:
chemComp = XmlIO.loadFromFile(project,
fileFound,
partialLoad=partialLoad)
#
return chemComp
def downloadChemCompXmlFile(repository, molType, ccpCode, showError=None):
"""
Fetch chemComp 'molType', 'ccpCode' to local repository 'repository'
from chemCompServer
showError is an error display function, passed in were appropriate for GUI
contexts
Returns name of copied file, or None if unsuccessful
"""
if showError is None:
showError = uniIo.printError
result = None
chemCompXmlFilePatt = re.compile("(" + molType + "\+" +
getCcpFileString(ccpCode) +
"\+[^\s\"\>]+\.xml)")
try:
urlLocation = "http://%s%s" % (chemCompServer,
os.path.join(chemCompWebPath, molType))
r1 = urllib.urlopen(os.path.join(urlLocation, "files.txt"))
try:
data = r1.read()
r1.close()
dataLines = data.split("\n")
chemCompXmlFile = None
for dataLine in dataLines:
chemCompSearch = chemCompXmlFilePatt.search(dataLine)
if chemCompSearch:
chemCompXmlFile = chemCompSearch.group(1)
if chemCompXmlFile:
urlLocation = os.path.join(urlLocation, chemCompXmlFile)
r2 = urllib.urlopen(urlLocation)
try:
data = r2.read()
r2.close()
try:
saveChemCompPath = repository.getFileLocation(
'ccp.molecule.ChemComp')
if not os.path.exists(saveChemCompPath):
os.makedirs(saveChemCompPath)
chemCompFile = os.path.join(saveChemCompPath,
chemCompXmlFile)
fout = open(chemCompFile, 'w')
fout.write(data)
fout.close()
print(
"Downloaded chemComp %s, %s from server %s, written to file %s!"
% (molType, ccpCode, chemCompServer, chemCompFile))
result = chemCompFile
except IOError, e:
showError(
"Cannot write file",
"Cannot write chemComp XML file %s, %s: %s" %
(molType, ccpCode, str(e)))
except IOError, e:
showError(
"Cannot read file", "Cannot read chemComp %s, %s: %s" %
(molType, ccpCode, str(e)))
else:
showError(
"Cannot find file",
"Cannot find chemComp XML file %s, %s." %
(molType, ccpCode))
def copyBaseToModifiedFile(project,
newBaseUnit,
origBaseUnit,
testMode,
repository,
replace=False):
#
# Reset the still empty new base unit parameters
#
newBaseUnit.__dict__['isLoaded'] = False
newBaseUnit.__dict__['isModified'] = False
newBaseUnit.__dict__['isStored'] = True
#
# Some pattern for identifying elements that have to be changed in the original file
#
ccpCodePatt = re.compile("ccpCode=\"([^ ]+)\"")
namePatt = re.compile("name=\"([^ ]+)\"")
guidPatt = re.compile("guid=\"([^ ]+)\"")
#
# Get the template (original) base unit file location
#
print origBaseUnit, testMode
origFilePath = findChemCompOrCoordFilePath(origBaseUnit, testMode=testMode)
#
# Get the repository path for the new base unit
#
packageName = newBaseUnit.packageLocator.targetName
repPath = repository.getFileLocation(packageName)
if not os.path.exists(repPath):
os.makedirs(repPath)
#
# Find out the file path for the new base unit
#
baseFileName = "%s" % (newBaseUnit.molType)
if newBaseUnit.className == 'ChemCompCoord':
baseFileName = "%s+" % (getCcpFileString(
newBaseUnit.sourceName)) + baseFileName
newFilePath = os.path.join(
repPath,
"%s+%s+" % (baseFileName, getCcpFileString(newBaseUnit.ccpCode)))
newFilePath += "%s.xml" % newBaseUnit.guid
#
# Read in the template file and modify it for the new base unit
#
fin = open(origFilePath)
lines = fin.readlines()
fin.close()
for lindex in range(len(lines)):
line = lines[lindex]
if line.count('<CHEM.NonStdChemComp') or line.count(
"<CCCO.ChemCompCoord"):
ccpCodeSearch = ccpCodePatt.search(line)
line = line.replace('ccpCode="%s"' % ccpCodeSearch.group(1),
'ccpCode="%s"' % newBaseUnit.ccpCode)
# Only relevant if name set to ccpCode...
nameSearch = namePatt.search(line)
if nameSearch and nameSearch.group(1) == ccpCodeSearch.group(1):
line = line.replace('name="%s"' % nameSearch.group(1),
'name="%s"' % newBaseUnit.ccpCode)
guidSearch = guidPatt.search(line)
line = line.replace('guid="%s"' % guidSearch.group(1),
'guid="%s"' % newBaseUnit.guid)
lines[lindex] = line
break
#
# If new file already exists, only replace it if replace flag set to True
#
if os.path.exists(newFilePath):
if replace:
os.remove(newFilePath)
else:
print " Modified chemComp already exists - aborting..."
return False
#
# Write out the new base unit file
#
fout = open(newFilePath, 'w')
fout.write(''.join(lines))
fout.close()
return True
if not customCcpCodeList:
targetCcpCodeList = getCcpCodeList(targetDir, prefix=prefix)
else:
targetCcpCodeList = customCcpCodeList
if prefix:
prefixText = "%s+" % prefix
else:
prefixText = ""
for (molType, ccpCodes) in targetCcpCodeList:
for ccpCode in ccpCodes:
chemCompFileSearchString = "%s%s+%s+*.xml" % (
prefixText, molType, getCcpFileString(ccpCode))
chemCompFileNameMatches = glob.glob(
os.path.join(targetDir, chemCompFileSearchString))
if molType == 'other':
sourceSubDir = os.path.join(molType, ccpCode[0])
else:
sourceSubDir = molType
if customCcpCodeList and not chemCompFileNameMatches:
# See if new file, copy over directly in this case
chemCompFileNameMatches = glob.glob(
os.path.join(sourceDir, sourceSubDir,
chemCompFileSearchString))
if chemCompFileNameMatches: