def fullLoadValidationStore(topObj):
"""hard load ValidationStore from old location
"""
from memops.format.xml import Util as xmlUtil
from memops.universal import Io as uniIo
from memops.format.xml import XmlIO
root = topObj.memopsRoot
locator = (
root.findFirstPackageLocator(targetName='ccp.molecule.Validation')
or root.findFirstPackageLocator(targetName='any'))
repository = locator.findFirstRepository()
#repository = topObj.activeRepositories[0]
fileLocation = repository.getFileLocation(
'ccp.molecule.StructureValidation')
filePath = uniIo.joinPath(fileLocation, xmlUtil.getTopObjectFile(topObj))
XmlIO.loadFromStream(open(filePath),
topObject=topObj,
topObjId=topObj.guid,
partialLoad=False)
def setupProject(self, fileName, projectName):
self.projectFileName = fileName
try:
self.ccpnProject = XmlIO.loadProjectFile(fileName)
print "Read existing CCPN project..."
except:
print "Creating new CCPN project..."
projectName = returnMemopsWord(projectName)
self.ccpnMemopsRoot = Implementation.MemopsRoot(name=projectName)
self.nmrProject = Nmr.NmrProject(self.ccpnProject,
name=self.ccpnProject.name)
#
# Set the location...
#
(path, file) = splitPath(fileName)
self.ccpnProject.path = file
self.ccpnProject.url.path = path
outputPath = os.path.join(path, projectName)
try:
os.stat(outputPath)
except:
os.mkdir(outputPath)
for url in self.ccpnProject.urls:
if url != self.ccpnProject.url:
url.path = outputPath
# TODO: check name of project: if not same CRASH OUT!
return self.ccpnProject
def loadProject(path,
projectName=None,
showWarning=None,
askFile=None,
askDir=None,
suppressGeneralDataDir=False):
"""
Loads a project file and checks and deletes unwanted project repositories and
changes the project repository path if the project has moved. Returns the project.
(The project repository path is effectively the userData repository.)
showWarning (if not None) has signature showWarning(title, message)
askFile (if not None) has signature askFile(title, message, initial_value = '')
askDir (if not None) has signature askDir(title, message, initial_value = '')
Throws an IOError if there is an I/O error.
Throws an ApiError if there is an API exception.
"""
from memops.format.xml import XmlIO
if not showWarning:
showWarning = printWarning
path = normalisePath(path, makeAbsolute=True)
# check if path exists and is directory
if not os.path.exists(path):
raise IOError('path "%s" does not exist' % path)
if not os.path.isdir(path):
raise IOError('path "%s" is not a directory' % path)
projectFile = xmlUtil.getProjectFile(path, projectName)
if projectName:
# projectName was specified so projectFile better exist
if not os.path.exists(projectFile):
raise IOError('project file "%s" does not exist' % projectFile)
else:
# projectName was not specified so default projectFile might not exist
if not os.path.exists(projectFile):
projectFiles = xmlUtil.getPossibleProjectFiles(path)
if len(projectFiles) == 0:
raise IOError('"%s" contains no project file' % path)
elif len(projectFiles) == 1:
projectFile = projectFiles[0]
elif askFile:
projectFile = askFile('Select project file',
'Select project file',
initial_value=projectFiles[0])
if not projectFile: # cancelled
raise IOError('Cancelled')
else:
raise IOError(
'"%s" contains %d project files, not sure which to use' %
(path, len(projectFiles)))
# TBD: should projectName be based on projectFile or on path???
# the way it is set here do not need to change project.name
# but if you used the path then you would need to change it
projectName = xmlUtil.getTopObjIdFromFileName(projectFile)
# doing the loadProject twice has a bit of an overhead, but not much
try:
# below assumes TopObjects exist where stated, so might fail
project = XmlIO.loadProject(path, projectName, partialLoad=False)
except:
print("\nFirst loading attempt failed - compatibility problem?.")
project = None
def isGeneralDataWriteable(generalDataRepository):
oldPath = generalDataRepository.url.path
return (isWindowsOS() or os.access(oldPath, os.W_OK | os.X_OK))
def isGeneralDataOk(project):
if suppressGeneralDataDir:
return True
generalDataRepository = project.findFirstRepository(name='generalData')
if generalDataRepository:
return isGeneralDataWriteable(generalDataRepository)
return True
if project is not None and (not xmlUtil.areAllTopObjectsPresent(project)
or not isGeneralDataOk(project)):
# if not all loaded (shell) TopObjects can be found, try again
project = None
###print "\nSome files unfindable - has project moved?."
if project is None:
###print "Re-trying, skipping cached TopObjects:"
project = XmlIO.loadProject(path, projectName, partialLoad=True)
warningMessages = []
# try and fix project repository path, if needed
packageLocator = project.packageLocator
repositories = packageLocator.repositories
for repository in repositories:
if repository.url.path == path:
oldPath = path
break
else:
# change first repository path to point to this one, and also change backup
repository = repositories[0]
oldPath = repository.url.path
warningMessages.append('Project file has moved from\n"%s"\nto\n"%s"' %
(oldPath, path))
repository.url = Implementation.Url(path=path)
# Necessary because activeRepositories are not set right
# if file names do not match:
project.__dict__['activeRepositories'].append(repository)
projectRepository = repository
# check backup path
backupRepository = project.findFirstRepository(name="backup")
if backupRepository:
backupUrl = backupRepository.url
oldBackupPath = backupUrl.path
newBackupPath = path + '_backup'
if oldBackupPath.startswith(oldPath): # hopefully true
if path != oldPath:
warningMessages.append(
'Backup is being changed from\n"%s"\nto\n"%s"' %
(oldBackupPath, newBackupPath))
backupRepository.url = Implementation.Url(path=newBackupPath)
elif not os.path.exists(oldBackupPath):
warningMessages.append(
'Backup is being changed from\n"%s"\nto\n"%s"' %
(oldBackupPath, newBackupPath))
backupRepository.url = Implementation.Url(path=newBackupPath)
# check if project repository is called 'userData'
if projectRepository.name != 'userData':
warningMessages.append(
'Project has non-standard repository name "%s"' %
projectRepository.name)
# repoint dataStores that are in same directory as project
# (but only if old path does not exist and new one does)
if path != oldPath:
oldDirectory = os.path.dirname(oldPath)
newDirectory = os.path.dirname(path)
for dataLocationStore in project.dataLocationStores:
for dataStore in dataLocationStore.dataStores:
fullPath = dataStore.fullPath
if not os.path.exists(fullPath):
dataUrl = dataStore.dataUrl
dataLocation = dataUrl.url.dataLocation
if dataLocation == oldDirectory or \
(dataLocation.startswith(oldDirectory) and dataLocation[len(oldDirectory)] == dirsep):
newDataUrlPath = newDirectory + dataLocation[
len(oldDirectory):]
newPath = joinPath(newDataUrlPath, dataStore.path)
if os.path.exists(newPath):
warningMessages.append(
'DataStore %s:%s path has been changed from\n"%s"\nto\n"%s"'
% (dataStore.dataLocationStore.name,
dataStore.serial, oldDirectory,
newDataUrlPath))
dataUrl.url = dataUrl.url.clone(
path=newDataUrlPath)
# change refData to current one if need be
refDataRepository = project.findFirstRepository(name='refData')
if refDataRepository:
oldPath = refDataRepository.url.path
newPath = normalisePath(getDataDirectory())
if newPath != oldPath:
warningMessages.append(
'refData has been changed from\n"%s"\nto\n"%s"' %
(oldPath, newPath))
refDataRepository.url = Implementation.Url(path=newPath)
else:
warningMessages.append('Project has no repository with name "refData"')
# change generalData to current one if need be
generalDataRepository = project.findFirstRepository(name='generalData')
if generalDataRepository and not suppressGeneralDataDir:
oldPath = generalDataRepository.url.path
if not os.path.exists(oldPath) or not isGeneralDataWriteable(
generalDataRepository):
newPath = normalisePath(os.path.expanduser('~/.ccpn/data'))
if not os.path.exists(newPath):
os.makedirs(newPath)
warningMessages.append(
'generalData has been changed from\n"%s"\nto\n"%s"' %
(oldPath, newPath))
generalDataRepository.url = Implementation.Url(path=newPath)
# check other repository paths
for repository in project.repositories:
if repository not in (projectRepository, refDataRepository,
backupRepository, generalDataRepository):
oldPath = repository.url.path
if not repository.stored:
title = 'Repository being deleted'
msg = 'Repository "%s" with path "%s" has no packageLocators, deleting' % (
repository.name, oldPath)
repository.delete()
elif not os.path.exists(oldPath):
title = 'Repository path does not exist'
if showWarning is printWarning:
tt = ''
else:
tt = ' (see console for packages)'
msg = 'Repository "%s" path "%s" does not exist%s' % (
repository.name, oldPath, tt)
print('List of packageLocators for repository "%s":' %
repository.name)
for packageLocator in repository.stored:
print(' %s' % packageLocator.targetName)
if askDir:
newPath = askDir(title,
msg + ': enter new path',
initial_value=oldPath)
while newPath and not os.path.exists(newPath):
msg = 'Path "%s" does not exist' % newPath
newPath = askDir(title,
msg + ': enter new path',
initial_value=newPath)
if newPath:
repository.url = Implementation.Url(
path=normalisePath(newPath))
else:
warningMessages.append(msg)
if warningMessages:
showWarning('Warnings', '\n\n'.join(warningMessages))
return project
addText = moleculeText + ':' + chainText + ':' + resCodesText
fout.write(" %-15s -> %-15s %s" %
("'" + resonanceName + "'",
string.join(atomNames, ','), addText))
else:
fout.write(" %-15s %-15s" %
("'" + resonanceName + "'", 'NOT LINKED'))
fout.write(newline)
return True
###################
# Main of program #
###################
if __name__ == "__main__":
inFile = sys.argv[1]
outFile = sys.argv[2]
# Read xml file
from memops.format.xml import XmlIO
proj = XmlIO.loadProjectFile(inFile)
writeMappingFile(proj, outFile)
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
from memops.format.xml import Util as xmlUtil
from memops.format.xml import XmlIO
from memops.universal import Io as uniIo
from memops.api import Implementation
import Tkinter
# standard project name
projectName = 'refIsotopeEditor'
# get or make project
repDir = uniIo.joinPath(uniIo.normalisePath(uniIo.os.getcwd()),
projectName)
projectFile = xmlUtil.getProjectFile(repDir, projectName=projectName)
if os.path.isfile(projectFile):
project = XmlIO.loadProjectFile(projectFile)
else:
project = Implementation.MemopsRoot(name=projectName)
# reorder to make sure data are saved in refData
labelingSchemeLocator = project.findFirstPackageLocator(
targetName='ccp.molecule.ChemCompLabel')
repositories = list(labelingSchemeLocator.repositories)
for rr in repositories:
if rr.name == 'refData':
refRepository = rr
break
else:
refRepository = None
if refRepository is not None:
repositories.remove(refRepository)
def loadProject(path, projectName=None, showWarning=None, askFile=None,
askDir=None, suppressGeneralDataDir = False):
"""
Loads a project file and checks and deletes unwanted project repositories and
changes the project repository path if the project has moved. Returns the project.
(The project repository path is effectively the userData repository.)
showWarning (if not None) has signature showWarning(title, message)
askFile (if not None) has signature askFile(title, message, initial_value = '')
askDir (if not None) has signature askDir(title, message, initial_value = '')
Throws an IOError if there is an I/O error.
Throws an ApiError if there is an API exception.
"""
from memops.format.xml import XmlIO
if not showWarning:
showWarning = printWarning
path = normalisePath(path, makeAbsolute=True)
# check if path exists and is directory
if not os.path.exists(path):
raise IOError('path "%s" does not exist' % path)
if not os.path.isdir(path):
raise IOError('path "%s" is not a directory' % path)
projectFile = xmlUtil.getProjectFile(path, projectName)
if projectName:
# projectName was specified so projectFile better exist
if not os.path.exists(projectFile):
raise IOError('project file "%s" does not exist' % projectFile)
else:
# projectName was not specified so default projectFile might not exist
if not os.path.exists(projectFile):
projectFiles = xmlUtil.getPossibleProjectFiles(path)
if len(projectFiles) == 0:
raise IOError('"%s" contains no project file' % path)
elif len(projectFiles) == 1:
projectFile = projectFiles[0]
elif askFile:
projectFile = askFile('Select project file', 'Select project file', initial_value=projectFiles[0])
if not projectFile: # cancelled
raise IOError('Cancelled')
else:
raise IOError('"%s" contains %d project files, not sure which to use' % (path, len(projectFiles)))
# TBD: should projectName be based on projectFile or on path???
# the way it is set here do not need to change project.name
# but if you used the path then you would need to change it
projectName = xmlUtil.getTopObjIdFromFileName(projectFile)
# doing the loadProject twice has a bit of an overhead, but not much
try:
# below assumes TopObjects exist where stated, so might fail
project = XmlIO.loadProject(path, projectName, partialLoad=False)
# check whether all topObject directories exist where they are said to exist
# if not then reload project with partialLoad = True
for repository in project.repositories:
if not os.path.exists(repository.getFileLocation()):
project = XmlIO.loadProject(path, projectName, partialLoad=True)
break
except: # this can happen if Implementation file is inconsistent with data model
project = XmlIO.loadProject(path, projectName, partialLoad=True)
# try and fix project repository path, if needed
packageLocator = project.packageLocator
repositories = packageLocator.repositories
for repository in repositories:
if repository.url.path == path:
oldPath = path
break
else:
# change first repository path to point to this one, and also change backup
repository = repositories[0]
oldPath = repository.url.path
showWarning('Project moved',
'Project file has moved from "%s" to "%s", updating path' \
% (oldPath, path))
repository.url = Implementation.Url(path=path)
projectRepository = repository
# check backup path
backupRepository = project.findFirstRepository(name="backup")
if backupRepository:
backupUrl = backupRepository.url
oldBackupPath = backupUrl.path
newBackupPath = path + '_backup'
if oldBackupPath.startswith(oldPath): # hopefully true
if path != oldPath:
showWarning('Backup changed',
'Backup is being changed from "%s" to "%s", updating path' \
% (oldBackupPath, newBackupPath))
backupRepository.url = Implementation.Url(path=newBackupPath)
elif not os.path.exists(oldBackupPath):
showWarning('Backup changed',
'Backup is being changed from "%s" to "%s", updating path' \
% (oldBackupPath, newBackupPath))
backupRepository.url = Implementation.Url(path=newBackupPath)
# check if project repository is called 'userData'
if projectRepository.name != 'userData':
showWarning('Project non-standard',
'Project has non-standard repository name "%s"' % projectRepository.name)
# change refData to current one if need be
refDataRepository = project.findFirstRepository(name='refData')
if refDataRepository:
oldPath = refDataRepository.url.path
newPath = normalisePath(getDataDirectory())
if newPath != oldPath:
showWarning('refData changed',
'refData has been changed from "%s" to "%s", updating paths' % (oldPath, newPath))
refDataRepository.url = Implementation.Url(path=newPath)
else:
showWarning('No refData repository',
'Project has no repository with name "refData"')
# change generalData to current one if need be
generalDataRepository = project.findFirstRepository(name='generalData')
if generalDataRepository and not suppressGeneralDataDir:
oldPath = generalDataRepository.url.path
if not os.path.exists(oldPath):
newPath = normalisePath(os.path.expanduser('~/.ccpn/data'))
if not os.path.exists(newPath):
os.makedirs(newPath)
showWarning('generalData changed',
'generalData has been changed from "%s" to "%s", updating paths' % (oldPath, newPath))
generalDataRepository.url = Implementation.Url(path=newPath)
# check other repository paths
for repository in project.repositories:
if repository not in (projectRepository, refDataRepository, backupRepository, generalDataRepository):
oldPath = repository.url.path
if not repository.stored:
title = 'Repository being deleted'
msg = 'Repository "%s" with path "%s" has no packageLocators, deleting' % (repository.name, oldPath)
repository.delete()
elif not os.path.exists(oldPath):
title = 'Repository path does not exist'
if showWarning is printWarning:
tt = ''
else:
tt = ' (see console for packages)'
msg = 'Repository "%s" path "%s" does not exist%s' % (repository.name, oldPath, tt)
print 'List of packageLocators for repository "%s":' % repository.name
for packageLocator in repository.stored:
print ' %s' % packageLocator.targetName
if askDir:
newPath = askDir(title, msg + ': enter new path', initial_value=oldPath)
while newPath and not os.path.exists(newPath):
msg = 'Path "%s" does not exist' % newPath
newPath = askDir(title, msg + ': enter new path', initial_value=newPath)
if newPath:
repository.url = Implementation.Url(path=normalisePath(newPath))
else:
showWarning(title, msg)
return project