def checkRemoveIfExists(path, removeExisting=False, showYesNo=None):
"""
If path already exists:
If removeExisting:
Delete the path
Return True
Else if showYesNo:
Ask the user if it is ok to delete the path
If yes, delete and return True. If no return None.
Else:
Raise an IOError
Else:
Return False
This function is not intended to be used outside this module but could be.
"""
if os.path.exists(path):
if removeExisting:
removePath(path)
return True
elif showYesNo:
if os.path.isdir(path):
files = os.listdir(path)
n = 5
if len(files) > n:
files = files[:n]
files.append('...')
ss = ', '.join(files)
message = '%s already exists, remove it and all of its contents (%s) (if no, then no action taken)?' % (
path, ss)
if not showYesNo('Remove directory', message):
return None
else:
removePath(path)
return True
else:
message = '%s already exists (not as a directory), remove it?' % path
if not showYesNo('Remove file', message):
return None
else:
removePath(path)
return True
else:
raise IOError('%s already exists' % path)
return False
def backupProject(project,
dataLocationStores=None,
skipRefData=True,
clearOutDir=False):
def modificationTime(path):
return os.stat(path)[8]
backupRepository = project.findFirstRepository(name="backup")
if not backupRepository:
print('Warning: no backup path set, so no backup done')
return
backupUrl = backupRepository.url
backupPath = backupUrl.path
if not dataLocationStores:
dataLocationStores = set()
if clearOutDir:
removePath(backupPath)
topObjects = tuple(project.topObjects) + (project, )
for topObject in topObjects:
if skipRefData:
repository = topObject.findFirstActiveRepository(name='refData')
if repository:
continue
if topObject.isModified:
topObject.backup()
else:
repository = topObject.findFirstActiveRepository()
if repository:
origFile = xmlUtil.findTopObjectPath(repository.url.path,
topObject)
if os.path.exists(origFile):
# problem with appending repository.name is that topObject.backup()
# above does not do it this way, so end up with inconsistent backup
###backupDir = joinPath(backupPath, repository.name)
# so use same backup pah as topObject.backup()
backupDir = backupPath
backupFile = xmlUtil.findTopObjectPath(
backupDir, topObject)
if not os.path.exists(backupFile) or \
(modificationTime(backupFile) < modificationTime(origFile)):
directory = os.path.dirname(backupFile)
if not os.path.exists(directory):
os.makedirs(directory)
shutil.copy(origFile, backupFile)
else:
# one is stuffed
print(
'Warning: could not backup %s since could not find original file "%s"'
% (topObject, origFile))
else:
# one is stuffed
print(
'Warning: could not backup %s since could not find repository'
% topObject)
dataBackupPath = joinPath(backupPath, 'data')
for dataLocationStore in dataLocationStores:
dataBackupDir = joinPath(dataBackupPath, dataLocationStore.name)
for dataStore in dataLocationStore.dataStores:
origFile = dataStore.dataUrl.url.path
backupFile = joinPath(dataBackupDir, dataStore.path)
if os.path.exists(origFile):
if not os.path.exists(backupFile) or \
(modificationTime(backupFile) < modificationTime(origFile)):
directory = os.path.dirname(backupFile)
if not os.path.exists(directory):
os.makedirs(directory)
shutil.copy(origFile, backupFile)
else:
print(
'Warning: could not backup dataStore "%s" because could not find original file "%s"'
% (dataStore.name, origFile))
def saveRepository(repository,
newPath=None,
createFallback=False,
removeExisting=False,
showYesNo=None):
"""
Save the repository to a location given by newPath (the url.path
of the repository) if set, or the existing location if not.
For the userData repository this just calls saveProject instead.
If createFallback, then makes copy of existing modified repository
files (in newPath, not oldPath) before doing save.
If newPath != oldPath and newPath exists (either as file or as directory):
If removeExisting:
Delete the newPath.
Else if showYesNo:
Ask the user if it is ok to delete the newPath
If yes, delete. If no, return without saving.
Else:
Raise an IOError
If there is no exception or early return then at end repository is pointing to newPath.
Return True if save done, False if not (unless there is an exception)
"""
project = repository.root
if repository.name == 'userData':
saveProject(project,
newPath=newPath,
createFallback=createFallback,
removeExisting=removeExisting,
showYesNo=showYesNo)
return False
oldPath = repository.url.path
if newPath:
# normalise path
newPath = normalisePath(newPath, makeAbsolute=True)
else:
newPath = oldPath
if newPath != oldPath:
answer = checkRemoveIfExists(newPath, removeExisting, showYesNo)
if answer is None:
return False
# check which topObjects have this repository as activeRepositories[0]
# and are modified but not deleted
topObjects = set()
for topObject in project.topObjects:
if topObject.isModified and not topObject.isDeleted and \
repository == topObject.findFirstActiveRepository():
topObjects.add(topObject)
# TBD: should this be done here?
for topObject in topObjects:
topObject.checkAllValid()
# copy repository files over
if newPath != oldPath:
if os.path.exists(oldPath):
# just copy everything from oldPath to newPath
shutil.copytree(oldPath, newPath)
# change repository url to point to new newPath
oldUrl = repository.url
repository.url = Implementation.Url(path=newPath)
# above will set project.isModified = True
# save modifications
try:
if createFallback:
for topObject in topObjects:
createTopObjectFallback(topObject)
for topObject in topObjects:
topObject.save()
# the paths have changed so also need to save project
project.save()
return True
except:
# something failed so revert to old path
if newPath != oldPath:
repository.url = oldUrl
try:
removePath(newPath)
except:
pass
raise
def saveProject(project,
newPath=None,
newProjectName=None,
changeBackup=True,
createFallback=False,
removeExisting=False,
showYesNo=None,
checkValid=False,
changeDataLocations=False,
showWarning=None,
revertToOriginal=False):
"""
Save the userData for a project to a location given by newPath (the url.path
of the userData repository) if set, or the existing location if not.
If userData does not exist then throws IOError.
If newPath is not specified then it is set to oldPath.
If newProjectName is not specified then it is set to oldProjectName if
newPath==oldPath, otherwise it is set to basename(newPath).
If changeBackup, then also changes backup URL path for project.
If createFallback, then makes copy of existing modified topObjects
files (in newPath, not oldPath) before doing save.
If newPath != oldPath and newPath exists (either as file or as directory):
If removeExisting:
Delete the newPath.
Else if showYesNo:
Ask the user if it is ok to delete the newPath
If yes, delete. If no, return without saving.
Else:
Raise an IOError
Elif newProjectName != oldProjectName and there exists corresponding path (file/directory):
If removeExisting:
Delete the path.
Else if showYesNo:
Ask the user if it is ok to delete the path.
If yes, delete. If no, return without saving.
Else:
Raise an IOError
If checkValid then does checkAllValid on project
If changeDataLocations then copy to project directory
If revertToOriginal then after the save changes paths back to as they were originally
If there is no exception or early return then at end userData is pointing to newPath.
Return True if save done, False if not (unless there is an exception)
"""
# check project valid (so don't save an obviously invalid project)
if checkValid:
project.checkAllValid()
# only want to change path for userData
userData = project.findFirstRepository(name='userData')
if not userData:
raise IOError('Problem: userData not found')
oldPath = userData.url.path
oldProjectName = project.name
if newPath:
# normalise newPath
newPath = normalisePath(newPath, makeAbsolute=True)
else:
newPath = oldPath
# if newProjectName isn't specified then use default
if not newProjectName:
if newPath == oldPath:
newProjectName = oldProjectName
else:
newProjectName = os.path.basename(newPath)
# below is because of data model limit
newProjectName = newProjectName[:32]
renameProject(project, newProjectName)
# if newPath same as oldPath, check if newProjectName already exists if it's not same as oldProjectName
if newPath == oldPath:
if newProjectName != oldProjectName:
location = xmlUtil.getTopObjectPath(project)
if os.path.exists(location):
answer = checkRemoveIfExists(location, removeExisting,
showYesNo)
if answer is None:
project.__dict__[
'name'] = oldProjectName # TBD: for now name is frozen so change this way
return False
else: # check instead if newPath already exists
if os.path.exists(newPath):
answer = checkRemoveIfExists(newPath, removeExisting, showYesNo)
if answer is None:
if newProjectName != oldProjectName:
project.__dict__[
'name'] = oldProjectName # TBD: for now name is frozen so change this way
return False
# TBD: should we be removing it?
removePath(newPath)
else:
# NBNB 2008/04/03 Rasmus Fogh. Added because it otherwise fell over when
# target path did not exist
upDir = os.path.dirname(newPath)
if not os.path.exists(upDir):
os.makedirs(upDir)
# check if any topObject activeRepository is not either of above
refData = project.findFirstRepository(name='refData')
genData = project.findFirstRepository(name='generalData')
topObjects = []
repositories = set()
for topObject in project.topObjects:
repository = topObject.findFirstActiveRepository()
if repository and repository not in (userData, refData, genData):
topObjects.append(topObject)
repositories.add(repository)
if topObjects:
print(
'Warning, topObjects %s, in repositories %s, being left in original locations'
% (topObjects, repositories))
try:
oldUrl = userData.url
if changeBackup:
# change project backup url to point to new path
backupRepository = project.findFirstRepository(name="backup")
if backupRepository:
oldBackupUrl = backupRepository.url
else:
changeBackup = False
# copy userData files over
if newPath != oldPath:
# if os.path.exists(oldPath): # only copy if this is a directory
if os.path.isdir(oldPath):
# just copy everything from oldPath to newPath
print(
'Copying directory %s to %s (this might take some time if there are big files)'
% (oldPath, newPath))
shutil.copytree(oldPath, newPath)
# but need toz remove all implementation files
implPath = joinPath(newPath, ImpConstants.modellingPackageName,
ImpConstants.implementationPackageName)
#implPath = pathImplDirectory(newPath)
removePath(implPath)
# and need to repoint dataUrl's that were copied over
oldPathP = oldPath + '/'
for dataLocationStore in project.dataLocationStores:
for dataStore in dataLocationStore.dataStores:
oldDataPath = dataStore.fullPath
if oldDataPath.startswith(oldPathP):
dataUrl = dataStore.dataUrl
oldDataUrlPath = dataUrl.url.dataLocation
if oldDataUrlPath.startswith(
oldPathP): # normally true
newDataUrlPath = newPath + oldDataUrlPath[
len(oldPath):]
dataUrl.url = Implementation.Url(
path=newDataUrlPath)
else: # path split awkwardly between absolute and relative
newDataUrlPath = newPath
dataUrl.url = Implementation.Url(
path=newDataUrlPath)
dataStore.path = oldDataPath[len(oldPath):]
# change userData url to point to new path
userData.url = Implementation.Url(path=newPath)
# above will set project.isModified = True
if changeBackup:
# change project backup repository url to point to new path
backupRepository.url = Implementation.Url(path=newPath +
'_backup')
# change project name
if newProjectName != oldProjectName:
if not project.isModified: # if it isModified it will be saved below
if createFallback:
createTopObjectFallback(project)
project.save()
# create fallbacks and keep track of modified topObjects
modifiedTopObjects = []
if createFallback:
for topObject in (project, ) + tuple(project.topObjects):
if not topObject.isDeleted and topObject.isModified:
createTopObjectFallback(topObject)
modifiedTopObjects.append(topObject)
if changeDataLocations:
dataLocationStores = project.sortedDataLocationStores()
userRepository = project.findFirstRepository(name='userData')
userPath = userRepository.url.dataLocation
# 2010 Aug 11: remove data directory from path
#dataPath = joinPath(userPath, 'data')
dataPath = userPath
# 2010 Aug 11: change name
#dataStorePrefix = 'dataStore'
dataStorePrefix = 'spectra'
if os.path.exists(dataPath):
files = [
xx for xx in os.listdir(dataPath)
if xx.startswith(dataStorePrefix)
]
offset = len(files)
else:
offset = 0
copyingList = []
dataUrlDict = {}
for dataLocationStore in dataLocationStores:
for dataStore in dataLocationStore.sortedDataStores():
# wb104: 24 Mar 2010: below check is a complete kludge
# we should check whether dataStore is instance of
# NumericMatrix, etc., but those are in ccp so should
# not be imported here
# in any case, there is no proper way to find out if
# a dataStore is used without explicit knowledge of class
knt = 0
# hicard = 1
for attr in ('nmrDataSourceImage', ):
if hasattr(dataStore, attr):
if getattr(dataStore, attr):
knt += 1
# hicard > 1
for attr in ('externalDatas', 'nmrDataSources'):
if hasattr(dataStore, attr):
knt += len(getattr(dataStore, attr))
if knt == 0:
continue
oldFullPath = dataStore.fullPath
if not oldFullPath.startswith(userPath + '/'):
# first figure out new dataUrl path
dataUrl = dataStore.dataUrl
oldPath = dataUrl.url.dataLocation
if dataUrl in dataUrlDict:
newUrl = dataUrlDict[dataUrl]
else:
offset += 1
newUrlPath = '%s%d' % (dataStorePrefix, offset)
newUrlPath = joinPath(dataPath, newUrlPath)
newUrl = dataUrlDict[dataUrl] = Implementation.Url(
path=newUrlPath)
# then add to list to copy over if original data exists
if os.path.exists(oldFullPath):
newFullPath = joinPath(newUrl.dataLocation,
dataStore.path)
copyingList.append((oldFullPath, newFullPath))
# now copy data files over
nfilesToCopy = len(copyingList)
for n, (oldFullPath, newFullPath) in enumerate(copyingList):
dirName = os.path.dirname(newFullPath)
if not os.path.exists(dirName):
os.makedirs(dirName)
print('Copying file %s to %s (%d of %d)' %
(oldFullPath, newFullPath, n + 1, nfilesToCopy))
shutil.copy(oldFullPath, newFullPath)
# finally change dataUrl paths
for dataUrl in dataUrlDict:
dataUrl.url = dataUrlDict[dataUrl]
# save modifications
# change way doing save in case exception is thrown
if createFallback:
for topObject in modifiedTopObjects:
try:
topObject.save()
except:
location = xmlUtil.getTopObjectPath(topObject)
print('Exception working on topObject %s, file %s' %
(topObject, location))
raise
# be safe and do below in case new modifications after
# modifiedTopObjects has been created
project.saveModified()
else:
project.saveModified()
if not isWindowsOS():
os.system('touch "%s"' %
newPath) # so that user can see which are most recent
badTopObjects = []
for topObject in modifiedTopObjects:
if not checkFileIntegrity(topObject):
badTopObjects.append(topObject)
if badTopObjects:
if showWarning:
showWarning(
'Incomplete save',
'It looks like one or more files did not save completely, see console for list'
)
print(
'It looks like one or more files did not save completely, you should check them:'
)
for topObject in badTopObjects:
print
print('%s, path:' % topObject)
print(xmlUtil.getTopObjectPath(topObject))
return False
if revertToOriginal: # TBD: the below does not change back dataUrl paths
if newProjectName != oldProjectName:
project.__dict__[
'name'] = oldProjectName # TBD: for now name is frozen so change this way
if newPath != oldPath:
userData.url = oldUrl
if changeBackup:
backupRepository.url = oldBackupUrl
return True
except:
# saveModified failed so revert to old values
if newProjectName != oldProjectName:
project.__dict__[
'name'] = oldProjectName # TBD: for now name is frozen so change this way
if newPath != oldPath:
userData.url = oldUrl
if changeBackup:
backupRepository.url = oldBackupUrl
try:
removePath(newPath)
except:
pass
raise
def saveProject(project, newPath = None, newProjectName = None, changeBackup = True,
createFallback = False, removeExisting = False, showYesNo = None,
checkValid = False):
"""
Save the userData for a project to a location given by newPath (the url.path
of the userData repository) if set, or the existing location if not.
If userData does not exist then throws IOError.
If newPath is not specified then it is set to oldPath.
If newProjectName is not specified then it is set to oldProjectName if
newPath==oldPath, otherwise it is set to basename(newPath).
If changeBackup, then also changes backup URL path for project.
If createFallback, then makes copy of existing modified topObjects
files (in newPath, not oldPath) before doing save.
If newPath != oldPath and newPath exists (either as file or as directory):
If removeExisting:
Delete the newPath.
Else if showYesNo:
Ask the user if it is ok to delete the newPath
If yes, delete. If no, return without saving.
Else:
Raise an IOError
Elif newProjectName != oldProjectName and there exists corresponding path (file/directory):
If removeExisting:
Delete the path.
Else if showYesNo:
Ask the user if it is ok to delete the path.
If yes, delete. If no, return without saving.
Else:
Raise an IOError
if checkValid then does checkAllValid on project
If there is no exception or early return then at end userData is pointing to newPath.
Return True if save done, False if not (unless there is an exception)
"""
# check project valid (so don't save an obviously invalid project)
if checkValid:
project.checkAllValid()
# only want to change path for userData
userData = project.findFirstRepository(name='userData')
if not userData:
raise IOError('Problem: userData not found')
oldPath = userData.url.path
oldProjectName = project.name
if newPath:
# normalise newPath
newPath = normalisePath(newPath, makeAbsolute=True)
else:
newPath = oldPath
# if newProjectName isn't specified then use default
if not newProjectName:
if newPath == oldPath:
newProjectName = oldProjectName
else:
newProjectName = os.path.basename(newPath)
# change project name
if newProjectName != oldProjectName:
project.override = True # TBD: for now name is frozen so change this way
try:
# below constraint is not checked in setName() if override is True so repeat here
isValid = newProjectName.isalnum() # superfluous but faster in most cases
if not isValid:
for cc in newProjectName:
if cc != '_' and not cc.isalnum():
isValid = False
break
else:
isValid = True
if (not (isValid)):
raise ApiError('project name must only have characters that are alphanumeric or underscore')
# below checks for length of name as well
project.name = newProjectName
finally:
project.override = False
# if newPath same as oldPath, check if newProjectName already exists if it's not same as oldProjectName
if newPath == oldPath:
if newProjectName != oldProjectName:
location = xmlUtil.getTopObjectPath(project)
if os.path.exists(location):
answer = checkRemoveIfExists(location, removeExisting, showYesNo)
if answer is None:
project.__dict__['name'] = oldProjectName # TBD: for now name is frozen so change this way
return False
else: # check instead if newPath already exists
if os.path.exists(newPath):
answer = checkRemoveIfExists(newPath, removeExisting, showYesNo)
if answer is None:
if newProjectName != oldProjectName:
project.__dict__['name'] = oldProjectName # TBD: for now name is frozen so change this way
return False
# TBD: should we be removing it?
removePath(newPath)
else:
# NBNB 2008/04/03 Rasmus Fogh. Added because it otherwise fell over when
# target path did not exist
upDir = os.path.dirname(newPath)
if not os.path.exists(upDir):
os.makedirs(upDir)
# check if any topObject activeRepository is not either of above
refData = project.findFirstRepository(name='refData')
genData = project.findFirstRepository(name='generalData')
topObjects = []
repositories = set()
for topObject in project.topObjects:
repository = topObject.findFirstActiveRepository()
if repository and repository not in (userData, refData, genData):
topObjects.append(topObject)
repositories.add(repository)
if topObjects:
print 'Warning, topObjects %s, in repositories %s, being left in original locations' % (topObjects, repositories)
try:
oldUrl = userData.url
if changeBackup:
# change project backup url to point to new path
backupRepository = project.findFirstRepository(name="backup")
if backupRepository:
oldBackupUrl = backupRepository.url
else:
changeBackup = False
# copy userData files over
if newPath != oldPath:
# if os.path.exists(oldPath): # only copy if this is a directory
if os.path.isdir(oldPath):
# just copy everything from oldPath to newPath
shutil.copytree(oldPath, newPath)
# but need to remove all implementation files
implPath = joinPath(newPath, ImpConstants.modellingPackageName,
ImpConstants.implementationPackageName)
#implPath = pathImplDirectory(newPath)
removePath(implPath)
# change userData url to point to new path
userData.url = Implementation.Url(path=newPath)
# above will set project.isModified = True
if changeBackup:
# change project backup repository url to point to new path
backupRepository.url = Implementation.Url(path=newPath+'_backup')
# change project name
if newProjectName != oldProjectName:
if not project.isModified: # if it isModified it will be saved below
if createFallback:
createTopObjectFallback(project)
project.save()
# create fallbacks
if createFallback:
for topObject in (project,)+tuple(project.topObjects):
if not topObject.isDeleted and topObject.isModified:
createTopObjectFallback(topObject)
# save modifications
project.saveModified()
if not isWindowsOS():
os.system('touch %s' % newPath) # so that user can see which are most recent
return True
except:
# saveModified failed so revert to old values
if newProjectName != oldProjectName:
project.__dict__['name'] = oldProjectName # TBD: for now name is frozen so change this way
if newPath != oldPath:
userData.url = oldUrl
if changeBackup:
backupRepository.url = oldBackupUrl
try:
removePath(newPath)
except:
pass
raise