def loadTopObject(repositoryPath, topObject):
""" Load given topObject
"""
filePath = xmlUtil.findTopObjectPath(repositoryPath, topObject)
topObjId = xmlUtil.getTopObjIdFromFileName(filePath, mustBeMultipart=True)
return loadFromStream(open(filePath),
topObjId=topObjId,
topObject=topObject)
def save(repositoryPath,
topObject,
mapping=None,
comment=None,
simplified=True,
compact=True,
expanded=False):
fileLocation = xmlUtil.findTopObjectPath(repositoryPath, topObject)
if os.path.exists(fileLocation):
# File that fits guid already exists - overwrite it
pass
else:
# file does not exist - make sure the directories are there.
dirName = os.path.dirname(fileLocation)
if not os.path.exists(dirName):
os.makedirs(dirName)
elif not os.path.isdir(dirName):
raise ApiError("%s exists and is not a directory" % dirName)
stream = open(fileLocation, 'w')
try:
saveToStream(stream, topObject, mapping, comment, simplified, compact)
finally:
stream.close()
def createTopObjectFallback(topObject):
"""
Create backup of topObject in same directory as original file but with '.bak' appended.
This function is not intended to be used outside this module but could be.
"""
location = xmlUtil.getTopObjectPath(topObject)
if not os.path.exists(location):
return
backupLocation = location + '.bak'
# copy rather than move because will need that much disk space in any case
# and sometimes move fails at OS level if file with that name already exists
directory = os.path.dirname(backupLocation)
if not os.path.exists(directory):
os.makedirs(directory)
shutil.copy(location, backupLocation)
def loadFromFile(memopsRoot, filePath, partialLoad=False):
""" Load topObject from filePath and MemopsRoot
"""
# open file
stream = open(filePath)
# load file
try:
topObjId = xmlUtil.getTopObjIdFromFileName(filePath,
mustBeMultipart=True)
topObject = loadFromStream(stream,
topObject=memopsRoot,
topObjId=topObjId,
partialLoad=partialLoad)
finally:
stream.close()
return topObject
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 loadProjectFile(filePath, partialLoad=False):
""" Load project by file name
"""
topObjId = xmlUtil.getTopObjIdFromFileName(filePath, mustBeMultipart=False)
filePath = os.path.abspath(filePath)
lowestDir = os.path.dirname(filePath)
project = loadFromStream(open(filePath),
topObjId=topObjId,
partialLoad=partialLoad)
activeRepositories = project.__dict__['activeRepositories']
if not activeRepositories:
for repository in project.packageLocator.repositories:
path = repository.getFileLocation('memops.Implementation')
if path == lowestDir:
activeRepositories.append(repository)
break
#
return project
def createTopObjectFallback(topObject):
"""
Create backup of topObject in same directory as original file but with '.bak' appended.
This function is not intended to be used outside this module but could be.
"""
location = xmlUtil.getTopObjectPath(topObject)
if not os.path.exists(location):
return
backupLocation = location + '.bak'
if not checkFileAtPath(location) and checkFileAtPath(backupLocation):
# current file no good and current backup good so do not do backup
print 'File at location "%s" not complete so not backing up' % location
return
# copy rather than move because will need that much disk space in any case
# and sometimes move fails at OS level if file with that name already exists
directory = os.path.dirname(backupLocation)
if not os.path.exists(directory):
os.makedirs(directory)
shutil.copy(location, backupLocation)
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 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
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 checkFileIntegrity(topObject):
"""Check that topObject file on disk ends correctly
"""
path = xmlUtil.getTopObjectPath(topObject)
return checkFileAtPath(path)
def loadProject(repositoryPath, projectName, partialLoad=False):
""" Load project by projectName
"""
filePath = xmlUtil.getProjectFile(repositoryPath, projectName)
return loadProjectFile(filePath, partialLoad=partialLoad)
if __name__ == '__main__':
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
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
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