def launchApplication(projectDir=None):
global top
root = Tkinter.Tk()
root.withdraw()
top = EntryCompletionGui(root)
project = None
if projectDir:
projectDir = normalisePath(projectDir)
askdir = lambda title, prompt, initial_value, default_dir: askDir(title, prompt,
initial_value, parent=top, extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(title, prompt,
initial_value, parent=top, extra_dismiss_text='Skip')
try:
project = loadProject(path=projectDir, showWarning=showWarning, askDir=askdir, askFile=askfile)
userRepos = project.findFirstRepository(name='userData')
chemCompPackLoc = project.findFirstPackageLocator(targetName='ccp.molecule.ChemComp')
if userRepos not in chemCompPackLoc.repositories:
chemCompPackLoc.addRepository(userRepos)
except ApiError, e:
showError('Reading project', e.error_msg, parent=top)
def launchApplication(projectDir=None):
global top
root = Tkinter.Tk()
root.withdraw(
) # get rid of the root window Tkinter would otherwise put up
top = ApplicationPopup(
root) # creates our controlled window (this class in fact)
project = None
if projectDir:
projectDir = normalisePath(projectDir)
askdir = lambda title, prompt, initial_value, default_dir: askDir(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip')
try:
project = loadProject(path=projectDir,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
except ApiError, e:
showError('Reading project', e.error_msg, parent=top)
def determineDir(self, directory):
directory = normalisePath(directory)
assert os.path.isdir(directory), '"%s" is not a directory' % directory
self.prev_directory = self.directory
if not os.path.isabs(directory):
if self.directory is None: # first time around
directory = joinPath(normalisePath(os.getcwd()), directory)
else:
directory = joinPath(self.directory, directory)
self.directory = directory
self.dirs = self.directory.split(dirsep)
def launchApplication(filename=None):
global top
root = Tkinter.Tk()
root.withdraw()
top = ApplicationPopup(root)
project = None
if filename:
file = normalisePath(filename)
askdir = lambda title, prompt, initial_value, default_dir: askDir(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip',
default_dir=default_dir)
askfile = lambda title, prompt, initial_value: askFile(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip')
try:
project = loadProject(path=file,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
except ApiError, e:
showError('Reading project', e.error_msg)
def setRepositoryPath(project, repositoryName, path):
from memops.api.Implementation import Url
repository = project.findFirstRepository(name=repositoryName)
if repository:
if path != repository.url.path:
# TBD: should we copy anything over from old url?
url = Url(path=normalisePath(path))
repository.url = url
def getDrives(self):
if isWindowsOS():
import win32api
drives = win32api.GetLogicalDriveStrings()
drives = drives.split('\x00')
drives = [normalisePath(drive) for drive in drives if drive]
drives.sort()
else:
drives = []
return drives
def __init__(self, projectFile):
# attributes
self.projectFile = normalisePath(projectFile, makeAbsolute=True)
self.sequenceFile = None
self.spectraFile = None
self.crosspeaksFile = None
self.binaryformat = 'bigendian'
# links
self.sequence = None
self.spectra = []
self.crosspeaks = []
self.resonances = set()
def addFile(self):
spectrum = self.spectrum
if not spectrum:
return
dataStore = spectrum.dataStore
if not dataStore:
showError('No dataStore',
'Spectrum does not have associated dataStore',
parent=self)
return
if not isinstance(dataStore, BlockedBinaryMatrix):
showError('No blockedBinaryMatrix',
'Spectrum dataStore is not a blockedBinaryMatrix',
parent=self)
return
if not dataStore.blockSizes:
showError('No blockSize',
'Spectrum dataStore does not have blockSize set',
parent=self)
return
blockSize = list(dataStore.blockSizes)
fileName = self.file_entry.get()
if not fileName:
showError('No filename', 'No filename given', parent=self)
return
fileName = normalisePath(fileName, makeAbsolute=True)
contourDir = spectrum.analysisSpectrum.contourDir.dataLocation
if fileName.startswith(contourDir):
path = fileName[len(contourDir) + 1:]
else:
path = os.path.basename(fileName)
if not os.path.exists(contourDir):
os.makedirs(contourDir)
print 'Copying %s to %s' % (fileName, contourDir)
shutil.copy(fileName, contourDir)
try:
header = getStoredContourHeader(fileName)
except Exception, e:
showError('File error', str(e), parent=self)
return
def launchApplication(projectDir=None):
global top
root = Tkinter.Tk()
root.withdraw()
top = ApplicationPopup(root)
project = None
if projectDir:
projectDir = normalisePath(projectDir)
try:
project = loadProject(top, path=projectDir)
except ApiError, e:
showError('Reading project', e.error_msg, parent=top)
def modifyPackageLocators(project,
repositoryName,
repositoryPath,
packageNames,
resetPackageLocator=True,
resetRepository=False):
"""
Resets package locators for specified packages to specified repository.
Use as, for example:
modifyPackageLocators(project,'newChemComps','/mydir/data/chemComps/',('ccp.molecule.ChemComp','ccp.molecule.ChemCompCoord'))
Additional args:
- resetPackageLocator: True will reset the package locator completely, removing old info
False will add the repository to the package locator.
- resetRepository: True will reset url for the repository, even if it already exists
False will not reset the url for the repository if it already exists
Returns the relevant repository.
"""
repository = project.findFirstRepository(name=repositoryName)
ss = normalisePath(repositoryPath)
if not repository:
repository = project.newRepository(name=repositoryName,
url=Implementation.Url(path=ss))
elif resetRepository and repository.url.path != repositoryPath:
repository.url = Implementation.Url(path=ss)
for packageName in packageNames:
packageLocator = project.findFirstPackageLocator(
targetName=packageName)
if not packageLocator:
raise ApiError("Cannot modify repository 'any' for package %s" %
packageName)
if resetPackageLocator:
packageLocator.repositories = (repository, )
elif not repository in packageLocator.repositories:
packageLocator.addRepository(repository)
return repository
def logMemoryStats(project, path):
"""
Logs stats for a project.
It appends information to the file given by path.
"""
path = normalisePath(path)
fp = open(path, 'a')
if fp:
t = time.ctime(time.time())
m = gc.collect()
n = len(gc.get_objects())
s = '%s: %d collected, %d objects' % (t, m, n)
fp.write('%s\n' % s)
print('logging: %s' % s)
fp.close()
def setDir(self):
directory = self.dir_entry.get()
if not directory:
showWarning('No directory',
'No directory specified, not setting backup directory',
parent=self)
return
if not os.path.abspath(directory):
directory = joinPath(os.getcwd(), directory)
if os.path.exists(directory):
if not os.path.isdir(directory):
showWarning('Path not directory',
'Path "%s" exists but is not a directory' %
directory,
parent=self)
return
else:
if showYesNo(
'Directory does not exist',
'Directory "%s" does not exist, should it be created?' %
directory,
parent=self):
os.mkdir(directory)
else:
showWarning(
'Directory not created',
'Directory "%s" not created so not setting backup directory'
% directory,
parent=self)
return
repository = self.project.findFirstRepository(name='backup')
if not repository:
showWarning(
'No backup repository',
'No backup repository found (something wrong somewhere)',
parent=self)
return
url = repository.url
if url.path != directory:
repository.url = Url(path=normalisePath(directory))
def __init__(self,
parent,
file=None,
files=None,
component=None,
selectionText='Select',
title=None,
format=None,
multiSelect=False):
#
# Also get format (from self?)
#
self.file = None # Use this to return single file info, for backward compat
if not multiSelect and file:
self.files = [file]
elif files:
self.files = files
else:
self.files = []
if self.files:
for i in range(len(self.files)):
self.files[i] = normalisePath(self.files[i])
self.component = component
self.fileSelected = False
self.selectionText = selectionText
self.format = format
self.multiSelect = multiSelect
if not title:
title = 'Select %s file' % component
BasePopup.__init__(self,
parent=parent,
title=title,
modal=True,
transient=True)
def newProject(projectName, path=None, removeExisting=False, showYesNo=None):
"""
Create, and return, a new project using a specified path (directory).
If path is not specified it takes the current working directory.
The path can be either absolute or relative.
The 'userData' repository is pointed to the path.
The 'backup' repository is pointed to the path + '_backup'.
If either of these paths already exist (either as files or as directories):
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 None.
Else:
Raise an IOError
"""
# relies on knowing that repositories to move have these names, and these values for path suffix
repositoryNameMap = {'userData': '', 'backup': '_backup'}
if not path:
path = os.getcwd()
for name in repositoryNameMap.keys():
fullPath = joinPath(path, projectName) + repositoryNameMap[name]
answer = checkRemoveIfExists(fullPath, removeExisting, showYesNo)
if answer is None:
return None
project = Implementation.MemopsRoot(name=projectName)
for name in repositoryNameMap.keys():
fullPath = normalisePath(joinPath(path, projectName) +
repositoryNameMap[name],
makeAbsolute=True)
repository = project.findFirstRepository(name=name)
repository.url = Implementation.Url(path=fullPath)
return project
def getDrives(self):
if isWindowsOS():
#import win32api
#drives = win32api.GetLogicalDriveStrings()
#drives = drives.split('\x00')
#drives = [normalisePath(drive) for drive in drives if drive]
#drives.sort()
# 19 Mar 2012: do not use win32api because not standard
from ctypes import windll
import string
drives = []
bitmask = windll.kernel32.GetLogicalDrives()
for letter in string.ascii_uppercase:
if bitmask & 1:
drives.append(letter)
bitmask >>= 1
drives = [drive + ':\\' for drive in drives]
drives = [normalisePath(drive) for drive in drives]
else:
drives = []
return drives
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
def __init__(self, parent, file_types = None, directory = None,
single_callback = None, double_callback = None,
prompt = None, show_file = True, file = '', multiSelect=False,
default_dir = None, getRowColor = None,
getExtraCell = None, extraHeadings = None, extraJustifies = None,
displayExtra = True, *args, **kw):
if file_types is None:
file_types = [ FileType("All", ["*"]) ]
if directory is None:
directory = normalisePath(os.getcwd())
if extraHeadings is None:
extraHeadings = ()
else:
extraHeadings = tuple(extraHeadings)
if extraJustifies is None:
extraJustifies = ()
else:
extraJustifies = tuple(extraJustifies)
if extraHeadings or extraJustifies:
assert len(extraHeadings) == len(extraJustifies)
assert getExtraCell
self.extraHeadings = extraHeadings
self.extraJustifies = extraJustifies
self.displayExtra = displayExtra
Frame.__init__(self, parent, *args, **kw)
self.file_types = file_types
self.fileType = file_types[0]
self.single_callback = single_callback
self.double_callback = double_callback
self.show_file = show_file
self.directory = None
self.historyBack = []
self.historyFwd = []
self.determineDir(directory)
self.default_dir = default_dir
self.getRowColor = getRowColor
self.getExtraCell = getExtraCell
self.grid_columnconfigure(0, weight=1)
row = 0
if prompt:
label = Label(self, text=prompt, grid=(row,0))
row += 1
self.grid_rowconfigure(row, weight=1)
if show_file:
headings = ('Name', 'Size', 'Date')
justifies = ('left','right','right')
else:
headings = ('Directory',)
justifies = ('left',)
self.normalHeadings = headings
self.normalJustifies = justifies
headings = headings + extraHeadings
justifies = justifies + extraJustifies
self.fileList = ScrolledMatrix(self, headingList=headings, justifyList=justifies,
initialRows=10, callback=self.singleCallback,
doubleCallback=self.doubleCallback,
multiSelect=multiSelect, grid=(row,0))
row += 1
texts = ['Back', 'Up', 'Forward', 'Top', 'Home', 'New', 'Refresh']
commands = [self.backDir, self.fwdDir, self.upDir, self.topDir,
self.homeDir, self.createDir, self.updateFileList ]
if self.default_dir:
texts.append('Default')
commands.append(self.setDefaultDir)
self.icons = []
for name in ICON_NAMES:
icon = Tkinter.PhotoImage(file=os.path.join(GFX_DIR,name+'.gif'))
self.icons.append(icon)
self.buttons = ButtonList(self, texts=texts, commands=commands,
images=self.icons, grid=(row,0))
if show_file:
row += 1
self.file_entry = LabeledEntry(self, label='File name',
label_width=10, entry_width=40,
returnCallback=self.setSelectedFile)
self.file_entry.grid(row=row, column=0, sticky=Tkinter.EW)
else:
self.file_entry = None
row += 1
self.directory_entry = LabeledEntry(self, label='Directory',
entry = directory,
label_width=10, entry_width=40,
returnCallback=self.entryDir)
self.directory_entry.grid(row=row, column=0, sticky=Tkinter.EW)
row += 1
subFrame = Frame(self, grid=(row,0))
subFrame.expandGrid(None,6)
if show_file:
label = Label(subFrame, text='File type:', grid=(0,0))
type_labels = self.determineTypeLabels()
self.fileType_menu = PulldownList(subFrame, callback=self.typeCallback,
texts=type_labels, objects=self.file_types,
grid=(0,1))
label = Label(subFrame, text=' Show hidden:', grid=(0,2))
self.hidden_checkbutton = CheckButton(subFrame, text='', selected=False,
callback=self.updateFileList, grid=(0,3))
label = Label(subFrame, text='Dir path:', grid=(0,4))
self.pathMenu = PulldownList(subFrame, callback=self.dirCallback,
objects=range(len(self.dirs)),
texts=self.dirs, index=len(self.dirs)-1,
indent=' ', prefix=dirsep, grid=(0,5))
self.updateFileList()
self.updateButtons()
if file:
self.setFile(file)
def parseFields(self, fields):
#
# This is taken almost directly from Wayne's AzaraParams.py file
#
key = fields[0]
assert key in self.allParKeys, 'key = %s' % key
parType = None
numFields = None
for tempParType in self.allPars.keys():
if key in self.parKeys[tempParType]:
for parInfo in self.allPars[tempParType]:
if key == parInfo[0]:
(origName,analysisName,numFields,default) = parInfo
parType = tempParType
break
if parType:
break
if not numFields:
return
if numFields == -1: # Basically any number of parameters!
valueList = []
for field in fields[1:]:
try:
x = int(field)
except:
x = float(field)
valueList.append(x)
if key == 'params':
dim = self.aPars.get('dim')
if dim is None:
raise Exception("'params' set before 'dim'")
npts = self.aPars.get('npts')
if not npts or len(npts) <= dim:
raise Exception("'params' set before 'npts'")
npts = npts[dim]
if len(valueList) != npts:
raise Exception("'params' set before 'npts'")
if parType == 'mainPars':
self.setValue(parInfo, tuple(valueList))
elif parType == 'dimPars':
assert self.aPars['dim'] >= 0, '"%s" must be after "dim"' % key
dim = self.aPars['dim']
self.setListValue(parInfo,dim,tuple(valueList))
# TBD: should this be done with a setValue somehow??
self.aPars['dimType'][dim] = self.dimTypeSampled
return
assert len(fields) == numFields, 'len(fields) = %d, should be %d' % (len(fields),numFields)
if numFields == 1:
if (key == 'little_endian'): # Int is now taken care of by dictionary!
self.setValue(parInfo,False)
else:
self.setValue(parInfo, True)
elif numFields == 2:
value = fields[1]
if parType == 'mainPars':
if (key == 'ndim'):
assert self.aPars['ndim'] == 0, 'repeated "ndim"'
self.setValue(parInfo, returnInt(value))
assert self.aPars['ndim'] > 0, 'ndim <= 0'
self.initDims()
elif (key == 'file'):
assert not self.aPars['file'], 'repeated "file"'
path = normalisePath(value)
if (path and (not os.path.isabs(path)) and os.path.isabs(self.name)):
path = joinPath(splitPath(self.name)[0], path)
self.setValue(parInfo,path)
elif (key == 'head'):
assert self.aPars['head'] == 0, 'repeated "head"'
self.setValue(parInfo, 4*int(value))
assert self.aPars['head'] >= 0, 'head < 0'
elif parType == 'dimPar':
if (key == 'dim'):
assert self.aPars['ndim'] > 0, '"dim" must be after "ndim"'
dim = self.aPars['dim']
self.setValue(parInfo, int(value) - 1)
assert self.aPars['dim'] != dim, 'repeated dim %d' % (dim+1)
assert self.aPars['dim'] >= 0, 'dim = %d <= 0' % (self.aPars['dim']+1)
assert self.aPars['dim'] < self.aPars['ndim'], 'dim = %d > ndim = %d' % (self.aPars['dim']+1, self.aPars['dim'])
elif parType == 'dimPars':
assert self.aPars['dim'] >= 0, '"%s" must be after "dim"' % key
dim = self.aPars['dim']
# can no longer do below because initDims() sets up default values
#assert getattr(self, key)[dim] is None, '%s repeated for dim %d' % (key, dim+1)
if (key in ('npts','block')):
v = int(value)
assert v > 0, '%s <= 0 for dim %d' % (key, dim+1)
self.setListValue(parInfo,dim,v)
elif (key == 'nuc'):
self.setListValue(parInfo,dim,standardNucleusName(value))
else:
self.setListValue(parInfo,dim,float(value))
def __init__(self,
parent,
file_types=None,
directory=None,
single_callback=None,
double_callback=None,
select_dir_callback=None,
change_dir_callback=None,
should_change_dir_callback=None,
prompt=None,
show_file=True,
file='',
multiSelect=False,
default_dir=None,
getRowColor=None,
getExtraCell=None,
extraHeadings=None,
extraJustifies=None,
displayExtra=True,
manualFileFilter=False,
extraTipTexts=None,
*args,
**kw):
if file_types is None:
file_types = [FileType("All", ["*"])]
if manualFileFilter:
self.manualFilter = FileType("Manual")
file_types.append(self.manualFilter)
else:
self.manualFilter = None
if directory is None:
directory = normalisePath(os.getcwd())
if extraHeadings is None:
extraHeadings = ()
else:
extraHeadings = tuple(extraHeadings)
if extraJustifies is None:
extraJustifies = ()
else:
extraJustifies = tuple(extraJustifies)
if extraHeadings or extraJustifies:
assert len(extraHeadings) == len(extraJustifies)
assert getExtraCell
self.extraHeadings = extraHeadings
self.extraJustifies = extraJustifies
self.extraTipTexts = extraTipTexts or []
self.displayExtra = displayExtra
Frame.__init__(self, parent, *args, **kw)
self.file_types = file_types
self.fileType = file_types[0]
self.single_callback = single_callback
self.double_callback = double_callback
self.select_dir_callback = select_dir_callback
self.change_dir_callback = change_dir_callback
self.should_change_dir_callback = should_change_dir_callback
self.show_file = show_file
self.directory = None
self.historyBack = []
self.historyFwd = []
self.determineDir(directory)
self.default_dir = default_dir
self.getRowColor = getRowColor
self.getExtraCell = getExtraCell
self.grid_columnconfigure(0, weight=1)
row = 0
if prompt:
label = Label(self, text=prompt, grid=(row, 0))
row += 1
self.grid_rowconfigure(row, weight=1)
if show_file:
headings = ('Name', 'Size', 'Date')
justifies = ('left', 'right', 'right')
tipTexts = [
'Name of file, directory or link', 'Size of file in bytes',
'Date of last modification'
]
else:
headings = ('Directory', )
justifies = ('left', )
tipTexts = ['Name of directory']
self.normalHeadings = headings
self.normalJustifies = justifies
self.normalTipTexts = tipTexts
headings = headings + extraHeadings
justifies = justifies + extraJustifies
tipTexts += [None] * len(extraHeadings)
self.fileList = ScrolledMatrix(self,
headingList=headings,
justifyList=justifies,
initialRows=10,
callback=self.singleCallback,
doubleCallback=self.doubleCallback,
tipTexts=tipTexts,
multiSelect=multiSelect,
grid=(row, 0))
row += 1
tipTexts = [
'Go to previous location in history',
'Go forward in location history', 'Go up one directory level',
'Go to root directory', 'Go to home directory',
'Make a new directory', 'Refresh directory listing'
]
texts = ['Back', 'Forward', 'Up', 'Top', 'Home', 'New', 'Refresh']
commands = [
self.backDir, self.fwdDir, self.upDir, self.topDir, self.homeDir,
self.createDir, self.updateFileList
]
if self.default_dir:
texts.append('Default')
commands.append(self.setDefaultDir)
tipTexts.append('Set the current directory as the default')
self.icons = []
for name in ICON_NAMES:
icon = Tkinter.PhotoImage(
file=os.path.join(GFX_DIR, name + '.gif'))
self.icons.append(icon)
self.buttons = ButtonList(self,
texts=texts,
commands=commands,
images=self.icons,
grid=(row, 0),
tipTexts=tipTexts)
if show_file:
row += 1
self.file_entry = LabeledEntry(self,
label='File name',
label_width=10,
entry_width=40,
returnCallback=self.setSelectedFile)
self.file_entry.grid(row=row, column=0, sticky=Tkinter.EW)
else:
self.file_entry = None
row += 1
self.directory_entry = LabeledEntry(self,
label='Directory',
entry=directory,
label_width=10,
entry_width=40,
returnCallback=self.entryDir)
self.directory_entry.grid(row=row, column=0, sticky=Tkinter.EW)
row += 1
subFrame = Frame(self, grid=(row, 0))
subFrame.expandGrid(None, 6)
if show_file:
label = Label(subFrame, text='File type:', grid=(0, 0))
type_labels = self.determineTypeLabels()
self.fileType_menu = PulldownList(
subFrame,
callback=self.typeCallback,
texts=type_labels,
objects=self.file_types,
grid=(0, 1),
tipText='Restrict listed files to selected suffix')
label = Label(subFrame, text=' Show hidden:', grid=(0, 2))
self.hidden_checkbutton = CheckButton(
subFrame,
text='',
selected=False,
callback=self.updateFileList,
grid=(0, 3),
tipText='Show hidden files beginning with "." etc.')
label = Label(subFrame, text='Dir path:', grid=(0, 4))
self.pathMenu = PulldownList(
subFrame,
callback=self.dirCallback,
objects=range(len(self.dirs)),
texts=self.dirs,
index=len(self.dirs) - 1,
indent=' ',
prefix=dirsep,
grid=(0, 5),
tipText='Directory navigation to current location')
if show_file and self.manualFilter is not None:
row += 1
self.manual_filter_entry = LabeledEntry(
self,
label='Manual Select',
entry=defaultFilter,
label_width=13,
entry_width=40,
returnCallback=self.entryFilter,
tipText=
'Path specification with wildcards to select multiple files')
self.manual_filter_entry.grid(row=row, column=0, sticky=Tkinter.EW)
self.updateFileList()
self.updateButtons()
if file:
self.setFile(file)
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 createFullProject(self, fileName):
if self.verbose == 1:
print "Writing %s project from file %s" % (self.formatLabel,
fileName)
self.file = self.projectIO.MarsProjectFile(fileName)
(fileDir, fileName) = os.path.split(fileName)
fileDir = normalisePath(fileDir)
marsInputDir = normalisePath(self.inputDirectory)
if marsInputDir != fileDir and marsInputDir.count(fileDir):
marsInputDir = marsInputDir.replace(fileDir, '')
if marsInputDir[0] == os.sep:
marsInputDir = marsInputDir[1:]
if not os.path.exists(marsInputDir):
os.mkdir(marsInputDir)
#
# Set tag for export/import cycle
#
#self.setDateTimeStamp(self.project,setTag,isUnique = False)
#self.setDateTimeStamp(self.chain,setTag,isUnique = True) # Only one export per chain!
#
# FASTA type sequence file
#
sequenceFileName = 'fastaSequence.tab'
self.file.files['sequence'] = os.path.join(marsInputDir,
sequenceFileName)
self.writeSequence(os.path.join(self.inputDirectory, sequenceFileName),
chains=[self.chain],
minimalPrompts=self.minimalPrompts)
#
# Chemical shift tab file - also used to set up spin system info
#
chemShiftFile = 'cs.tab'
self.file.files['csTab'] = os.path.join(marsInputDir, chemShiftFile)
if self.useFixedConnection:
ignoreFixedConnection = True
else:
ignoreFixedConnection = False
# Need to keep track of info in measurement file
self.writeShifts(os.path.join(self.inputDirectory, chemShiftFile),
measurementList=self.shiftList,
chains=[self.chain],
ignoreFixedConnection=ignoreFixedConnection,
noWrite=True,
minimalPrompts=self.minimalPrompts)
self.measurementFile.write(**self.writeKeywds)
#
# Fixed connection info - TODO make a ccp/format level file for this? Or not worth it?
#
if self.useFixedConnection:
fixedConnectionFile = 'fix_con.tab'
self.file.files['fixConn'] = os.path.join(marsInputDir,
fixedConnectionFile)
fixConnOut = open(
os.path.join(self.inputDirectory, fixedConnectionFile), 'w')
# Ignore info written in chemical shift file - is already filtered to not include chain-linked spin systems
ignoreSsSerials = []
for ssSerial in self.measurementFile.spinSystemLinks.keys():
ignoreSsSerials.append(ssSerial)
ignoreSsSerials.append(
self.measurementFile.spinSystemLinks[ssSerial][-1])
# Now go over spins systems, and print out links
serialConnections = []
for spinSystem in self.spinSystemList:
ssSerial = spinSystem.serial
if ssSerial in ignoreSsSerials:
continue
# Only report spin systems that are part of the chemical shift tab file!!
if not self.spinSystemToPrevId.has_key(
spinSystem) or not self.spinSystemToPrevId[spinSystem]:
continue
refResonanceToSpinSystem = self.spinSystemToResonanceDict[
spinSystem][0]
serialKey = None
if refResonanceToSpinSystem.linkedSpinSystems.has_key(1):
serialKey = (
spinSystem.serial,
refResonanceToSpinSystem.linkedSpinSystems[1].serial)
elif refResonanceToSpinSystem.linkedSpinSystems.has_key(-1):
serialKey = (
refResonanceToSpinSystem.linkedSpinSystems[-1].serial,
spinSystem.serial)
if serialKey and serialKey not in serialConnections:
serialConnections.append(serialKey)
for serialKey in serialConnections:
fixConnOut.write("%-4d %-4d" % (serialKey[0], serialKey[1]) +
newline)
fixConnOut.close()
#
# Fixed assignment info - TODO make a ccp/format level file for this? Or not worth it?
#
if self.useFixedAssignments:
fixedAssignmentFile = 'fix_ass.tab'
self.file.files['fixAss'] = os.path.join(marsInputDir,
fixedAssignmentFile)
fixAssOut = open(
os.path.join(self.inputDirectory, fixedAssignmentFile), 'w')
# Go over spins systems, and print out info if available
ssInfo = []
for spinSystem in self.spinSystemList:
# Only report spin systems that are part of the chemical shift tab file!!
if not self.spinSystemToPrevId.has_key(
spinSystem) or not self.spinSystemToPrevId[spinSystem]:
continue
seqIdList = []
resCodeList = []
# First use 'clean' information
if spinSystem.residue:
if spinSystem.residue.chain == self.chain:
seqIdList.append(spinSystem.residue.seqId)
else:
# Don't use if residue in wrong chain
continue
else:
if spinSystem.residueProbs:
for residueProb in spinSystem.residueProbs:
residue = residueProb.possibility
if residue.chain == self.chain:
seqIdList.append(residue.seqId)
# Don't use if all residues are in wrong chain
if not seqIdList:
continue
elif spinSystem.ccpCode:
resCodeList.append(
self.getCode1Letter(spinSystem.ccpCode))
else:
for residueTypeProb in spinSystem.residueTypeProbs:
code1Letter = self.getCode1Letter(
residueTypeProb.possibility.ccpCode)
if not code1Letter in resCodeList:
resCodeList.append(code1Letter)
if seqIdList or resCodeList:
ssInfo.append((spinSystem.serial, seqIdList, resCodeList))
for (ssSerial, seqIdList, resCodeList) in ssInfo:
fixAssOut.write("%-4d " % ssSerial)
if seqIdList:
for seqId in seqIdList:
fixAssOut.write("%d " % seqId)
if resCodeList:
fixAssOut.write("%s" % string.join(resCodeList, ''))
fixAssOut.write(newline)
fixAssOut.close()
#
# Finish up
#
self.file.write()
return self.file
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 body(self, master):
master.grid_columnconfigure(0, weight=1)
master.grid_rowconfigure(0, weight=1)
master.grid_rowconfigure(1, weight=1)
self.geometry('500x500')
fileNames = []
# All files have to be in same directory!
if self.files and self.files[0].find(dirsep) > -1:
(path, fileName) = splitPath(self.files[0])
directory = path
fileNames.append(fileName)
for file in self.files[1:]:
(path, fileName) = splitPath(file)
fileNames.append(fileName)
else:
path = None
directory = normalisePath(os.path.abspath(os.curdir))
fileNames = []
#print directory
#print fileName
file_types = []
if fileTypeDict.has_key(self.component):
if self.format and fileTypeDict[self.component].has_key(
self.format):
file_types.extend([
FileType(self.format,
fileTypeDict[self.component][self.format])
])
if fileTypeDict[self.component].has_key('generic'):
file_types.extend([
FileType('generic',
fileTypeDict[self.component]['generic'])
])
file_types.extend([FileType('All', ['*'])])
self.file_select = FileSelect(master,
file_types=file_types,
directory=directory,
double_callback=self.ok,
multiSelect=self.multiSelect)
if self.multiSelect:
self.file_select.setFiles(fileNames)
else:
if fileNames:
fileName = fileNames[0]
else:
fileName = ''
self.file_select.setFile(fileName)
self.file_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
texts = [self.selectionText]
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands)
buttons.grid(row=1, column=0, sticky=Tkinter.EW)
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
print 'must specify project directory'
sys.exit()
path = sys.argv[1]
import Tkinter
from memops.gui.DataEntry import askDir, askFile
from memops.gui.MessageReporter import showWarning
from memops.general.Io import loadProject
from memops.universal.Io import normalisePath
# This needs to be above loadProject because that can pop up
# dialogs, and it will create a root if one has not been created
# already, and that will lead to the later code crashing
r = Tkinter.Tk()
path = normalisePath(path)
askdir = lambda title, prompt, initial_value: askDir(
title, prompt, initial_value, parent=top, extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(
title, prompt, initial_value, parent=top, extra_dismiss_text='Skip')
project = loadProject(path,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
popup = DataLocationPopup(r, project)
r.withdraw()
r.mainloop()
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 parseFields(self, fields):
key = fields[0]
if (not (key in self.keys1 or key in self.keys2 or key in self.keys3)):
raise ApiError(
'unknown keyword (first few characters = "%s") in par file "%s"'
% (key[:10], self.parFile))
if (key in self.keys3):
return
if (key in self.keys1):
if (key != 'params' and len(fields) != 2):
raise ApiError(
'for key "%s", number of args = %d, should be 1' %
(key, len(fields) - 1))
elif (key in self.keys2):
if (len(fields) != 1):
raise ApiError(
'for key "%s", number of args = %d, should be 0' %
(key, len(fields) - 1))
if (key in self.keys2):
if (key == 'int'):
self.integer = True
elif (key == 'little_endian'):
self.big_endian = False
else:
setattr(self, key, True)
return
if len(fields) == 2:
value = fields[1]
else:
value = fields[1:]
if (key == 'ndim'):
if (self.ndim != 0):
raise ApiError('repeated "ndim"')
try:
self.ndim = int(value)
except:
raise ApiError('"ndim" value not an int')
if (self.ndim <= 0):
raise ApiError('ndim <= 0')
self.initDims()
elif (key == 'file'):
if (self.dataFile):
raise ApiError('repeated "file"')
path = normalisePath(value)
if not os.path.isabs(path):
directory = os.path.dirname(self.parFile)
if not directory:
directory = os.getcwd()
path = joinPath(directory, path)
self.dataFile = path
elif (key == 'head'):
if (self.head != 0):
raise ApiError('repeated "head"')
try:
self.head = 4 * int(value)
except:
raise ApiError('"head" value not an int')
if (self.head < 0):
raise ApiError('head < 0')
elif (key == 'dim'):
if (self.ndim <= 0):
raise ApiError('"dim" must be after "ndim"')
dim = self.dim
try:
self.dim = int(value) - 1
except:
raise ApiError('"dim" value not an int')
if (self.dim == dim):
raise ApiError('repeated dim %d' % (dim + 1))
if (self.dim < 0):
raise ApiError('dim = %d <= 0' % (self.dim + 1))
if (self.dim >= self.ndim):
raise ApiError('dim = %d > ndim = %d' %
(self.dim + 1, self.ndim))
else:
if (self.dim < 0):
raise ApiError('keyword "%s" must be after "dim"' % key)
dim = self.dim
# can no longer do below because initDims() sets up default values
#assert getattr(self, key)[dim] is None, '%s repeated for dim %d' % (key, dim+1)
if (key == 'npts'):
try:
v = int(value)
except:
raise ApiError('"npts" value not an int')
if (v <= 0):
raise ApiError('npts <= 0 for dim %d' % (key, dim + 1))
self.npts[dim] = v
elif (key == 'block'):
try:
v = int(value)
except:
raise ApiError('"block" value not an int')
if (v <= 0):
raise ApiError('block <= 0 for dim %d' % (key, dim + 1))
self.block[dim] = v
elif (key == 'nuc'):
self.nuc[dim] = self.standardNucleusName(value)
elif (key in ('sw', 'sf', 'refppm', 'refpt')):
try:
v = float(value)
except:
raise ApiError('"%s" value not a float' % key)
if (key == 'sw'):
self.sw[dim] = v
elif (key == 'sf'):
self.sf[dim] = v
elif (key == 'refppm'):
self.refppm[dim] = v
elif (key == 'refpt'):
self.refpt[dim] = v
elif (key == 'params'):
self.dimType[dim] = self.sampledDimType
try:
self.pointValues[dim] = [float(v) for v in value]
except:
raise ApiError('%s input %s not valid input to float' %
(key, value))
