def getFilterFiles(self, directory):
isDir = os.path.isdir
filterFiles = set()
for filtr in self.fileType.filters:
# have to use fullfilter rather than filter because cwd is not directory in general
fullfilter = joinPath(directory, filtr)
filterFiles.update(glob.glob(fullfilter))
# remove directory from file names
n = len(directory)
if directory[-1] != dirsep:
n = n + 1
filterFiles = list(set([x[n:] for x in filterFiles if not isDir(x)]))
filterFiles.sort()
# add in subdirectories
subDirs = [
x for x in os.listdir(directory) if isDir(joinPath(directory, x))
]
subDirs.sort()
return subDirs + filterFiles
def singleCallback(self, entry, row, col):
file = joinPath(self.directory, entry)
if os.path.isdir(file):
if not self.show_file:
self.directory_entry.setEntry(joinPath(self.directory, entry))
else:
if self.show_file:
self.file_entry.setEntry(entry)
if self.single_callback:
self.single_callback(file)
def showAminoPlot(self):
matrix = self.matrix
binWidth = self.binWidth
canvas = self.canvas
itemconf = canvas.itemconfigure
scaleColorQuick = self.scaleColorQuick
if self.aminoAcid:
colors = self.canvasDict.get(self.aminoAcid)
if not colors:
# fileName is the name of a PGM file in P2 format
fileName = joinPath(self.bitmapDir,
'log_%s.pgm' % self.aminoAcid.upper())
colors = self.readPGM(fileName)
self.canvasDict[self.aminoAcid] = colors
if not colors:
showWarning(
'Warning',
'Ramachandran plot data for %s does not exist! Using default'
% self.aminoAcid)
fileName = joinPath(self.bitmapDir, 'log_ALL.pgm')
colors = self.readPGM(fileName)
self.canvasDict[self.aminoAcid] = colors
else:
colors = self.canvasDict.get('ALL')
if not colors:
fileName = joinPath(self.bitmapDir, 'log_ALL.pgm')
colors = self.readPGM(fileName)
self.canvasDict['ALL'] = colors
for i in range(len(colors)):
for j in range(len(colors[0])):
item = matrix[i][j]
color = colors[i][j]
itemconf(item, fill=color)
if binWidth < 7:
itemconf(item, outline=color)
elif binWidth < 12:
itemconf(item, outline=scaleColorQuick(color, 0.9))
else:
itemconf(item, outline=scaleColorQuick(color, 0.8))
itemconf(self.title, text=self.aminoAcid or 'All Residue Types')
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 __init__(self, parent, selectionList, title = 'Select', text = 'Select', topText = None, dismissText = None, selected = None, selectionDict = None, urlFile = None, dismissButton = True, modal = False):
self.selectionList = selectionList
self.selectionDict = selectionDict
self.text = text
self.dismissButton = dismissButton
if dismissButton:
if dismissText:
self.dismissText = dismissText
else:
self.dismissText = 'dismiss'
self.topText = topText
self.isSelected = None
if not selected:
self.selectedIndex = 0
else:
self.selectedIndex = self.selectionList.index(selected)
if urlFile:
self.help_url = joinPath(getHelpUrlDir(),urlFile + '.html')
else:
self.help_url = None
TemporaryBasePopup.__init__(self,parent = parent, title = title, modal = modal, transient=True)
def updateInfo(self, *extra):
projName = self.proj_name_entry.get()
directory = self.proj_dir_select.getDirectory()
directory = joinPath(directory, projName)
self.proj_dir_label.set(directory)
def save(self):
projName = self.proj_name_entry.get()
directory = self.proj_dir_select.getDirectory()
directory = joinPath(directory, projName)
if self.isProjectDirectory(directory):
if not showOkCancel('Overwrite directory',
'Overwrite existing project directory?',
parent=self):
return
self.updateInfo()
self.did_save = False
changeDataLocations = self.dataCheckButton.isSelected()
done = False
try:
done = Io.saveProject(self.project,
newPath=directory,
newProjectName=projName,
createFallback=True,
showYesNo=showYesNo,
changeDataLocations=changeDataLocations,
showWarning=showWarning)
if done:
showInfo('Project saved', 'Project saved successfully')
self.did_save = True
if self.callback:
self.callback(self.project)
elif self.modal:
return # give another chance
except Implementation.ApiError, e:
showError('Save project', e.error_msg)
def __init__(self,
parent,
message,
nmrRes,
optionList,
title,
urlFile=None):
# Constructor doesn't do much except call body
# The parent is self.parent (parent of the popup)
self.singleResonanceStatus = None
self.message = message
self.optionList = optionList
self.nmrRes = nmrRes
if urlFile:
self.help_url = joinPath(getHelpUrlDir(), urlFile + '.html')
else:
self.help_url = None
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(self,
parent=parent,
title=title,
modal=True,
transient=True)
def callback(key, values, comment):
if key == 'control':
if project.foundControl:
raise AnsigParseException('control found twice')
project.foundControl = True
controlKeywordDict = {
'help_dir': (False, 1, (None, )),
'html_viewer': (False, 1, (None, )),
'dictionary': (False, 1, (None, )),
'gr_translate': (False, 1, (None, )),
'sequence': (False, 1, (None, )),
'spectra': (False, 1, (None, )),
'crosspeaks': (False, 1, (None, )),
'backup': (False, 1, (None, )),
'initialize': (False, 1, (None, )),
'exit': (False, 1, (None, )),
'binaryformat': (False, 1, (None, )),
'font': (False, 1, (None, )),
}
return controlKeywordDict
elif key in ('sequence', 'spectra', 'crosspeaks', 'binaryformat'):
value = values[0]
if key != 'binaryformat':
key = key + 'File'
if not os.path.isabs(value):
base = os.path.dirname(project.projectFile)
value = joinPath(base, value)
setattr(project, key, value)
def __init__(self, parent, matchName, chemAtomList, chemAtomDict, propagateList, ccpCode, shifts, matchType = 'Resonance', matchInfoPopup = None, selectedIndex = 4, title = 'Select resonance atom match', helpUrl = 'AtomSelect.html', headerLines = None, modal = False):
self.help_url = joinPath(getHelpUrlDir(),helpUrl)
# Constructor doesn't do much except call body
# The parent is self.parent (parent of the popup)
self.chemAtomOrSets = None
self.propagate = None
self.matchName = matchName
self.matchType = matchType
self.matchInfoPopup = matchInfoPopup
self.chemAtomList = chemAtomList
self.chemAtomDict = chemAtomDict
self.propagateList = propagateList
self.ccpCode = ccpCode
self.shifts = shifts
self.guiParent = parent
self.headerLines = headerLines
self.selectedIndex = selectedIndex
# modal = true means that it won't continue unless this one returns value
TemporaryBasePopup.__init__(self, parent=parent, title=title, modal=modal, transient=True)
def fcImportAllData(self):
# These files have to be correct, no preparsing necessary.
self.fcImportFile('sequence', 'dyana',
joinPath(self.importDir, "1bc6.seq"))
self.fcImportFile('distanceConstraints', 'dyana',
joinPath(self.importDir, "1bc6.restr"))
self.fcImportFile('coordinates',
'pdb',
joinPath(self.importDir, "1bc6.pdb"),
addKeywords={'forceDefaultChainMapping': True})
self.formatConversion.linkResonances(setSingleProchiral=True)
# This should be modifiable...
self.ccpnProject.saveModified()
def getEntryInfo(self, entry):
file = joinPath(self.directory, entry)
if os.path.islink(file):
# plain arrow: u' \u2192 '
entry = entry + u' \u21D2 ' + unicode(os.readlink(file), 'utf-8')
size = None
color = '#E0D0C0'
elif os.path.isdir(file):
if not self.isRootDirectory(entry):
entry = entry + dirsep
size = None
color = '#C0D0C0'
else:
color = '#C0C0D0'
if self.show_file:
try:
size = str(os.path.getsize(file))
except:
size = None
else:
size = None
try:
fileTime = self.fileTime(file)
except:
fileTime = ''
return (entry, size, fileTime, color)
def getAquaAtomInfo(chemCompCodes = {}):
aquaRefDir = getDataPath('ccp', 'aqua')
files = os.listdir(aquaRefDir)
for file in files:
if file[0:8] == 'AtomLIB-':
format = file[8:]
readAquaFormats(joinPath(aquaRefDir,file),format,chemCompCodes)
for file in files:
if file[-8:] == 'LIB-aqua':
info = file[0:-8]
readAquaDefs(joinPath(aquaRefDir,file),info,chemCompCodes)
return chemCompCodes
def doubleCallback(self, entry, row, col):
# TODO: need to worry about symbolic links leading you astray on path
file = joinPath(self.directory, entry)
if (self.show_file or not self.double_callback) and os.path.isdir(file):
self.changeDir(file)
elif self.double_callback:
self.double_callback(file)
class ImportFormatComponentPopup(GenericFormatPopup):
help_url = joinPath(getHelpUrlDir(),'ImportFormatComponent.html')
def setImportExportFlag(self):
self.importExportFlag = 'import'
self.titleText = "Project '%s': " % self.project.name + '%s %s %s' % (self.format,self.component,self.importExportFlag)
def getIntensityValue(self, phi, psi):
intensities = self.intensityDict.get(self.aminoAcid)
if not intensities:
if self.aminoAcid:
fileName = joinPath(self.bitmapDir,
'log_%s.pgm' % self.aminoAcid.upper())
else:
fileName = joinPath(self.bitmapDir, 'log_ALL.pgm')
self.readPGM(fileName)
intensities = self.intensityDict[self.aminoAcid]
i = int((phi + 180) / self.binSize)
j = int((psi - 180) / -self.binSize)
return intensities[i][j]
def setFileUpdates(self, fileUpdates=None, refresh=False, passwd=None):
# Synchronise the server - This is the admin upload part
if not fileUpdates:
fileUpdates = self.fileUpdates
if passwd is None:
if self.parent.isGraphical:
passwd = askPassword(
'Password Request',
'Enter password for %s@%s' % (self.uid, self.location))
else:
self.parent.warningMessage(
'Warning',
'Password must be specified when setting updates in non graphical mode'
)
if not passwd:
return False
# Clean server files
self.deleteFile(passwd, '__temp_*')
added = 0
if self.fileUpdates:
fileName = joinPath(self.parent.tempDir, self.dataFile)
file = open(fileName, 'w')
file.write('%s\n' % self.parent.version)
for x in self.fileUpdates:
if (not x.isNew) and refresh and (x in fileUpdates):
if not x.getIsUpToDate():
x.timestamp()
x.isNew = True
data = fieldSep.join([
x.fileName, x.filePath, x.storedAs, x.language, x.date,
x.details,
str(x.priority)
])
file.write('%s\n' % data)
if x.isNew:
copyfile(x.installedFile, x.tempFile)
self.uploadFile(passwd, x.tempFile, x.storedAs)
added += 1
file.close()
self.uploadFile(passwd, fileName, self.dataFile)
else:
self.deleteFile(passwd, self.dataFile)
self.parent.warningMessage('Notice',
'Server Update of %d files' % added)
return True
class NamingSystemPopup(TemporaryBasePopup):
help_url = joinPath(getHelpUrlDir(), 'NamingSystem.html')
def __init__(self, parent, namingSysList=None, namingSysDict=None):
# Constructor doesn't do much except call body
# The parent is self.parent (parent of the popup)
self.namingSys = None
self.namingSysList = namingSysList
self.namingSysDict = namingSysDict
# modal = true means that it won't continue unless this one returns value
TemporaryBasePopup.__init__(self,
parent=parent,
title='Choose namingSys',
modal=False,
transient=True)
def body(self, master):
#
# Popup gui
#
# First row
row = 0
label = Label(master, text="Choose a naming system:")
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
label = Label(master, text="(% matches in brackets)")
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
self.menu = PulldownMenu(master, entries=self.namingSysList)
self.menu.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Exit',
help_url=self.help_url)
buttons.grid(row=row, column=0)
def apply(self):
self.namingSysName = self.namingSysDict[self.menu.getSelected()]
return True
def __init__(self, procpar_file, data_file=None, **kw):
if not data_file:
data_file = joinPath(os.path.dirname(procpar_file), 'datdir', 'phasefile')
self.procpar_file = procpar_file
self.data_file = data_file
ExternalParams.__init__(self, **kw)
def topDir(self):
if self.directory:
isRoot = self.isRootDirectory
dirName = self.directory
while not isRoot(dirName):
dirName = joinPath(dirName, os.pardir)
self.changeDir(dirName)
def getFile(self, full_path=True):
if self.show_file:
file = self.file_entry.getEntry()
if file and full_path:
file = joinPath(self.directory, file)
else: # ignore full_path
file = self.directory_entry.getEntry()
return file
def cingProjectDownload(self, outputDir):
#
# Put in CCPN project as default. Always usea time-stamped directory name.
#
if not outputDir:
outputDir = self.ccpnProject.findFirstRepository(
name='userData').url.path
outputDir = os.path.join(outputDir, 'cing',
self.getFileTimeString())
#
# Make sure output dir exists
#
if not os.path.exists(outputDir):
os.makedirs(outputDir)
#
# Get the CING project name - safer in case changed on server side
#
projectPage = self.cingRequest("ProjectName")
pyDict = eval(projectPage)
projectName = pyDict['Result']
#
# Now download the file - first wait a bit just in case
#
time.sleep(20)
cingZipFile = "%s_CING_report.zip" % projectName
cingZipFileHttp = os.path.join(self.cingDownload, self.userId,
self.accessKey, cingZipFile)
# Try to re-download if not found.
outputData = None
while (not outputData or outputData.count("Not Found")):
time.sleep(20)
outputData = getDataFromHttp(cingZipFileHttp)
#
# And write it out...
#
self.cingZipFileOut = joinPath(outputDir, cingZipFile)
fout = open(self.cingZipFileOut, 'w')
fout.write(outputData)
fout.close()
def callHttpScript(self, passwd, script, data):
auth = base64.encodestring(self.uid + ":" + passwd)[:-1]
authheader = 'Basic %s' % auth
uri = 'http://' + joinPath(self.location, 'cgi-bin', self.httpDir,
script)
req = urllib2.Request(uri)
req.add_header("Authorization", authheader)
req.add_data(data)
uu = urllib2.urlopen(req)
print uu.read()
def getFilterFiles(self, directory):
filterFiles = set()
for filter in self.fileType.filters:
# have to use fullfilter rather than filter because cwd is not directory in general
fullfilter = joinPath(directory, filter)
filterFiles.update(glob.glob(fullfilter))
# remove directory from file names
n = len(directory)
if directory[-1] != dirsep:
n = n + 1
filterFiles = set([x[n:] for x in filterFiles])
# add in subdirectories
filterFiles.update([x for x in os.listdir(directory) if os.path.isdir(joinPath(directory, x))])
return list(filterFiles)
def uploadFile(self, passwd, localFile, serverFile):
cc = open(localFile).read()
ss = joinPath(self.basedir, serverFile)
data = urllib.urlencode({'content': cc, 'file': ss})
try:
# 18 Aug 08: TEMP: TBD: remove Temp when Jenny password protects directory
self.callHttpScript(passwd, 'uploadFileTemp', data)
except Exception, e:
self.parent.warningMessage('Server',
'Server exception: %s' % str(e))
def decomposeMultipleFileText(self,text):
files = []
if text:
textItems = text.split("\n")
if len(textItems) == 2:
(path,fileNameText) = textItems
for fileName in fileNameText.split(', '):
files.append(joinPath(path,fileName))
return files
class TextOutputPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'TextOutput.html')
def __init__(self, parent, title='Text output'):
BasePopup.__init__(self,
parent=parent,
title=title,
modal=False,
transient=False)
def body(self, master):
self.text = ScrolledText(master)
self.text.pack(side=Tkinter.TOP, expand=Tkinter.YES, fill=Tkinter.BOTH)
texts = ['Save text']
commands = [self.saveText]
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.pack()
def saveText(self):
fileSelectPopup = FileSelectPopup(
self,
file_types=[
FileType('Text', ['*.txt', '*.out', '*.text']),
FileType('All', ['*'])
],
title='Select text output save file')
fileName = fileSelectPopup.getFile()
if fileName:
writeFile = 1
if os.path.exists(fileName):
if not showYesNo('Overwrite file',
'Overwrite existing file %s?' % fileName):
writeFile = 0
if writeFile:
fout = open(fileName, 'w')
fout.write(self.text.text_area.getText())
fout.close()
def apply(self):
return True
class ChemCompSelectionPopup(TemporaryBasePopup):
help_url = joinPath(getHelpUrlDir(), 'ChemCompSelection.html')
def __init__(self, parent, project, **keywds):
self.project = project
self.keywds = keywds
origCode = self.keywds['origCode']
del self.keywds['origCode']
TemporaryBasePopup.__init__(
self,
parent=parent,
title="Project '%s': " % project.name +
"ChemComp selection for code '%s'" % origCode,
modal=False,
transient=False,
width=200)
def body(self, master):
self.frame = ChemCompFrame(master, self.project, **self.keywds)
self.frame.pack(side=Tkinter.TOP,
expand=Tkinter.YES,
fill=Tkinter.BOTH)
texts = ['OK']
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel',
help_url=self.help_url)
buttons.pack()
def apply(self):
if self.frame.getSelectedChemComp():
return True
else:
showInfo(
'No selection',
'Please select a chemCompVar from the bottom half of the window, or press Cancel to quit.'
)
return False
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 unpackRelease(self):
os.chdir('%s/%s' % (self.baseDir, self.releaseDir))
gzippedTarFile = self.releaseFile
cmds = []
if gzippedTarFile.endswith('.tar.gz'):
tarFile = gzippedTarFile[:-3]
sourceEnvFile = joinPath(self.baseDir, self.installDir, 'c',
environmentFile)
destEnvFile = joinPath(self.baseDir, self.releaseDir,
self.ccpnmrTopDir, self.ccpnmrCodeDir, 'c',
environmentFile)
cmds.append('gunzip %s' % gzippedTarFile)
cmds.append('tar xvf %s' % tarFile)
cmds.append('gzip %s' % tarFile)
cmds.append('cp %s %s' % (sourceEnvFile, destEnvFile))
else:
cmds.append('tar xvfz %s' % gzippedTarFile)
self.runCmds(cmds)