def loadRequiredPackages(required, loadingProgressBar):
try: # protect the required functions in a try statement, we want to load these things and they should be there but we can't force it to exist in older schemas, so this is in a try.
required = cPickle.loads(required)
if len(required) > 0:
if 'CRANrepos' in redREnviron.settings.keys():
repo = redREnviron.settings['CRANrepos']
else:
repo = None
loadingProgressBar.setLabelText(_('Loading required R Packages. If not found they will be downloaded.\n This may take a while...'))
RSession.require_librarys(required['R'], repository=repo)
installedPackages = redRPackageManager.getInstalledPackages()
downloadList = {}
print type(required['RedR'])
#print required['RedR']
for name,package in required['RedR'].items():
#print package
if (package['Name'] not in installedPackages.keys()) or (float(package['Version']['Number']) > float(installedPackages[package['Name']]['Version']['Number'])):
print 'my package number %s' % str(float(installedPackages[package['Name']]['Version']['Number'])), 'their package number %s' % str(float(package['Version']['Number']))
downloadList[package['Name']] = {'Version':unicode(package['Version']['Number']), 'installed':False}
if len(downloadList.keys()) > 0:
pm = redRPackageManager.packageManager(canvasDlg)
pm.show()
pm.askToInstall(downloadList, _('The following packages need to be installed before the session can be loaded.'))
except Exception as inst:
redRLog.log(redRLog.REDRCORE, redRLog.ERROR, _('redRSaveLoad loadRequiredPackages; error loading package %s') % inst)
def loadBaseLibs():
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
RSession.updatePackages(repository = redREnviron.settings['CRANrepos'])
RSession.install_libraries(['RSvgDevice', 'reshape', 'lattice', 'hexbin', 'ggplot2', 'graph', 'grid', 'limma', 'gregmisc', 'MASS', 'Matrix', 'RSQLite', 'splines'], repository = redREnviron.settings['CRANrepos'])
finally:
QApplication.restoreOverrideCursor()
def setMirror(self):
# print 'setMirror'
item = self.libListBox.currentRow()
self.settings['CRANrepos'] = unicode(self.libs['URL'][item])
RSession.Rcommand('local({r <- getOption("repos"); r["CRAN"] <- "' + unicode(self.libs['URL'][item]) + '"; options(repos=r)})')
#print self.settings['CRANrepos']
self.libInfo.setText('Repository URL changed to: '+unicode(self.libs['URL'][item]))
def loadMirrors(self):
self.libMessageBox.clear()
if not redREnviron.checkInternetConnection():
self.libMessageBox.setText(
_('No Internet Connection, please try again'))
return
self.libs = RSession.Rcommand('getCRANmirrors()')
self.libListBox.update(self.libs['Name'])
def require_librarys(self, librarys, repository=None):
qApp.setOverrideCursor(Qt.WaitCursor)
if not repository and 'CRANrepos' in redREnviron.settings.keys():
repository = redREnviron.settings['CRANrepos']
#print _('Loading required librarys')
success = RSession.require_librarys(librarys=librarys,
repository=repository)
self.requiredRLibraries.extend(librarys)
qApp.restoreOverrideCursor()
return success
def loadRequiredPackages(required, loadingProgressBar):
try: # protect the required functions in a try statement, we want to load these things and they should be there but we can't force it to exist in older schemas, so this is in a try.
required = cPickle.loads(required)
if len(required) > 0:
if 'CRANrepos' in redREnviron.settings.keys():
repo = redREnviron.settings['CRANrepos']
else:
repo = None
loadingProgressBar.setLabelText(
_('Loading required R Packages. If not found they will be downloaded.\n This may take a while...'
))
RSession.require_librarys(required['R'], repository=repo)
installedPackages = redRPackageManager.packageManager.getInstalledPackages(
)
downloadList = {}
print type(required['RedR'])
#print required['RedR']
for name, package in required['RedR'].items():
#print package
if not (package['Name'] in installedPackages.keys()
and package['Version']['Number'] == installedPackages[
package['Name']]['Version']['Number']):
downloadList[package['Name']] = {
'Version': unicode(package['Version']['Number']),
'installed': False
}
if len(downloadList.keys()) > 0:
pm = redRPackageManager.packageManagerDialog()
pm.show()
pm.askToInstall(
downloadList,
_('The following packages need to be installed before the session can be loaded.'
))
except Exception as inst:
redRLog.log(
redRLog.REDRCORE, redRLog.ERROR,
_('redRSaveLoad loadRequiredPackages; error loading package %s') %
inst)
def R(self,
query,
callType='getRData',
processingNotice=False,
silent=False,
showException=True,
wantType='convert',
listOfLists=True):
self.setRIndicator(True)
#try:
if processingNotice:
self.status.setStatus(4)
qApp.setOverrideCursor(Qt.WaitCursor)
try:
commandOutput = RSession.Rcommand(query=query,
silent=silent,
wantType=wantType,
listOfLists=listOfLists)
except RuntimeError as inst:
#print _('asdfasdfasdf'), inst
redRLog.log(redRLog.REDRCORE, redRLog.ERROR,
redRLog.formatException())
qApp.restoreOverrideCursor()
self.setRIndicator(False)
if showException:
QMessageBox.information(self, _('Red-R Canvas'),
_('R Error: ') + unicode(inst),
QMessageBox.Ok + QMessageBox.Default)
raise RuntimeError(unicode(inst))
return None # now processes can catch potential errors
#except:
# print _('R exception occurred')
self.processing = False
if processingNotice:
self.status.setStatus(5)
#self.progressBarFinished()
if not silent:
OWRpy.globalRHistory.append(query)
self.widgetRHistory.append(query)
self.ROutput.setCursorToEnd()
self.ROutput.append(
'> ' + query
) #Keep track automatically of what R functions were performed.
qApp.restoreOverrideCursor()
self.setRIndicator(False)
return commandOutput
def assignR(self, name, object):
assignOK = RSession.assign(name, object)
if not assignOK:
QMessageBox.information(self, _('Red-R Canvas'),_('Object was not assigned correctly in R, please tell package manager.'),
QMessageBox.Ok + QMessageBox.Default)
raise Exception, _('Object was not assigned correctly in R, please tell package manager.')
else:
histquery = _('Assign ')+unicode(name)+_(' to ')+unicode(object)
OWRpy.globalRHistory.append(histquery)
self.widgetRHistory.append(histquery)
self.ROutput.setCursorToEnd()
self.ROutput.append('> '+ histquery)
def onTabChange(self,index):
# print 'onTabChange',index
# get a data frame (dict) of r libraries
if self.tabs.tabText(index) != _('R Settings'):
return
try:
if not self.libListBox: return
except:
redRLog.log(redRLog.REDRCORE, redRLog.ERROR, redRLog.formatException())
self.libs = RSession.Rcommand('getCRANmirrors()')
# place a listBox in the widget and fill it with a list of mirrors
self.libListBox = redRlistBox(self.rlibrariesBox, label = _('Mirrors'),
items = self.libs['Name'], callback = self.setMirror)
def require_librarys(self, librarys, repository = None, load = True):
"""Load R libraries using the :mod:`RSession` require_librarys function.
Takes a list of strings as R libraries to load. These should be valid R packages or an error will occur. repository is an optional argument to specity a custom repository if the library is not in a standard location.
"""
qApp.setOverrideCursor(Qt.WaitCursor)
if not repository and 'CRANrepos' in redREnviron.settings.keys():
repository = redREnviron.settings['CRANrepos']
#print _('Loading required librarys')
try:
success = RSession.require_librarys(librarys = librarys, repository = repository, load = load)
self.requiredRLibraries.extend(librarys)
finally:
qApp.restoreOverrideCursor()
return success
def assignR(self, name, object):
assignOK = RSession.assign(name, object)
if not assignOK:
QMessageBox.information(
self, _('Red-R Canvas'),
_('Object was not assigned correctly in R, please tell package manager.'
), QMessageBox.Ok + QMessageBox.Default)
raise Exception, _(
'Object was not assigned correctly in R, please tell package manager.'
)
else:
histquery = _('Assign ') + unicode(name) + _(' to ') + unicode(
object)
OWRpy.globalRHistory.append(histquery)
self.widgetRHistory.append(histquery)
self.ROutput.setCursorToEnd()
self.ROutput.append('> ' + histquery)
def R(self, query):
return RSession.Rcommand(query = query)
def require_librarys(self, libraries):
return RSession.require_librarys(libraries)
def require_librarys(self, libraries):
return RSession.require_librarys(libraries)
def resolveRDependencies(self, packageList):
import RSession
packageList = [x.strip() for x in packageList]
RSession.require_librarys(packageList)
def loadDocument180(filename, caption=None, freeze=0, importing=0):
global sessionID
import redREnviron
if filename.split('.')[-1] in ['rrts']:
tmp = True
elif filename.split('.')[-1] in ['rrs']:
tmp = False
else:
QMessageBox.information(
self, _('Red-R Error'),
_('Cannot load file with extension %s') %
unicode(filename.split('.')[-1]),
QMessageBox.Ok + QMessageBox.Default)
return
loadingProgressBar = startProgressBar(
_('Loading %s') % unicode(os.path.basename(filename)),
_('Loading ') + unicode(filename), 2)
## What is the purpose of this???
if not os.path.exists(filename):
if os.path.splitext(filename)[1].lower() != ".tmp":
QMessageBox.critical(self, _('Red-R Canvas'),
_('Unable to locate file "%s"') % filename,
QMessageBox.Ok)
return
loadingProgressBar.hide()
loadingProgressBar.close()
###
# set cursor
qApp.setOverrideCursor(Qt.WaitCursor)
if os.path.splitext(filename)[1].lower() == ".rrs":
schemaPath, _schemaName = os.path.split(filename)
canvasDlg.setCaption(caption or _schemaName)
if importing: # a normal load of the session
_schemaName = ""
loadingProgressBar.setLabelText(_('Loading Schema Data, please wait'))
### unzip the file ###
zfile = zipfile.ZipFile(unicode(filename), "r")
for name in zfile.namelist():
file(
os.path.join(redREnviron.directoryNames['tempDir'],
os.path.basename(name)), 'wb'
).write(
zfile.read(name)
) ## put the data into the tempdir for this session for each file that was in the temp dir for the last schema when saved.
doc = parse(
os.path.join(redREnviron.directoryNames['tempDir'], 'tempSchema.tmp')
) # load the doc data for the data in the temp dir.
## get info from the schema
schema = doc.firstChild
widgets = schema.getElementsByTagName("widgets")[0]
lines = schema.getElementsByTagName('channels')[0]
f = open(
os.path.join(redREnviron.directoryNames['tempDir'], 'settings.pickle'))
settingsDict = eval(unicode(f.read()))
f.close()
#settingsDict = eval(unicode(settings[0].getAttribute("settingsDictionary")))
loadedSettingsDict = settingsDict
loadRequiredPackages(settingsDict['_requiredPackages'],
loadingProgressBar=loadingProgressBar)
## make sure that there are no duplicate widgets.
if not tmp:
## need to load the r session before we can load the widgets because the signals will beed to check the classes on init.
if not checkWidgetDuplication(widgets=widgets):
QMessageBox.information(
self, _('Schema Loading Failed'),
_('Duplicated widgets were detected between this schema and the active one. Loading is not possible.'
), QMessageBox.Ok + QMessageBox.Default)
return
RSession.Rcommand('load("' +
os.path.join(redREnviron.directoryNames['tempDir'],
"tmp.RData").replace('\\', '/') + '")')
loadingProgressBar.setLabelText(_('Loading Widgets'))
loadingProgressBar.setMaximum(
len(widgets.getElementsByTagName("widget")) + 1)
loadingProgressBar.setValue(0)
globalData.globalData = cPickle.loads(loadedSettingsDict['_globalData'])
(loadedOkW,
tempFailureTextW) = loadWidgets180(widgets=widgets,
loadingProgressBar=loadingProgressBar,
loadedSettingsDict=loadedSettingsDict,
tmp=tmp)
lineList = lines.getElementsByTagName("channel")
loadingProgressBar.setLabelText(_('Loading Lines'))
(loadedOkL,
tempFailureTextL) = loadLines(lineList,
loadingProgressBar=loadingProgressBar,
freeze=freeze,
tmp=tmp)
#for widget in redRObjects.instances(): widget.updateTooltip()
#activeCanvas().update()
#saveTempDoc()
if not loadedOkW and loadedOkL:
failureText = tempFailureTextW + tempFailureTextL
QMessageBox.information(
canvasDlg, _('Schema Loading Failed'),
_('The following errors occured while loading the schema: <br><br>'
) + failureText, QMessageBox.Ok + QMessageBox.Default)
for widget in redRObjects.instances():
widget.setLoadingSavedSession(False)
qApp.restoreOverrideCursor()
qApp.restoreOverrideCursor()
qApp.restoreOverrideCursor()
loadingProgressBar.hide()
loadingProgressBar.close()
if tmp:
sessionID += 1
def loadDocument(filename, caption=None, freeze=0, importing=0):
global _schemaName
global schemaPath
global globalNotes
redRLog.log(redRLog.REDRCORE, redRLog.INFO,
_('Loading Document %s') % filename)
import redREnviron
if filename.split('.')[-1] in ['rrts']:
tmp = True
pipe = False
elif filename.split('.')[-1] in ['rrs']:
tmp = False
pipe = False
elif filename.split('.')[-1] in [
'rrpipe'
]: ## pipeline, no data but everything else there.
pipe = True
tmp = False
else:
QMessageBox.information(
None, 'Red-R Error',
_('Cannot load file with extension %s') %
unicode(filename.split('.')[-1]),
QMessageBox.Ok + QMessageBox.Default)
return
loadingProgressBar = startProgressBar(
_('Loading %s') % unicode(os.path.basename(filename)),
_('Loading %s') % unicode(filename), 2)
# set cursor
qApp.setOverrideCursor(Qt.WaitCursor)
if os.path.splitext(filename)[1].lower() == ".rrs":
schemaPath, _schemaName = os.path.split(filename)
canvasDlg.setCaption(caption or _schemaName)
if importing: # a normal load of the session
_schemaName = ""
loadingProgressBar.setLabelText(_('Loading Schema Data, please wait'))
### unzip the file ###
zfile = zipfile.ZipFile(unicode(filename), "r")
for name in zfile.namelist():
file(
os.path.join(redREnviron.directoryNames['tempDir'],
os.path.basename(name)), 'wb'
).write(
zfile.read(name)
) ## put the data into the tempdir for this session for each file that was in the temp dir for the last schema when saved.
doc = parse(
os.path.join(redREnviron.directoryNames['tempDir'], 'tempSchema.tmp')
) # load the doc data for the data in the temp dir.
## get info from the schema
schema = doc.firstChild
try:
version = schema.getElementsByTagName("header")[0].getAttribute(
'version')
if not version:
redRLog.log(
redRLog.REDRCORE, redRLog.WARNING,
_('Version Tag Missing, using Red-R 1.80 loading specifications'
)
) ## we should move everything to the earlier versions of orngDoc for loading.
loadDocument180(filename, caption=None, freeze=0, importing=0)
loadingProgressBar.hide()
loadingProgressBar.close()
return
else:
print _('The version is:%s') % version
except Exception as inst:
redRLog.log(redRLog.REDRCORE, redRLog.ERROR, redRLog.formatException())
redRLog.log(
redRLog.REDRCORE, redRLog.WARNING,
_('Error in loading the schema %s, reverting to load with 1.80 settings'
) % inst)
loadDocument180(filename, caption=None, freeze=0, importing=0)
loadingProgressBar.hide()
loadingProgressBar.close()
return
widgets = schema.getElementsByTagName("widgets")[0]
tabs = schema.getElementsByTagName("tabs")[0]
#settings = schema.getElementsByTagName("settings")
f = open(
os.path.join(redREnviron.directoryNames['tempDir'], 'settings.pickle'))
settingsDict = eval(unicode(f.read()))
f.close()
## load the required packages
loadRequiredPackages(settingsDict['_requiredPackages'],
loadingProgressBar=loadingProgressBar)
## make sure that there are no duplicate widgets.
if not tmp and not pipe:
## need to load the r session before we can load the widgets because the signals will beed to check the classes on init.
if not checkWidgetDuplication(widgets=widgets):
QMessageBox.information(
canvasDlg, _('Schema Loading Failed'),
_('Duplicated widgets were detected between this schema and the active one. Loading is not possible.'
), QMessageBox.Ok + QMessageBox.Default)
return
RSession.Rcommand('load("' +
os.path.join(redREnviron.directoryNames['tempDir'],
"tmp.RData").replace('\\', '/') + '")')
loadingProgressBar.setLabelText(_('Loading Widgets'))
loadingProgressBar.setMaximum(
len(widgets.getElementsByTagName("widget")) + 1)
loadingProgressBar.setValue(0)
if not tmp:
globalData.globalData = cPickle.loads(settingsDict['_globalData'])
if notesTextWidget and ('none' in globalData.globalData.keys()) and (
'globalNotes' in globalData.globalData['none'].keys()):
notesTextWidget.setHtml(
globalData.globalData['none']['globalNotes']['data'])
(loadedOkW,
tempFailureTextW) = loadWidgets(widgets=widgets,
loadingProgressBar=loadingProgressBar,
loadedSettingsDict=settingsDict,
tmp=tmp)
## LOAD tabs
##### move through all of the tabs and load them.
(loadedOkT,
tempFailureTextT) = loadTabs(tabs=tabs,
loadingProgressBar=loadingProgressBar,
tmp=tmp,
loadedSettingsDict=settingsDict)
if not tmp:
redRLog.log(10, 9, 3, _('Setting Signals'))
for widget in redRObjects.instances():
redRLog.log(10, 9, 9, _('Setting Signals for %s') % widget)
try:
if widget.widgetID not in settingsDict.keys(): continue
widget.outputs.setOutputs(
cPickle.loads(
settingsDict[widget.widgetID]['connections']), tmp)
except Exception as inst:
redRLog.log(redRLog.REDRCORE, redRLog.ERROR,
redRLog.formatException())
redRLog.log(
1, 9, 1,
_('Error setting signals %s, Settings are %s') %
(inst, settingsDict[widget.widgetID].keys()))
else:
for widget in redRObjects.instances():
if widget.tempID and widget.tempID in settingsDict.keys():
widget.outputs.setOutputs(
cPickle.loads(settingsDict[widget.tempID]['connections']),
tmp)
if pipe: ## send none through all of the data.
for w in redRObjects.instances():
w.outputs.propogateNone(ask=False)
for widget in redRObjects.instances():
widget.tempID = None ## we set the temp ID to none so that there won't be a conflict with other temp loading.
## some saved sessions may have widget instances that are available but that do not match to icons. This shouldn't happen normally but if it does then we have instances that can persist without us knowing about it. We clear those here.
for i in redRObjects.instances():
try:
redRObjects.getWidgetByInstance(i)
except:
redRLog.log(redRLog.REDRCORE, redRLog.ERROR,
redRLog.formatException())
try:
redRObjects.removeWidgetInstance(i)
except:
redRLog.log(redRLog.REDRCORE, redRLog.ERROR,
redRLog.formatException())
pass
qApp.restoreOverrideCursor()
qApp.restoreOverrideCursor()
qApp.restoreOverrideCursor()
loadingProgressBar.hide()
loadingProgressBar.close()
redRObjects.updateLines()
def save(filename=None, template=False, copy=False, pipe=False):
global _schemaName
global schemaPath
global notesTextWidget
#redRLog.log(redRLog.REDRCORE, redRLog.ERROR, '%s' % filename)
if filename == None and not copy:
filename = os.path.join(schemaPath, _schemaName)
elif copy:
filename = os.path.join(redREnviron.directoryNames['tempDir'],
'copy.rrts')
#redRLog.log(redRLog.REDRCORE, redRLog.ERROR, 'Saveing file as name %s' % filename)
progressBar = startProgressBar(
_('Saving ') + unicode(os.path.basename(filename)),
_('Saving ') + unicode(os.path.basename(filename)),
len(redRObjects.instances()) + len(redRObjects.lines()) + 3)
progress = 0
# create xml document
(doc, schema, header, widgets, lines, settings, required, tabs,
saveTagsList, saveDescription) = makeXMLDoc()
requiredRLibraries = {}
#save widgets
tempWidgets = redRObjects.instances(
wantType='dict'
) ## all of the widget instances, these are not the widget icons
(widgets, settingsDict,
requireRedRLibraries) = saveInstances(tempWidgets, widgets, doc,
progressBar)
# save tabs and the icons and the channels
if not copy or template:
#tabs.setAttribute('tabNames', unicode(self.canvasTabs.keys()))
for t in redRObjects.tabNames():
temp = doc.createElement('tab')
temp.setAttribute('name', t)
## set all of the widget icons on the tab
widgetIcons = doc.createElement('widgetIcons')
for wi in redRObjects.getIconsByTab(
t
)[t]: ## extract only the list for this tab thus the [t] syntax
saveIcon(widgetIcons, wi, doc)
# tabLines = doc.createElement('tabLines')
# for line in self.widgetLines(t)[t]:
# saveLine(tabLines, line)
temp.appendChild(
widgetIcons) ## append the widgetIcons XML to the global XML
#temp.appendChild(tabLines) ## append the tabLines XML to the global XML
tabs.appendChild(temp)
## save the global settings ##
if notesTextWidget:
globalData.setGlobalData('Notes', 'globalNotes',
unicode(notesTextWidget.toHtml()))
settingsDict['_globalData'] = cPickle.dumps(globalData.globalData, 2)
settingsDict['_requiredPackages'] = cPickle.dumps(
{
'R': requiredRLibraries.keys(),
'RedR': requireRedRLibraries
}, 2)
#print requireRedRLibraries
file = open(
os.path.join(redREnviron.directoryNames['tempDir'], 'settings.pickle'),
"wt")
file.write(unicode(settingsDict))
file.close()
if template:
taglist = unicode(tempDialog.tagsList.text())
tempDescription = unicode(tempDialog.descriptionEdit.toPlainText())
saveTagsList.setAttribute("tagsList", taglist)
saveDescription.setAttribute("tempDescription", tempDescription)
xmlText = doc.toprettyxml()
progress += 1
progressBar.setValue(progress)
if not template and not copy and not pipe:
tempschema = os.path.join(redREnviron.directoryNames['tempDir'],
"tempSchema.tmp")
tempR = os.path.join(redREnviron.directoryNames['tempDir'],
"tmp.RData").replace('\\', '/')
file = open(tempschema, "wt")
file.write(xmlText)
file.close()
doc.unlink()
progressBar.setLabelText('Saving Data...')
progress += 1
progressBar.setValue(progress)
RSession.Rcommand('save.image("' + tempR + '")') # save the R data
createZipFile(
filename, [], [redREnviron.directoryNames['tempDir']]
) # collect the files that are in the tempDir and save them into the zip file.
elif template:
tempschema = os.path.join(redREnviron.directoryNames['tempDir'],
"tempSchema.tmp")
file = open(tempschema, "wt")
file.write(xmlText)
file.close()
zout = zipfile.ZipFile(filename, "w")
zout.write(tempschema, "tempSchema.tmp")
zout.write(
os.path.join(redREnviron.directoryNames['tempDir'],
'settings.pickle'), 'settings.pickle')
zout.close()
doc.unlink()
elif copy:
tempschema = os.path.join(redREnviron.directoryNames['tempDir'],
"tempSchema.tmp")
file = open(tempschema, "wt")
file.write(xmlText)
file.close()
zout = zipfile.ZipFile(filename, "w")
zout.write(tempschema, "tempSchema.tmp")
zout.write(
os.path.join(redREnviron.directoryNames['tempDir'],
'settings.pickle'), 'settings.pickle')
zout.close()
doc.unlink()
loadTemplate(filename)
progress += 1
progressBar.setValue(progress)
progressBar.close()
if os.path.splitext(filename)[1].lower() == ".rrs":
(schemaPath, schemaName) = os.path.split(filename)
redREnviron.settings["saveSchemaDir"] = schemaPath
canvasDlg.toolbarFunctions.addToRecentMenu(filename)
canvasDlg.setCaption(schemaName)
redRLog.log(redRLog.REDRCORE, redRLog.INFO,
'Document Saved Successfully to %s' % filename)
return True
