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()
"""!@#$ Is this still required? If packages request R libraries then we don't really need to install them again, we just need to resolve the packages."""
requiredRLibraries = {}
#save widgets
tempWidgets = redRObjects.instances(wantType = 'dict') ## all of the widget instances, these are not the widget icons
"""This is where we save the instances to the file."""
print 'Saving widget instances ', tempWidgets
(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)
temp.appendChild(widgetIcons) ## append the widgetIcons 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.encode('utf-8', 'replace'))
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
def __init__(self, **kwargs):
OWRpy.__init__(self, wantGUIDialog = 1, **kwargs)
self.setRvariableNames(['summaryData'])
""".. rrsignals::"""
self.inputs.addInput('id1', _('Input Data Table'), [signals.base.TableView, signals.base.RDataFrame], self.dataset)
self.data = {} # dict containing the table infromation
self.dataParent = None
self.showMetas = {} # key: id, value: (True/False, columnList)
self.showMeta = 1
self.showAttributeLabels = 1
self.showDistributions = 1
self.distColorRgb = (220,220,220, 255)
self.distColor = QColor(*self.distColorRgb)
self.locale = QLocale()
self.currentLinks = {}
#R modifications
self.currentData = None
self.dataTableIndex = {}
self.supressTabClick = False
self.mylink = ''
self.link = {}
#The settings
self.advancedOptions = redRGUI.base.tabWidget(self.GUIDialog, position = QTabWidget.West) #orientation = 'vertical')
self.GUIDialog.layout().setAlignment(self.advancedOptions,Qt.AlignTop)
diBox = self.advancedOptions.createTabPage(_("Data Information"))
vbox = redRGUI.base.widgetBox(diBox)
self.infoBox = redRGUI.base.groupBox(vbox, label=_("Data Information"))
self.infoBox.setHidden(False)
redRGUI.base.widgetLabel(self.infoBox, label = _("A summary of your data will be displayed below when data is available."), wordWrap = True)
self.rowColCount = redRGUI.base.widgetLabel(self.infoBox)
summaryBox = redRGUI.base.groupBox(vbox, label=_("Selected Data Summary"))
self.customSummary = redRGUI.base.lineEdit(summaryBox, label = _('Custom Summary:'), toolTip = _('Place a custom summary function in here which will be added to the regular summary, use {Col} for the column number. Ex. mean({Col})'))
self.summaryLabel = redRGUI.base.textEdit(summaryBox, label = _('Summary'),displayLabel=False)
#saveTab = self.tabWidgeta.createTabPage('Save Data')
sdBox = self.advancedOptions.createTabPage(_("Save Data"))
saveTab = redRGUI.base.groupBox(sdBox,label=_('Save Data'),orientation='horizontal')
#redRGUI.base.widgetLabel(saveTab, label=_("Saves the current table to a file."))
#redRGUI.base.button(saveTab, label=_("Set File"), callback = self.chooseDirectory)
#self.fileName = redRGUI.base.widgetLabel(saveTab, label="")
self.separator = redRGUI.base.comboBox(saveTab, label = 'Seperator:',
items = [_('Comma'), _('Tab'), _('Space')], orientation = 'horizontal')
save = redRGUI.base.button(saveTab, label=_("Save As File"), callback=self.writeFile,
toolTip = _("Write the table to a text file."))
saveTab.layout().setAlignment(save,Qt.AlignRight)
#links:
linkBox = self.advancedOptions.createTabPage(_('Links to Websites'), canScroll = True)
linksTab = redRGUI.base.groupBox(linkBox, _('Links to Websites'))
self.linksListBox = redRGUI.base.listBox(linksTab,label=_('Links to Websites'),displayLabel=False)
self.linksListBox.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.customLink = redRGUI.base.lineEdit(linksTab, label = _('Add Link:'), includeInReports=False)
hbox = redRGUI.base.widgetBox(linksTab,orientation='horizontal')
b = redRGUI.base.button(hbox, label = _('Add'), toolTip = _('Adds a link to the link section for interactive data exploration.\nThe link must have a marker for the row information in the form\n{column number}\n\nFor example:http://www.google.com/#q=%s, would do a search Google(TM) for whatever was in the cell you clicked.\nYou can test this if you want using the example.'), callback=self.addCustomLink)
redRGUI.base.button(hbox, label = _('Clear Links'), toolTip = _('Clears the links from the links section'),
callback = self.clearLinks)
hbox.layout().setAlignment(Qt.AlignRight)
redRGUI.base.widgetLabel(linksTab,label ="""
Creating new links:
http://www.ncbi.nlm.nih.gov/gene/{gene_id}
- Here {gene_id} is a place holder and should be
the column name in your table.
- The value in that column and selected row will
replace the place holder.
""")
#The table
self.tableBox = redRGUI.base.widgetBox(self.controlArea)
self.tableBox.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
#boxSettings = redRGUI.base.groupBox(self.advancedOptions, label = _("Settings"))
self.table = redRGUI.base.filterTable(self.tableBox,label = _('Data Table'),displayLabel=False, sortable=True,
filterable=True,selectionBehavior = QAbstractItemView.SelectItems, callback=self.itemClicked,selectionCallback=self.cellSelection)
# self.table = filterTable2(self.tableBox, sortable=True,
# filterable=True,selectionBehavior = QAbstractItemView.SelectItems, callback=self.itemClicked)
##########################################################
# self.R('data <- data.frame(a=rnorm(1000),b=c("a","b","c","d","e"))')
# self.data = 'iris'
# self.table.setRTable(self.data)
##########################################################
globalData.setGlobalData(self, 'links', [('http://www.google.com/search?q=%s', 'Google'), ('http://en.wikipedia.org/w/index.php?title=Special:Search&search=%s', 'Wikipedia')])
self.setLinks()
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
