class ResonanceSelectPopup(BasePopup):
def __init__(self,
parent,
resonanceList,
resonanceDict,
code3Letter,
resName,
helpText,
multi,
title='Select resonances'):
# Constructor doesn't do much except call body
# The parent is self.parent (parent of the popup)
self.selectedResonances = None
self.resonanceList = resonanceList
self.resonanceDict = resonanceDict
self.code3Letter = code3Letter
self.resName = resName
self.helpText = helpText
if multi:
self.selectmode = Tkinter.MULTIPLE
else:
self.selectmode = Tkinter.SINGLE
# 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 body(self, master):
master.grid_columnconfigure(0, weight=1)
for i in range(6):
master.grid_rowconfigure(i, weight=1)
self.geometry('600x400')
#
# Popup window
#
row = 0
label = Label(master, text="Residue type '%s'" % self.code3Letter)
label.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text="Resonance '%s'" % self.resName)
label.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text="Pick resonance(s):")
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
self.list = ScrolledListbox(master,
width=50,
height=5,
selectmode=self.selectmode,
initial_list=self.resonanceList)
self.list.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text=self.helpText, fg='blue')
label.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)
buttons.grid(row=row, column=0)
def apply(self):
selectedResNames = self.list.getSelectedItems()
#
# Return value depends on whether multi or not
#
if selectedResNames:
if type(selectedResNames) == type([]):
self.selectedResonances = []
for selectedResName in selectedResNames:
self.selectedResonances.append(
self.resonanceDict[selectedResName])
else:
self.selectedResonances = [
self.resonanceDict[selectedResNames]
]
else:
return False
return True
class CreateShiftListPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'CreateShiftList.html')
def __init__(self, parent, project):
self.project = project
self.peakLists = []
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Create shift list from peak lists',
modal=False,
transient=True)
def body(self, master):
#
# Peaklist setup
#
self.peakListDict = {}
for experiment in self.project.currentNmrProject.sortedExperiments():
for dataSource in experiment.sortedDataSources():
for peakList in dataSource.sortedPeakLists():
peakListLabel = "%s:%s:%d:%s" % (
experiment.name, dataSource.name, peakList.serial,
peakList.name)
self.peakListDict[peakListLabel] = peakList
peakListLabels = self.peakListDict.keys()
peakListLabels.sort()
#
# chemical shift list setup
#
self.shiftListDict = {}
self.shiftListDict['None'] = None
for shiftList in self.project.currentNmrProject.findAllMeasurementLists(
className='ShiftList'):
shiftListLabel = "%d:%s" % (shiftList.serial, shiftList.name)
self.shiftListDict[shiftListLabel] = shiftList
shiftListLabels = self.shiftListDict.keys()
shiftListLabels.sort()
row = 0
label = Label(master, text="Generation of chemical shift list")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row += 1
label = Label(master, text="Peak lists:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.peakListBox = ScrolledListbox(master,
width=50,
height=5,
selectmode=Tkinter.MULTIPLE,
initial_list=peakListLabels)
self.peakListBox.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use existing shift list:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master, entries=shiftListLabels)
self.shiftListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use multiple assignments:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.useAllContribs = CheckButton(master)
self.useAllContribs.grid(row=row, column=1, sticky=Tkinter.W)
#
# Setup the default shift error per nucleus
#
self.defaultShiftError = {}
for (nucl, text, defValue) in [('1H', 'proton', '0.002'),
('13C', 'carbon', '0.1'),
('15N', 'nitrogen', '0.1')]:
row += 1
label = Label(master, text="Default %s shift error:" % text)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.defaultShiftError[nucl] = Entry(master, text=defValue)
self.defaultShiftError[nucl].grid(row=row,
column=1,
sticky=Tkinter.W)
row += 1
texts = ['Create shift list']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, columnspan=2, column=0)
def apply(self):
selectedPeakLists = self.peakListBox.getSelectedItems()
for peakListLabel in selectedPeakLists:
self.peakLists.append(self.peakListDict[peakListLabel])
chemShiftList = self.shiftListDict[self.shiftListSelect.getSelected()]
if not chemShiftList:
chemShiftListName = askString("Enter chemical shift list name",
"New chemical shift list name", '',
self)
else:
chemShiftListName = chemShiftList.name
useAllContribs = self.useAllContribs.isSelected()
defaultShiftError = {}
for nucl in self.defaultShiftError.keys():
defaultShiftError[nucl] = returnFloat(
self.defaultShiftError[nucl].get())
listCreated = createChemShifts(self.peakLists,
guiParent=self.parent,
multiDialog=self.parent.multiDialog,
shiftList=chemShiftList,
useAllContribs=useAllContribs,
defaultShiftError=defaultShiftError,
shiftListName=chemShiftListName)
if listCreated:
showInfo(
"Success",
"Succesfully created a chemical shift list from peaklist(s)")
return True
class RepositoryFrame(Frame):
def __init__(self, guiParent, basePopup):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
# should the screen autorefresh
self.autoRefresh = False
# add this to shortcuts to ease navigation
self.basePopup.frameShortcuts['Repository'] = self
# get a port proxy instance
# this should probably belong to the repository directly
# or else should belong in a dictionary in the main gui
# layer when it can be picked up easily
# FIXME JMCI
# need to work out how to get a number of these!
loc = SharedBeanServiceLocator()
self.port = loc.getSharedBean()
self.registerNotify = basePopup.registerNotify
self.unregisterNotify = basePopup.unregisterNotify
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=20)
self.grid_columnconfigure(1, weight=1, minsize=10)
self.grid_columnconfigure(2, weight=0, minsize=20)
self.grid_rowconfigure(0, weight=0, minsize=5)
self.grid_rowconfigure(1, weight=0, minsize=0)
self.grid_rowconfigure(2, weight=0, minsize=10)
self.grid_rowconfigure(3, weight=0, minsize=10)
self.grid_rowconfigure(4, weight=0, minsize=10)
self.grid_rowconfigure(5, weight=1, minsize=10)
self.grid_rowconfigure(6, weight=0, minsize=10)
self.grid_rowconfigure(7, weight=0, minsize=10)
# widgets for view when no data
self.noDataWidgets = []
self.noRepLabel = Label(self, text='No repository currently selected.')
self.noDataWidgets.append(self.noRepLabel)
# widgets for view when current repository set
self.dataWidgets = []
self.repTitle = Label(self, text='Repository:', font='Helvetica16')
self.dataWidgets.append(self.repTitle)
#self.repLabel = Label(self,text='All Projects in Repository')
#self.dataWidgets.append(self.repLabel)
self.repTree = Tree(self, doubleCallback=self.goto_project_tab)
self.dataWidgets.append(self.repTree)
sel = 1
if self.autoRefresh:
sel = 0
self.autoRefreshSwitchLabel = Label(self, text='Auto Refresh')
self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'],
select_callback=self.set_refresh,
selected_index=sel)
# need to decide whether this is static or not
r_button_texts = [
'Add to Basket', ' Import ', ' Export ', ' Refresh ',
'Properties'
]
r_button_cmds = [
self.tmpCall, self.import_project, self.export_project,
self.drawFrame, self.goto_project_tab
]
self.rep_button_list = ButtonList(self, r_button_texts, r_button_cmds)
self.dataWidgets.append(self.rep_button_list)
self.filterFrame = FilterFrame(self, self.basePopup, text='Filter')
self.dataWidgets.append(self.filterFrame)
baskets = ('basket1', 'basket2', 'basket3')
self.basketSelect = PulldownList(self, self.tmpCall, baskets)
self.dataWidgets.append(self.basketSelect)
basketElements = ('1ay3', '1ay7')
self.basketList = ScrolledListbox(self, basketElements, 25, 18)
self.dataWidgets.append(self.basketList)
b_button_texts = ['Remove from Basket', 'New Basket']
b_button_cmds = [self.tmpCall, self.tmpCall]
self.b_button_list = ButtonList(self, b_button_texts, b_button_cmds)
self.dataWidgets.append(self.b_button_list)
# draw if not automatically refreshing
if sel == 1:
self.drawFrame()
# set up a loop
self.refresh()
def drawFrame(self):
if self.basePopup.repList.currentRepository == None:
for widget in self.dataWidgets:
widget.grid_remove()
self.noRepLabel.grid(row=1, column=1, sticky='n')
else:
self.repository = self.basePopup.repList.currentRepository
for widget in self.noDataWidgets:
widget.grid_remove()
# Column headers
# want to have a general admin panel; current repository, button to change, info
# about login and so on
self.repTitle.set('Repository: ' + self.repository.user + '@' +
self.repository.name + ' ( ' +
self.repository.connect + ' )')
self.repTitle.grid(row=1, column=1, sticky='w')
# self.repLabel.grid(row=2, column=1, sticky='w')
# Repository block
#grid and update
self.repTree.grid(row=3, column=1, rowspan=3, sticky='nsew')
self.updateRepTree()
self.autoRefreshSwitchLabel.grid(row=6,
column=1,
padx=10,
sticky='w')
self.autoRefreshSwitch.grid(row=6, column=1, padx=10, sticky='e')
# the buttons for functionality in repository area
self.rep_button_list.grid(row=7, column=1, padx=3, sticky='ew')
# filter frame
self.filterFrame.grid(row=3, column=2, stick='nsew')
# list of baskest. Will callback to change current basket
self.basketSelect.grid(row=4, column=2, padx=10, stick='w')
# lists projects per basket
self.basketList.grid(row=5,
rowspan=2,
column=2,
padx=10,
stick='nsew')
self.b_button_list.grid(row=7, column=2, padx=5, stick='ew')
def openLink(self, node):
tree = node.tree
par = node.object
# this should be associated with the repository object
request = getList()
# FIXME JMCI
# 1. Potentially need to traverse up the node tree
# 2. Currently there is bug in expansion/contraction
# 3. Search needs to work off proxy method (not off
# generated stubs
# pass the parent name for now. may need other criteria later
h1 = {'name': par.__str__()}
h2 = {'project': h1}
wsstr_in = WSString(h2)
request._arg0 = 'org.pimslims.applet.server.ProjectVersionBean'
request._arg1 = 'getListWithFields'
request._arg2 = wsstr_in.str
# get the response
response = self.port.getList(request)
# currently we just get a list of numbers. May want to send
# all the fields for every object too to cut down on db calls
wsstr_out = WSString(response._return)
ss = wsstr_out.getStruct()
for hm in ss:
print 'handling ', hm, ', ', hm['status'].__str__()
#if hm['status'].__str__() == 'AVAILABLE':
icon = 'text-x-generic'
#else:
# icon='emblem-readonly'
pv = par.__str__() + '::' + hm['versionTag'].__str__()
obj = pv
text = hm['versionTag'].__str__()
callback = None
tree.add(node, obj, text, icon, callback)
def set_refresh(self, text):
print 'setting refresh ', text
if text == 'on':
self.autoRefresh = True
else:
self.autoRefresh = False
def refresh(self):
if self.autoRefresh:
print 'refreshing frame ', time.time()
self.drawFrame()
self.after(5000, self.refresh)
# FIME JMCI
# it would probably be a good idea to have a method that allowed
# a user to unlock a given project version. Would need to check
# permissions very carefully, though
def unlock_project_version(self):
pass
def goto_project_tab(self, node=None):
if node is None:
# get the selected node
selected_nodes = self.repTree.getSelectedNodes()
# restrict the choice to one
node = selected_nodes[0]
# we really need to traverse the tree a lot more carefully
pv = node.object.__str__()
print 'GOTO PROJECT ', pv, ', ', node, ', ', node.object
pat = re.compile('::')
matcher = pat.search(pv, 0)
name = pv[0:matcher.start()]
versionTag = pv[matcher.end():]
print 'GOTO PROJECT ', name, ', ', versionTag
#versionTag = node.object.__str__()
#name = node.parent.object.__str__()
#print node.__dict__
#print node.parent.__dict__
self.basePopup.repList.currentRepository.currentProjectName = name
self.basePopup.repList.currentRepository.currentVersionTag = versionTag
# this is going to have to be keyed on a natural key that then
# gets set into the criteria of a ws query
# hack for now. build in later. Essentially, we have to handle two
# cases; that of a specific projectVersion request and that of a
# request on a project alone. Probably the best behaviour would be
# for the project-only request to default to the latest trunk
# version of the project and the most elegent way of triggering
# this would probably be to have this as a property of the project
# returned in the main hash from Project.getFields().
self.basePopup.tabbedFrame.select(1)
if self.basePopup.frameShortcuts.has_key('Project'):
self.basePopup.frameShortcuts['Project'].drawFrame()
def import_project(self):
# FIXME JMCI
# need to preserve the current status. Take default from the
# Wms layer
rootDir = self.basePopup.repList.current_import_dir
fileSelectPopup = FileSelectPopup(self, None, rootDir)
new_project_dir = fileSelectPopup.getDirectory()
self.basePopup.repList.current_import_dir = new_project_dir
print 'in import project with directory', new_project_dir
idx = new_project_dir.rfind('/')
new_project_name = new_project_dir[idx + 1:]
print 'in import project with project', new_project_name
# FIXME
# need to set the project version number somewhere. For now set to none
# and this gets picked up and set to a default 1.1 later
self.repository.import_project(new_project_name, None, new_project_dir)
self.drawFrame()
def export_project(self):
# get the selected node
selected_nodes = self.repTree.getSelectedNodes()
# restrict the choice to one
node = selected_nodes[0]
# we really need to traverse the tree a lot more carefully
name = node.parent.object.__str__()
versionTag = node.object.__str__()[len(name) + 2:]
# need to preserve the current status. Take a default from the
# Wms layer
rootDir = self.basePopup.repList.current_export_dir
# This should be obtained from a query box. Hard code for now
fileSelectPopup = FileSelectPopup(self, None, rootDir)
exp_project_dir = fileSelectPopup.getDirectory()
self.basePopup.repList.current_export_dir = exp_project_dir
self.repository.export_project(name, versionTag, exp_project_dir)
def disconnectRepository(self):
# do we need to formally break a connection and destroy the session?
# yes we probably should.
# need an "are you sure" dialog box
# need to protect
self.repository.repList.repositories.remove(self.repository)
self.grid_remove()
for ff in self.guiParent.guiParent.parent.frames[0].children.values():
ff.drawFrame()
def tmpCall(self):
return
# This will need a separate call to the WS with an additional
# criterion (picking up the checkout version)
def updateRepTree(self):
texts = []
icons = []
parents = []
callbacks = []
objects = []
# OK, this would be a good point to access the list
# this should be associated with the repository object
loc = SharedBeanServiceLocator()
port = loc.getSharedBean()
request = getList()
# these are actually static
request._arg0 = 'org.pimslims.applet.server.ProjectBean'
request._arg1 = 'getList'
request._arg2 = ''
# get the response
response = port.getList(request)
# this is a hack at present. It needs to be written properly
wsstr = WSString(response._return)
ss = wsstr.getStruct()
for strg in ss:
texts.append(strg)
icons.append('folder')
parents.append(None)
objects.append(strg)
callbacks.append(self.openLink)
print 'UPDATE ', ss
print 'UPDATE ', len(ss)
if len(ss) > 0:
print 'UPDATE: updating '
self.repTree.update(parents, objects, texts, icons, callbacks)
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
class MultiSelectionListSkeleton:
def __init__(self, parent, selectionList, selectionDict = {}, selectedItems = [], title = 'MultiSelect', text = 'MultiSelect', endText = None, dismissText = 'dismiss', urlFile = None, modal = False):
self.selectionList = selectionList
self.selectionDict = selectionDict
self.selectedItems = selectedItems
self.text = text
self.endText = endText
self.dismissText = dismissText
self.isSelectedList = None
self.setUrlFile(urlFile)
self.startBasePopup(parent,title,modal,True)
def startBasePopup(self,parent,title,modal,True):
pass
def setUrlFile(self,urlFile):
self.help_url = None
def body(self, master):
#
# Popup window
#
row = 0
label = Label(master, text= self.text)
label.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
self.multiSelect = ScrolledListbox(master,
width = 50,
height = 5,
selectmode = Tkinter.MULTIPLE,
initial_list = self.selectionList)
self.multiSelect.grid(row=row, column=0, sticky=Tkinter.E, ipadx = 20)
master.grid_columnconfigure(0, weight=1)
master.grid_rowconfigure(row, weight=1)
if self.selectedItems:
self.multiSelect.setSelectedItems(self.selectedItems)
if self.endText:
row = row + 1
label = Label(master, text= self.endText)
label.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 = self.dismissText, help_url=self.help_url)
buttons.grid(row=row, column=0)
def apply(self):
self.isSelectedList = []
for selectedItem in self.multiSelect.getSelectedItems():
if self.selectionDict.has_key(selectedItem):
self.isSelectedList.append(self.selectionDict[selectedItem])
else:
self.isSelectedList.append(selectedItem)
return True
class WriteMappingPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(),'WriteMapping.html')
def __init__(self, parent, project):
self.project = project
self.selectedFormats = []
self.defaultText = 'Select file'
self.formats = allFormatsDict.keys()
self.formats.sort()
BasePopup.__init__(self, parent=parent, title= "Project '%s': " % project.name + 'Write ccpNmr mapping file', modal=False, transient=True)
def body(self, master):
row = 0
label = Label(master, text= "CcpNmr resonance -> atom mapping file writer.")
label.grid(row=row, column=0, columnspan = 2, sticky=Tkinter.W)
row += 1
label = Label(master, text= "File formats:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.formatListBox = ScrolledListbox(master, width = 50, height = 5, selectmode = Tkinter.MULTIPLE,
initial_list = self.formats)
self.formatListBox.grid(row=row, column=1, sticky=Tkinter.EW)
# Default is all formats selected...
self.formatListBox.setSelectedItems(self.formatListBox.getItems())
row += 1
label = Label(master, text= "Mapping output file:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.fileButton = Tkinter.Button(master, text = self.defaultText, command = self.selectFile)
self.fileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
texts = [ 'Write mapping' ]
commands = [ self.ok ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url)
buttons.grid(row=row, columnspan = 2, column=0)
def selectFile(self):
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
fileName = 'ccpNmr.map'
popup = FormatFilePopup(self, file = fileName, component = 'mapping', format = ccpNmr_kw)
if popup.fileSelected:
self.fileButton.config(text = popup.file)
popup.destroy()
def apply(self):
self.selectedFormats = self.formatListBox.getSelectedItems()
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
return False
fileCreated = writeMappingFile(self.project,fileName,originalFormats = self.selectedFormats)
if fileCreated:
showInfo("Success","Succesfully wrote mapping file")
else:
showError("Not written","Error writing file %s. File not written" % fileName)
return False
return True