def on_save_settings(self, evt):
# for saving the experimental file, the text file may have the following nomenclature
# Date(YYYY_MM_DD)_ExperimenterNumber_Experimenter Name_ first 20 words from the aim
meta = ExperimentSettings.getInstance()
#-- Get Experimental Date/number ---#
exp_date = meta.get_field('Overview|Project|ExptDate')
exp_num = meta.get_field('Overview|Project|ExptNum')
exp_title = meta.get_field('Overview|Project|Title')
if None not in [exp_date, exp_num, exp_title]:
day, month, year = exp_date.split('/')
filename = '%s%s%s_%s_%s.txt' % (year, month, day, exp_num,
exp_title)
else:
filename = 'new_experiment.txt'
dlg = wx.FileDialog(None,
message='Saving experimental metadata...',
defaultDir=os.getcwd(),
defaultFile=filename,
wildcard='.txt',
style=wx.SAVE | wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(dlg.GetPath())[0])
ExperimentSettings.getInstance().save_to_file(dlg.GetPath())
def on_load_settings(self, evt):
dlg = wx.FileDialog(
None,
"Select the file containing your ProtocolNavigator workspace...",
defaultDir=os.getcwd(),
style=wx.OPEN | wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
ExperimentSettings.getInstance().load_from_file(dlg.GetPath())
def on_load_settings(self, evt):
meta = ExperimentSettings.getInstance()
dlg = wx.FileDialog(
None,
"Select the file containing your ProtocolNavigator workspace...",
defaultDir=os.getcwd(),
style=wx.OPEN | wx.FD_CHANGE_DIR,
)
if dlg.ShowModal() == wx.ID_OK:
ExperimentSettings.getInstance().load_from_file(dlg.GetPath(), self.loadSettingsMenuItem)
if meta.get_field("Overview|Project|Title") is not None:
self.settings_frame.SetTitle("ProtocolNavigator - %s" % meta.get_field("Overview|Project|Title"))
def on_save_settings(self, evt):
# for saving the experimental file, the text file may have the following nomenclature
# Date(YYYY_MM_DD)_ExperimenterNumber_Experimenter Name_ first 20 words from the aim
meta = ExperimentSettings.getInstance()
if meta.get_field("Overview|Project|Title") is not None:
self.settings_frame.SetTitle("ProtocolNavigator - %s" % meta.get_field("Overview|Project|Title"))
meta.save_file_dialogue()
def OnAddStep(self, event):
meta = ExperimentSettings.getInstance()
steps = sorted([step for step in self.curr_protocol.keys()
if not step.startswith('ADMIN')] , key = meta.stringSplitByNumbers)
for step in steps:
if not self.curr_protocol[step]:
dial = wx.MessageDialog(None, 'Please fill the description in %s !!' %step, 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
ctrl = event.GetEventObject()
#Rearrange the steps numbers in the experimental settings
temp_steps = {}
for step in steps:
stepNo = int(step.split('Step')[1])
step_info = self.curr_protocol[step]
if stepNo > ctrl.GetId() and temp_steps[stepNo] is not []:
temp_steps[stepNo+1] =self.curr_protocol[step]
del self.curr_protocol[step]
else:
temp_steps[stepNo] = self.curr_protocol[step]
temp_steps[stepNo+1] = []
del self.curr_protocol[step]
for stepNo in sorted(temp_steps.iterkeys()):
self.curr_protocol['Step%s'%str(stepNo)] = temp_steps[stepNo]
self.fgs.Clear(deleteWindows=True)
self.showSteps()
def OnAddStep(self, event):
meta = ExperimentSettings.getInstance()
#if meta.get_field(self.tag_stump+'|ProtocolName|'+self.instance) is None:
#dial = wx.MessageDialog(None, 'Please fill the Title/Name filed!!', 'Error', wx.OK | wx.ICON_ERROR)
#dial.ShowModal()
#return
# also check whether the description field has been filled by users
steps = sorted(meta.get_attribute_list_by_instance(
self.tag_stump + '|Step', self.instance),
key=meta.stringSplitByNumbers)
for step in steps:
step_info = meta.get_field(self.tag_stump + '|%s|%s' %
(step, self.instance))
if not step_info[0]:
dial = wx.MessageDialog(
None, 'Please fill the description in %s !!' % step,
'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
ctrl = event.GetEventObject()
## Rearrange the steps numbers in the experimental settings
temp_steps = {}
for step in steps:
stepNo = int(step.split('Step')[1])
if stepNo > ctrl.GetId() and temp_steps[stepNo] is not []:
temp_steps[stepNo +
1] = meta.get_field(self.tag_stump + '|%s|%s' %
(step, self.instance))
meta.remove_field(self.tag_stump + '|%s|%s' %
(step, self.instance))
else:
temp_steps[stepNo] = meta.get_field(self.tag_stump + '|%s|%s' %
(step, self.instance))
temp_steps[stepNo + 1] = []
meta.remove_field(self.tag_stump + '|%s|%s' %
(step, self.instance))
for stepNo in sorted(temp_steps.iterkeys()):
meta.set_field(
self.tag_stump + '|%s|%s' %
('Step%s' % str(stepNo), self.instance), temp_steps[stepNo])
#clear the bottom panel
self.fgs.Clear(deleteWindows=True)
#redraw the panel
self.showSteps()
def on_save_settings(self, evt):
# for saving the experimental file, the text file may have the following nomenclature
# Date(YYYY_MM_DD)_ExperimenterNumber_Experimenter Name_ first 20 words from the aim
meta = ExperimentSettings.getInstance()
#-- Get Experimental Date/number ---#
exp_date = meta.get_field('Overview|Project|ExptDate')
exp_num = meta.get_field('Overview|Project|ExptNum')
exp_title = meta.get_field('Overview|Project|Title')
if None not in [exp_date, exp_num, exp_title]:
day, month, year = exp_date.split('/')
filename = '%s%s%s_%s_%s.txt'%(year, month, day , exp_num, exp_title)
else:
filename = 'new_experiment.txt'
dlg = wx.FileDialog(None, message='Saving experimental metadata...',
defaultDir=os.getcwd(), defaultFile=filename,
wildcard='.txt',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(dlg.GetPath())[0])
ExperimentSettings.getInstance().save_to_file(dlg.GetPath())
def OnAddStep(self, event):
meta = ExperimentSettings.getInstance()
#if meta.get_field(self.tag_stump+'|ProtocolName|'+self.instance) is None:
#dial = wx.MessageDialog(None, 'Please fill the Title/Name filed!!', 'Error', wx.OK | wx.ICON_ERROR)
#dial.ShowModal()
#return
# also check whether the description field has been filled by users
steps = sorted(meta.get_attribute_list_by_instance(self.tag_stump+'|Step', self.instance), key = meta.stringSplitByNumbers)
for step in steps:
step_info = meta.get_field(self.tag_stump+'|%s|%s' %(step, self.instance))
if not step_info[0]:
dial = wx.MessageDialog(None, 'Please fill the description in %s !!' %step, 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
ctrl = event.GetEventObject()
## Rearrange the steps numbers in the experimental settings
temp_steps = {}
for step in steps:
stepNo = int(step.split('Step')[1])
if stepNo > ctrl.GetId() and temp_steps[stepNo] is not []:
temp_steps[stepNo+1] = meta.get_field(self.tag_stump+'|%s|%s' %(step, self.instance))
meta.remove_field(self.tag_stump+'|%s|%s' %(step, self.instance))
else:
temp_steps[stepNo] = meta.get_field(self.tag_stump+'|%s|%s' %(step, self.instance))
temp_steps[stepNo+1] = []
meta.remove_field(self.tag_stump+'|%s|%s' %(step, self.instance))
for stepNo in sorted(temp_steps.iterkeys()):
meta.set_field(self.tag_stump+'|%s|%s' %('Step%s'%str(stepNo), self.instance), temp_steps[stepNo])
#clear the bottom panel
self.fgs.Clear(deleteWindows=True)
#redraw the panel
self.showSteps()
def OnAddStep(self, event):
meta = ExperimentSettings.getInstance()
steps = sorted([
step for step in self.curr_protocol.keys()
if not step.startswith('ADMIN')
],
key=meta.stringSplitByNumbers)
for step in steps:
if not self.curr_protocol[step]:
dial = wx.MessageDialog(
None, 'Please fill the description in %s !!' % step,
'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
ctrl = event.GetEventObject()
#Rearrange the steps numbers in the experimental settings
temp_steps = {}
for step in steps:
stepNo = int(step.split('Step')[1])
step_info = self.curr_protocol[step]
if stepNo > ctrl.GetId() and temp_steps[stepNo] is not []:
temp_steps[stepNo + 1] = self.curr_protocol[step]
del self.curr_protocol[step]
else:
temp_steps[stepNo] = self.curr_protocol[step]
temp_steps[stepNo + 1] = []
del self.curr_protocol[step]
for stepNo in sorted(temp_steps.iterkeys()):
self.curr_protocol['Step%s' % str(stepNo)] = temp_steps[stepNo]
self.fgs.Clear(deleteWindows=True)
self.showSteps()
def on_load_settings(self, evt):
dlg = wx.FileDialog(None, "Select the file containing your CPAnalyst workspace...",
defaultDir=os.getcwd(), style=wx.OPEN|wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
ExperimentSettings.getInstance().load_from_file(dlg.GetPath())
def on_new_experiment(self, evt):
'''clears the existing Experiment settings
'''
return ExperimentSettings.getInstance().clear()
exp_num = meta.get_field('Overview|Project|ExptNum')
exp_title = meta.get_field('Overview|Project|Title')
if None not in [exp_date, exp_num, exp_title]:
day, month, year = exp_date.split('/')
filename = '%s%s%s_%s_%s.txt'%(year, month, day , exp_num, exp_title)
else:
filename = 'new_experiment.txt'
dlg = wx.FileDialog(None, message='Saving experimental metadata...',
defaultDir=os.getcwd(), defaultFile=filename,
wildcard='.txt',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(dlg.GetPath())[0])
ExperimentSettings.getInstance().save_to_file(dlg.GetPath())
def on_load_settings(self, evt):
dlg = wx.FileDialog(None, "Select the file containing your CPAnalyst workspace...",
defaultDir=os.getcwd(), style=wx.OPEN|wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
ExperimentSettings.getInstance().load_from_file(dlg.GetPath())
if __name__ == '__main__':
app = LineageProfiler(redirect=False)
# Load a settings file if passed in args
if len(sys.argv) > 1:
ExperimentSettings.getInstance().load_from_file(sys.argv[1])
app.MainLoop()
def on_save_as_settings(self, evt):
meta = ExperimentSettings.getInstance()
if meta.get_field("Overview|Project|Title") is not None:
self.settings_frame.SetTitle("ProtocolNavigator - %s" % meta.get_field("Overview|Project|Title"))
meta.save_as_file_dialogue()
def decode_event_description(self, protocol):
meta = ExperimentSettings.getInstance()
instance = exp.get_tag_attribute(protocol)
header = ''
footer = []
info = []
if exp.get_tag_type(protocol) == 'Overview':
header += meta.get_field('Overview|Project|Title', default='Not specified')
info.append(('Aims', meta.get_field('Overview|Project|Aims', default='Not specified')))
info.append(('Funding Code', meta.get_field('Overview|Project|Fund', default='Not specified')))
info.append(('Keywords', meta.get_field('Overview|Project|Keywords', default='Not specified')))
info.append(('Experiment Number', meta.get_field('Overview|Project|ExptNum', default='Not specified')))
info.append(('Experiment date', meta.get_field('Overview|Project|ExptDate', default='Not specified')))
info.append(('Relevant publications', meta.get_field('Overview|Project|Publications', default='Not specified')))
info.append(('Experimenter', meta.get_field('Overview|Project|Experimenter', default='Not specified')))
info.append(('Institution', meta.get_field('Overview|Project|Institution', default='Not specified')))
info.append(('Department', meta.get_field('Overview|Project|Department', default='Not specified')))
info.append(('Address', meta.get_field('Overview|Project|Address', default='Not specified')))
info.append(('Experiment Status', meta.get_field('Overview|Project|Status', default='Not specified')))
return (header, info)
if exp.get_tag_type(protocol) == 'StockCulture':
header += '%s cell line (Authority %s, Ref: %s) was used. This will be referred as Stock Instance %s' %(meta.get_field('StockCulture|Sample|CellLine|%s'%instance, default='Not specified'),
meta.get_field('StockCulture|Sample|Authority|%s'%instance, default='Not specified'),
str(instance),
meta.get_field('StockCulture|Sample|CatalogueNo|%s'%instance, default='Not specified'),
str(instance))
info.append(('Depositors', meta.get_field('StockCulture|Sample|Depositors|%s'%instance, default='Not specified')))
info.append(('Biosafety Level', meta.get_field('StockCulture|Sample|Biosafety|%s'%instance, default='Not specified')))
info.append(('Shipment', meta.get_field('StockCulture|Sample|Shipment|%s'%instance, default='Not specified')))
info.append(('Permit', meta.get_field('StockCulture|Sample|Permit|%s'%instance, default='Not specified')))
info.append(('Growth Property', meta.get_field('StockCulture|Sample|GrowthProperty|%s'%instance, default='Not specified')))
info.append(('Organism', meta.get_field('StockCulture|Sample|Organism|%s'%instance, default='Not specified')))
info.append(('Morphology', meta.get_field('StockCulture|Sample|Morphology|%s'%instance, default='Not specified')))
info.append(('Organ', meta.get_field('StockCulture|Sample|Organ|%s'%instance, default='Not specified')))
info.append(('Disease', meta.get_field('StockCulture|Sample|Disease|%s'%instance, default='Not specified')))
info.append(('Products', meta.get_field('StockCulture|Sample|Products|%s'%instance, default='Not specified')))
info.append(('Applications', meta.get_field('StockCulture|Sample|Applications|%s'%instance, default='Not specified')))
info.append(('Receptors', meta.get_field('StockCulture|Sample|Receptors|%s'%instance, default='Not specified')))
info.append(('Antigen', meta.get_field('StockCulture|Sample|Antigen|%s'%instance, default='Not specified')))
info.append(('DNA', meta.get_field('StockCulture|Sample|DNA|%s'%instance, default='Not specified')))
info.append(('Cytogenetic', meta.get_field('StockCulture|Sample|Cytogenetic|%s'%instance, default='Not specified')))
info.append(('Isoenzymes', meta.get_field('StockCulture|Sample|Isoenzymes|%s'%instance, default='Not specified')))
info.append(('Age of Organism (days)', meta.get_field('StockCulture|Sample|Age|%s'%instance, default='Not specified')))
info.append(('Gender', meta.get_field('StockCulture|Sample|Gender|%s'%instance, default='Not specified')))
info.append(('Ethnicity', meta.get_field('StockCulture|Sample|Ethnicity|%s'%instance, default='Not specified')))
info.append(('Comments', meta.get_field('StockCulture|Sample|Comments|%s'%instance, default='Not specified')))
info.append(('Publications', meta.get_field('StockCulture|Sample|Publications|%s'%instance, default='Not specified')))
info.append(('Related Products', meta.get_field('StockCulture|Sample|RelProduct|%s'%instance, default='Not specified')))
info.append(('Original Passage Number', meta.get_field('StockCulture|Sample|OrgPassageNo|%s'%instance, default='Not specified')))
info.append(('Preservation', meta.get_field('StockCulture|Sample|Preservation|%s'%instance, default='Not specified')))
info.append(('GrowthMedium', meta.get_field('StockCulture|Sample|GrowthMedium|%s'%instance, default='Not specified')))
passages = [attr for attr in meta.get_attribute_list_by_instance('StockCulture|Sample', instance)
if attr.startswith('Passage')]
if passages:
footer += '%s passages were carried out according to the specifications' %str(len(passages))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Microscope':
header += '%s settings' %meta.get_field('Instrument|Microscope|ChannelName|%s'%instance, default = 'Not specified')
if meta.get_field('Instrument|Microscope|Stand|%s'%instance) is not None:
info.append(('Component', 'Stand'))
info.append(('Type', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[2]))
info.append(('Orientation', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[3]))
info.append(('Number of Lampss', str(meta.get_field('Instrument|Microscope|Stand|%s'%instance)[4])))
info.append(('Number of Detectors', str(meta.get_field('Instrument|Microscope|Stand|%s'%instance)[5])))
if meta.get_field('Instrument|Microscope|Condensor|%s'%instance) is not None:
info.append(('Component', 'Condensor'))
info.append(('Type', meta.get_field('Instrument|Microscope|Condensor|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Condensor|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Condensor|%s'%instance)[2]))
if meta.get_field('Instrument|Microscope|Stage|%s'%instance) is not None:
info.append(('Component', 'Stage'))
info.append(('Type', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[2]))
info.append(('Stage Holder', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[3]))
info.append(('Holder Code', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[4]))
if meta.get_field('Instrument|Microscope|Incubator|%s'%instance) is not None:
info.append(('Component', 'Incubator'))
info.append(('Make', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[0]))
info.append(('Model', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[1]))
info.append(('Temperature(C)', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[2]))
info.append(('CO2%', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[3]))
info.append(('Humidity', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[4]))
info.append(('Pressure', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[5]))
if meta.get_field('Instrument|Microscope|LightSource|%s'%instance) is not None:
info.append(('Component', 'Light Source'))
info.append(('Type', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[0]))
info.append(('Source', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[1]))
info.append(('Make', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[2]))
info.append(('Model', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[3]))
info.append(('Measured Power (User)', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[4]))
info.append(('Measured Power (Instrument)', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[5]))
info.append(('Shutter Used', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[6]))
info.append(('Shutter Type', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[7]))
info.append(('Shutter Make', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[8]))
info.append(('Shutter Model', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[9]))
if meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance) is not None:
info.append(('Component', 'Excitation Filter'))
info.append(('Wavelength Range (nm)', str(meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[0])+' - '+str(meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[1])))
info.append(('Make', meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[2]))
info.append(('Model', meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[3]))
if meta.get_field('Instrument|Microscope|Mirror|%s'%instance) is not None:
info.append(('Component', 'Dichroic Mirror'))
info.append(('Wavelength Range (nm)', str(meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[0])+' - '+str(meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[1])))
info.append(('Mode', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[2]))
info.append(('Make', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[3]))
info.append(('Model', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[4]))
info.append(('Modification', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[5]))
if meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance) is not None:
info.append(('Component', 'Emission Filter'))
info.append(('Wavelength Range (nm)', str(meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[0])+' - '+str(meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[1])))
info.append(('Make', meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[2]))
info.append(('Model', meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[3]))
if meta.get_field('Instrument|Microscope|Lens|%s'%instance) is not None:
info.append(('Component', 'Lens'))
info.append(('Make', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[0]))
info.append(('Model', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[1]))
info.append(('Objective Magnification', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[2]))
info.append(('Objective NA', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[3]))
info.append(('Calibrated Magnification', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[4]))
info.append(('Immersion', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[5]))
info.append(('Correction Collar', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[6]))
info.append(('Correction Value', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[7]))
info.append(('Correction Type', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[8]))
if meta.get_field('Instrument|Microscope|Lens|%s'%instance) is not None:
info.append(('Component', 'Detector'))
info.append(('Type', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[2]))
info.append(('Binning', str(meta.get_field('Instrument|Microscope|Detector|%s'%instance)[3])))
info.append(('Exposure Time', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[4]+' '+meta.get_field('Instrument|Microscope|Detector|%s'%instance)[5]))
info.append(('Gain', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[6]+' '+meta.get_field('Instrument|Microscope|Detector|%s'%instance)[7]))
info.append(('Offset', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[8]+' '+meta.get_field('Instrument|Microscope|Detector|%s'%instance)[9]))
return (header, info)
if exp.get_tag_event(protocol) == 'Flowcytometer':
header += meta.get_field('Instrument|Flowcytometer|Manufacter|%s'%instance, default='')
if meta.get_field('Instrument|Flowcytometer|Model|%s'%instance) is not None:
header += '(model: %s)' %meta.get_field('Instrument|Flowcytometer|Model|%s'%instance, default = 'not specified')
header += ' was used. '
for attribute, description in sorted(meta.get_attribute_dict('Instrument|Flowcytometer|%s'%instance).iteritems()):
if attribute.startswith('Manufacter') or attribute.startswith('Model'):
continue
else:
info.append((attribute, description)) # attribute is Ch# and description is the component list
return(header, info)
if exp.get_tag_event(protocol) == 'Seed':
if meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance) is not None:
header += meta.get_field('StockCulture|Sample|CellLine|%s'%meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance))
header += ' cells were seeded with a density of %s from the stock flask (Instance %s). ' %(meta.get_field('CellTransfer|Seed|SeedingDensity|%s'%instance, default = ''), meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance))
#if meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance) is not None:
#header += meta.get_field('StockCulture|Sample|CellLine|%s'%meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance))
#header += ' cells were seeded with a density of %s from the Wells depicted bellow. ' %meta.get_field('CellTransfer|Seed|SeedingDensity|%s'%instance, default = '')
if meta.get_field('CellTransfer|Seed|MediumUsed|%s'%instance) is not None:
header += meta.get_field('CellTransfer|Seed|MediumUsed|%s'%instance)+' medium was used '
if meta.get_field('CellTransfer|Seed|MediumAddatives|%s'%instance) is not None:
header += 'with following medium additives: %s. ' %meta.get_field('CellTransfer|Seed|MediumAddatives|%s'%instance)
if meta.get_field('CellTransfer|Seed|Trypsinizatiton|%s'%instance) is 'Yes':
header += 'Also trypsinisation was performed'
return (header, info)
if exp.get_tag_event(protocol) == 'Chem':
if meta.get_field('Perturbation|Chem|ChemName|%s'%instance) is not None:
header += meta.get_field('Perturbation|Chem|ChemName|%s'%instance)
subtext = '%s,%s' %(meta.get_field('Perturbation|Chem|Manufacturer|%s'%instance, default=''), meta.get_field('Perturbation|Chem|CatNum|%s'%instance, default=''))
if re.search('\w+', subtext): #if the mfg and or cat number of the chemical is mentioned
header += '[%s]'%subtext
header += ' was added'
if meta.get_field('Perturbation|Chem|Conc|%s'%instance) is not None:
header += ' with a concentration of %s %s' %(meta.get_field('Perturbation|Chem|Conc|%s'%instance), meta.get_field('Perturbation|Chem|Unit|%s'%instance, default=''))
if meta.get_field('Perturbation|Chem|Additives|%s'%instance) is not None:
header += '. Following additives were included: %s' %meta.get_field('Perturbation|Chem|Additives|%s'%instance)
if meta.get_field('Perturbation|Chem|Other|%s'%instance) is not None:
header += '. Other information: %s'%meta.get_field('Perturbation|Chem|Other|%s'%instance)
return (header, info)
if exp.get_tag_event(protocol) == 'Bio':
header += 'Biological perturbation was done with following agent'
info.append(('RNAi Sequence', meta.get_field('Perturbation|Bio|SeqName|%s'%instance, default = 'Not specified')))
info.append(('Acession Number', meta.get_field('Perturbation|Bio|AccessNumber|%s'%instance, default = 'Not specified')))
info.append(('Target Gene Accession Number', meta.get_field('Perturbation|Bio|TargetGeneAccessNum|%s'%instance, default = 'Not specified')))
info.append(('Concentration', meta.get_field('Perturbation|Bio|Conc|%s'%instance, default = 'Not specified')+' '+meta.get_field('Perturbation|Bio|Unit|%s'%instance, default = '')))
info.append(('Additives', meta.get_field('Perturbation|Bio|Additives|%s'%instance, default = 'Not specified')))
info.append(('Other Information', meta.get_field('Perturbation|Bio|Other|%s'%instance, default = 'Not specified')))
return (header, info)
if exp.get_tag_event(protocol) == 'Dye':
header += meta.get_field('Staining|Dye|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('Staining|Dye|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('Staining|Dye|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Immuno':
header += meta.get_field('Staining|Immuno|ProtocolName|%s'%instance)
if meta.get_field('Staining|Immuno|Target|%s'%instance) is not None:
footer.append('Target antibody %s was used.'%meta.get_field('Staining|Immuno|Target|%s'%instance))
if meta.get_field('Staining|Immuno|Clonality|%s'%instance) is not None:
footer.append('Clonality was %s.'%meta.get_field('Staining|Immuno|Clonality|%s'%instance))
if meta.get_field('Staining|Immuno|Primary|%s'%instance) is not None:
token =''
token += 'Primary antibody %s was used'%meta.get_field('Staining|Immuno|Primary|%s'%instance)[0]
if len(meta.get_field('Staining|Immuno|Primary|%s'%instance)[1])>0:
token += ' with %s'%meta.get_field('Staining|Immuno|Primary|%s'%instance)[1]
footer.append(token)
if meta.get_field('Staining|Immuno|Secondary|%s'%instance) is not None:
token =''
token += 'Secondary antibody %s was used'%meta.get_field('Staining|Immuno|Secondary|%s'%instance)[0]
if len(meta.get_field('Staining|Immuno|Secondary|%s'%instance)[1])>0:
token += ' with %s'%meta.get_field('Staining|Immuno|Secondary|%s'%instance)[1]
footer.append(token)
if meta.get_field('Staining|Immuno|Tertiary|%s'%instance) is not None:
token =''
token += 'Tertiary antibody %s was used'%meta.get_field('Staining|Immuno|Tertiary|%s'%instance)[0]
if len(meta.get_field('Staining|Immuno|Tertiary|%s'%instance)[1])>0:
token += ' with %s'%meta.get_field('Staining|Immuno|Tertiary|%s'%instance)[1]
footer.append(token)
steps = sorted(meta.get_attribute_list_by_instance('Staining|Immuno|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('Staining|Immuno|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Genetic':
header += meta.get_field('Staining|Genetic|ProtocolName|%s'%instance)
footer.append(('Target Sequence', meta.get_field('Staining|Genetic|Target|%s'%instance, default = 'Not specified')))
footer.append(('Primer Sequence', meta.get_field('Staining|Genetic|Primer|%s'%instance, default = 'Not specified')))
footer.append(('Temperature', meta.get_field('Staining|Genetic|Temp|%s'%instance, default = 'Not specified')))
footer.append(('Temperature', meta.get_field('Staining|Genetic|GC|%s'%instance, default = 'Not specified')))
steps = sorted(meta.get_attribute_list_by_instance('Staining|Genetic|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('Staining|Genetic|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Spin':
header += meta.get_field('AddProcess|Spin|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Spin|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Spin|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Wash':
header += meta.get_field('AddProcess|Wash|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Wash|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Wash|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Dry':
header += meta.get_field('AddProcess|Dry|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Dry|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Dry|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Medium':
header += meta.get_field('AddProcess|Medium|ProtocolName|%s'%instance)
if meta.get_field('AddProcess|Medium|MediumAdditives|%s'%instance) is not None:
footer.append('Medium additives used: %s'%meta.get_field('AddProcess|Medium|MediumAdditives|%s'%instance))
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Medium|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Medium|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Incubator':
header += meta.get_field('AddProcess|Incubator|ProtocolName|%s'%instance)
footer.append(('Incubator settings', ''))
footer.append(('Manufacturer', meta.get_field('AddProcess|Incubator|Manufacter|%s'%instance, default = 'Not specified')))
footer.append(('Model', meta.get_field('AddProcess|Incubator|Model|%s'%instance, default = 'Not specified')))
footer.append(('Temperature', meta.get_field('AddProcess|Incubator|Temp|%s'%instance, default = 'Not specified')))
footer.append(('CO2%', meta.get_field('AddProcess|Incubator|CO2|%s'%instance, default = 'Not specified')))
footer.append(('Humidity', meta.get_field('AddProcess|Incubator|Humidity|%s'%instance, default = 'Not specified')))
footer.append(('Pressure', meta.get_field('AddProcess|Incubator|Pressure|%s'%instance, default = 'Not specified')))
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Medium|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Medium|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'TLM':
if meta.get_field('DataAcquis|TLM|MicroscopeInstance|%s'%instance) is not None:
ch_name = meta.get_field('DataAcquis|TLM|MicroscopeInstance|%s'%instance)
cytometer_instance=meta.get_instance_by_field_value('Instrument|Microscope|ChannelName|', ch_name)
header += ch_name+' channel was used (see microscope instance %s for details)'%cytometer_instance
info.append(('Image Format', meta.get_field('DataAcquis|TLM|Format|%s'%instance, default = 'Not specified')))
info.append(('Time Interval (min)', meta.get_field('DataAcquis|TLM|TimeInterval|%s'%instance, default = 'Not specified')))
info.append(('Total Frame/Pane Number', meta.get_field('DataAcquis|TLM|FrameNumber|%s'%instance, default = 'Not specified')))
info.append(('Stacking Order', meta.get_field('DataAcquis|TLM|StackProcess|%s'%instance, default = 'Not specified')))
info.append(('Pixel Size', meta.get_field('DataAcquis|TLM|PixelSize|%s'%instance, default = 'Not specified')))
info.append(('Pixel Conversion', meta.get_field('DataAcquis|TLM|PixelConvert|%s'%instance, default = 'Not specified')))
info.append(('Software', meta.get_field('DataAcquis|TLM|Software|%s'%instance, default = 'Not specified')))
return (header, info)
if exp.get_tag_event(protocol) == 'HCS':
if meta.get_field('DataAcquis|HCS|MicroscopeInstance|%s'%instance) is not None:
ch_name = meta.get_field('DataAcquis|HCS|MicroscopeInstance|%s'%instance)
cytometer_instance=meta.get_instance_by_field_value('Instrument|Microscope|ChannelName|', ch_name)
header += ch_name+' channel was used (see microscope instance %s for details)'%cytometer_instance
info.append(('Image Format', meta.get_field('DataAcquis|HCS|Format|%s'%instance, default = 'Not specified')))
info.append(('Pixel Size', meta.get_field('DataAcquis|HCS|PixelSize|%s'%instance, default = 'Not specified')))
info.append(('Pixel Conversion', meta.get_field('DataAcquis|HCS|PixelConvert|%s'%instance, default = 'Not specified')))
info.append(('Software', meta.get_field('DataAcquis|HCS|Software|%s'%instance, default = 'Not specified')))
return (header, info)
if exp.get_tag_event(protocol) == 'FCS':
if meta.get_field('DataAcquis|FCS|FlowcytInstance|%s'%instance) is not None:
cytometer_instance = meta.get_field('DataAcquis|FCS|FlowcytInstance|%s'%instance)
header += meta.get_field('Instrument|Flowcytometer|Manufacter|%s'%cytometer_instance, default='')+' flowcytometer '
if meta.get_field('Instrument|Flowcytometer|Model|%s'%cytometer_instance) is not None:
header += '(model: %s)' %meta.get_field('Instrument|Flowcytometer|Model|%s'%cytometer_instance, default = 'not specified')
header += ' was used (see flowcytometer instance %s for details).'%cytometer_instance
if meta.get_field('DataAcquis|FCS|Software|%s'%instance) is not None:
info.append(meta.get_field('DataAcquis|FCS|Software|%s'%instance)+' software was used for data acquisition. ')
if meta.get_field('DataAcquis|FCS|Format|%s'%instance) is not None:
info.append('FCS files in %s'%meta.get_field('DataAcquis|FCS|Format|%s'%instance)+' format were saved in following location\n')
return (header, info)
def decode_event_description(self, protocol): meta = ExperimentSettings.getInstance()