def Main(args):
# The logger!!
logger = Logger(DATA_DIR)
try:
# Let's set ourselves up for success!
runtimeArgs = Setup()
# Let's make the dialog box:
DialogBox = WgstDlg()
if not DialogBox.Show():
bns.Stop()
# Start the calculation
Run(runtimeArgs)
except:
e = traceback.format_exc()
logger._log(e)
MessageBox('Error', e, '')
finally:
logger._save()
def Main(args):
winId = 1
#pick up previously used settings
tmpNameFieldId = ''
tmpNameHistoryFieldId = ''
tmpCharViewId = ''
tmpThresholds = [0.5, 1, 5, 10]
tmpSplitNames = False
tmpMinPresenceThreshold = 0.95
settingsKey = "hierarchical_strain_nomenclature"
settings = bns.Database.Db.Info.LoadSetting(settingsKey, True)
if settings:
root = ET.fromstring(settings)
n = root.find('nameFieldId')
if n is not None: tmpNameFieldId = n.text
n = root.find('nameHistoryFieldId')
if n is not None: tmpNameHistoryFieldId = n.text
n = root.find('charViewId')
if n is not None: tmpCharViewId = n.text
n = root.find('thresholds')
if n is not None: tmpThresholds = [float(f) for f in n.text.split('|')]
n = root.find('splitNames')
if n is not None: tmpSplitNames = n.text == '1'
n = root.find('minPresenceThreshold')
if n is not None: tmpMinPresenceThreshold = float(n.text)
#show the dialog
currSchema = Schema.GetCurrent()
wgmlstExperType = bns.Database.ExperimentType(currSchema.WgMLSTExperTypeID)
dlg = CalcStrainNamesDlg(wgmlstExperType, tmpNameFieldId, tmpNameHistoryFieldId, tmpCharViewId, tmpThresholds, tmpSplitNames, tmpMinPresenceThreshold)
if not dlg.Show():
bns.Stop()
#store the current settings
settings = ET.Element("hierarchical_strain_nomenclature_settings")
ET.SubElement(settings, 'nameFieldId').text = dlg.selectedField
ET.SubElement(settings, 'nameHistoryFieldId').text = dlg.selectedHistoryField
ET.SubElement(settings, 'charViewId').text = dlg.selectedCharView
ET.SubElement(settings, 'thresholds').text = '|'.join(str(f) for f in dlg.selectedThresholds)
ET.SubElement(settings, 'splitNames').text = '1'if dlg.selectedSplitNames else '0'
ET.SubElement(settings, 'minPresenceThreshold').text = str(dlg.minPresenceThreshold)
settings = bns.Database.Db.Info.SaveSetting(settingsKey, ET.tostring(settings), True)
#calculate the damn thing
allNamesFlName = os.path.join(bns.Database.Db.Info.SourceFilesDir, '9strain_naming_names_{}_{}.txt.gz'.format(wgmlstExperType.ID, dlg.selectedCharView))
allProfilesFlName = os.path.join(bns.Database.Db.Info.SourceFilesDir, '9strain_naming_profiles_{}_{}.txt.gz'.format(wgmlstExperType.ID, dlg.selectedCharView))
ok = os.path.isfile(allNamesFlName) and os.path.isfile(allProfilesFlName)
if not ok:
#put out a warning
#delete files if only one is present
if os.path.isfile(allNamesFlName): os.remove(allNamesFlName)
if os.path.isfile(allProfilesFlName): os.remove(allProfilesFlName)
calculator = Calculator(wgmlstExperType, dlg.selectedField, dlg.selectedHistoryField, dlg.selectedCharView, dlg.selectedThresholds, dlg.selectedSplitNames, dlg.minPresenceThreshold, allNamesFlName, allProfilesFlName)
#calculator.DoCalc({})
bns.Windows.BnsWindow(winId).StartAsyncCalculation(calculator.DoCalc, calculator.DoRefresh, async=False)