def covar_handle5():
covarlned = {'columns': None}
covarlned['columns'] = string_to_list('TEMP, TAG')
covarini = ini.InputHandler(name='covarinfo',
tablename='covartable',
lnedentry=covarlned)
return covarini
def covar_handle_3_biomass():
covarlned = {'columns': None}
covarlned['columns'] = string_to_list('temp')
covarini = ini.InputHandler(name='covarinfo',
tablename='covartable',
lnedentry=covarlned)
return covarini
def submit_change(self):
sender = self.sender()
self.cbindlned = {
'column_1': self.lnedColumn1.text().strip(),
'column_2': self.lnedColumn2.text().strip()
}
self.cbindini = ini.InputHandler(name='cbind',
lnedentry=self.cbindlned)
self.facade.input_register(self.cbindini)
self.facade.create_log_record('cbind')
self._log = self.facade._tablelog['cbind']
if self.previous_click is True:
self.viewEdit = view.PandasTableModelEdit(None)
else:
pass
try:
self.cbindtable = hlp.cbind(self.facade._data,
self.cbindlned['column_1'],
self.cbindlned['column_2'])
except Exception as e:
print(str(e))
self.error.showMessage('Could combine column values: ' + str(e))
hlp.write_column_to_log(self.cbindlned, self._log, 'cbind')
if sender is self.btnPreview:
self.viewEdit.set_data(self.cbindtable)
self.preview.tabviewPreview.setModel(self.viewEdit)
self.preview.show()
elif sender is self.btnSaveClose:
self.facade._data = self.cbindtable
self.update_data.emit('update')
self.close()
def meta_handler(self):
'''
Method to pass the user input about metadata to the mainwindow
(where the facade class is instantiated).
'''
entries = {
'globalid': int(self.lnedGlobalId.text().strip()),
'metaurl': self.lnedMetadataUrl.text().strip(),
'lter': self.cboxLTERloc.currentText().strip()
}
self.metaini = ini.InputHandler(name='metacheck',
tablename=None,
lnedentry=entries,
verify=self.verify)
self.facade.input_register(self.metaini)
try:
print(self.metaini.lnedentry['metaurl'])
self.facade.meta_verify()
self.webview_url.emit(self.metaini.lnedentry['metaurl'])
self.message.about(self, 'Status', 'Entries recorded')
except Exception as e:
print(str(e))
self.error.showMessage('Invalid entries: ' + str(e))
raise LookupError('Invalid metadata entries')
def covar_handle_2_density():
covarlned = {'columns': None}
covarlned['columns'] = string_to_list('AREA, VIS, OBS_CODE')
covarini = ini.InputHandler(name='covarinfo',
tablename='covartable',
lnedentry=covarlned)
return covarini
def project_handle_1_count():
studytype = namedtuple('studytype', 'checked entry unit')
# derived
derived = namedtuple('derived', 'checked entry unit')
# treatments
treatments = namedtuple('treatments', 'checked entry unit')
# Contacts: author, contact email
contacts = namedtuple('contacts', 'checked entry unit')
# Community
community = namedtuple('community', 'checked entry unit')
# SamplingFreq
sampfreq = namedtuple('sampfreq', 'checked entry unit')
# Datatype/units
dtype = namedtuple('dtype', 'checked entry unit')
# organism structure
structure = namedtuple('structure', 'checked entry unit')
# Spatial extent
ext = namedtuple('spatial_ext', 'checked entry unit')
form_dict = OrderedDict(
(('samplingunits', dtype(False,
'', None)), ('datatype',
dtype(True, 'count', None)),
('structured_type_1', structure(True, 'size',
'cm')), ('structured_type_2',
structure(False, '', '')),
('structured_type_3',
structure(False, '',
'')), ('samplefreq', sampfreq(True, 'month:yr', None)),
('studytype', studytype(True, 'obs',
None)), ('community',
community(True, True, None)),
('spatial_replication_level_1_extent',
ext(True, '100',
'm2')), ('spatial_replication_level_2_extent',
ext(True, '10',
'm2')), ('spatial_replication_level_3_extent',
ext(False, '', '')),
('spatial_replication_level_4_extent',
ext(False, '', '')), ('spatial_replication_level_5_extent',
ext(False, '',
'')), ('treatment_type_1',
treatments(False, 'NULL', None)),
('treatment_type_2',
treatments(False, 'NULL',
None)), ('treatment_type_3',
treatments(False, 'NULL',
None)), ('derived',
derived(True, 'no', None)),
('authors',
contacts(True, 'AJ Bibian, TEX Miller',
None)), ('authors_contact',
contacts(True, '[email protected], [email protected]',
None))))
main_input = ini.InputHandler(name='maininfo',
tablename='project_table',
lnedentry=form_dict)
return main_input
def file_handler(self):
'''
Method to pass the user input about the file to load
'''
lned = {
'sheet': self.lnedExcelSheet.text().strip(),
'delim': self.lnedDelimiter.text().strip(),
'tskip': self.lnedSkipTop.text().strip(),
'bskip': self.lnedSkipBottom.text().strip(),
'header': ''
}
rbtn = {
'csv': self.rbtnCsv.isChecked(),
'xlsx': self.rbtnExcel.isChecked(),
'txt': self.rbtnTxt.isChecked()
}
name = QtGui.QFileDialog.getOpenFileName(self, 'Select File')
headers = self.ckHeader.isChecked()
self.fileini = ini.InputHandler(name='fileoptions',
tablename=None,
rbtns=rbtn,
lnedentry=lned,
filename=name,
checks=headers)
self.facade.input_register(self.fileini)
try:
self.facade.load_data()
self.raw_data_model.emit('loaded_data')
except Exception as e:
self.filetypeReceive.emit(str(e))
def meta_handler(self):
'''
Method to verify the user input regarding the metadata
record (globalid/url) they'll be working from.
Url is passed to main window up verification.Note,
take user input and wraps it in a InputHandler class.
'''
entries = {
'globalid': int(self.lnedGlobalId.text().strip()),
'metaurl': self.lnedMetadataUrl.text().strip(),
'lter': self.cboxLTERloc.currentText().strip()
}
self.metaini = ini.InputHandler(name='metacheck',
tablename=None,
lnedentry=entries,
verify=self.verify)
self.facade.input_register(self.metaini)
try:
print(self.metaini.lnedentry['metaurl'])
self.facade.meta_verify()
self.webview_url.emit(self.metaini.lnedentry['metaurl'])
self.message.about(self, 'Status', 'Entries recorded')
except Exception as e:
print(str(e))
self.error.showMessage('Invalid entries: ' + str(e))
raise LookupError('Invalid metadata entries')
def file_handler(self):
'''
Method to pass the user input about the file to load.
Note this is only tested for CSV file: Still have
to run more test to make it more flexible. Note,
takes user input and wraps it in a InputHandler class.
'''
lned = {
'sheet': str(self.lnedExcelSheet.text().strip()),
'delim': str(self.lnedDelimiter.text().strip()),
'tskip': str(self.lnedSkipTop.text().strip()),
'bskip': str(self.lnedSkipBottom.text().strip()),
'header': ''
}
rbtn = {
'csv': self.rbtnCsv.isChecked(),
'xlsx': self.rbtnExcel.isChecked(),
'txt': self.rbtnTxt.isChecked()
}
name = str(QtGui.QFileDialog.getOpenFileName(self, 'Select File'))
headers = self.ckHeader.isChecked()
self.fileini = ini.InputHandler(name='fileoptions',
tablename=None,
rbtns=rbtn,
lnedentry=lned,
filename=name,
checks=headers)
self.facade.input_register(self.fileini)
try:
self.facade.load_data()
self.raw_data_model.emit('loaded_data')
except Exception as e:
raise IOError('Could not load data')
def count_handle2():
obslned = OrderedDict(
(('spatial_replication_level_2', 'transect'),
('spatial_replication_level_3', ''), ('spatial_replication_level_4',
''), ('structured_type_1', ''),
('structured_type_2', ''), ('structured_type_3', ''),
('treatment_type_1', ''), ('treatment_type_2', ''),
('treatment_type_3', ''), ('unitobs', 'count')))
obsckbox = OrderedDict(
(('spatial_replication_level_2', True), ('spatial_replication_level_3',
False),
('spatial_replication_level_4', False), ('structured_type_1', False),
('structured_type_2', False), ('structured_type_3', False),
('treatment_type_1', False), ('treatment_type_2', False),
('treatment_type_3', False), ('unitobs', True)))
available = [
x for x, y in zip(list(obslned.keys()), list(obsckbox.values()))
if y is True
]
countini = ini.InputHandler(name='rawinfo',
tablename='count_table',
lnedentry=extract(obslned, available),
checks=obsckbox)
return countini
def taxa_handle2():
taxalned = OrderedDict(
(('sppcode', ''), ('kingdom', ''), ('subkingdom', ''),
('infrakingdom', ''), ('superdivision', ''), ('divsion', ''),
('subdivision', ''), ('superphylum', ''), ('phylum', ''),
('subphylum', ''), ('clss', ''), ('subclass', ''), ('ordr', ''),
('family', ''), ('genus', 'genus'), ('species', 'species')))
taxackbox = OrderedDict(
(('sppcode', False), ('kingdom', False), ('subkingdom', False),
('infrakingdom', False), ('superdivision', False), ('divsion', False),
('subdivision', False), ('superphylum', False), ('phylum', False),
('subphylum', False), ('clss', False), ('subclass', False),
('ordr', False), ('family', False), ('genus', True), ('species',
True)))
taxacreate = {'taxacreate': False}
available = [
x for x, y in zip(list(taxalned.keys()), list(taxackbox.values()))
if y is True
]
taxaini = ini.InputHandler(name='taxainfo',
tablename='taxa_table',
lnedentry=extract(taxalned, available),
checks=taxacreate)
return taxaini
def covar_handle_4_percent_cover():
covarlned = {'columns': None}
covarlned['columns'] = string_to_list('Precip')
covarini = ini.InputHandler(name='covarinfo',
tablename='covartable',
lnedentry=covarlned)
return covarini
def metahandle_bad():
lentry = {'globalid': 2, 'metaurl': 'http://test', 'lter': 'SBC'}
ckentry = {}
metainput = ini.InputHandler(name='metacheck',
tablename=None,
lnedentry=lentry,
checks=ckentry)
return metainput
def submit_change(self):
self.lter = self.facade._valueregister['lterid']
# Registering information to facade class
self.sitelned = {'siteid': self.lnedSiteID.text().strip()}
self.siteloc['siteid'] = self.lnedSiteID.text().strip()
self.facade.create_log_record('climatesite')
self._log = self.facade._tablelog['climatesite']
if self.ckCreate.isChecked() is True:
print('Box is checked')
print('Site line entry: ', self.siteloc['siteid'])
print('facade data (before): ', self.facade._data)
self.facade._data[self.siteloc[
'study_site_key']] = self.siteloc['study_site_key']
print('facade data (after): ', self.facade._data)
else:
pass
try:
self.facade._data[self.siteloc['siteid']]
except Exception as e:
print(str(e))
self._log.debug(str(e))
self.error.showMessage(self.siteloc['siteid'] +
' not in dataframe')
raise KeyError(self.siteloc['siteid'] + ' not in dataframe')
self.siteini = ini.InputHandler(name='siteinfo',
tablename='sitetable',
lnedentry=self.sitelned,
verify=self.verify)
self.facade.input_register(self.siteini)
self.facade._valueregister['siteid'] = self.siteloc['siteid']
self.message.about(self, 'Status', 'Information recorded')
# Make table and Register site levels with facade
self.sitedirector = self.facade.make_table('siteinfo')
self.rawdata = (self.sitedirector._availdf.sort_values(
by='siteid'))
self.facade.register_site_levels(
self.rawdata['siteid'].drop_duplicates().values.tolist())
# Performing query
self.sitelevels = self.facade._valueregister['sitelevels']
self._log.debug('sitelevels (submit): ' +
' '.join(self.sitelevels))
# Setting Table Model View
self.sitetablemodel = self.viewEdit(self.rawdata)
self.listviewSiteLabels.setModel(self.sitetablemodel)
self.btnSiteID.setEnabled(False)
def real_data():
rbtn = {'csv': False, 'xlsx': False, 'txt': True}
lned = {'sheet': '', 'delim': '\t', 'tskip': '', 'bskip': '', 'header': ''}
fname = (rootpath + end + 'data' + end + 'SGS_LTER_Humus_canopyCover.txt')
user_input = ini.InputHandler(name='fileoptions',
lnedentry=lned,
rbtns=rbtn,
filename=fname,
checks=False)
return user_input
def submit_change(self):
sender = self.sender()
self.widetolonglned = {
'value_columns':
hlp.string_to_list(self.lnedValuecolumns.text()),
'datatype_name': self.cboxDatatypecolumn.currentText(),
'panel_data': self.ckPaneldata.isChecked()
}
self.widetolongini = ini.InputHandler(
name='widetolong', lnedentry=self.widetolonglned)
self.facade.input_register(self.widetolongini)
self.facade.create_log_record('widetolong')
self._log = self.facade._tablelog['widetolong']
try:
if self.widetolonglned['panel_data'] is False:
self.widetolongtable = hlp.wide_to_long(
self.facade._data,
value_columns=self.widetolonglned['value_columns'],
value_column_name=self.widetolonglned['datatype_name'])
else:
temp = self.facade._data.copy()
temp['id'] = temp.index
self.widetolongtable = wide_to_long(
temp,
self.widetolonglned['value_columns'],
i="id",
j=self.widetolonglned['datatype_name'])
self.widetolongtable[self.widetolonglned[
'datatype_name']] = self.widetolongtable.index.get_level_values(
self.widetolonglned['datatype_name'])
self.widetolongtable.reset_index(drop=True, inplace=True)
except Exception as e:
print(str(e))
self.error.showMessage('Could not melt data: ', str(e))
try:
assert self.widetolonglned['datatype_name'] != 'NULL'
except Exception as e:
print(str(e))
self.error.showMessage('Invalid datatype column: ' + str(e))
return
if sender is self.btnPreview:
self.widetolongmodel = view.PandasTableModel(
self.widetolongtable)
self.preview.tabviewPreview.setModel(self.widetolongmodel)
self.preview.show()
elif sender is self.btnSaveClose:
hlp.write_column_to_log(self.widetolonglned, self._log,
'widetolong')
self.facade._data = self.widetolongtable
self.update_data.emit('update')
self.close()
def user_input():
rbtn = {'csv': True, 'xlsx': False, 'txt': False}
lned = {'sheet': '', 'delim': '', 'tskip': '', 'bskip': '', 'header': ''}
fname = (rootpath + end + 'Datasets_manual_test' + end +
'raw_data_test_1.csv')
user_input = ini.InputHandler(name='fileoptions',
lnedentry=lned,
rbtns=rbtn,
filename=fname,
checks=False)
return user_input
def file_handle_free():
ckentry = {}
rbtn = {'.csv': True, '.txt': False, '.xlsx': False}
lned = {'sheet': '', 'delim': '', 'tskip': '', 'bskip': '', 'header': ''}
fileinput = ini.InputHandler(name='fileoptions',
tablename=None,
lnedentry=lned,
rbtns=rbtn,
checks=ckentry,
session=True,
filename=(rootpath + end + 'data' + end +
'PLT-OTH-1509-Garden_1_0.csv'))
return fileinput
def file_handle5():
ckentry = {}
rbtn = {'.csv': True, '.txt': False, '.xlsx': False}
lned = {'sheet': '', 'delim': '', 'tskip': '', 'bskip': '', 'header': ''}
fileinput = ini.InputHandler(
name='fileoptions',
tablename=None,
lnedentry=lned,
rbtns=rbtn,
checks=ckentry,
session=True,
filename=(rootpath + end + 'test' + end + 'Datasets_manual_test' +
end + 'raw_data_test_5.csv'))
return fileinput
def submit_change(self):
sender = self.sender()
self.replacevaluelned = {
'column_name': self.lnedColumnname.text().strip(),
'value_from': self.lnedFrom.text(),
'value_to': self.lnedTo.text().strip(),
'all_columns': self.ckAllcolumns.isChecked()
}
self.replacevalueini = ini.InputHandler(
name='replacevalue', lnedentry=self.replacevaluelned)
self.facade.input_register(self.replacevalueini)
self.facade.create_log_record('replacevalue')
self._log = self.facade._tablelog['replacevalue']
if self.previous_click is True:
self.viewEdit = view.PandasTableModelEdit(None)
else:
pass
try:
if self.replacevaluelned['all_columns'] is True:
self.replacevaluetable = self.facade._data.replace({
self.replacevaluelned['value_from']:
self.replacevaluelned['value_to']
})
else:
columntochange = self.replacevaluelned['column_name']
assert (columntochange is not '') is True
self.replacevaluetable = self.facade._data.replace({
columntochange: {
self.replacevaluelned['value_from']:
self.replacevaluelned['value_to']
}
})
self.previous_click = True
except Exception as e:
print(str(e))
self.error.showMessage('Could not replace values: ' + str(e))
hlp.write_column_to_log(self.replacevaluelned, self._log,
'replacevalue')
if sender is self.btnPreview:
self.viewEdit.set_data(self.replacevaluetable)
self.preview.tabviewPreview.setModel(self.viewEdit)
self.preview.show()
elif sender is self.btnSaveClose:
self.facade._data = self.replacevaluetable
self.update_data.emit('replace_mod')
self.close()
def filehandle():
ckentry = {}
rbtn = {'.csv': True, '.txt': False, '.xlsx': False}
lned = {'sheet': '', 'delim': '', 'tskip': '', 'bskip': ''}
fileinput = ini.InputHandler(
name='fileoptions',
tablename=None,
lnedentry=lned,
rbtns=rbtn,
checks=ckentry,
session=True,
filename='Datasets_manual_test/raw_data_test_2.csv')
return fileinput
def metahandle():
lentry = {
'globalid':
1,
'metaurl': ('http://sbc.lternet.edu/cgi-bin/showDataset' +
'.cgi?docid=knb-lter-sbc.18'),
'lter':
'SBC'
}
metainput = ini.InputHandler(name='metacheck',
tablename=None,
lnedentry=lentry,
checks=True)
return metainput
def time_handle_1_count():
d = {
'dayname': 'date',
'dayform': 'dd-mm-YYYY (Any Order)',
'monthname': 'date',
'monthform': 'dd-mm-YYYY (Any Order)',
'yearname': 'date',
'yearform': 'dd-mm-YYYY (Any Order)',
'jd': False,
'hms': False
}
timeini = ini.InputHandler(name='timeinfo',
tablename='timetable',
lnedentry=d)
return timeini
def commit_data(self):
''' Method to call the upload to database command '''
commithandle = ini.InputHandler(name='updateinfo',
tablename='updatetable')
self.facade.input_register(commithandle)
try:
self.facade.push_merged_data()
self.actionCommit.setEnabled(False)
self.message.about(self, 'Status', 'Database transaction complete')
except Exception as e:
print(str(e))
self.facade._tablelog['project_table'].debug(str(e))
self.error.showMessage('Datbase transaction error: ' + str(e) +
'. May need to alter site abbreviations.')
raise ValueError(str(e))
def time_handle5():
d = {
'dayname': '',
'dayform': 'NULL',
'monthname': '',
'monthform': 'NULL',
'yearname': 'YEAR',
'yearform': 'YYYY',
'jd': False,
'hms': False
}
timeini = ini.InputHandler(name='timeinfo',
tablename='timetable',
lnedentry=d)
return timeini
def meta_handle_free():
lentry = {
'globalid':
312,
'metaurl':
('http://gce-lter.marsci.uga.edu/public/app/dataset_details.asp?accession=PLT-GCES-0706'
),
'lter':
'GCE'
}
ckentry = {}
metainput = ini.InputHandler(name='metacheck',
tablename=None,
lnedentry=lentry,
checks=ckentry)
return metainput
def filehandle():
ckentry = {}
rbtn = {'.csv': False, '.txt': False, '.xlsx': True}
lned = {'sheet': '', 'delim': '', 'tskip': '', 'bskip': ''}
fileinput = ini.InputHandler(name='fileoptions',
tablename=None,
lnedentry=lned,
rbtns=rbtn,
checks=ckentry,
session=True,
verify='climatesite',
filename=str(os.getcwd()) +
'/Datasets_manual_test/' +
'climate_precip.txt')
return fileinput
def submit_change(self):
sender = self.sender()
self.covarlned['columns'] = hlp.string_to_list(self.lnedColumns.text())
self.covarini = ini.InputHandler(name='covarinfo',
tablename='covartable',
lnedentry=self.covarlned)
self.facade.input_register(self.covarini)
self.facade.create_log_record('covartable')
self._log = self.facade._tablelog['covartable']
if self.covarlned['columns'][0] == '':
print('in pass')
pass
else:
try:
self.facade._data[self.covarlned['columns']]
except Exception as e:
print(str(e))
self._log.debug(str(e))
self.error.showMessage(
'Column names not valid: Check spacing ' + 'and headers.')
raise ValueError('Column names are incorrect')
try:
self.covardata = ddf.DictionaryDataframe(
self.facade._data,
self.covarlned['columns']).convert_records()
except Exception as e:
print(str(e))
self._log.debug(str(e))
self.error.showMessage('Could not concatenate columns')
raise TypeError('Could not concatenate columns')
self.facade.push_tables['covariates'] = self.covardata
if sender is self.btnColumns:
self.message.about(self, 'Status', 'Columns recorded')
elif sender is self.btnPreview:
self.covarmodel = views.PandasTableModelEdit(self.covardata)
self.preview.tabviewPreview.setModel(self.covarmodel)
self.preview.show()
elif sender is self.btnSaveClose:
hlp.write_column_to_log(self.covarlned, self._log, 'covartable')
self.close()
def submit_change(self):
sender = self.sender()
self.addsitecolumn = {'addsite': self.lnedAddsite.text()}
# Input handler
self.addsiteini = ini.InputHandler(name='addsite',
lnedentry=self.addsitecolumn)
self.facade.input_register(self.addsiteini)
self.sitelabel = self.addsitecolumn['addsite']
# Logger
self.facade.create_log_record('addsite')
self._log = self.facade._tablelog['addsite']
if sender is self.btnAddsite:
try:
self.facade._data['site_added'] = self.sitelabel
self.message.about(self, 'Status', 'Site column added')
except Exception as e:
print(str(e))
self._log.debug(str(e))
self.error.showMessage('Could create column for sites: ' +
str(e))
raise ValueError('Could create column for sites: ' +
str(e))
if sender is self.btnSaveClose:
hlp.write_column_to_log(self.addsitecolumn, self._log,
'addsite')
try:
assert 'site_added' in self.facade._data.columns.values.tolist(
)
except Exception as e:
print(str(e))
raise AttributeError(str(e))
self.error.showMessage('Could not add site column: ' +
str(e))
self.close()
elif sender is self.btnCancel:
self.close()