def __init__(self, parent=None):
super().__init__(parent)
self.setupUi(self)
# Facade set up for the taxa dialog
# box. These inputs will have been already
# logged in the computer in order to
# reach this phase
self.facade = face.Facade()
self.facade.input_register(metahandle)
self.facade.meta_verify()
self.facade.input_register(filehandle)
self.facade.load_data()
self.facade.input_register(sitehandle)
sitelevels = self.facade._data['SITE'].drop_duplicates(
).values.tolist()
self.facade.register_site_levels(sitelevels)
self.facade.input_register(taxahandle)
self.sitelabel = None
# Actions
self.btnAddsite.clicked.connect(self.submit_change)
self.btnSaveClose.clicked.connect(self.submit_change)
self.btnCancel.clicked.connect(self.close)
# Update boxes/preview box
self.message = QtGui.QMessageBox
self.error = QtGui.QErrorMessage()
def __init__(self, parent=None):
super().__init__(parent)
self.setupUi(self)
# Facade set up
self.facade = face.Facade()
self.facade.input_register(meta_handle_1_count)
self.facade.meta_verify()
self.facade.input_register(file_handle_split_columns)
self.facade.load_data()
self.previous_click = False
# Place holders for user inputs
self.splitcolumnlned = {}
# Place holder: Data Model/ Data model view
self.splitcolumnmodel = None
self.viewEdit = view.PandasTableModelEdit(None)
# Placeholders: Data tables
self.splitcolumntable = None
# Actions
self.btnPreview.clicked.connect(self.submit_change)
self.btnSaveClose.clicked.connect(self.submit_change)
self.btnCancel.clicked.connect(self.close)
# Update boxes/preview box
self.message = QtGui.QMessageBox
self.error = QtGui.QErrorMessage()
self.preview = tprev.TablePreview()
def __init__(self, parent=None):
super().__init__(parent)
# attributes
self.setupUi(self)
# ------- SITE DIALOG CONSTRUCTOR ARGS ----- #
self.facade = face.Facade()
self.dsite = SiteDialog()
# Actions
self.actionSiteTable.triggered.connect(self.site_display)
# Custom Signals
self.dsite.site_unlocks.connect(self.site_complete_enable)
self.dsite.update_data
# ------ SESSION DIALOG CONSTRUCTOR ARGS ----- #
# Dialog boxes for user feedback
self.dsession = logicsess.SessionDialog()
self.error = QtGui.QErrorMessage()
self.message = QtGui.QMessageBox
# Custom signals
self.dsession.raw_data_model.connect(self.update_data_model)
# actions
self.actionStart_Session.triggered.connect(self.session_display)
self.mdiArea.addSubWindow(self.subwindow_2)
self.mdiArea.addSubWindow(self.subwindow_1)
metadf = read_csv(rootpath + end + 'data' + end +
'Cataloged_Data_Current_sorted.csv',
encoding='iso-8859-11')
metamodel = view.PandasTableModel(
metadf[['global_id', 'lter', 'title', 'site_metadata']])
self.tblViewMeta.setModel(metamodel)
def __init__(self, parent=None):
super().__init__(parent)
self.setupUi(self)
# Facade set up for the taxa dialog
# box. These inputs will have been already
# logged in the computer in order to
# reach this phase
self.facade = face.Facade()
self.facade.input_register(meta_handle_free)
self.facade.meta_verify()
self.facade.input_register(file_handle_free)
self.facade.load_data()
self.facade.input_register(site_handle_free)
sitelevels = self.facade._data[site_handle_free.lnedentry[
'study_site_key']].drop_duplicates().values.tolist()
self.facade.register_site_levels(sitelevels)
# Place holders for user inputs
self.obslned = {}
self.obsckbox = {}
self.obsraw = {}
self.available = None
self.null = None
# Place holder: Data Model/ Data model view
self.obsmodel = None
self.viewEdit = view.PandasTableModelEdit
# Placeholders: Data tables
self.obstable = None
# Placeholder: Director (table builder), log
self.obsdirector = None
self._log = None
# Placeholder for maindata Orms
self.obsorms = {}
# Actions
self.btnPreview.clicked.connect(self.submit_change)
self.btnSaveClose.clicked.connect(self.submit_change)
self.btnCancel.clicked.connect(self.close)
self.tablename = None
self.table = None
# Update boxes/preview box
self.message = QtGui.QMessageBox
self.error = QtGui.QErrorMessage()
self.preview = prev.TablePreview()
def __init__(self, parent=None):
super().__init__(parent)
# attributes
self.setupUi(self)
# ------- SITE DIALOG CONSTRUCTOR ARGS ----- #
self.facade = face.Facade()
self.dsite = s_.SiteDialog()
self.climatesite = ClimateSite()
self.climatesite.climatesite_unlocks.connect(
self.climate_site_complete_enabled)
# Actions
self.actionSiteTable.triggered.connect(self.site_display)
self.actionClimateSiteTable.triggered.connect(
self.climate_site_display)
# Custom Signals
# ------ SESSION DIALOG CONSTRUCTOR ARGS ----- #
# Dialog boxes for user feedback
self.dsession = logicsess.SessionDialog()
self.dsession.raw_data_model.connect(self.update_data_model)
self.climatesession = logicsess.SessionDialog()
self.climatesession.raw_data_model.connect(self.update_data_model)
self.error = QtGui.QErrorMessage()
self.message = QtGui.QMessageBox
# actions
self.actionStart_Session.triggered.connect(self.session_display)
self.actionNew_Climate.triggered.connect(
self.climate_session_display)
self.mdiArea.addSubWindow(self.subwindow_2)
self.mdiArea.addSubWindow(self.subwindow_1)
# Dialog boxes for user feedback
self.error = QtGui.QErrorMessage()
self.message = QtGui.QMessageBox
metadf = read_csv(metapath, encoding='iso-8859-11')
metamodel = view.PandasTableModel(metadf)
self.tblViewMeta.setModel(metamodel)
def __init__(self, parent=None):
super().__init__(parent)
# attributes
self.setupUi(self)
self.facade = face.Facade()
self.dsession = SessionDialog()
# Dialog boxes for user feedback
self.error = QtGui.QErrorMessage()
self.message = QtGui.QMessageBox
# Custom signals
self.dsession.raw_data_model.connect(self.update_data_model)
# actions
self.actionStart_Session.triggered.connect(self.session_display)
self.mdiArea.addSubWindow(self.subwindow_2)
self.mdiArea.addSubWindow(self.subwindow_1)
def __init__(self, parent=None):
super().__init__(parent)
self.setupUi(self)
self.facade = face.Facade()
self.facade.input_register(meta_handle7)
self.facade.meta_verify()
self.facade.input_register(file_handle5)
self.facade.load_data()
self.facade.input_register(site_handle5)
sitelevels = self.facade._data[
site_handle5.lnedentry['study_site_key']
].drop_duplicates().values.tolist()
self.facade.register_site_levels(sitelevels)
self.facade.input_register(taxa_handle5)
self.mainini = None
# Place holder: Data Model/ Data model view
self.mainmodel = None
self.viewEdit = view.PandasTableModelEdit
self.form_entries = None
# Placeholders: Data tables
self.project_table = None
# Placeholder: Director (table builder), log
self.maindirector = None
self._log = None
# Actions
self.btnPreview.clicked.connect(self.submit_change)
self.btnSaveClose.clicked.connect(self.submit_change)
self.btnCancel.clicked.connect(self.close)
self.preview = tprev.TablePreview()
self.message = QtGui.QMessageBox
self.error = QtGui.QErrorMessage()
def __init__(self, parent=None):
super().__init__(parent)
self.setupUi(self)
# Facade set up for the taxa dialog
# box. These inputs will have been already
# logged in the computer in order to
# reach this phase
self.facade = face.Facade()
self.facade.input_register(meta_handle_free)
self.facade.meta_verify()
self.facade.input_register(file_handle_wide_to_long)
self.facade.load_data()
self.facade.input_register(site_handle_wide_to_long)
sitelevels = self.facade._data[
self.facade._inputs['siteinfo'].
lnedentry['study_site_key']].drop_duplicates().values.tolist()
self.facade.register_site_levels(sitelevels)
# Place holders for user inputs
self.widetolonglned = {}
# Place holder: Data Model/ Data model view
self.widetolongmodel = None
self.viewEdit = view.PandasTableModel
# Placeholders: Data tables
self.widetolongtable = None
# Actions
self.btnPreview.clicked.connect(self.submit_change)
self.btnSaveClose.clicked.connect(self.submit_change)
self.btnCancel.clicked.connect(self.close)
# Update boxes/preview box
self.message = QtGui.QMessageBox
self.error = QtGui.QErrorMessage()
self.preview = tprev.TablePreview()
def test_site_in_project_key_number_two(MergeToUpload, site_handle2,
file_handle2, meta_handle2,
project_handle2, taxa_handle2,
time_handle2, count_handle2,
covar_handle2):
facade = face.Facade()
facade.input_register(meta_handle2)
facade.meta_verify()
facade.input_register(file_handle2)
facade.load_data()
facade.input_register(site_handle2)
sitedirector = facade.make_table('siteinfo')
study_site_table = sitedirector._availdf
siteid = site_handle2.lnedentry['study_site_key']
sitelevels = facade._data[siteid].drop_duplicates().values.tolist()
facade.register_site_levels(sitelevels)
print('test2 sitelevels: ', sitelevels)
facade._valueregister['siteid'] = siteid
print('study_site_table (test): ', study_site_table)
facade.create_log_record('study_site_table')
lter = meta_handle2.lnedentry['lter']
ltercol = produce_null_df(1, ['lter_table_fkey'], len(study_site_table),
lter)
study_site_table = concat([study_site_table, ltercol], axis=1)
study_site_table_og_col = study_site_table.columns.values.tolist()
study_site_table_single = study_site_table.iloc[0, :]
study_site_table_single_df = DataFrame([study_site_table_single])
study_site_table_single_df.columns = study_site_table_og_col
print('study site single: ', study_site_table_single)
study_site_table_single_df.loc[0, 'study_site_key'] = 'NULL'
print('study_site_table: ', study_site_table_single_df)
facade.push_tables['study_site_table'] = study_site_table_single_df
facade.input_register(project_handle2)
maindirector = facade.make_table('maininfo')
project_table = maindirector._availdf.copy().reset_index(drop=True)
orm.convert_types(project_table, orm.project_types)
facade.push_tables['project_table'] = project_table
facade.create_log_record('project_table')
facade.input_register(taxa_handle2)
taxadirector = facade.make_table('taxainfo')
taxa_table = taxadirector._availdf
facade.push_tables['taxa_table'] = taxa_table
print('taxa columns after make taxa table: ', taxa_table.columns)
facade.create_log_record('taxa_table')
print('taxa columns before time_table: ', taxa_table.columns)
facade.input_register(time_handle2)
timetable = tparse.TimeParse(facade._data,
time_handle2.lnedentry).formater()
facade.push_tables['timetable'] = timetable
facade.create_log_record('timetable')
print('taxa columns before count_table: ', taxa_table.columns)
facade.input_register(count_handle2)
rawdirector = facade.make_table('rawinfo')
rawtable = rawdirector._availdf
print(rawtable)
facade.push_tables[count_handle2.tablename] = rawtable
facade.create_log_record(count_handle2.tablename)
print('taxa columns before covar_table: ', taxa_table.columns)
facade.input_register(covar_handle2)
covartable = ddf.DictionaryDataframe(
facade._data, covar_handle2.lnedentry['columns']).convert_records()
facade.push_tables['covariates'] = covartable
facade.create_log_record('covartable')
facade._valueregister['globalid'] = meta_handle2.lnedentry['globalid']
facade._valueregister['lter'] = meta_handle2.lnedentry['lter']
facade._valueregister['siteid'] = siteid
timetable_og_cols = timetable.columns.values.tolist()
timetable.columns = [x + '_derived' for x in timetable_og_cols]
observationdf = facade._data
observation_time_df = concat([timetable, observationdf], axis=1)
print('merge class obs_time columns: ', observation_time_df.columns)
print('merge class project table: ', project_table)
study_site_table.to_sql('study_site_table',
orm.conn,
if_exists='append',
index=False)
project_table['lter_project_fkey'] = facade._valueregister['lter']
project_table.to_sql('project_table',
orm.conn,
if_exists='append',
index=False)
print('taxa columns before site_in_proj method: ', taxa_table.columns)
merge_object = MergeToUpload()
site_in_project_key_df = merge_object.site_in_proj_key_df(
studysitetabledf=study_site_table,
projecttabledf=project_table,
observationtabledf=observation_time_df,
lterlocation=facade._valueregister['lter'],
studysitelabel=siteid,
studysitelevels=sitelevels)
print('taxa columns before user taxa merge method: ', taxa_table.columns)
merge_object.merge_for_taxa_table_upload(
formated_taxa_table=taxa_table,
siteinprojkeydf=site_in_project_key_df,
sitelabel=siteid)
taxa_column_in_data = [
x[0] for x in list(facade._inputs['taxainfo'].lnedentry.items())
]
taxa_column_in_push_table = [
x[1] for x in list(facade._inputs['taxainfo'].lnedentry.items())
]
merge_object.merge_for_datatype_table_upload(
raw_dataframe=observation_time_df,
formated_dataframe=rawtable,
formated_dataframe_name='{}'.format(
re.sub('_table', '', facade._inputs['rawinfo'].tablename)),
covariate_dataframe=covartable,
siteinprojkeydf=site_in_project_key_df,
raw_data_taxa_columns=taxa_column_in_data,
uploaded_taxa_columns=taxa_column_in_push_table)
def __init__(self, parent=None):
super().__init__(parent)
# attributes
self.setupUi(self)
self.facade = face.Facade()
self._log = None
self.dsite = sitelogic.SiteDialog()
self.dsession = sesslogic.SessionDialog()
self.dmain = mainlogic.MainDialog()
self.dtaxa = taxalogic.TaxaDialog()
self.dtime = timelogic.TimeDialog()
self.draw = rawlogic.ObsDialog()
self.dcovar = covarlogic.CovarDialog()
self.dclimatesite = climsitelogic.ClimateSite()
self.dclimatesession = sesslogic.SessionDialog()
self.dwidetolong = widetolonglogic.WidetoLongDialog()
self.dsplitcolumn = splitcolumnlogic.SplitColumnDialog()
self.dreplacevalue = replacelogic.ReplaceValueDialog()
self.dcbind = cbindlogic.CbindDialog()
self.data_model = view.PandasTableModelEdit(None)
self.data_model.log_change.connect(self.write_to_log)
self.change_count = 0
# Actions
self.actionUndo.triggered.connect(self.undo_data_mod)
self.actionCombine_Columns.triggered.connect(self.cbind_display)
self.actionReplace.triggered.connect(self.replace_value_display)
self.actionConvert_Wide_to_Long.triggered.connect(
self.wide_to_long_display)
self.actionSplit_Column_By.triggered.connect(self.split_column_display)
self.actionSiteTable.triggered.connect(self.site_display)
self.actionStart_Session.triggered.connect(self.session_display)
self.actionEnd_Session.triggered.connect(self.end_session)
self.actionMainTable.triggered.connect(self.main_display)
self.actionTaxaTable.triggered.connect(self.taxa_display)
self.actionTimeFormat.triggered.connect(self.time_display)
self.actionRawTable.triggered.connect(self.obs_display)
self.actionCovariates.triggered.connect(self.covar_display)
self.actionCommit.triggered.connect(self.commit_data)
self.actionClimateSiteTable.triggered.connect(
self.climate_site_display)
self.actionNew_Climate.triggered.connect(self.climate_session_display)
self.mdiArea.addSubWindow(self.subwindow_2)
self.mdiArea.addSubWindow(self.subwindow_1)
# Custom Signals
self.dsite.site_unlocks.connect(self.site_complete_enable)
self.dwidetolong.update_data.connect(self.update_data_model)
self.dsplitcolumn.update_data.connect(self.update_data_model)
self.dreplacevalue.update_data.connect(self.update_data_model)
self.dcbind.update_data.connect(self.update_data_model)
self.dclimatesite.climatesite_unlocks.connect(
self.climate_site_complete_enabled)
self.dsession.raw_data_model.connect(self.update_data_model)
self.dclimatesession.raw_data_model.connect(self.update_data_model)
# Dialog boxes for user feedback
self.error = QtGui.QErrorMessage()
self.message = QtGui.QMessageBox
metadf = read_csv(metapath, encoding='iso-8859-11')
metamodel = view.PandasTableModel(
metadf[['global_id', 'lter', 'title', 'site_metadata',
'temp_int']])
self.tblViewMeta.setModel(metamodel)
self.tblViewMeta.resizeColumnsToContents()
self.tblViewRaw.horizontalHeader().sectionDoubleClicked.connect(
self.changeHorizontalHeader)
self.tblViewRaw.resizeColumnsToContents()
def test_site_in_project_key(MergeToUpload, site_handle_corner_case,
file_handle_corner_case, meta_handle_corner_case,
project_handle_corner_case,
taxa_handle_corner_case, time_handle_corner_case,
percent_cover_handle_corner_case,
covar_handle_corner_case):
facade = face.Facade()
facade.input_register(meta_handle_corner_case)
facade.meta_verify()
facade.input_register(file_handle_corner_case)
facade.load_data()
siteid = site_handle_corner_case.lnedentry['study_site_key']
facade._data[siteid].replace(
{
'C': 'site_jrn_zone_creosotebush',
'G': 'site_jrn_zone_grassland'
},
inplace=True)
facade.input_register(site_handle_corner_case)
sitedirector = facade.make_table('siteinfo')
study_site_table = sitedirector._availdf
print('study_site_table (test): ', study_site_table)
facade.create_log_record('study_site_table')
lter = meta_handle_corner_case.lnedentry['lter']
ltercol = produce_null_df(1, ['lter_table_fkey'], len(study_site_table),
lter)
study_site_table = concat([study_site_table, ltercol], axis=1)
print('study_site_table: ', study_site_table)
facade.push_tables['study_site_table'] = study_site_table
sitelevels = facade._data[siteid].drop_duplicates().values.tolist()
facade.register_site_levels(sitelevels)
facade._valueregister['siteid'] = siteid
facade.input_register(project_handle_corner_case)
maindirector = facade.make_table('maininfo')
project_table = maindirector._availdf.copy().reset_index(drop=True)
orm.convert_types(project_table, orm.project_types)
facade.push_tables['project_table'] = project_table
facade.create_log_record('project_table')
facade.input_register(taxa_handle_corner_case)
taxadirector = facade.make_table('taxainfo')
taxa_table = taxadirector._availdf
facade.push_tables['taxa_table'] = taxa_table
facade.create_log_record('taxa_table')
facade.input_register(time_handle_corner_case)
timetable = tparse.TimeParse(facade._data,
time_handle_corner_case.lnedentry).formater()
facade.push_tables['timetable'] = timetable
facade.create_log_record('timetable')
facade.input_register(percent_cover_handle_corner_case)
rawdirector = facade.make_table('rawinfo')
rawtable = rawdirector._availdf
print(rawtable)
facade.push_tables[percent_cover_handle_corner_case.tablename] = rawtable
facade.create_log_record(percent_cover_handle_corner_case.tablename)
facade.input_register(covar_handle_corner_case)
covartable = ddf.DictionaryDataframe(
facade._data,
covar_handle_corner_case.lnedentry['columns']).convert_records()
facade.push_tables['covariates'] = covartable
facade.create_log_record('covartable')
facade._valueregister['globalid'] = meta_handle_corner_case.lnedentry[
'globalid']
facade._valueregister['lter'] = meta_handle_corner_case.lnedentry['lter']
facade._valueregister['siteid'] = siteid
timetable_og_cols = timetable.columns.values.tolist()
timetable.columns = [x + '_derived' for x in timetable_og_cols]
observationdf = facade._data
observation_time_df = concat([timetable, observationdf], axis=1)
print('merge class obs_time columns: ', observation_time_df.columns)
print('merge class project table: ', project_table)
# try:
# study_site_table.to_sql(
# 'study_site_table',
# orm.conn, if_exists='append', index=False)
# except Exception as e:
# print('Sites in db: ', str(e))
project_table['lter_project_fkey'] = facade._valueregister['lter']
project_table.to_sql('project_table',
orm.conn,
if_exists='append',
index=False)
merge_object = MergeToUpload()
site_in_project_key_df = merge_object.site_in_proj_key_df(
studysitetabledf=study_site_table,
projecttabledf=project_table,
observationtabledf=observation_time_df,
lterlocation=facade._valueregister['lter'],
studysitelabel=siteid,
studysitelevels=sitelevels)
merge_object.merge_for_taxa_table_upload(
formated_taxa_table=taxa_table,
siteinprojkeydf=site_in_project_key_df,
sitelabel=siteid)
taxa_column_in_push_table = [
x[0] for x in list(facade._inputs['taxainfo'].lnedentry.items())
]
taxa_column_in_data = [
x[1] for x in list(facade._inputs['taxainfo'].lnedentry.items())
]
merge_object.merge_for_datatype_table_upload(
raw_dataframe=observation_time_df,
formated_dataframe=rawtable,
formated_dataframe_name='{}'.format(
re.sub('_table', '', facade._inputs['rawinfo'].tablename)),
covariate_dataframe=covartable,
siteinprojkeydf=site_in_project_key_df,
raw_data_taxa_columns=taxa_column_in_data,
uploaded_taxa_columns=taxa_column_in_push_table)
obs_columns_in_data = [
x[1] for x in list(facade._inputs['rawinfo'].lnedentry.items())
]
obs_columns_in_push_table = [
x[0] for x in list(facade._inputs['rawinfo'].lnedentry.items())
]
merge_object.update_project_table(
spatial_rep_columns_from_og_df=obs_columns_in_data,
spatial_rep_columns_from_formated_df=obs_columns_in_push_table)
# Creating dictionaries for data from different tables
site_dict = meta.table_data('sitetable').iloc[0]
obs_dict = meta.table_data('rawtable').iloc[0]
taxa_dict = meta.table_data('taxatable').iloc[0]
main_dict = meta.table_data('maintable').iloc[0] # Units and extent
main_dict_updated = meta.table_data('maintable').iloc[
1] # Time & labels
time_dict = meta.table_data('timetable').iloc[0]
covar_dict = meta.table_data('covartable').iloc[0]
sitecolumn = list(set(main_dict_updated['sp_rep1_label'][1]))[0]
# -------------------------------------------------------------------
# Begin concatenating data for reload to popler3
# -------------------------------------------------------------------
facade = face.Facade()
# ---------------------
# Create METADATA HANDLE
# --------------------
lentry = {
'globalid':
z,
'metaurl':
metadata_file[metadata_file['global_id'] == z]
['site_metadata'].iloc[0],
'lter':
metadata_file[metadata_file['global_id'] == z]['lter'].iloc[0]
}
ckentry = {}
metainput = ini.InputHandler(name='metacheck',