def add_tsn(self, index):
try:
indexes = self.ui.table_results.selectionModel().selectedRows()
selected_indices = [int(index.row()) for index in list(indexes)]
df = self.ui.table_results.model().dataframe()
indexes = df.index[selected_indices]
if df.shape[0] == 1:
index = 0
elif selected_indices:
index = selected_indices[0]
else:
return
if 'combinedName' in df.columns:
item_name = df.iloc[index]['combinedName']
else:
item_name = str(df.iloc[index]['commonName'])
tsn = df.iloc[index]['tsn']
i = self.selected_items_df.index.max() + 1
if pd.isnull(i):
i = 0
self.selected_items_df.loc[i] = [str(item_name), tsn]
self.selected_model = utils.PandasModel(self.selected_items_df)
self.ui.table_include.setModel(self.selected_model)
except AttributeError:
pass
def __init__(self, xml=None, fgdc_function=None, parent=None):
QWidget.__init__(self, parent=parent)
self.build_ui()
self.connect_events()
self.selected_items_df = pd.DataFrame(columns=['item', 'tsn'])
self.selected_model = utils.PandasModel(self.selected_items_df)
self.ui.table_include.setModel(self.selected_model)
self._from_xml(xml)
self.fgdc_function = fgdc_function
def search_itis(self):
if str(self.ui.combo_search_type.currentText()) == 'Scientific name':
results = taxonomy.search_by_scientific_name(
str(self.ui.search_term.text()))
else:
results = taxonomy.search_by_common_name(
str(self.ui.search_term.text()))
model = utils.PandasModel(results)
self.ui.table_results.setModel(model)
def search_itis(self):
QApplication.setOverrideCursor(Qt.WaitCursor)
if str(self.ui.combo_search_type.currentText()) == 'Scientific name':
results = taxonomy.search_by_scientific_name(
str(self.ui.search_term.text()))
else:
results = taxonomy.search_by_common_name(
str(self.ui.search_term.text()))
model = utils.PandasModel(results)
self.ui.table_results.setModel(model)
QApplication.restoreOverrideCursor()
def __init__(self, parent=None):
WizardWidget.__init__(self, parent=parent)
self.selected_items_df = pd.DataFrame(columns=['item', 'tsn'])
self.selected_model = utils.PandasModel(self.selected_items_df)
self.ui.table_include.setModel(self.selected_model)
self.ui.frame_included_species.hide()
# This dictionary contains copies of each unique taxonomy xml created
# so that we need not generate them more than once
self.xml_lookup = {}
def _from_xml(self, taxonomy_element):
if taxonomy_element is not None:
i = 0
for common_node in taxonomy_element.findall('.//common'):
if common_node.text.startswith('TSN: '):
tsn = common_node.text[5:]
scientific_name = taxonomy.get_full_record_from_tsn(
tsn)['scientificName']['combinedName']
self.selected_items_df.loc[i] = [scientific_name, tsn]
i += 1
self.selected_model = utils.PandasModel(self.selected_items_df)
self.ui.table_include.setModel(self.selected_model)
def _from_xml(self, taxonomy_element):
self.ui.rbtn_yes.setChecked(True)
self.selected_items_df = pd.DataFrame(columns=['item', 'tsn'])
i = 0
for common_node in taxonomy_element.findall('.//common'):
if common_node.text.startswith('TSN: '):
tsn = common_node.text[5:]
self.selected_items_df.loc[i] = ['...', tsn]
# try:
# scientific_name = taxonomy.get_full_record_from_tsn(tsn)['scientificName']['combinedName']
# self.selected_items_df.loc[i] = [scientific_name, tsn]
# except:
# self.selected_items_df.loc[i] = ['...', tsn]
# i += 1
self.selected_model = utils.PandasModel(self.selected_items_df)
self.ui.table_include.setModel(self.selected_model)
def add_tsn(self, index):
indexes = self.ui.table_results.selectionModel().selectedRows()
selected_indices = [int(index.row()) for index in list(indexes)]
df = self.ui.table_results.model().dataframe()
indices = df.index[selected_indices]
for index in indices:
if "combinedName" in df.columns:
item_name = df.iloc[index]["combinedName"]
else:
item_name = str(df.iloc[index]["commonName"])
tsn = df.iloc[index]["tsn"]
i = self.selected_items_df.index.max() + 1
if pd.isnull(i):
i = 0
self.selected_items_df.loc[i] = [str(item_name), tsn]
self.selected_model = utils.PandasModel(self.selected_items_df)
self.table_include.setModel(self.selected_model)
def search_itis(self):
QApplication.setOverrideCursor(Qt.WaitCursor)
try:
if str(self.ui.combo_search_type.currentText()
) == "Scientific name":
results = taxonomy.search_by_scientific_name(
str(self.ui.search_term.text()))
else:
results = taxonomy.search_by_common_name(
str(self.ui.search_term.text()))
model = utils.PandasModel(results)
self.ui.table_results.setModel(model)
QApplication.restoreOverrideCursor()
except requests.exceptions.ConnectionError:
QApplication.restoreOverrideCursor()
msg = "This functionality requires an internet connection."
msg += "\n Please retry latter."
QMessageBox.information(None, "No internet connection", msg)
self.close()
def add_tsn(self, index):
try:
indexes = self.ui.table_results.selectionModel().selectedRows()
selected_indices = [int(index.row()) for index in list(indexes)]
df = self.ui.table_results.model().dataframe()
indexes = df.index[selected_indices]
if df.shape[0] == 1:
index = 0
elif selected_indices:
index = selected_indices[0]
else:
return
if "combinedName" in df.columns:
item_name = df.iloc[index]["combinedName"]
else:
try:
item_name = str(df.iloc[index]["commonName"])
except KeyError:
msg = "Error, No taxon was selected in the Search Results table!"
msg += "\nMake sure the ITIS search returned results and select one before clicking Add Selection. "
QMessageBox.information(None,
"Problem adding taxon",
msg,
parent=self)
return None
tsn = df.iloc[index]["tsn"]
i = self.selected_items_df.index.max() + 1
if pd.isnull(i):
i = 0
self.selected_items_df.loc[i] = [str(item_name), tsn]
self.selected_model = utils.PandasModel(self.selected_items_df)
self.ui.table_include.setModel(self.selected_model)
except AttributeError:
pass
