def data_package_id(filename=None):
form = DataPackageIDForm()
eml_node = load_eml(filename=filename)
# Process POST
# if request.method == 'POST' and form.validate_on_submit():
if request.method == 'POST':
save = False
if is_dirty_form(form):
save = True
if save:
data_package_id = form.data_package_id.data
create_data_package_id(data_package_id, filename)
set_active_packageid(data_package_id)
form.md5.data = form_md5(form)
new_page = PAGE_TITLE
this_page = PAGE_DATA_PACKAGE_ID
new_page = handle_hidden_buttons(new_page, this_page)
return redirect(url_for(new_page, filename=filename))
# Process GET
data_package_id = eml_node.attribute_value('packageId')
form.data_package_id.data = data_package_id if data_package_id else ''
form.md5.data = form_md5(form)
set_current_page('data_package_id')
help = get_helps(['data_package_id'])
return render_template('data_package_id.html',
form=form,
help=help,
title='Data Package ID')
def rp_select_get(filename=None,
form=None,
rp_name=None,
rp_singular=None,
rp_plural=None,
help=None,
node_id=None,
project_node_id=None):
# Process GET
eml_node = load_eml(filename=filename)
rp_list = list_responsible_parties(eml_node,
rp_name,
project_node_id=project_node_id)
title = rp_plural # rp_name.capitalize()
related_project = project_node_id is not None
if related_project:
rp_singular = 'Related ' + rp_singular
rp_plural = 'Related ' + rp_plural
return render_template('responsible_party_select.html',
title=title,
rp_list=rp_list,
form=form,
rp_singular=rp_singular,
rp_plural=rp_plural,
help=help,
relatedProject=related_project)
def taxonomic_coverage_select(filename=None):
form = TaxonomicCoverageSelectForm(filename=filename)
# Process POST
if request.method == 'POST':
form_value = request.form
form_dict = form_value.to_dict(flat=False)
url = select_post(filename, form, form_dict, 'POST',
PAGE_TAXONOMIC_COVERAGE_SELECT,
PAGE_TEMPORAL_COVERAGE_SELECT, PAGE_MAINTENANCE,
PAGE_TAXONOMIC_COVERAGE)
return redirect(url)
# Process GET
title = "Taxonomic Coverage"
txc_list = []
eml_node = load_eml(filename=filename)
if eml_node:
dataset_node = eml_node.find_child(names.DATASET)
if dataset_node:
txc_list = list_taxonomic_coverages(dataset_node)
set_current_page('taxonomic_coverage')
help = [get_help('taxonomic_coverages')]
return render_template('taxonomic_coverage_select.html',
title=title,
txc_list=txc_list,
form=form,
help=help)
def check_eml(filename: str):
# global evaluation, metapype_validation_errs, metapype_evaluation
global evaluation
evaluation = []
eml_node = load_eml(filename)
check_dataset_title(eml_node, filename)
check_data_tables(eml_node, filename)
check_creators(eml_node, filename)
check_contacts(eml_node, filename)
check_associated_parties(eml_node, filename)
check_metadata_providers(eml_node, filename)
check_dataset_abstract(eml_node, filename)
check_keywords(eml_node, filename)
check_intellectual_rights(eml_node, filename)
check_coverage(eml_node, filename)
check_geographic_coverage(eml_node, filename)
check_maintenance(eml_node, filename)
check_method_steps(eml_node, filename)
check_project(eml_node, filename)
check_other_entities(eml_node, filename)
check_data_package_id(eml_node, filename)
return format_output(evaluation)
def geographic_coverage_select(filename=None):
form = GeographicCoverageSelectForm(filename=filename)
# Process POST
if request.method == 'POST':
form_value = request.form
form_dict = form_value.to_dict(flat=False)
url = select_post(filename, form, form_dict, 'POST',
PAGE_GEOGRAPHIC_COVERAGE_SELECT,
PAGE_INTELLECTUAL_RIGHTS,
PAGE_TEMPORAL_COVERAGE_SELECT,
PAGE_GEOGRAPHIC_COVERAGE)
return redirect(url)
# Process GET
gc_list = []
title = "Geographic Coverage"
eml_node = load_eml(filename=filename)
if eml_node:
dataset_node = eml_node.find_child(names.DATASET)
if dataset_node:
gc_list = list_geographic_coverages(dataset_node)
set_current_page('geographic_coverage')
help = get_helps(['geographic_coverages', 'geographic_coverages_csv_file'])
return render_template('geographic_coverage_select.html',
title=title,
gc_list=gc_list,
form=form,
help=help)
def cull_uploads(package_name=None):
# Remove uploads not represented in the metadata.
# Formerly, Import Package removed all uploads on the assumption that it was a new package.
# But, we may want to replace the metadata without losing the uploads. This is especially
# true when the "without data" form of the package is being used to replace the existing
# package in order to update the metadata without losing the uploads.
eml_node = load_eml(filename=package_name)
# Get all of the uploads represented in the metadata
object_names = []
object_name_nodes = []
eml_node.find_all_descendants(names.OBJECTNAME, object_name_nodes)
for object_name_node in object_name_nodes:
if object_name_node.content:
object_names.append(object_name_node.content)
# Remove any uploads that aren't in the list
user_path = user_data.get_user_folder_name(
) # os.path.join(current_path, USER_DATA_DIR)
upload_folder = os.path.join(user_path, 'uploads', package_name)
to_delete = [
file for file in os.listdir(upload_folder) if file not in object_names
]
for file in to_delete:
os.remove(os.path.join(user_path, 'uploads', package_name, file))
def funding_award_select(filename=None, project_node_id=None):
form = AwardSelectForm(filename=filename)
# Process POST
if request.method == 'POST':
form_value = request.form
form_dict = form_value.to_dict(flat=False)
node_id = None
new_page = PAGE_FUNDING_AWARD_SELECT
if form_dict:
for key in form_dict:
val = form_dict[key][0] # value is the first list element
if val == BTN_SAVE_AND_CONTINUE:
new_page = PAGE_PROJECT
elif val[0:4] == 'Back':
new_page = PAGE_PROJECT
elif val == BTN_EDIT:
new_page = PAGE_FUNDING_AWARD
node_id = key
elif val == BTN_REMOVE:
new_page = PAGE_FUNDING_AWARD_SELECT
node_id = key
eml_node = load_eml(filename=filename)
remove_child(node_id=node_id)
save_both_formats(filename=filename, eml_node=eml_node)
elif val == UP_ARROW:
new_page = PAGE_FUNDING_AWARD_SELECT
node_id = key
process_up_button(filename, node_id)
elif val == DOWN_ARROW:
new_page = PAGE_FUNDING_AWARD_SELECT
node_id = key
process_down_button(filename, node_id)
elif val[0:3] == 'Add':
new_page = PAGE_FUNDING_AWARD
node_id = '1'
else:
new_page = check_val_for_hidden_buttons(
val, new_page, PAGE_FUNDING_AWARD_SELECT)
if form.validate_on_submit():
if node_id and project_node_id:
url = url_for(new_page,
filename=filename,
node_id=node_id,
project_node_id=project_node_id)
elif project_node_id:
url = url_for(new_page,
filename=filename,
project_node_id=project_node_id)
else:
url = url_for(new_page, filename=filename, node_id=node_id)
return redirect(url)
# Process GET
return funding_award_select_get(filename=filename,
form=form,
project_node_id=project_node_id)
def get_abstract(filename, form):
# Process GET
eml_node = load_eml(filename=filename)
abstract_node = eml_node.find_single_node_by_path(
[names.DATASET, names.ABSTRACT])
if abstract_node:
try:
form.abstract.data = display_texttype_node(abstract_node)
except InvalidXMLError as exc:
flash('The XML is invalid. Please make corrections.', 'error')
return render_get_abstract_page(form, filename)
def clear_taxonomic_coverage(package_name):
# When user selects Clear Taxonomic Coverage to get rid of coverage imported from XML, we delete it and
# set the flag that says its OK for ezEML to handle even though the package was imported from XML.
eml_node = load_eml(filename=package_name)
coverage_node = eml_node.find_single_node_by_path([names.DATASET, names.COVERAGE])
if coverage_node:
taxonomic_coverage_nodes = coverage_node.find_all_children(names.TAXONOMICCOVERAGE)
for taxonomic_coverage_node in taxonomic_coverage_nodes:
coverage_node.remove_child(taxonomic_coverage_node)
Node.delete_node_instance(taxonomic_coverage_node.id)
clear_taxonomy_imported_from_xml(eml_node, package_name)
def render_get_abstract_page(form, filename):
eml_node = load_eml(filename)
form.md5.data = form_md5(form)
set_current_page('abstract')
help = [get_help('abstract'), get_help('nav')]
return render_template(
'abstract.html',
title='Abstract',
model_has_complex_texttypes=model_has_complex_texttypes(eml_node),
filename=filename,
form=form,
help=help)
def publication_info(filename=None):
form = PublicationInfoForm()
# Process POST
# if request.method == 'POST' and form.validate_on_submit():
if request.method == 'POST':
if 'Next' in request.form:
new_page = PAGE_METHOD_STEP_SELECT
elif BTN_HIDDEN_CHECK in request.form:
new_page = PAGE_CHECK
elif BTN_HIDDEN_SAVE in request.form:
new_page = PAGE_PUBLICATION_INFO
elif BTN_HIDDEN_DOWNLOAD in request.form:
new_page = PAGE_DOWNLOAD
elif BTN_HIDDEN_NEW in request.form:
new_page = PAGE_CREATE
elif BTN_HIDDEN_OPEN in request.form:
new_page = PAGE_OPEN
elif BTN_HIDDEN_CLOSE in request.form:
new_page = PAGE_CLOSE
else:
new_page = PAGE_PUBLISHER
save = False
if is_dirty_form(form):
save = True
if save:
pubplace = form.pubplace.data
pubdate = form.pubdate.data
create_pubinfo(pubplace=pubplace,
pubdate=pubdate,
filename=filename)
return redirect(url_for(new_page, filename=filename))
# Process GET
eml_node = load_eml(filename=filename)
pubplace_node = eml_node.find_single_node_by_path(
[names.DATASET, names.PUBPLACE])
if pubplace_node:
form.pubplace.data = pubplace_node.content
pubdate_node = eml_node.find_single_node_by_path(
[names.DATASET, names.PUBDATE])
if pubdate_node:
form.pubdate.data = pubdate_node.content
form.md5.data = form_md5(form)
set_current_page('publication_info')
help = get_helps(['pubplace', 'pubdate'])
return render_template('publication_info.html',
help=help,
form=form,
title='Publication Info')
def maintenance(filename=None):
form = MaintenanceForm(filename=filename)
eml_node = load_eml(filename=filename)
if eml_node:
dataset_node = eml_node.find_child(names.DATASET)
if not dataset_node:
dataset_node = Node(names.DATASET, parent=eml_node)
add_child(eml_node, dataset_node)
# Process POST
if request.method == 'POST' and BTN_CANCEL in request.form:
url = url_for(PAGE_MAINTENANCE, filename=filename)
return redirect(url)
if request.method == 'POST' and form.validate_on_submit():
save = False
if is_dirty_form(form):
save = True
if save:
maintenace_description = form.description.data
valid, msg = is_valid_xml_fragment(maintenace_description, names.MAINTENANCE)
if not valid:
flash(invalid_xml_error_message(msg, False, names.DESCRIPTION), 'error')
return render_get_maintenance_page(eml_node, form, filename)
update_frequency = form.update_frequency.data
create_maintenance(dataset_node, maintenace_description, update_frequency)
save_both_formats(filename=filename, eml_node=eml_node)
form_value = request.form
form_dict = form_value.to_dict(flat=False)
new_page = PAGE_MAINTENANCE
if form_dict:
for key in form_dict:
val = form_dict[key][0] # value is the first list element
if val == BTN_SAVE_AND_CONTINUE:
new_page = PAGE_PUBLISHER
else:
new_page = handle_hidden_buttons(new_page, PAGE_MAINTENANCE)
return redirect(url_for(new_page, filename=filename))
# Process GET
if dataset_node:
maintenance_node = dataset_node.find_child(names.MAINTENANCE)
if maintenance_node:
populate_maintenance_form(form, maintenance_node)
return render_get_maintenance_page(eml_node, form, filename)
def remove_keyword(filename, node_id):
eml_node = load_eml(filename=filename)
if node_id:
keyword_node = Node.get_node_instance(node_id)
if keyword_node:
keyword_set_node = keyword_node.parent
remove_child(node_id=node_id)
# if we've just removed the last keyword under the keywordSet, remove the keywordSet
if not keyword_set_node.find_all_children(names.KEYWORD):
parent_node = keyword_set_node.parent
parent_node.remove_child(keyword_set_node)
save_both_formats(filename=filename, eml_node=eml_node)
def access_select_get(filename=None, form=None):
# Process GET
access_rules_list = []
title = 'Access Rules'
eml_node = load_eml(filename=filename)
if eml_node:
access_rules_list = list_access_rules(eml_node)
return render_template('access_select.html',
title=title,
filename=filename,
ar_list=access_rules_list,
form=form)
def render_get_intellectual_rights_page(form, filename, font_family):
eml_node = load_eml(filename)
form.md5.data = form_md5(form)
set_current_page('intellectual_rights')
help = [get_help('intellectual_rights')]
return render_template(
'intellectual_rights.html',
title='Intellectual Rights',
font_family=font_family,
model_has_complex_texttypes=model_has_complex_texttypes(eml_node),
filename=filename,
form=form,
help=help)
def title(filename=None):
form = TitleForm()
# Process POST
# if request.method == 'POST' and form.validate_on_submit():
if request.method == 'POST':
new_page = PAGE_DATA_TABLE_SELECT
save = False
if is_dirty_form(form):
save = True
if save:
create_title(title=form.title.data, filename=filename)
form.md5.data = form_md5(form)
if 'Next' in request.form:
new_page = PAGE_DATA_TABLE_SELECT
elif BTN_HIDDEN_CHECK in request.form:
new_page = PAGE_CHECK
elif BTN_HIDDEN_SAVE in request.form:
new_page = PAGE_TITLE
elif BTN_HIDDEN_DOWNLOAD in request.form:
new_page = PAGE_DOWNLOAD
elif BTN_HIDDEN_NEW in request.form:
new_page = PAGE_CREATE
elif BTN_HIDDEN_OPEN in request.form:
new_page = PAGE_OPEN
elif BTN_HIDDEN_CLOSE in request.form:
new_page = PAGE_CLOSE
return redirect(url_for(new_page, filename=filename))
# Process GET
eml_node = load_eml(filename=filename)
dataset_node = eml_node.find_child(child_name=names.DATASET)
title_node = dataset_node.find_child(names.TITLE)
if title_node:
form.title.data = title_node.content
form.md5.data = form_md5(form)
set_current_page('title')
help = get_helps(['title', 'nav', 'welcome'])
first_usage = is_first_usage()
return render_template('title.html',
title='Title',
form=form,
help=help,
is_first_usage=first_usage)
def data_package_id(filename=None):
form = DataPackageIDForm()
eml_node = load_eml(filename=filename)
# Process POST
# if request.method == 'POST' and form.validate_on_submit():
if request.method == 'POST':
new_page = PAGE_TITLE
save = False
if is_dirty_form(form):
save = True
if save:
data_package_id = form.data_package_id.data
create_data_package_id(data_package_id, filename)
set_active_packageid(data_package_id)
form.md5.data = form_md5(form)
if 'Next' in request.form:
new_page = PAGE_CHECK
elif BTN_HIDDEN_CHECK in request.form:
new_page = PAGE_CHECK
elif BTN_HIDDEN_SAVE in request.form:
new_page = PAGE_DATA_PACKAGE_ID
elif BTN_HIDDEN_DOWNLOAD in request.form:
new_page = PAGE_DOWNLOAD
elif BTN_HIDDEN_NEW in request.form:
new_page = PAGE_CREATE
elif BTN_HIDDEN_OPEN in request.form:
new_page = PAGE_OPEN
elif BTN_HIDDEN_CLOSE in request.form:
new_page = PAGE_CLOSE
return redirect(url_for(new_page, filename=filename))
# Process GET
data_package_id = eml_node.attribute_value('packageId')
form.data_package_id.data = data_package_id if data_package_id else ''
form.md5.data = form_md5(form)
set_current_page('data_package_id')
help = get_helps(['data_package_id'])
return render_template('data_package_id.html',
form=form,
help=help,
title='Data Package ID')
def funding_award_select_get(filename=None, form=None, node_id=None):
# Process GET
title = 'Funding Awards'
# entity_name = ''
eml_node = load_eml(filename=filename)
funding_award_list = list_funding_awards(eml_node, node_id)
set_current_page('project')
related_project = node_id is not None
help = [get_help('awards')]
return render_template('award_select.html',
title=title,
filename=filename,
award_list=funding_award_list,
form=form,
help=help,
related_project=related_project)
def publisher(filename=None):
method = request.method
node_id = '1'
if filename:
eml_node = load_eml(filename=filename)
dataset_node = eml_node.find_child(names.DATASET)
if dataset_node:
publisher_node = dataset_node.find_child(names.PUBLISHER)
if publisher_node:
node_id = publisher_node.id
set_current_page('publisher')
help = [get_help('publisher')]
return responsible_party(filename=filename, node_id=node_id,
method=method, node_name=names.PUBLISHER,
back_page=PAGE_CONTACT_SELECT, title='Publisher',
next_page=PAGE_PUBLICATION_INFO,
save_and_continue=True, help=help)
def keyword_select_get(filename=None, form=None):
# Process GET
kw_list = []
title = 'Keywords'
eml_node = load_eml(filename=filename)
if eml_node:
kw_list = list_keywords(eml_node)
set_current_page('keyword')
help = [get_help('keywords')]
return render_template('keyword_select.html',
title=title,
filename=filename,
kw_list=kw_list,
form=form,
help=help)
def related_project_select_get(filename=None, form=None):
# Process GET
project_list = []
title = 'Related Projects'
eml_node = load_eml(filename=filename)
if eml_node:
project_list = list_related_projects(eml_node)
set_current_page('project')
help = [get_help('related_project')]
return render_template('related_project_select.html',
title=title,
filename=filename,
project_list=project_list,
form=form,
help=help)
def access_select_post(filename=None,
form=None,
form_dict=None,
method=None,
this_page=None,
back_page=None,
next_page=None,
edit_page=None):
node_id = ''
new_page = ''
if form_dict:
for key in form_dict:
val = form_dict[key][0] # value is the first list element
if val == 'Back':
new_page = back_page
elif val == 'Next':
new_page = next_page
elif val == 'Edit':
new_page = edit_page
node_id = key
elif val == 'Remove':
new_page = this_page
node_id = key
eml_node = load_eml(filename=filename)
remove_child(node_id=node_id)
save_both_formats(filename=filename, eml_node=eml_node)
elif val == UP_ARROW:
new_page = this_page
node_id = key
process_up_button(filename, node_id)
elif val == DOWN_ARROW:
new_page = this_page
node_id = key
process_down_button(filename, node_id)
elif val[0:3] == 'Add':
new_page = edit_page
node_id = '1'
if form.validate_on_submit():
if new_page == edit_page:
return url_for(new_page, filename=filename, node_id=node_id)
elif new_page == this_page:
return url_for(new_page, filename=filename, node_id=node_id)
elif new_page == back_page or new_page == next_page:
return url_for(new_page, filename=filename)
def load_geo_coverage_from_csv(csv_filename, filename):
eml_node = load_eml(filename=filename)
data_frame = pd.read_csv(csv_filename, comment='#', encoding='utf8')
required_columns = ['geographicDescription',
'northBoundingCoordinate',
'southBoundingCoordinate',
'eastBoundingCoordinate',
'westBoundingCoordinate']
optional_columns = ['minimumAltitude',
'maximumAltitude',
'altitudeUnits']
has_required_columns = False
has_optional_columns = False
if list(data_frame.columns) == required_columns:
has_required_columns = True
if list(data_frame.columns) == required_columns + optional_columns:
has_required_columns = True
has_optional_columns = True
if not has_required_columns:
raise ValueError('Geographic coverage file does not have expected column names.')
expected_types_error_msg = 'Geographic coverage file does not have expected variable types in columns. Note that ' \
'numerical values must be written with a decimal point.'
if not has_optional_columns:
if list(data_frame.dtypes) != [np.object, np.float64, np.float64, np.float64, np.float64]:
raise ValueError(expected_types_error_msg)
else:
if list(data_frame.dtypes)[1:-1] != [np.float64, np.float64, np.float64, np.float64, np.float64, np.float64]:
raise ValueError(expected_types_error_msg)
for index, row in data_frame.iterrows():
if has_optional_columns:
add_geo_coverage_node(eml_node, row[0], row[1], row[2], row[3], row[4],
str(row[5]) if not pd.isna(row[5]) else None,
str(row[6]) if not pd.isna(row[6]) else None,
str(row[7]) if not pd.isna(row[7]) else None)
else:
add_geo_coverage_node(eml_node, row[0], row[1], row[2], row[3], row[4])
save_both_formats(filename=filename, eml_node=eml_node)
def abstract(filename=None):
form = AbstractForm(filename=filename)
# Process POST
if request.method == 'POST':
if 'Next' in request.form:
new_page = PAGE_KEYWORD_SELECT
elif BTN_HIDDEN_CHECK in request.form:
new_page = PAGE_CHECK
elif BTN_HIDDEN_SAVE in request.form:
new_page = PAGE_ABSTRACT
elif BTN_HIDDEN_DOWNLOAD in request.form:
new_page = PAGE_DOWNLOAD
elif BTN_HIDDEN_NEW in request.form:
new_page = PAGE_CREATE
elif BTN_HIDDEN_OPEN in request.form:
new_page = PAGE_OPEN
elif BTN_HIDDEN_CLOSE in request.form:
new_page = PAGE_CLOSE
else:
submit_type = None
new_page = PAGE_KEYWORD_SELECT
if form.validate_on_submit():
if is_dirty_form(form):
abstract = add_paragraph_tags(form.abstract.data)
create_abstract(filename=filename, abstract=abstract)
return redirect(url_for(new_page, filename=filename))
# Process GET
eml_node = load_eml(filename=filename)
abstract_node = eml_node.find_single_node_by_path(
[names.DATASET, names.ABSTRACT])
if abstract_node:
form.abstract.data = remove_paragraph_tags(abstract_node.content)
form.md5.data = form_md5(form)
set_current_page('abstract')
help = [get_help('abstract'), get_help('nav')]
return render_template('abstract.html',
title='Abstract',
filename=filename,
form=form,
help=help)
def publication_info(filename=None):
form = PublicationInfoForm()
# Process POST
# if request.method == 'POST' and form.validate_on_submit():
if request.method == 'POST':
new_page = PAGE_METHOD_STEP_SELECT
this_page = PAGE_PUBLICATION_INFO
new_page = handle_hidden_buttons(new_page, this_page)
save = False
if is_dirty_form(form):
save = True
if save:
pubplace = form.pubplace.data
pubdate = form.pubdate.data
create_pubinfo(pubplace=pubplace,
pubdate=pubdate,
filename=filename)
return redirect(url_for(new_page, filename=filename))
# Process GET
eml_node = load_eml(filename=filename)
pubplace_node = eml_node.find_single_node_by_path(
[names.DATASET, names.PUBPLACE])
if pubplace_node:
form.pubplace.data = pubplace_node.content
pubdate_node = eml_node.find_single_node_by_path(
[names.DATASET, names.PUBDATE])
if pubdate_node:
form.pubdate.data = pubdate_node.content
form.md5.data = form_md5(form)
set_current_page('publication_info')
help = get_helps(['pubplace', 'pubdate'])
return render_template('publication_info.html',
help=help,
form=form,
title='Publication Info')
def get_intellectual_rights(filename, form):
eml_node = load_eml(filename=filename)
intellectual_rights_node = eml_node.find_single_node_by_path(
[names.DATASET, names.INTELLECTUALRIGHTS])
if intellectual_rights_node:
ir_content = display_texttype_node(intellectual_rights_node)
if INTELLECTUAL_RIGHTS_CC0 in ir_content:
form.intellectual_rights_radio.data = 'CC0'
form.intellectual_rights.data = ''
elif INTELLECTUAL_RIGHTS_CC_BY in ir_content:
form.intellectual_rights_radio.data = 'CCBY'
form.intellectual_rights.data = ''
else:
form.intellectual_rights_radio.data = "Other"
form.intellectual_rights.data = display_texttype_node(
intellectual_rights_node)
font_family = 'Courier' if node_has_literal_children(
intellectual_rights_node) else ''
return render_get_intellectual_rights_page(filename=filename,
form=form,
font_family=font_family)
def title(filename=None):
log_info(f'Title')
form = TitleForm()
# Process POST
if request.method == 'POST' and form.validate_on_submit():
save = False
if is_dirty_form(form):
save = True
if save:
create_title(title=form.title.data, filename=filename)
form.md5.data = form_md5(form)
new_page = PAGE_DATA_TABLE_SELECT
this_page = PAGE_TITLE
new_page = handle_hidden_buttons(new_page, this_page)
return redirect(url_for(new_page, filename=filename))
# Process GET
eml_node = load_eml(filename=filename)
dataset_node = eml_node.find_child(child_name=names.DATASET)
title_node = dataset_node.find_child(names.TITLE)
if title_node:
form.title.data = title_node.content
form.md5.data = form_md5(form)
set_current_page('title')
help = get_helps(['title', 'nav', 'welcome'])
first_usage = is_first_usage()
return render_template('title.html',
title='Title',
form=form,
help=help,
is_first_usage=first_usage)
def load_geo_coverage_from_csv(csv_filename, filename):
eml_node = load_eml(filename=filename)
data_frame = pd.read_csv(csv_filename, comment='#', encoding='utf8')
if list(data_frame.columns) != [
'geographicDescription', 'northBoundingCoordinate',
'southBoundingCoordinate', 'eastBoundingCoordinate',
'westBoundingCoordinate'
]:
raise ValueError(
'Geographic coverage file does not have expected column names.')
if list(data_frame.dtypes) != [
np.object, np.float64, np.float64, np.float64, np.float64
]:
raise ValueError(
'Geographic coverage file does not have expected variable types in columns.'
)
for index, row in data_frame.iterrows():
add_geo_coverage_node(eml_node, row[0], row[1], row[2], row[3], row[4])
save_both_formats(filename=filename, eml_node=eml_node)
def access(filename=None, node_id=None):
eml_node = load_eml(filename=filename)
if eml_node:
access_node = eml_node.find_child(names.ACCESS)
else:
return
if not access_node:
access_node = Node(names.ACCESS, parent=eml_node)
add_child(eml_node, access_node)
form = AccessForm(filename=filename, node_id=node_id)
# form = AccessForm()
# Process POST
if request.method == 'POST':
if BTN_CANCEL in request.form:
url = url_for(PAGE_ACCESS_SELECT, filename=filename)
return redirect(url)
next_page = PAGE_ACCESS_SELECT # Save or Back sends us back to the list of access rules
if form.validate_on_submit():
if is_dirty_form(form):
submit_type = 'Save Changes'
else:
submit_type = 'Back'
if submit_type == 'Save Changes':
userid = form.userid.data
permission = form.permission.data
allow_node = Node(names.ALLOW, parent=access_node)
create_access_rule(allow_node, userid, permission)
if node_id and len(node_id) != 1:
old_allow_node = Node.get_node_instance(node_id)
if old_allow_node:
access_parent_node = old_allow_node.parent
access_parent_node.replace_child(
old_allow_node, allow_node)
else:
msg = f"No 'allow' node found in the node store with node id {node_id}"
raise Exception(msg)
else:
add_child(access_node, allow_node)
save_both_formats(filename=filename, eml_node=eml_node)
url = url_for(next_page, filename=filename)
return redirect(url)
# Process GET
if node_id == '1':
form.init_md5()
else:
allow_nodes = access_node.find_all_children(names.ALLOW)
if allow_nodes:
for allow_node in allow_nodes:
if node_id == allow_node.id:
populate_access_rule_form(form, allow_node)
break
return render_template('access.html',
title='Access Rule',
form=form,
filename=filename)
def taxonomic_coverage(filename=None, node_id=None, taxon=None):
form = TaxonomicCoverageForm(filename=filename)
# Process POST
if request.method == 'POST' and BTN_CANCEL in request.form:
url = url_for(PAGE_TAXONOMIC_COVERAGE_SELECT, filename=filename)
return redirect(url)
if request.method == 'POST' and form.validate_on_submit():
save = False
if is_dirty_form(form):
save = True
# flash(f'save: {save}')
form_value = request.form
have_links = False
if 'Fill' in form_value:
source = form.taxonomic_authority.data
if source == 'ITIS':
source_type = TaxonomySourceEnum.ITIS
elif source == 'NCBI':
source_type = TaxonomySourceEnum.NCBI
elif source == "WORMS":
source_type = TaxonomySourceEnum.WORMS
try:
source_name = ''
for choice in form.taxonomic_authority.choices:
if choice[0] == source:
source_name = choice[1]
break
hierarchy = fill_taxonomic_coverage(form.taxon_value.data,
source_type, source_name)
if hierarchy:
# set the taxon rank dropdown appropriately
rank = hierarchy[0][0].capitalize()
if (rank, rank) in form.taxon_rank.choices:
form.taxon_rank.data = rank
# see if we should display a Links column
for taxon in hierarchy:
if taxon[4]:
have_links = True
break
except ValueError as e:
flash(str(e))
hierarchy = [(form.taxon_rank.data, form.taxon_value.data, '',
'')]
form.hierarchy.data = hierarchy
form.hidden_taxon_rank.data = form.taxon_rank.data
form.hidden_taxon_value.data = form.taxon_value.data
form.hidden_taxonomic_authority.data = form.taxonomic_authority.data
help = get_helps(['taxonomic_coverage_fill_hierarchy'])
return render_template(
'taxonomic_coverage.html',
title='Taxonomic Coverage',
form=form,
hierarchy=hierarchy,
taxon_rank=form.taxon_rank.data,
taxon_value=form.taxon_value.data,
taxonomic_authority=form.taxonomic_authority.data,
help=help,
have_links=have_links)
form_dict = form_value.to_dict(flat=False)
new_page = PAGE_TAXONOMIC_COVERAGE_SELECT
if form_dict:
for key in form_dict:
val = form_dict[key][0] # value is the first list element
if val == BTN_HIDDEN_NEW:
new_page = PAGE_CREATE
break
elif val == BTN_HIDDEN_OPEN:
new_page = PAGE_OPEN
break
elif val == BTN_HIDDEN_CLOSE:
new_page = PAGE_CLOSE
break
if save:
if not form.taxon_value.data and not form.taxon_rank.data:
return redirect(url_for(new_page, filename=filename))
submitted_hierarchy = form_value.get('hierarchy')
if isinstance(form_value.get('hierarchy'),
str) and form_value.get('hierarchy'):
# convert hierarchy string to list
submitted_hierarchy = ast.literal_eval(
form_value.get('hierarchy'))
form.hierarchy.data = submitted_hierarchy
# if we're saving after doing 'Fill Hierarchy', fill in the values we've been passed
if form_value.get('hidden_taxon_rank'):
form.taxon_rank.data = form_value.get('hidden_taxon_rank')
form.taxon_value.data = form_value.get('hidden_taxon_value')
form.taxonomic_authority.data = form_value.get(
'hidden_taxonomic_authority')
elif not submitted_hierarchy:
# we don't have a hierarchy, so construct a fake hierarchy to be used by create_taxonomic_coverage()
form.hierarchy.data = [(form_value.get('taxon_rank'),
form_value.get('taxon_value'), '', '',
'', '')]
if not form_value.get('taxon_rank'):
flash('Taxon Rank is required.')
return redirect(
url_for(PAGE_TAXONOMIC_COVERAGE,
filename=filename,
node_id=node_id,
taxon=form.taxon_value.data))
eml_node = load_eml(filename=filename)
dataset_node = eml_node.find_child(names.DATASET)
if not dataset_node:
dataset_node = Node(names.DATASET)
coverage_node = dataset_node.find_child(names.COVERAGE)
if not coverage_node:
coverage_node = Node(names.COVERAGE, parent=dataset_node)
add_child(dataset_node, coverage_node)
txc_node = Node(names.TAXONOMICCOVERAGE, parent=coverage_node)
create_taxonomic_coverage(txc_node,
form.general_taxonomic_coverage.data,
form.hierarchy.data,
form.taxonomic_authority.data)
if node_id and len(node_id) != 1:
old_txc_node = Node.get_node_instance(node_id)
if old_txc_node:
coverage_parent_node = old_txc_node.parent
coverage_parent_node.replace_child(old_txc_node, txc_node)
else:
msg = f"No node found in the node store with node id {node_id}"
raise Exception(msg)
else:
add_child(coverage_node, txc_node)
save_both_formats(filename=filename, eml_node=eml_node)
return redirect(url_for(new_page, filename=filename))
# Process GET
have_links = False
if node_id == '1':
form.init_md5()
if taxon:
form.taxon_value.data = taxon
else:
eml_node = load_eml(filename=filename)
dataset_node = eml_node.find_child(names.DATASET)
if dataset_node:
coverage_node = dataset_node.find_child(names.COVERAGE)
if coverage_node:
txc_nodes = coverage_node.find_all_children(
names.TAXONOMICCOVERAGE)
if txc_nodes:
for txc_node in txc_nodes:
if node_id == txc_node.id:
have_links = populate_taxonomic_coverage_form(
form, txc_node)
help = get_helps(['taxonomic_coverage_fill_hierarchy'])
set_current_page('taxonomic_coverage')
return render_template('taxonomic_coverage.html',
title='Taxonomic Coverage',
form=form,
hierarchy=form.hierarchy.data,
have_links=have_links,
help=help)
