def populate_award_form(form: AwardForm, award_node: Node): funder_name = '' award_title = '' funder_identifier = '' # FIX ME - should be list award_number = '' award_url = '' if award_node: funder_name_node = award_node.find_child(names.FUNDERNAME) if funder_name_node and funder_name_node.content: funder_name = funder_name_node.content award_title_node = award_node.find_child(names.TITLE) if award_title_node and award_title_node.content: award_title = award_title_node.content funder_identifiers = [] funder_identifier_nodes = award_node.find_all_children( names.FUNDERIDENTIFIER) for funder_identifier_node in funder_identifier_nodes: if funder_identifier_node.content: funder_identifiers.append(funder_identifier_node.content) funder_identifier = ','.join(funder_identifiers) award_number_node = award_node.find_child(names.AWARDNUMBER) if award_number_node and award_number_node.content: award_number = award_number_node.content award_url_node = award_node.find_child(names.AWARDURL) if award_url_node and award_url_node.content: award_url = award_url_node.content form.funder_name.data = funder_name form.award_title.data = award_title form.funder_identifier.data = funder_identifier form.award_number.data = award_number form.award_url.data = award_url
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)
def temporal_coverage(filename=None, node_id=None): form = TemporalCoverageForm(filename=filename) tc_node_id = node_id # Process POST if request.method == 'POST' and BTN_CANCEL in request.form: url = url_for(PAGE_TEMPORAL_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 form_value = request.form form_dict = form_value.to_dict(flat=False) new_page = PAGE_TEMPORAL_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 url = url_for(new_page, filename=filename) if save: 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) tc_node = Node(names.TEMPORALCOVERAGE, parent=coverage_node) begin_date_str = form.begin_date.data end_date_str = form.end_date.data create_temporal_coverage(tc_node, begin_date_str, end_date_str) if node_id and len(node_id) != 1: old_tc_node = Node.get_node_instance(node_id) if old_tc_node: coverage_parent_node = old_tc_node.parent coverage_parent_node.replace_child(old_tc_node, tc_node) else: msg = f"No node found in the node store with node id {node_id}" raise Exception(msg) else: add_child(coverage_node, tc_node) tc_node_id = tc_node.id flash_msg = compare_begin_end_dates(begin_date_str, end_date_str) if flash_msg: flash(flash_msg) url = (url_for(PAGE_TEMPORAL_COVERAGE, filename=filename, node_id=tc_node_id)) save_both_formats(filename=filename, eml_node=eml_node) return redirect(url) # Process GET if node_id == '1': form.init_md5() 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: tc_nodes = coverage_node.find_all_children( names.TEMPORALCOVERAGE) if tc_nodes: for tc_node in tc_nodes: if node_id == tc_node.id: populate_temporal_coverage_form(form, tc_node) set_current_page('temporal_coverage') return render_template('temporal_coverage.html', title='Temporal Coverage', form=form)
def geographic_coverage(filename=None, node_id=None): form = GeographicCoverageForm(filename=filename) # Process POST if request.method == 'POST' and BTN_CANCEL in request.form: url = url_for(PAGE_GEOGRAPHIC_COVERAGE_SELECT, filename=filename) return redirect(url) if request.method == 'POST' and form.validate_on_submit(): submit_type = None if is_dirty_form(form): submit_type = 'Save Changes' form_value = request.form form_dict = form_value.to_dict(flat=False) new_page = PAGE_GEOGRAPHIC_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 url = url_for(new_page, filename=filename) if submit_type == 'Save Changes': 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) geographic_description = form.geographic_description.data wbc = form.wbc.data if form.wbc.data is not None else '' ebc = form.ebc.data if form.ebc.data is not None else '' nbc = form.nbc.data if form.nbc.data is not None else '' sbc = form.sbc.data if form.sbc.data is not None else '' gc_node = Node(names.GEOGRAPHICCOVERAGE, parent=coverage_node) create_geographic_coverage(gc_node, geographic_description, wbc, ebc, nbc, sbc) if node_id and len(node_id) != 1: old_gc_node = Node.get_node_instance(node_id) if old_gc_node: coverage_parent_node = old_gc_node.parent coverage_parent_node.replace_child(old_gc_node, gc_node) else: msg = f"No node found in the node store with node id {node_id}" raise Exception(msg) else: add_child(coverage_node, gc_node) if nbc and sbc and nbc < sbc: flash('North should be greater than or equal to South') url = (url_for(PAGE_GEOGRAPHIC_COVERAGE, filename=filename, node_id=gc_node.id)) if ebc and wbc and ebc < wbc: flash('East should be greater than or equal to West') url = (url_for(PAGE_GEOGRAPHIC_COVERAGE, filename=filename, node_id=gc_node.id)) save_both_formats(filename=filename, eml_node=eml_node) return redirect(url) # Process GET if node_id == '1': form.init_md5() 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: gc_nodes = coverage_node.find_all_children( names.GEOGRAPHICCOVERAGE) if gc_nodes: for gc_node in gc_nodes: if node_id == gc_node.id: populate_geographic_coverage_form(form, gc_node) set_current_page('geographic_coverage') help = [ get_help('geographic_coverages'), get_help('geographic_description'), get_help('bounding_coordinates') ] return render_template('geographic_coverage.html', title='Geographic Coverage', form=form, help=help)
def method_step(filename=None, node_id=None): eml_node = load_eml(filename=filename) dataset_node = eml_node.find_child(names.DATASET) if dataset_node: methods_node = dataset_node.find_child(names.METHODS) else: dataset_node = Node(names.DATASET, parent=eml_node) add_child(eml_node, dataset_node) if not methods_node: methods_node = Node(names.METHODS, parent=dataset_node) add_child(dataset_node, methods_node) form = MethodStepForm(filename=filename, node_id=node_id) # Process POST if request.method == 'POST' and BTN_CANCEL in request.form: url = url_for(PAGE_METHOD_STEP_SELECT, filename=filename) return redirect(url) if request.method == 'POST' and form.validate_on_submit(): new_page = PAGE_METHOD_STEP_SELECT # Save or Back sends us back to the list of method steps form_value = request.form form_dict = form_value.to_dict(flat=False) 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 submit_type = None if is_dirty_form(form): submit_type = 'Save Changes' if submit_type == 'Save Changes': description = add_paragraph_tags(form.description.data) instrumentation = form.instrumentation.data method_step_node = Node(names.METHODSTEP, parent=methods_node) create_method_step(method_step_node, description, instrumentation) if node_id and len(node_id) != 1: old_method_step_node = Node.get_node_instance(node_id) if old_method_step_node: method_step_parent_node = old_method_step_node.parent method_step_parent_node.replace_child( old_method_step_node, method_step_node) else: msg = f"No methodStep node found in the node store with node id {node_id}" raise Exception(msg) else: add_child(methods_node, method_step_node) save_both_formats(filename=filename, eml_node=eml_node) url = url_for(new_page, filename=filename) return redirect(url) # Process GET if node_id == '1': form.init_md5() else: method_step_nodes = methods_node.find_all_children(names.METHODSTEP) if method_step_nodes: for ms_node in method_step_nodes: if node_id == ms_node.id: populate_method_step_form(form, ms_node) break set_current_page('method_step') help = [ get_help('method_step_description'), get_help('method_step_instrumentation') ] return render_template('method_step.html', title='Method Step', form=form, filename=filename, help=help)
def keyword(filename=None, node_id=None): eml_node = load_eml(filename=filename) 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) form = KeywordForm(filename=filename, node_id=node_id) form.init_keywords() # Process POST if request.method == 'POST' and BTN_CANCEL in request.form: url = url_for(PAGE_KEYWORD_SELECT, filename=filename) return redirect(url) # if request.method == 'POST' and form.validate_on_submit(): if request.method == 'POST': form_value = request.form form_dict = form_value.to_dict(flat=False) new_page = PAGE_KEYWORD_SELECT if form_dict: for key in form_dict: val = form_dict[key][0] # value is the first list element new_page = check_val_for_hidden_buttons( val, new_page, new_page) submit_type = None if is_dirty_form(form): submit_type = 'Save Changes' # flash(f'submit_type: {submit_type}') if submit_type == 'Save Changes': keyword = form.keyword.data keyword_type = form.keyword_type.data keyword_thesaurus = form.keyword_thesaurus.data # If so thesaurus was specified, see if the LTER Controlled Vocabulary applies if not keyword_thesaurus: lter_keywords = get_keywords('LTER') if keyword in lter_keywords: keyword_thesaurus = 'LTER Controlled Vocabulary' keyword_set_nodes = [] eml_node.find_all_descendants(names.KEYWORDSET, keyword_set_nodes) keyword_set_node = None for kws_node in keyword_set_nodes: keyword_thesaurus_node = kws_node.find_child( names.KEYWORDTHESAURUS) if keyword_thesaurus_node and keyword_thesaurus_node.content == keyword_thesaurus: keyword_set_node = kws_node break if not keyword_thesaurus_node and not keyword_thesaurus: keyword_set_node = kws_node break if not keyword_set_node: keyword_set_node = Node(names.KEYWORDSET, parent=dataset_node) add_child(dataset_node, keyword_set_node) if keyword_thesaurus: keyword_thesaurus_node = Node(names.KEYWORDTHESAURUS, parent=keyword_set_node) keyword_thesaurus_node.content = keyword_thesaurus keyword_set_node.children.append(keyword_thesaurus_node) keyword_node = Node(names.KEYWORD, parent=keyword_set_node) create_keyword(keyword_node, keyword, keyword_type) if node_id and len(node_id) != 1: old_keyword_node = Node.get_node_instance(node_id) if old_keyword_node: keyword_parent_node = old_keyword_node.parent keyword_parent_node.replace_child(old_keyword_node, keyword_node) else: msg = f"No keyword node found in the node store with node id {node_id}" raise Exception(msg) else: add_child(keyword_set_node, keyword_node) save_both_formats(filename=filename, eml_node=eml_node) url = url_for(new_page, filename=filename) return redirect(url) # Process GET if node_id == '1': form.init_md5() else: keyword_set_nodes = [] eml_node.find_all_descendants(names.KEYWORDSET, keyword_set_nodes) found = False for keyword_set_node in keyword_set_nodes: keyword_nodes = keyword_set_node.find_all_children(names.KEYWORD) keyword_thesaurus_node = keyword_set_node.find_child( names.KEYWORDTHESAURUS) if keyword_nodes: for kw_node in keyword_nodes: if node_id == kw_node.id: populate_keyword_form(form, kw_node, keyword_thesaurus_node) found = True break if found: break set_current_page('keyword') help = [get_help('keywords')] return render_template('keyword.html', title='Keyword', form=form, filename=filename, help=help)
def populate_responsible_party_form(form: ResponsiblePartyForm, node: Node): in_node = node.find_child(names.INDIVIDUALNAME) if in_node: salutation_node = in_node.find_child(names.SALUTATION) if salutation_node: form.salutation.data = salutation_node.content gn_nodes = in_node.find_all_children(names.GIVENNAME) if gn_nodes: form.gn.data = gn_nodes[0].content if len(gn_nodes) > 1: form.mn.data = gn_nodes[1].content sn_node = in_node.find_child(names.SURNAME) if sn_node: form.sn.data = sn_node.content user_id_node = node.find_child(names.USERID) if user_id_node: form.user_id.data = user_id_node.content organization_node = node.find_child(names.ORGANIZATIONNAME) if organization_node: form.organization.data = organization_node.content position_name_node = node.find_child(names.POSITIONNAME) if position_name_node: form.position_name.data = position_name_node.content address_node = node.find_child(names.ADDRESS) if address_node: delivery_point_nodes = \ address_node.find_all_children(names.DELIVERYPOINT) if len(delivery_point_nodes) > 0: form.address_1.data = delivery_point_nodes[0].content if len(delivery_point_nodes) > 1: form.address_2.data = delivery_point_nodes[1].content city_node = address_node.find_child(names.CITY) if city_node: form.city.data = city_node.content administrative_area_node = \ address_node.find_child(names.ADMINISTRATIVEAREA) if administrative_area_node: form.state.data = administrative_area_node.content postal_code_node = address_node.find_child(names.POSTALCODE) if postal_code_node: form.postal_code.data = postal_code_node.content country_node = address_node.find_child(names.COUNTRY) if country_node: form.country.data = country_node.content phone_node = node.find_child(names.PHONE) if phone_node: form.phone.data = phone_node.content phone_nodes = node.find_all_children(names.PHONE) for phone_node in phone_nodes: phone_type = phone_node.attribute_value('phonetype') if phone_type == 'facsimile': form.fax.data = phone_node.content else: form.phone.data = phone_node.content email_node = node.find_child(names.ELECTRONICMAILADDRESS) if email_node: form.email.data = email_node.content online_url_node = node.find_child(names.ONLINEURL) if online_url_node: form.online_url.data = online_url_node.content role_node = node.find_child(names.ROLE) if role_node: form.role.data = role_node.content form.md5.data = form_md5(form)
def method_step(filename=None, node_id=None): eml_node = load_eml(filename=filename) dataset_node = eml_node.find_child(names.DATASET) if dataset_node: methods_node = dataset_node.find_child(names.METHODS) else: dataset_node = Node(names.DATASET, parent=eml_node) add_child(eml_node, dataset_node) if not methods_node: methods_node = Node(names.METHODS, parent=dataset_node) add_child(dataset_node, methods_node) form = MethodStepForm(filename=filename, node_id=node_id) # Process POST if request.method == 'POST' and BTN_CANCEL in request.form: url = url_for(PAGE_METHOD_STEP_SELECT, filename=filename) return redirect(url) if request.method == 'POST' and form.validate_on_submit(): new_page = PAGE_METHOD_STEP_SELECT # Save or Back sends us back to the list of method steps form_value = request.form form_dict = form_value.to_dict(flat=False) if form_dict: for key in form_dict: val = form_dict[key][0] # value is the first list element new_page = check_val_for_hidden_buttons( val, new_page, PAGE_METHOD_STEP) submit_type = None if is_dirty_form(form): submit_type = 'Save Changes' if submit_type == 'Save Changes': description = form.description.data valid, msg = is_valid_xml_fragment(description, names.MAINTENANCE) if not valid: flash(invalid_xml_error_message(msg, False, names.DESCRIPTION), 'error') return render_get_method_step_page(eml_node, form, filename) instrumentation = form.instrumentation.data data_sources = form.data_sources.data method_step_node = Node(names.METHODSTEP, parent=methods_node) create_method_step(method_step_node, description, instrumentation, data_sources, data_sources_marker_begin, data_sources_marker_end) if node_id and len(node_id) != 1: old_method_step_node = Node.get_node_instance(node_id) if old_method_step_node: method_step_parent_node = old_method_step_node.parent method_step_parent_node.replace_child( old_method_step_node, method_step_node) else: msg = f"No methodStep node found in the node store with node id {node_id}" raise Exception(msg) else: add_child(methods_node, method_step_node) save_both_formats(filename=filename, eml_node=eml_node) url = url_for(new_page, filename=filename) return redirect(url) # Process GET if node_id == '1': form.init_md5() else: method_step_nodes = methods_node.find_all_children(names.METHODSTEP) if method_step_nodes: for ms_node in method_step_nodes: if node_id == ms_node.id: populate_method_step_form(form, ms_node) break return render_get_method_step_page(eml_node, form, filename)