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Source code for galaxy.webapps.galaxy.controllers.forms

import copy
import logging
import re

from markupsafe import escape

from galaxy import model, util
from galaxy.web.framework.helpers import grids, iff, time_ago
from galaxy.webapps.base.controller import BaseUIController, web

log = logging.getLogger(__name__)

VALID_FIELDNAME_RE = re.compile(r"^[a-zA-Z0-9\_]+$")

[docs]class FormsGrid(grids.Grid): # Custom column types
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, form): return escape(form.latest_form.name)
[docs] class DescriptionColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, form): return escape(form.latest_form.desc)
[docs] class TypeColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, form): return form.latest_form.type
[docs] class StatusColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, user): if user.deleted: return "deleted" return "active"
# Grid definition title = "Forms" model_class = model.FormDefinitionCurrent default_sort_key = "-update_time" num_rows_per_page = 50 use_paging = True default_filter = dict(deleted="False") columns = [ NameColumn("Name", key="name", model_class=model.FormDefinition, link=(lambda item: iff(item.deleted, None, dict(controller="admin", action="form/edit_form", id=item.id))), attach_popup=True, filterable="advanced"), DescriptionColumn("Description", key="desc", model_class=model.FormDefinition, filterable="advanced"), TypeColumn("Type"), grids.GridColumn("Last Updated", key="update_time", format=time_ago), StatusColumn("Status"), grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced") ] columns.append(grids.MulticolFilterColumn("Search", cols_to_filter=[columns[0], columns[1]], key="free-text-search", visible=False, filterable="standard")) operations = [ grids.GridOperation("Delete", allow_multiple=True, condition=(lambda item: not item.deleted)), grids.GridOperation("Undelete", condition=(lambda item: item.deleted)), ] global_actions = [ grids.GridAction("Create new form", dict(controller="admin", action="form/create_form")) ]
[docs] def build_initial_query(self, trans, **kwargs): return trans.sa_session.query(self.model_class).join(model.FormDefinition, self.model_class.latest_form_id == model.FormDefinition.id)
[docs]class Forms(BaseUIController): forms_grid = FormsGrid()
[docs] @web.legacy_expose_api @web.require_admin def forms_list(self, trans, payload=None, **kwd): message = kwd.get('message', '') status = kwd.get('status', '') if 'operation' in kwd: id = kwd.get('id') if not id: return self.message_exception(trans, f'Invalid form id ({str(id)}) received.') ids = util.listify(id) operation = kwd['operation'].lower() if operation == 'delete': message, status = self._delete_form(trans, ids) elif operation == 'undelete': message, status = self._undelete_form(trans, ids) if message and status: kwd['message'] = util.sanitize_text(message) kwd['status'] = status return self.forms_grid(trans, **kwd)
[docs] @web.legacy_expose_api @web.require_admin def create_form(self, trans, payload=None, **kwd): if trans.request.method == 'GET': fd_types = sorted(trans.app.model.FormDefinition.types.__members__.items()) return { 'title': 'Create new form', 'inputs': [{ 'name': 'name', 'label': 'Name' }, { 'name': 'desc', 'label': 'Description' }, { 'name': 'type', 'type': 'select', 'options': [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types], 'label': 'Type' }, { 'name': 'csv_file', 'label': 'Import from CSV', 'type': 'upload', 'help': 'Import fields from CSV-file with the following format: Label, Help, Type, Value, Options, Required=True/False.' }] } else: # csv-file format: label, helptext, type, default, selectlist, required ''' csv_file = payload.get('csv_file') index = 0 if csv_file: lines = csv_file.splitlines() for line in lines: row = line.split(',') if len(row) >= 6: prefix = 'fields_%i|' % index payload[f"{prefix}name"] = '%i_imported_field' % (index + 1) payload[f"{prefix}label"] = row[0] payload[f"{prefix}helptext"] = row[1] payload[f"{prefix}type"] = row[2] payload[f"{prefix}default"] = row[3] payload[f"{prefix}selectlist"] = row[4].split(',') payload[f"{prefix}required"] = row[5].lower() == 'true' index = index + 1 new_form, message = self.save_form_definition(trans, None, payload) if new_form is None: return self.message_exception(trans, message) imported = (' with %i imported fields' % index) if index > 0 else '' message = f"The form '{payload.get('name')}' has been created{imported}." return {'message': util.sanitize_text(message)}
[docs] @web.legacy_expose_api @web.require_admin def edit_form(self, trans, payload=None, **kwd): id = kwd.get('id') if not id: return self.message_exception(trans, 'No form id received for editing.') form = get_form(trans, id) latest_form = form.latest_form if trans.request.method == 'GET': fd_types = sorted(trans.app.model.FormDefinition.types.__members__.items()) ff_types = [(t.__name__.replace('Field', ''), t.__name__) for t in trans.model.FormDefinition.supported_field_types] field_cache = [] field_inputs = [{ 'name': 'name', 'label': 'Name', 'value': 'field_name', 'help': 'The field name must be unique for each field and must contain only alphanumeric characters and underscore.' }, { 'name': 'label', 'label': 'Label', 'value': 'Field label' }, { 'name': 'helptext', 'label': 'Help text' }, { 'name': 'type', 'label': 'Type', 'type': 'select', 'options': ff_types }, { 'name': 'default', 'label': 'Default value' }, { 'name': 'selectlist', 'label': 'Options', 'help': '*Only for fields which allow multiple selections, provide comma-separated values.' }, { 'name': 'required', 'label': 'Required', 'type': 'boolean', 'value': 'false' }] form_dict = { 'title': 'Edit form for \'%s\'' % (util.sanitize_text(latest_form.name)), 'inputs': [{ 'name': 'name', 'label': 'Name', 'value': latest_form.name }, { 'name': 'desc', 'label': 'Description', 'value': latest_form.desc }, { 'name': 'type', 'type': 'select', 'options': [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types], 'label': 'Type', 'value': latest_form.type }, { 'name': 'fields', 'title': 'Field', 'type': 'repeat', 'cache': field_cache, 'inputs': field_inputs }] } for field in latest_form.fields: new_field = copy.deepcopy(field_inputs) for field_input in new_field: field_value = field.get(field_input['name']) if field_value: if isinstance(field_value, list): field_value = ','.join(field_value) field_input['value'] = str(field_value) field_cache.append(new_field) return form_dict else: new_form, message = self.save_form_definition(trans, id, payload) if new_form is None: return self.message_exception(trans, message) message = f"The form '{payload.get('name')}' has been updated." return {'message': util.sanitize_text(message)}
[docs] def get_current_form(self, trans, payload=None, **kwd): ''' This method gets all the unsaved user-entered form details and returns a dictionary containing the name, desc, type, layout & fields of the form ''' name = payload.get('name') desc = payload.get('desc') or '' type = payload.get('type') fields = [] index = 0 while True: prefix = 'fields_%i|' % index if f"{prefix}label" in payload: field_attributes = ['name', 'label', 'helptext', 'required', 'type', 'selectlist', 'default'] field_dict = {attr: payload.get(f'{prefix}{attr}') for attr in field_attributes} field_dict['visible'] = True field_dict['required'] = field_dict['required'] == 'true' if isinstance(field_dict['selectlist'], str): field_dict['selectlist'] = field_dict['selectlist'].split(',') else: field_dict['selectlist'] = [] fields.append(field_dict) index = index + 1 else: break return dict(name=name, desc=desc, type=type, layout=[], fields=fields)
[docs] def save_form_definition(self, trans, form_id=None, payload=None, **kwd): ''' This method saves a form given an id ''' if not payload.get('name'): return None, 'Please provide a form name.' if payload.get('type') == 'none': return None, 'Please select a form type.' current_form = self.get_current_form(trans, payload) # validate fields field_names_dict = {} for field in current_form['fields']: if not field['label']: return None, 'All the field labels must be completed.' if not VALID_FIELDNAME_RE.match(field['name']): return None, f"{field['name']} is not a valid field name." if field['name'] in field_names_dict: return None, f"Each field name must be unique in the form definition. {field['name']} is not unique." else: field_names_dict[field['name']] = 1 # create a new form definition form_definition = trans.app.model.FormDefinition(name=current_form['name'], desc=current_form['desc'], fields=current_form['fields'], form_definition_current=None, form_type=current_form['type'], layout=current_form['layout']) # save changes to the existing form if form_id: form_definition_current = trans.sa_session.query(trans.app.model.FormDefinitionCurrent).get(trans.security.decode_id(form_id)) if form_definition_current is None: return None, f'Invalid form id ({form_id}) provided. Cannot save form.' else: form_definition_current = trans.app.model.FormDefinitionCurrent() # create corresponding row in the form_definition_current table form_definition.form_definition_current = form_definition_current form_definition_current.latest_form = form_definition trans.sa_session.add(form_definition_current) trans.sa_session.flush() return form_definition, None
@web.expose @web.require_admin def _delete_form(self, trans, ids): for form_id in ids: form = get_form(trans, form_id) form.deleted = True trans.sa_session.add(form) trans.sa_session.flush() return ('Deleted %i form(s).' % len(ids), 'done') @web.expose @web.require_admin def _undelete_form(self, trans, ids): for form_id in ids: form = get_form(trans, form_id) form.deleted = False trans.sa_session.add(form) trans.sa_session.flush() return ('Undeleted %i form(s).' % len(ids), 'done')
# ---- Utility methods -------------------------------------------------------
[docs]def get_form(trans, form_id): """Get a FormDefinition from the database by id.""" form = trans.sa_session.query(trans.app.model.FormDefinitionCurrent).get(trans.security.decode_id(form_id)) if not form: return trans.show_error_message(f"Form not found for id ({str(form_id)})") return form