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Merge branch 'replace_page_edit_form' into dev

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This commit is contained in:
Dannon Baker
2017-09-28 12:57:20 -04:00
parent f4941e5422 a8f59a46a9
commit 297cb2da4b
12 changed files with 170 additions and 181 deletions
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client/galaxy/scripts/apps/analysis.js
+10
View File
@@ -46,6 +46,8 @@ window.app = function app( options, bootstrapped ){
'(/)user(/)(:form_id)' : 'show_user_form',
'(/)workflow(/)' : 'show_workflows',
'(/)workflow/run(/)' : 'show_run',
'(/)pages(/)create(/)' : 'show_pages_create',
'(/)pages(/)edit(/)' : 'show_pages_edit',
'(/)pages(/)(:action_id)' : 'show_pages',
'(/)visualizations(/)edit(/)' : 'show_visualizations_edit',
'(/)visualizations/(:action_id)' : 'show_visualizations',
@@ -114,6 +116,14 @@ window.app = function app( options, bootstrapped ){
this.page.display( new GridShared.View( { action_id: action_id, plural: 'Pages', item: 'page' } ) );
},
show_pages_create : function() {
this.page.display( new FormWrapper.View ( { url : 'page/create', redirect: 'pages/list' } ) );
},
show_pages_edit : function() {
this.page.display( new FormWrapper.View ( { url : 'page/edit?id=' + QueryStringParsing.get( 'id' ), redirect: 'pages/list' } ) );
},
show_workflows : function(){
this.page.display( new Workflows.View() );
},
lib/galaxy/web/base/controller.py
+4 -1
View File
@@ -183,13 +183,16 @@ class BaseUIController(BaseController):
try:
return BaseController.get_object(self, trans, id, class_name,
check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
except exceptions.MessageException:
raise # handled in the caller
except:
log.exception("Exception in get_object check for %s %s:", class_name, str(id))
raise Exception('Server error retrieving %s id ( %s ).' % (class_name, str(id)))
def message_exception(self, trans, message):
trans.response.status = 400
return {'err_msg': util.sanitize_text(message)}
class BaseAPIController(BaseController):
lib/galaxy/webapps/galaxy/buildapp.py
+2
View File
@@ -121,6 +121,8 @@ def paste_app_factory(global_conf, **kwargs):
webapp.add_client_route('/visualizations/edit')
webapp.add_client_route('/pages/list')
webapp.add_client_route('/pages/list_published')
webapp.add_client_route('/pages/create')
webapp.add_client_route('/pages/edit')
webapp.add_client_route('/histories/list')
webapp.add_client_route('/histories/list_published')
webapp.add_client_route('/histories/list_shared')
lib/galaxy/webapps/galaxy/controllers/admin.py
+35 -40
View File
@@ -547,13 +547,13 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
if 'operation' in kwargs:
id = kwargs.get('id')
if not id:
return message_exception(trans, 'Invalid quota id (%s) received.' % str(id))
return self.message_exception(trans, 'Invalid quota id (%s) received.' % str(id))
quotas = []
for quota_id in util.listify(id):
try:
quotas.append(get_quota(trans, quota_id))
except MessageException as e:
return message_exception(trans, str(e))
return self.message_exception(trans, str(e))
operation = kwargs.pop('operation').lower()
try:
if operation == 'delete':
@@ -618,14 +618,14 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
quota, message = self._create_quota(util.Params(payload), decode_id=trans.security.decode_id)
return {'message': message}
except ActionInputError as e:
return message_exception(trans, e.err_msg)
return self.message_exception(trans, e.err_msg)
@web.expose_api
@web.require_admin
def rename_quota(self, trans, payload=None, **kwd):
id = kwd.get('id')
if not id:
return message_exception(trans, 'No quota id received for renaming.')
return self.message_exception(trans, 'No quota id received for renaming.')
quota = get_quota(trans, id)
if trans.request.method == 'GET':
return {
@@ -644,14 +644,14 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
try:
return {'message': self._rename_quota(quota, util.Params(payload))}
except ActionInputError as e:
return message_exception(trans, e.err_msg)
return self.message_exception(trans, e.err_msg)
@web.expose_api
@web.require_admin
def manage_users_and_groups_for_quota(self, trans, payload=None, **kwd):
quota_id = kwd.get('id')
if not quota_id:
return message_exception(trans, 'Invalid quota id (%s) received' % str(quota_id))
return self.message_exception(trans, 'Invalid quota id (%s) received' % str(quota_id))
quota = get_quota(trans, quota_id)
if trans.request.method == 'GET':
in_users = []
@@ -680,14 +680,14 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
try:
return {'message': self._manage_users_and_groups_for_quota(quota, util.Params(payload), decode_id=trans.security.decode_id)}
except ActionInputError as e:
return message_exception(trans, e.err_msg)
return self.message_exception(trans, e.err_msg)
@web.expose_api
@web.require_admin
def edit_quota(self, trans, payload=None, **kwd):
id = kwd.get('id')
if not id:
return message_exception(trans, 'No quota id received for renaming.')
return self.message_exception(trans, 'No quota id received for renaming.')
quota = get_quota(trans, id)
if trans.request.method == 'GET':
return {
@@ -708,14 +708,14 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
try:
return {'message': self._edit_quota(quota, util.Params(payload))}
except ActionInputError as e:
return message_exception(trans, e.err_msg)
return self.message_exception(trans, e.err_msg)
@web.expose_api
@web.require_admin
def set_quota_default(self, trans, payload=None, **kwd):
id = kwd.get('id')
if not id:
return message_exception(trans, 'No quota id received for renaming.')
return self.message_exception(trans, 'No quota id received for renaming.')
quota = get_quota(trans, id)
if trans.request.method == 'GET':
default_value = quota.default[0].type if quota.default else 'no'
@@ -736,7 +736,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
try:
return {'message': self._set_quota_default(quota, util.Params(payload))}
except ActionInputError as e:
return message_exception(trans, e.err_msg)
return self.message_exception(trans, e.err_msg)
@web.expose
@web.require_admin
@@ -984,11 +984,11 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))]
in_groups = [trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_groups'))]
if not name or not description:
return message_exception(trans, 'Enter a valid name and a description.')
return self.message_exception(trans, 'Enter a valid name and a description.')
elif trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == name).first():
return message_exception(trans, 'Role names must be unique and a role with that name already exists, so choose another name.')
return self.message_exception(trans, 'Role names must be unique and a role with that name already exists, so choose another name.')
elif None in in_users or None in in_groups:
return message_exception(trans, 'One or more invalid user/group id has been provided.')
return self.message_exception(trans, 'One or more invalid user/group id has been provided.')
else:
# Create the role
role = trans.app.model.Role(name=name, description=description, type=trans.app.model.Role.types.ADMIN)
@@ -1004,7 +1004,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
if auto_create_checked:
# Check if role with same name already exists
if trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name).first():
return message_exception(trans, 'A group with that name already exists, so choose another name or disable group creation.')
return self.message_exception(trans, 'A group with that name already exists, so choose another name or disable group creation.')
# Create the group
group = trans.app.model.Group(name=name)
trans.sa_session.add(group)
@@ -1025,7 +1025,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
def rename_role(self, trans, payload=None, **kwd):
id = kwd.get('id')
if not id:
return message_exception(trans, 'No role id received for renaming.')
return self.message_exception(trans, 'No role id received for renaming.')
role = get_role(trans, id)
if trans.request.method == 'GET':
return {
@@ -1045,11 +1045,11 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
new_name = util.restore_text(payload.get('name'))
new_description = util.restore_text(payload.get('description'))
if not new_name:
return message_exception(trans, 'Enter a valid role name.')
return self.message_exception(trans, 'Enter a valid role name.')
else:
existing_role = trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == new_name).first()
if existing_role and existing_role.id != role.id:
return message_exception(trans, 'A role with that name already exists.')
return self.message_exception(trans, 'A role with that name already exists.')
else:
if not (role.name == new_name and role.description == new_description):
role.name = new_name
@@ -1063,7 +1063,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
def manage_users_and_groups_for_role(self, trans, payload=None, **kwd):
role_id = kwd.get('id')
if not role_id:
return message_exception(trans, 'Invalid role id (%s) received' % str(role_id))
return self.message_exception(trans, 'Invalid role id (%s) received' % str(role_id))
role = get_role(trans, role_id)
if trans.request.method == 'GET':
in_users = []
@@ -1092,7 +1092,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))]
in_groups = [trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_groups'))]
if None in in_users or None in in_groups:
return message_exception(trans, 'One or more invalid user/group id has been provided.')
return self.message_exception(trans, 'One or more invalid user/group id has been provided.')
for ura in role.users:
user = trans.sa_session.query(trans.app.model.User).get(ura.user_id)
if user not in in_users:
@@ -1178,7 +1178,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
if 'operation' in kwargs:
id = kwargs.get('id')
if not id:
return message_exception(trans, 'Invalid group id (%s) received.' % str(id))
return self.message_exception(trans, 'Invalid group id (%s) received.' % str(id))
ids = util.listify(id)
operation = kwargs['operation'].lower().replace('+', ' ')
if operation == 'delete':
@@ -1198,7 +1198,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
def rename_group(self, trans, payload=None, **kwd):
id = kwd.get('id')
if not id:
return message_exception(trans, 'No group id received for renaming.')
return self.message_exception(trans, 'No group id received for renaming.')
group = get_group(trans, id)
if trans.request.method == 'GET':
return {
@@ -1213,11 +1213,11 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
old_name = group.name
new_name = util.restore_text(payload.get('name'))
if not new_name:
return message_exception(trans, 'Enter a valid group name.')
return self.message_exception(trans, 'Enter a valid group name.')
else:
existing_group = trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == new_name).first()
if existing_group and existing_group.id != group.id:
return message_exception(trans, 'A group with that name already exists.')
return self.message_exception(trans, 'A group with that name already exists.')
else:
if not (group.name == new_name):
group.name = new_name
@@ -1230,7 +1230,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
def manage_users_and_roles_for_group(self, trans, payload=None, **kwd):
group_id = kwd.get('id')
if not group_id:
return message_exception(trans, 'Invalid group id (%s) received' % str(group_id))
return self.message_exception(trans, 'Invalid group id (%s) received' % str(group_id))
group = get_group(trans, group_id)
if trans.request.method == 'GET':
in_users = []
@@ -1259,7 +1259,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))]
in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))]
if None in in_users or None in in_roles:
return message_exception(trans, 'One or more invalid user/role id has been provided.')
return self.message_exception(trans, 'One or more invalid user/role id has been provided.')
trans.app.security_agent.set_entity_group_associations(groups=[group], users=in_users, roles=in_roles)
trans.sa_session.refresh(group)
return {'message' : 'Group \'%s\' has been updated with %d associated users and %d associated roles.' % (group.name, len(in_users), len(in_roles))}
@@ -1297,11 +1297,11 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))]
in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))]
if not name:
return message_exception(trans, 'Enter a valid name.')
return self.message_exception(trans, 'Enter a valid name.')
elif trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name).first():
return message_exception(trans, 'Group names must be unique and a group with that name already exists, so choose another name.')
return self.message_exception(trans, 'Group names must be unique and a group with that name already exists, so choose another name.')
elif None in in_users or None in in_roles:
return message_exception(trans, 'One or more invalid user/role id has been provided.')
return self.message_exception(trans, 'One or more invalid user/role id has been provided.')
else:
# Create the role
group = trans.app.model.Group(name=name)
@@ -1317,7 +1317,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
if auto_create_checked:
# Check if role with same name already exists
if trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == name).first():
return message_exception(trans, 'A role with that name already exists, so choose another name or disable role creation.')
return self.message_exception(trans, 'A role with that name already exists, so choose another name or disable role creation.')
# Create the role
role = trans.app.model.Role(name=name, description='Role for group %s' % name)
trans.sa_session.add(role)
@@ -1396,16 +1396,16 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
password = payload.get('password')
confirm = payload.get('confirm')
if len(password) < 6:
return message_exception(trans, 'Use a password of at least 6 characters.')
return self.message_exception(trans, 'Use a password of at least 6 characters.')
elif password != confirm:
return message_exception(trans, 'Passwords do not match.')
return self.message_exception(trans, 'Passwords do not match.')
for user in users.itervalues():
user.set_password_cleartext(password)
trans.sa_session.add(user)
trans.sa_session.flush()
return {'message': 'Passwords reset for %d user(s).' % len(users)}
else:
return message_exception(trans, 'Please specify user ids.')
return self.message_exception(trans, 'Please specify user ids.')
def _delete_user(self, trans, ids):
message = 'Deleted %d users: ' % len(ids)
@@ -1510,7 +1510,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
def manage_roles_and_groups_for_user(self, trans, payload=None, **kwd):
user_id = kwd.get('id')
if not user_id:
return message_exception(trans, 'Invalid user id (%s) received' % str(user_id))
return self.message_exception(trans, 'Invalid user id (%s) received' % str(user_id))
user = get_user(trans, user_id)
if trans.request.method == 'GET':
in_roles = []
@@ -1542,7 +1542,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))]
in_groups = [trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_groups'))]
if None in in_groups or None in in_roles:
return message_exception(trans, 'One or more invalid role/group id has been provided.')
return self.message_exception(trans, 'One or more invalid role/group id has been provided.')
# make sure the user is not dis-associating himself from his private role
private_role = trans.app.security_agent.get_private_user_role(user)
@@ -1715,11 +1715,6 @@ def build_select_input(name, label, options, value):
'value' : value}
def message_exception(trans, message):
trans.response.status = 400
return {'err_msg': sanitize_text(message)}
def get_user(trans, user_id):
"""Get a User from the database by id."""
user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
lib/galaxy/webapps/galaxy/controllers/forms.py
+4 -9
View File
@@ -87,7 +87,7 @@ class Forms(BaseUIController):
if 'operation' in kwd:
id = kwd.get('id')
if not id:
return message_exception(trans, 'Invalid form id (%s) received.' % str(id))
return self.message_exception(trans, 'Invalid form id (%s) received.' % str(id))
ids = util.listify(id)
operation = kwd['operation'].lower()
if operation == 'delete':
@@ -147,7 +147,7 @@ class Forms(BaseUIController):
index = index + 1
new_form, message = self.save_form_definition(trans, None, payload)
if new_form is None:
return message_exception(trans, message)
return self.message_exception(trans, message)
imported = (' with %i imported fields' % index) if index > 0 else ''
message = 'The form \'%s\' has been created%s.' % (payload.get('name'), imported)
return {'message': util.sanitize_text(message)}
@@ -157,7 +157,7 @@ class Forms(BaseUIController):
def edit_form(self, trans, payload=None, **kwd):
id = kwd.get('id')
if not id:
return message_exception(trans, 'No form id received for editing.')
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':
@@ -232,7 +232,7 @@ class Forms(BaseUIController):
else:
new_form, message = self.save_form_definition(trans, id, payload)
if new_form is None:
return message_exception(trans, message)
return self.message_exception(trans, message)
message = 'The form \'%s\' has been updated.' % payload.get('name')
return {'message': util.sanitize_text(message)}
@@ -331,11 +331,6 @@ class Forms(BaseUIController):
# ---- Utility methods -------------------------------------------------------
def message_exception(trans, message):
trans.response.status = 400
return {'err_msg': util.sanitize_text(message)}
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))
lib/galaxy/webapps/galaxy/controllers/history.py
+1 -6
View File
@@ -1245,7 +1245,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
def rename(self, trans, payload=None, **kwd):
id = kwd.get('id')
if not id:
return message_exception(trans, 'No history id received for renaming.')
return self.message_exception(trans, 'No history id received for renaming.')
user = trans.get_user()
id = listify(id)
histories = []
@@ -1330,8 +1330,3 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
new_history = trans.new_history(name)
return self.history_data(trans, new_history)
# TODO: /history/current to do all of the above: if ajax, return json; if post, read id and set to current
def message_exception(trans, message):
trans.response.status = 400
return {'err_msg': sanitize_text(message)}
lib/galaxy/webapps/galaxy/controllers/page.py
+101 -93
View File
@@ -32,7 +32,7 @@ class PageListGrid(grids.Grid):
default_filter = {"published": "All", "tags": "All", "title": "All", "sharing": "All"}
default_sort_key = "-update_time"
columns = [
grids.TextColumn("Title", key="title", attach_popup=True, filterable="advanced"),
grids.TextColumn("Title", key="title", attach_popup=True, filterable="advanced", link=(lambda item: dict(action="display_by_username_and_slug", username=item.user.username, slug=item.slug))),
URLColumn("Public URL"),
grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced"),
grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid"),
@@ -45,13 +45,13 @@ class PageListGrid(grids.Grid):
cols_to_filter=[columns[0], columns[2]],
key="free-text-search", visible=False, filterable="standard"))
global_actions = [
grids.GridAction("Add new page", dict(action='create'), target="inbound")
grids.GridAction("Add new page", dict(controller="", action="pages/create"))
]
operations = [
grids.DisplayByUsernameAndSlugGridOperation("View", allow_multiple=False),
grids.GridOperation("Edit content", allow_multiple=False, url_args=dict(action='edit_content')),
grids.GridOperation("Edit attributes", allow_multiple=False, url_args=dict(action='edit')),
grids.GridOperation("Share or Publish", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(action='sharing')),
grids.GridOperation("Edit content", allow_multiple=False, url_args=dict(action="edit_content")),
grids.GridOperation("Edit attributes", allow_multiple=False, url_args=dict(controller="", action="pages/edit")),
grids.GridOperation("Share or Publish", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(action="sharing")),
grids.GridOperation("Delete", confirm="Are you sure you want to delete this page?"),
]
@@ -348,107 +348,115 @@ class PageController(BaseUIController, SharableMixin,
'slug' : p.page.slug,
'title' : p.page.title} for p in shared_by_others]
@web.expose
@web.expose_api
@web.require_login("create pages")
def create(self, trans, page_title="", page_slug="", page_annotation=""):
def create(self, trans, payload=None, **kwd):
"""
Create a new page
Create a new page.
"""
user = trans.get_user()
page_title_err = page_slug_err = page_annotation_err = ""
if trans.request.method == "POST":
if not page_title:
page_title_err = "Page name is required"
elif not page_slug:
page_slug_err = "Page id is required"
elif not self._is_valid_slug(page_slug):
page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character"
elif trans.sa_session.query(model.Page).filter_by(user=user, slug=page_slug, deleted=False).first():
page_slug_err = "Page id must be unique"
if trans.request.method == 'GET':
return {
'title' : 'Create a new page',
'inputs' : [{
'name' : 'title',
'label' : 'Name'
}, {
'name' : 'slug',
'label' : 'Identifier',
'help' : 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).'
}, {
'name' : 'annotation',
'label' : 'Annotation',
'help' : 'A description of the page. The annotation is shown alongside published pages.'
}]
}
else:
user = trans.get_user()
p_title = payload.get('title')
p_slug = payload.get('slug')
p_annotation = payload.get('annotation')
if not p_title:
return self.message_exception(trans, 'Please provide a page name is required.')
elif not p_slug:
return self.message_exception(trans, 'Please provide a unique identifier.')
elif not self._is_valid_slug(p_slug):
return self.message_exception(trans, 'Page identifier can only contain lowercase letters, numbers, and dashes (-).')
elif trans.sa_session.query(model.Page).filter_by(user=user, slug=p_slug, deleted=False).first():
return self.message_exception(trans, 'Page id must be unique.')
else:
# Create the new stored page
page = model.Page()
page.title = page_title
page.slug = page_slug
page_annotation = sanitize_html(page_annotation, 'utf-8', 'text/html')
self.add_item_annotation(trans.sa_session, trans.get_user(), page, page_annotation)
page.user = user
p = model.Page()
p.title = p_title
p.slug = p_slug
p.user = user
if p_annotation:
p_annotation = sanitize_html(p_annotation, 'utf-8', 'text/html')
self.add_item_annotation(trans.sa_session, user, p, p_annotation)
# And the first (empty) page revision
page_revision = model.PageRevision()
page_revision.title = page_title
page_revision.page = page
page.latest_revision = page_revision
page_revision.content = ""
p_revision = model.PageRevision()
p_revision.title = p_title
p_revision.page = p
p.latest_revision = p_revision
p_revision.content = ""
# Persist
session = trans.sa_session
session.add(page)
session.flush()
# Display the management page
# trans.set_message( "Page '%s' created" % page.title )
return trans.response.send_redirect(web.url_for(controller='pages', action='list'))
return trans.show_form(
web.FormBuilder(web.url_for(controller='page', action='create'), "Create new page", submit_text="Submit")
.add_text("page_title", "Page title", value=page_title, error=page_title_err)
.add_text("page_slug", "Page identifier", value=page_slug, error=page_slug_err,
help="""A unique identifier that will be used for
public links to this page. A default is generated
from the page title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""")
.add_text("page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err,
help="A description of the page; annotation is shown alongside published pages."),
template="page/create.mako")
trans.sa_session.add(p)
trans.sa_session.flush()
return {'message': 'Page \'%s\' successfully created.' % p.title, 'status': 'success'}
@web.expose
@web.expose_api
@web.require_login("edit pages")
def edit(self, trans, id, page_title="", page_slug="", page_annotation=""):
def edit(self, trans, payload=None, **kwd):
"""
Edit a page's attributes.
"""
encoded_id = id
id = self.decode_id(id)
session = trans.sa_session
page = session.query(model.Page).get(id)
user = trans.user
assert page.user == user
page_title_err = page_slug_err = page_annotation_err = ""
if trans.request.method == "POST":
if not page_title:
page_title_err = "Page name is required"
elif not page_slug:
page_slug_err = "Page id is required"
elif not self._is_valid_slug(page_slug):
page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character"
elif page_slug != page.slug and trans.sa_session.query(model.Page).filter_by(user=user, slug=page_slug, deleted=False).first():
page_slug_err = "Page id must be unique"
elif not page_annotation:
page_annotation_err = "Page annotation is required"
else:
page.title = page_title
page.slug = page_slug
page_annotation = sanitize_html(page_annotation, 'utf-8', 'text/html')
self.add_item_annotation(trans.sa_session, trans.get_user(), page, page_annotation)
session.flush()
# Redirect to page list.
return trans.response.send_redirect(web.url_for(controller='pages', action='list'))
id = kwd.get('id')
if not id:
return self.message_exception(trans, 'No page id received for editing.')
decoded_id = self.decode_id(id)
user = trans.get_user()
p = trans.sa_session.query(model.Page).get(decoded_id)
if trans.request.method == 'GET':
if p.slug is None:
self.create_item_slug(trans.sa_session, p)
return {
'title' : 'Edit page attributes',
'inputs' : [{
'name' : 'title',
'label' : 'Name',
'value' : p.title
}, {
'name' : 'slug',
'label' : 'Identifier',
'value' : p.slug,
'help' : 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).'
}, {
'name' : 'annotation',
'label' : 'Annotation',
'value' : self.get_item_annotation_str(trans.sa_session, user, p),
'help' : 'A description of the page. The annotation is shown alongside published pages.'
}]
}
else:
page_title = page.title
page_slug = page.slug
page_annotation = self.get_item_annotation_str(trans.sa_session, trans.user, page)
if not page_annotation:
page_annotation = ""
return trans.show_form(
web.FormBuilder(web.url_for(controller='page', action='edit', id=encoded_id), "Edit page attributes", submit_text="Submit")
.add_text("page_title", "Page title", value=page_title, error=page_title_err)
.add_text("page_slug", "Page identifier", value=page_slug, error=page_slug_err,
help="""A unique identifier that will be used for
public links to this page. A default is generated
from the page title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""")
.add_text("page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err,
help="A description of the page; annotation is shown alongside published pages."),
template="page/create.mako")
p_title = payload.get('title')
p_slug = payload.get('slug')
p_annotation = payload.get('annotation')
if not p_title:
return self.message_exception(trans, 'Please provide a page name is required.')
elif not p_slug:
return self.message_exception(trans, 'Please provide a unique identifier.')
elif not self._is_valid_slug(p_slug):
return self.message_exception(trans, 'Page identifier can only contain lowercase letters, numbers, and dashes (-).')
elif p_slug != p.slug and trans.sa_session.query(model.Page).filter_by(user=p.user, slug=p_slug, deleted=False).first():
return self.message_exception(trans, 'Page id must be unique.')
else:
p.title = p_title
p.slug = p_slug
if p_annotation:
p_annotation = sanitize_html(p_annotation, 'utf-8', 'text/html')
self.add_item_annotation(trans.sa_session, user, p, p_annotation)
trans.sa_session.add(p)
trans.sa_session.flush()
return {'message': 'Attributes of \'%s\' successfully saved.' % p.title, 'status': 'success'}
@web.expose
@web.require_login("edit pages")
lib/galaxy/webapps/galaxy/controllers/visualization.py
+6 -11
View File
@@ -570,7 +570,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
"""
id = kwd.get('id')
if not id:
return message_exception(trans, 'No visualization id received for editing.')
return self.message_exception(trans, 'No visualization id received for editing.')
v = self.get_visualization(trans, id, check_ownership=True)
if trans.request.method == 'GET':
if v.slug is None:
@@ -585,7 +585,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
'name' : 'slug',
'label' : 'Identifier',
'value' : v.slug,
'help' : 'A unique identifier that will be used for public links to this visualization. A default is generated from the visualization title, but can be edited. This field must contain only lowercase letters, numbers, and the \'-\' character.'
'help' : 'A unique identifier that will be used for public links to this visualization. This field can only contain lowercase letters, numbers, and dashes (-).'
}, {
'name' : 'dbkey',
'label' : 'Build',
@@ -607,13 +607,13 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
v_dbkey = payload.get('dbkey')
v_annotation = payload.get('annotation')
if not v_title:
return message_exception(trans, 'Please provide a visualization name is required.')
return self.message_exception(trans, 'Please provide a visualization name is required.')
elif not v_slug:
return message_exception(trans, 'Please provide a unique identifier.')
return self.message_exception(trans, 'Please provide a unique identifier.')
elif not self._is_valid_slug(v_slug):
return message_exception(trans, 'Visualization identifier must consist of only lowercase letters, numbers, and the \'-\' character.')
return self.message_exception(trans, 'Visualization identifier can only contain lowercase letters, numbers, and dashes (-).')
elif v_slug != v.slug and trans.sa_session.query(model.Visualization).filter_by(user=v.user, slug=v_slug, deleted=False).first():
return message_exception(trans, 'Visualization id must be unique.')
return self.message_exception(trans, 'Visualization id must be unique.')
else:
v.title = v_title
v.slug = v_slug
@@ -967,8 +967,3 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
name = fields[4]
rows.append([location, name])
return {'data': rows}
def message_exception(trans, message):
trans.response.status = 400
return {'err_msg': sanitize_text(message)}
static/scripts/bundled/analysis.bundled.js
+5 -5
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static/scripts/bundled/analysis.bundled.js.map
+1 -1
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static/scripts/bundled/libs.bundled.js.map
+1 -1
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templates/webapps/galaxy/page/create.mako
-14
View File
@@ -1,14 +0,0 @@
<%inherit file="/form.mako"/>
<%def name="javascripts()">
${parent.javascripts()}
<script type="text/javascript">
$(function(){
var page_name = $("input[name=page_title]");
var page_slug = $("input[name=page_slug]");
page_name.keyup(function(){
page_slug.val( $(this).val().replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() )
});
})
</script>
</%def>