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Source code for galaxy.webapps.galaxy.controllers.page
from markupsafe import escape
from sqlalchemy import (
and_,
desc,
false,
true
)
from sqlalchemy.orm import (
eagerload,
undefer
)
from galaxy import (
exceptions,
model,
util,
web
)
from galaxy.managers.hdas import HDAManager
from galaxy.managers.histories import HistoryManager, HistorySerializer
from galaxy.managers.pages import (
get_page_identifiers,
PageContentProcessor,
PageManager,
)
from galaxy.model.item_attrs import UsesItemRatings
from galaxy.util import unicodify
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import (
error,
url_for
)
from galaxy.web.framework.helpers import (
grids,
time_ago
)
from galaxy.webapps.base.controller import (
BaseUIController,
SharableMixin,
UsesStoredWorkflowMixin,
UsesVisualizationMixin
)
[docs]class PageListGrid(grids.Grid):
# Custom column.
[docs] class URLColumn(grids.PublicURLColumn):
[docs] def get_value(self, trans, grid, item):
return url_for(controller='page', action='display_by_username_and_slug', username=item.user.username, slug=item.slug)
# Grid definition
use_panels = True
title = "Pages"
model_class = model.Page
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", 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"),
grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False),
grids.GridColumn("Created", key="create_time", format=time_ago),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
]
columns.append(grids.MulticolFilterColumn(
"Search",
cols_to_filter=[columns[0], columns[2]],
key="free-text-search", visible=False, filterable="standard"))
global_actions = [
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(controller="", action="pages/edit")),
grids.GridOperation("Share or Publish", allow_multiple=False, condition=(lambda item: not item.deleted), url_args=dict(controller="", action="pages/sharing")),
grids.GridOperation("Delete", confirm="Are you sure you want to delete this page?"),
]
[docs] def apply_query_filter(self, trans, query, **kwargs):
return query.filter_by(user=trans.user, deleted=False)
[docs]class PageAllPublishedGrid(grids.Grid):
# Grid definition
use_panels = True
title = "Published Pages"
model_class = model.Page
default_sort_key = "update_time"
default_filter = dict(title="All", username="All")
columns = [
grids.PublicURLColumn("Title", key="title", filterable="advanced"),
grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced"),
grids.OwnerColumn("Owner", key="username", model_class=model.User, filterable="advanced"),
grids.CommunityRatingColumn("Community Rating", key="rating"),
grids.CommunityTagsColumn("Community Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid"),
grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago)
]
columns.append(
grids.MulticolFilterColumn(
"Search title, annotation, owner, and tags",
cols_to_filter=[columns[0], columns[1], columns[2], columns[4]],
key="free-text-search", visible=False, filterable="standard")
)
[docs] def build_initial_query(self, trans, **kwargs):
# See optimization description comments and TODO for tags in matching public histories query.
return trans.sa_session.query(self.model_class).join("user").options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
[docs] def apply_query_filter(self, trans, query, **kwargs):
return query.filter(self.model_class.deleted == false()).filter(self.model_class.published == true())
[docs]class ItemSelectionGrid(grids.Grid):
""" Base class for pages' item selection grids. """
# Custom columns.
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, item):
if hasattr(item, "get_display_name"):
return escape(item.get_display_name())
else:
return escape(item.name)
# Grid definition.
show_item_checkboxes = True
default_filter = {"deleted": "False", "sharing": "All"}
default_sort_key = "-update_time"
use_paging = True
num_rows_per_page = 10
[docs] def apply_query_filter(self, trans, query, **kwargs):
return query.filter_by(user=trans.user)
[docs]class HistorySelectionGrid(ItemSelectionGrid):
""" Grid for selecting histories. """
# Grid definition.
title = "Saved Histories"
model_class = model.History
columns = [
ItemSelectionGrid.NameColumn("Name", key="name", filterable="advanced"),
grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False, visible=False),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search", visible=False, filterable="standard")
)
[docs] def apply_query_filter(self, trans, query, **kwargs):
return query.filter_by(user=trans.user, purged=False)
[docs]class HistoryDatasetAssociationSelectionGrid(ItemSelectionGrid):
""" Grid for selecting HDAs. """
# Grid definition.
title = "Saved Datasets"
model_class = model.HistoryDatasetAssociation
columns = [
ItemSelectionGrid.NameColumn("Name", key="name", filterable="advanced"),
grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False, visible=False),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search", visible=False, filterable="standard")
)
[docs] def apply_query_filter(self, trans, query, **kwargs):
# To filter HDAs by user, need to join HDA and History table and then filter histories by user. This is necessary because HDAs do not have
# a user relation.
return query.select_from(model.HistoryDatasetAssociation.table.join(model.History.table)).filter(model.History.user == trans.user)
[docs]class WorkflowSelectionGrid(ItemSelectionGrid):
""" Grid for selecting workflows. """
# Grid definition.
title = "Saved Workflows"
model_class = model.StoredWorkflow
columns = [
ItemSelectionGrid.NameColumn("Name", key="name", filterable="advanced"),
grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False, visible=False),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search", visible=False, filterable="standard")
)
[docs]class PageSelectionGrid(ItemSelectionGrid):
""" Grid for selecting pages. """
# Grid definition.
title = "Saved Pages"
model_class = model.Page
columns = [
grids.TextColumn("Title", key="title", filterable="advanced"),
grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False, visible=False),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search", visible=False, filterable="standard")
)
[docs]class VisualizationSelectionGrid(ItemSelectionGrid):
""" Grid for selecting visualizations. """
# Grid definition.
title = "Saved Visualizations"
model_class = model.Visualization
columns = [
grids.TextColumn("Title", key="title", filterable="advanced"),
grids.TextColumn("Type", key="type"),
grids.IndividualTagsColumn("Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid"),
grids.SharingStatusColumn("Sharing", key="sharing", filterable="advanced", sortable=False),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[columns[0], columns[2]],
key="free-text-search", visible=False, filterable="standard")
)
# Adapted from the _BaseHTMLProcessor class of https://github.com/kurtmckee/feedparser
[docs]class PageController(BaseUIController, SharableMixin,
UsesStoredWorkflowMixin, UsesVisualizationMixin, UsesItemRatings):
_page_list = PageListGrid()
_all_published_list = PageAllPublishedGrid()
_history_selection_grid = HistorySelectionGrid()
_workflow_selection_grid = WorkflowSelectionGrid()
_datasets_selection_grid = HistoryDatasetAssociationSelectionGrid()
_page_selection_grid = PageSelectionGrid()
_visualization_selection_grid = VisualizationSelectionGrid()
[docs] def __init__(self, app):
super(PageController, self).__init__(app)
self.page_manager = PageManager(app)
self.history_manager = HistoryManager(app)
self.history_serializer = HistorySerializer(self.app)
self.hda_manager = HDAManager(app)
[docs] @web.expose
@web.json
@web.require_login()
def list(self, trans, *args, **kwargs):
""" List user's pages. """
# Handle operation
if 'operation' in kwargs and 'id' in kwargs:
session = trans.sa_session
operation = kwargs['operation'].lower()
ids = util.listify(kwargs['id'])
for id in ids:
item = session.query(model.Page).get(self.decode_id(id))
if operation == "delete":
item.deleted = True
session.flush()
# Build grid dictionary.
grid = self._page_list(trans, *args, **kwargs)
grid['shared_by_others'] = self._get_shared(trans)
return grid
[docs] @web.expose
@web.json
def list_published(self, trans, *args, **kwargs):
grid = self._all_published_list(trans, *args, **kwargs)
grid['shared_by_others'] = self._get_shared(trans)
return grid
def _get_shared(self, trans):
"""Identify shared pages"""
shared_by_others = trans.sa_session \
.query(model.PageUserShareAssociation) \
.filter_by(user=trans.get_user()) \
.join(model.Page.table) \
.filter(model.Page.deleted == false()) \
.order_by(desc(model.Page.update_time)) \
.all()
return [{'username' : p.page.user.username,
'slug' : p.page.slug,
'title' : p.page.title} for p in shared_by_others]
[docs] @web.legacy_expose_api
@web.require_login("create pages")
def create(self, trans, payload=None, **kwd):
"""
Create a new page.
"""
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:
try:
page = self.page_manager.create(trans, payload)
except exceptions.MessageException as e:
return self.message_exception(trans, unicodify(e))
return {'message': 'Page \'%s\' successfully created.' % page.title, 'status': 'success'}
[docs] @web.legacy_expose_api
@web.require_login("edit pages")
def edit(self, trans, payload=None, **kwd):
"""
Edit a page's attributes.
"""
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:
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)
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'}
[docs] @web.expose
@web.require_login("edit pages")
def edit_content(self, trans, id):
"""
Render the main page editor interface.
"""
id = self.decode_id(id)
page = trans.sa_session.query(model.Page).get(id)
assert page.user == trans.user
return trans.fill_template("page/editor.mako", page=page)
[docs] @web.expose
@web.require_login()
def save(self, trans, id, content):
id = self.decode_id(id)
page = trans.sa_session.query(model.Page).get(id)
assert page.user == trans.user
self.page_manager.save_new_revision(trans, page, {"content": content})
[docs] @web.expose
@web.require_login()
def display(self, trans, id):
id = self.decode_id(id)
page = trans.sa_session.query(model.Page).get(id)
if not page:
raise web.httpexceptions.HTTPNotFound()
return self.display_by_username_and_slug(trans, page.user.username, page.slug)
[docs] @web.expose
def display_by_username_and_slug(self, trans, username, slug):
""" Display page based on a username and slug. """
# Get page.
session = trans.sa_session
user = session.query(model.User).filter_by(username=username).first()
page = trans.sa_session.query(model.Page).filter_by(user=user, slug=slug, deleted=False).first()
if page is None:
raise web.httpexceptions.HTTPNotFound()
# Security check raises error if user cannot access page.
self.security_check(trans, page, False, True)
# Process page content.
processor = PageContentProcessor(trans, self._get_embed_html)
processor.feed(page.latest_revision.content)
# Output is string, so convert to unicode for display.
page_content = unicodify(processor.output(), 'utf-8')
# Get rating data.
user_item_rating = 0
if trans.get_user():
user_item_rating = self.get_user_item_rating(trans.sa_session, trans.get_user(), page)
if user_item_rating:
user_item_rating = user_item_rating.rating
else:
user_item_rating = 0
ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, page)
return trans.fill_template_mako("page/display.mako", item=page,
item_data=page_content,
user_item_rating=user_item_rating,
ave_item_rating=ave_item_rating,
num_ratings=num_ratings,
content_only=True)
[docs] @web.expose
@web.require_login("use Galaxy pages")
def set_accessible_async(self, trans, id=None, accessible=False):
""" Set page's importable attribute and slug. """
page = self.get_page(trans, id)
# Only set if importable value would change; this prevents a change in the update_time unless attribute really changed.
importable = accessible in ['True', 'true', 't', 'T']
if page.importable != importable:
if importable:
self._make_item_accessible(trans.sa_session, page)
else:
page.importable = importable
trans.sa_session.flush()
return
[docs] @web.expose
@web.require_login("rate items")
@web.json
def rate_async(self, trans, id, rating):
""" Rate a page asynchronously and return updated community data. """
page = self.get_page(trans, id, check_ownership=False, check_accessible=True)
if not page:
return trans.show_error_message("The specified page does not exist.")
# Rate page.
self.rate_item(trans.sa_session, trans.get_user(), page, rating)
return self.get_ave_item_rating_data(trans.sa_session, page)
[docs] @web.expose
def get_embed_html_async(self, trans, id):
""" Returns HTML for embedding a workflow in a page. """
# TODO: user should be able to embed any item he has access to. see display_by_username_and_slug for security code.
page = self.get_page(trans, id)
if page:
return "Embedded Page '%s'" % page.title
[docs] @web.expose
@web.json
@web.require_login("use Galaxy pages")
def get_name_and_link_async(self, trans, id=None):
""" Returns page's name and link. """
page = self.get_page(trans, id)
if self.create_item_slug(trans.sa_session, page):
trans.sa_session.flush()
return_dict = {"name": page.title, "link": url_for(controller='page',
action="display_by_username_and_slug",
username=page.user.username,
slug=page.slug)}
return return_dict
[docs] @web.expose
@web.json
@web.require_login("select a history from saved histories")
def list_histories_for_selection(self, trans, **kwargs):
""" Returns HTML that enables a user to select one or more histories. """
return self._history_selection_grid(trans, **kwargs)
[docs] @web.expose
@web.json
@web.require_login("select a workflow from saved workflows")
def list_workflows_for_selection(self, trans, **kwargs):
""" Returns HTML that enables a user to select one or more workflows. """
return self._workflow_selection_grid(trans, **kwargs)
[docs] @web.expose
@web.json
@web.require_login("select a visualization from saved visualizations")
def list_visualizations_for_selection(self, trans, **kwargs):
""" Returns HTML that enables a user to select one or more visualizations. """
return self._visualization_selection_grid(trans, **kwargs)
[docs] @web.expose
@web.json
@web.require_login("select a page from saved pages")
def list_pages_for_selection(self, trans, **kwargs):
""" Returns HTML that enables a user to select one or more pages. """
return self._page_selection_grid(trans, **kwargs)
[docs] @web.expose
@web.json
@web.require_login("select a dataset from saved datasets")
def list_datasets_for_selection(self, trans, **kwargs):
""" Returns HTML that enables a user to select one or more datasets. """
return self._datasets_selection_grid(trans, **kwargs)
[docs] @web.expose
def get_editor_iframe(self, trans):
""" Returns the document for the page editor's iframe. """
return trans.fill_template("page/wymiframe.mako")
[docs] def get_page(self, trans, id, check_ownership=True, check_accessible=False):
"""Get a page from the database by id."""
# Load history from database
id = self.decode_id(id)
page = trans.sa_session.query(model.Page).get(id)
if not page:
error("Page not found")
else:
return self.security_check(trans, page, check_ownership, check_accessible)
def _get_embedded_history_html(self, trans, decoded_id):
"""
Returns html suitable for embedding in another page.
"""
# histories embedded in pages are set to importable when embedded, check for access here
history = self.history_manager.get_accessible(decoded_id, trans.user, current_history=trans.history)
# create ownership flag for template, dictify models
# note: adding original annotation since this is published - get_dict returns user-based annos
user_is_owner = trans.user == history.user
history.annotation = self.get_item_annotation_str(trans.sa_session, history.user, history)
# include all datasets: hidden, deleted, and purged
history_dictionary = self.history_serializer.serialize_to_view(
history, view='detailed', user=trans.user, trans=trans
)
contents = self.history_serializer.serialize_contents(history, 'contents', trans=trans, user=trans.user)
history_dictionary['annotation'] = history.annotation
filled = trans.fill_template("history/embed.mako",
item=history,
user_is_owner=user_is_owner,
history_dict=history_dictionary,
content_dicts=contents)
return filled
def _get_embedded_visualization_html(self, trans, encoded_id):
"""
Returns html suitable for embedding visualizations in another page.
"""
visualization = self.get_visualization(trans, encoded_id, False, True)
visualization.annotation = self.get_item_annotation_str(trans.sa_session, visualization.user, visualization)
if not visualization:
return None
# Fork to template based on visualization.type (registry or builtin).
if((trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins) and
(visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS)):
# if a registry visualization, load a version into an iframe :(
# TODO: simplest path from A to B but not optimal - will be difficult to do reg visualizations any other way
# TODO: this will load the visualization twice (once above, once when the iframe src calls 'saved')
encoded_visualization_id = trans.security.encode_id(visualization.id)
return trans.fill_template('visualization/embed_in_frame.mako',
item=visualization,
encoded_visualization_id=encoded_visualization_id,
content_only=True)
return trans.fill_template("visualization/embed.mako", item=visualization, item_data=None)
def _get_embed_html(self, trans, item_class, item_id):
""" Returns HTML for embedding an item in a page. """
item_class = self.get_class(item_class)
encoded_id, decoded_id = get_page_identifiers(item_id, trans.app)
if item_class == model.History:
return self._get_embedded_history_html(trans, decoded_id)
elif item_class == model.HistoryDatasetAssociation:
dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
dataset = self.hda_manager.error_if_uploading(dataset)
dataset.annotation = self.get_item_annotation_str(trans.sa_session, dataset.history.user, dataset)
if dataset:
data = self.hda_manager.text_data(dataset)
return trans.fill_template("dataset/embed.mako", item=dataset, item_data=data)
elif item_class == model.StoredWorkflow:
workflow = self.get_stored_workflow(trans, encoded_id, False, True)
workflow.annotation = self.get_item_annotation_str(trans.sa_session, workflow.user, workflow)
if workflow:
self.get_stored_workflow_steps(trans, workflow)
return trans.fill_template("workflow/embed.mako", item=workflow, item_data=workflow.latest_workflow.steps)
elif item_class == model.Visualization:
return self._get_embedded_visualization_html(trans, encoded_id)
elif item_class == model.Page:
pass