def __init__(self, app):
super().__init__(app)
self.page_manager = PageManager(app)
self.history_manager = HistoryManager(app)
self.history_serializer = HistorySerializer(self.app)
self.hda_manager = HDAManager(app)
self.workflow_manager = WorkflowsManager(app)
class PageRevisionsController(BaseAPIController, SharableItemSecurityMixin,
UsesAnnotations, SharableMixin):
def __init__(self, app):
super(PageRevisionsController, self).__init__(app)
self.manager = PageManager(app)
@expose_api
def index(self, trans, page_id, **kwd):
"""
index( self, trans, page_id, **kwd )
* GET /api/pages/{page_id}/revisions
return a list of Page revisions
:param page_id: Display the revisions of Page with ID=page_id
:rtype: list
:returns: dictionaries containing different revisions of the page
"""
page = get_object(trans,
page_id,
'Page',
check_ownership=False,
check_accessible=True)
r = trans.sa_session.query(
trans.app.model.PageRevision).filter_by(page_id=page.id)
out = []
for page in r:
as_dict = self.encode_all_ids(trans, page.to_dict(), True)
self.manager.rewrite_content_for_export(trans, as_dict)
out.append(as_dict)
return out
@expose_api
def create(self, trans, page_id, payload, **kwd):
"""
create( self, trans, page_id, payload **kwd )
* POST /api/pages/{page_id}/revisions
Create a new revision for a page
:param page_id: Add revision to Page with ID=page_id
:param payload: A dictionary containing::
'title' = New title of the page
'content' = New content of the page
:rtype: dictionary
:returns: Dictionary with 'success' or 'error' element to indicate the result of the request
"""
page = get_object(trans, page_id, 'Page', check_ownership=True)
page_revision = self.manager.save_new_revision(trans, page, payload)
rval = self.encode_all_ids(trans,
page_revision.to_dict(view="element"), True)
self.manager.rewrite_content_for_export(trans, rval)
return rval
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)
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()
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)
@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
@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]
@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.'
}, {
'name' : 'content_format',
'label' : 'Content Format',
'type' : 'select',
'options' : [('HTML', 'html'), ('Markdown', 'markdown')],
'help' : 'Use the traditional rich HTML editor or the newer experimental Markdown editor to create the page content. The HTML editor has several known bugs, is unmaintained and pages created with it will be read-only in future releases of Galaxy.'
}]
}
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'}
@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'}
@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)
@web.expose
@web.require_login("use Galaxy pages")
def share(self, trans, id, email="", use_panels=False):
""" Handle sharing with an individual user. """
msg = mtype = None
page = trans.sa_session.query(model.Page).get(self.decode_id(id))
if email:
other = trans.sa_session.query(model.User) \
.filter(and_(model.User.table.c.email == email,
model.User.table.c.deleted == false())) \
.first()
if not other:
mtype = "error"
msg = ("User '%s' does not exist" % escape(email))
elif other == trans.get_user():
mtype = "error"
msg = ("You cannot share a page with yourself")
elif trans.sa_session.query(model.PageUserShareAssociation) \
.filter_by(user=other, page=page).count() > 0:
mtype = "error"
msg = ("Page already shared with '%s'" % escape(email))
else:
share = model.PageUserShareAssociation()
share.page = page
share.user = other
session = trans.sa_session
session.add(share)
self.create_item_slug(session, page)
session.flush()
page_title = escape(page.title)
other_email = escape(other.email)
trans.set_message("Page '%s' shared with user '%s'" % (page_title, other_email))
return trans.response.send_redirect(url_for("/pages/sharing?id=%s" % id))
return trans.fill_template("/ind_share_base.mako",
message=msg,
messagetype=mtype,
item=page,
email=email,
use_panels=use_panels)
@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)
@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)
latest_revision = page.latest_revision
if latest_revision.content_format == "html":
# 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')
template = "page/display.mako"
else:
page_content = trans.security.encode_id(page.id)
template = "page/display_markdown.mako"
# 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(template, 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)
@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
@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)
@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
@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
@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)
@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)
@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)
@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)
@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)
@web.expose
def get_editor_iframe(self, trans):
""" Returns the document for the page editor's iframe. """
return trans.fill_template("page/wymiframe.mako")
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_item(self, trans, id):
return self.get_page(trans, id)
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
def __init__(self, app):
super().__init__(app)
self.manager = PageManager(app)
def __init__(self, app):
super(PagesController, self).__init__(app)
self.manager = PageManager(app)
self.serializer = PageSerializer(app)
class PagesController(BaseAPIController, SharableItemSecurityMixin,
UsesAnnotations, SharableMixin):
"""
RESTful controller for interactions with pages.
"""
def __init__(self, app):
super(PagesController, self).__init__(app)
self.manager = PageManager(app)
self.serializer = PageSerializer(app)
@expose_api_anonymous_and_sessionless
def index(self, trans, deleted=False, **kwd):
"""
index( self, trans, deleted=False, **kwd )
* GET /api/pages
return a list of Pages viewable by the user
:param deleted: Display deleted pages
:rtype: list
:returns: dictionaries containing summary or detailed Page information
"""
out = []
if trans.user_is_admin:
r = trans.sa_session.query(trans.app.model.Page)
if not deleted:
r = r.filter_by(deleted=False)
for row in r:
out.append(self.encode_all_ids(trans, row.to_dict(), True))
else:
# Transaction user's pages (if any)
user = trans.get_user()
r = trans.sa_session.query(
trans.app.model.Page).filter_by(user=user)
if not deleted:
r = r.filter_by(deleted=False)
for row in r:
out.append(self.encode_all_ids(trans, row.to_dict(), True))
# Published pages from other users
r = trans.sa_session.query(trans.app.model.Page).filter(
trans.app.model.Page.user != user).filter_by(published=True)
if not deleted:
r = r.filter_by(deleted=False)
for row in r:
out.append(self.encode_all_ids(trans, row.to_dict(), True))
return out
@expose_api
def create(self, trans, payload, **kwd):
"""
create( self, trans, payload, **kwd )
* POST /api/pages
Create a page and return dictionary containing Page summary
:param payload: dictionary structure containing::
'slug' = The title slug for the page URL, must be unique
'title' = Title of the page
'content' = contents of the first page revision (type dependent on content_format)
'content_format' = 'html' or 'markdown'
'annotation' = Annotation that will be attached to the page
:rtype: dict
:returns: Dictionary return of the Page.to_dict call
"""
page = self.manager.create(trans, payload)
rval = self.encode_all_ids(trans, page.to_dict(), True)
rval['content'] = page.latest_revision.content
self.manager.rewrite_content_for_export(trans, rval)
return rval
@expose_api
def delete(self, trans, id, **kwd):
"""
delete( self, trans, id, **kwd )
* DELETE /api/pages/{id}
Create a page and return dictionary containing Page summary
:param id: ID of page to be deleted
:rtype: dict
:returns: Dictionary with 'success' or 'error' element to indicate the result of the request
"""
page = get_object(trans, id, 'Page', check_ownership=True)
# Mark a page as deleted
page.deleted = True
trans.sa_session.flush()
return '' # TODO: Figure out what to return on DELETE, document in guidelines!
@expose_api_anonymous_and_sessionless
def show(self, trans, id, **kwd):
"""
show( self, trans, id, **kwd )
* GET /api/pages/{id}
View a page summary and the content of the latest revision
:param id: ID of page to be displayed
:rtype: dict
:returns: Dictionary return of the Page.to_dict call with the 'content' field populated by the most recent revision
"""
page = get_object(trans,
id,
'Page',
check_ownership=False,
check_accessible=True)
rval = self.encode_all_ids(trans, page.to_dict(), True)
rval['content'] = page.latest_revision.content
rval['content_format'] = page.latest_revision.content_format
self.manager.rewrite_content_for_export(trans, rval)
return rval
@expose_api_raw_anonymous_and_sessionless
def show_pdf(self, trans, id, **kwd):
"""
show( self, trans, id, **kwd )
* GET /api/pages/{id}.pdf
View a page summary and the content of the latest revision as PDF.
:param id: ID of page to be displayed
:rtype: dict
:returns: Dictionary return of the Page.to_dict call with the 'content' field populated by the most recent revision
"""
page = get_object(trans,
id,
'Page',
check_ownership=False,
check_accessible=True)
if page.latest_revision.content_format != "markdown":
raise RequestParameterInvalidException(
"PDF export only allowed for Markdown based pages")
internal_galaxy_markdown = page.latest_revision.content
trans.response.set_content_type("application/pdf")
return internal_galaxy_markdown_to_pdf(trans, internal_galaxy_markdown,
'page')
def __init__(self, app):
super(PageRevisionsController, self).__init__(app)
self.manager = PageManager(app)
def __init__(self, app):
super().__init__(app)
self.manager = PageManager(app)
self.serializer = PageSerializer(app)