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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]def format_bool(b): if b: return "yes" else: return ""
[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("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)
[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("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)
[docs] 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