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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.managers.workflows import WorkflowsManager
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").filter( model.User.deleted == false()).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().__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)
[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': form_title = "Create new Page" title = "" slug = "" content = "" content_format_hide = False content_hide = True if "invocation_id" in kwd: invocation_id = kwd.get("invocation_id") form_title = form_title + " from Invocation Report" slug = "invocation-report-" + invocation_id invocation_report = self.workflow_manager.get_invocation_report(trans, invocation_id) title = invocation_report.get("title") content = invocation_report.get("markdown") content_format_hide = True content_hide = False return { 'title' : form_title, 'inputs' : [{ 'name' : 'title', 'label' : 'Name', 'value' : title, }, { '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 (-).', 'value' : slug, }, { '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', 'hidden' : content_format_hide, 'options' : [('Markdown', 'markdown'), ('HTML', 'html')], '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.' }, { 'name' : 'content', 'label' : 'Content', 'area' : True, 'value' : content, 'hidden' : content_hide, }] } 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. """ return trans.fill_template("page/editor.mako", id=id)
[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(f"Page '{page_title}' shared with user '{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 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) 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)
[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