Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.webapps.galaxy.controllers.page

import re
from json import loads

from markupsafe import escape
from six.moves.html_entities import name2codepoint
from six.moves.html_parser import HTMLParser
from sqlalchemy import (
    and_,
    desc,
    false,
    true
)
from sqlalchemy.orm import (
    eagerload,
    undefer
)

from galaxy import (
    managers,
    model,
    util,
    web
)
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.base.controller import (
    BaseUIController,
    SharableMixin,
    UsesStoredWorkflowMixin,
    UsesVisualizationMixin
)
from galaxy.web.framework.helpers import (
    grids,
    time_ago
)


# Copied from https://github.com/kurtmckee/feedparser
_cp1252 = {
    128: u'\u20ac',  # euro sign
    130: u'\u201a',  # single low-9 quotation mark
    131: u'\u0192',  # latin small letter f with hook
    132: u'\u201e',  # double low-9 quotation mark
    133: u'\u2026',  # horizontal ellipsis
    134: u'\u2020',  # dagger
    135: u'\u2021',  # double dagger
    136: u'\u02c6',  # modifier letter circumflex accent
    137: u'\u2030',  # per mille sign
    138: u'\u0160',  # latin capital letter s with caron
    139: u'\u2039',  # single left-pointing angle quotation mark
    140: u'\u0152',  # latin capital ligature oe
    142: u'\u017d',  # latin capital letter z with caron
    145: u'\u2018',  # left single quotation mark
    146: u'\u2019',  # right single quotation mark
    147: u'\u201c',  # left double quotation mark
    148: u'\u201d',  # right double quotation mark
    149: u'\u2022',  # bullet
    150: u'\u2013',  # en dash
    151: u'\u2014',  # em dash
    152: u'\u02dc',  # small tilde
    153: u'\u2122',  # trade mark sign
    154: u'\u0161',  # latin small letter s with caron
    155: u'\u203a',  # single right-pointing angle quotation mark
    156: u'\u0153',  # latin small ligature oe
    158: u'\u017e',  # latin small letter z with caron
    159: u'\u0178',  # latin capital letter y with diaeresis
}


PAGE_MAXRAW = 10**15


def _get_page_identifiers(item_id, app):
    # Assume if item id is integer and less than 10**15, it's unencoded.
    try:
        decoded_id = int(item_id)
        if decoded_id >= PAGE_MAXRAW:
            raise ValueError("Identifier larger than maximum expected raw int, must be already encoded.")
        encoded_id = app.security.encode_id(item_id)
    except ValueError:
        # It's an encoded id.
        encoded_id = item_id
        decoded_id = app.security.decode_id(item_id)
    return (encoded_id, decoded_id)


[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 class _PageContentProcessor(HTMLParser, object): """ Processes page content to produce HTML that is suitable for display. For now, processor renders embedded objects. """ bare_ampersand = re.compile(r"&(?!#\d+;|#x[0-9a-fA-F]+;|\w+;)") elements_no_end_tag = set([ 'area', 'base', 'basefont', 'br', 'col', 'command', 'embed', 'frame', 'hr', 'img', 'input', 'isindex', 'keygen', 'link', 'meta', 'param', 'source', 'track', 'wbr' ]) def __init__(self, trans, render_embed_html_fn): HTMLParser.__init__(self) self.trans = trans self.ignore_content = False self.num_open_tags_for_ignore = 0 self.render_embed_html_fn = render_embed_html_fn def reset(self): self.pieces = [] HTMLParser.reset(self) def _shorttag_replace(self, match): tag = match.group(1) if tag in self.elements_no_end_tag: return '<' + tag + ' />' else: return '<' + tag + '></' + tag + '>' def feed(self, data): data = re.compile(r'<!((?!DOCTYPE|--|\[))', re.IGNORECASE).sub(r'&lt;!\1', data) data = re.sub(r'<([^<>\s]+?)\s*/>', self._shorttag_replace, data) data = data.replace('&#39;', "'") data = data.replace('&#34;', '"') HTMLParser.feed(self, data) HTMLParser.close(self) def handle_starttag(self, tag, attrs): """ Called for each start tag attrs is a list of (attr, value) tuples, e.g. for <pre class='screen'>, tag='pre', attrs=[('class', 'screen')] """ # If ignoring content, just increment tag count and ignore. if self.ignore_content: self.num_open_tags_for_ignore += 1 return # Not ignoring tag; look for embedded content. embedded_item = False for attribute in attrs: if (attribute[0] == "class") and ("embedded-item" in attribute[1].split(" ")): embedded_item = True break # For embedded content, set ignore flag to ignore current content and add new content for embedded item. if embedded_item: # Set processing attributes to ignore content. self.ignore_content = True self.num_open_tags_for_ignore = 1 # Insert content for embedded element. for attribute in attrs: name = attribute[0] if name == "id": # ID has form '<class_name>-<encoded_item_id>' item_class, item_id = attribute[1].split("-") embed_html = self.render_embed_html_fn(self.trans, item_class, item_id) self.pieces.append(embed_html) return # Default behavior: not ignoring and no embedded content. uattrs = [] strattrs = '' if attrs: for key, value in attrs: value = value.replace('>', '&gt;').replace('<', '&lt;').replace('"', '&quot;') value = self.bare_ampersand.sub("&amp;", value) uattrs.append((key, value)) strattrs = ''.join(' %s="%s"' % (k, v) for k, v in uattrs) if tag in self.elements_no_end_tag: self.pieces.append('<%s%s />' % (tag, strattrs)) else: self.pieces.append('<%s%s>' % (tag, strattrs)) def handle_endtag(self, tag): """ Called for each end tag E.g. for </pre>, tag will be 'pre' """ # If ignoring content, see if current tag is the end of content to ignore. if self.ignore_content: self.num_open_tags_for_ignore -= 1 if self.num_open_tags_for_ignore == 0: # Done ignoring content. self.ignore_content = False return # Default behavior: reconstruct the original end tag. if tag not in self.elements_no_end_tag: self.pieces.append("</%s>" % tag) def handle_charref(self, ref): # called for each character reference, e.g. for '&#160;', ref will be '160' # Reconstruct the original character reference. ref = ref.lower() if ref.startswith('x'): value = int(ref[1:], 16) else: value = int(ref) if value in _cp1252: self.pieces.append('&#%s;' % hex(ord(_cp1252[value]))[1:]) else: self.pieces.append('&#%s;' % ref) def handle_entityref(self, ref): # called for each entity reference, e.g. for '&copy;', ref will be 'copy' # Reconstruct the original entity reference. if ref in name2codepoint or ref == 'apos': self.pieces.append('&%s;' % ref) else: self.pieces.append('&amp;%s' % ref) def handle_data(self, text): """ Called for each block of plain text Called outside of any tag and not containing any character or entity references. Store the original text verbatim. """ if self.ignore_content: return self.pieces.append(text) def handle_comment(self, text): # called for each HTML comment, e.g. <!-- insert Javascript code here --> # Reconstruct the original comment. self.pieces.append('<!--%s-->' % text) def handle_decl(self, text): # called for the DOCTYPE, if present, e.g. # <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" # "http://www.w3.org/TR/html4/loose.dtd"> # Reconstruct original DOCTYPE self.pieces.append('<!%s>' % text) def handle_pi(self, text): # called for each processing instruction, e.g. <?instruction> # Reconstruct original processing instruction. self.pieces.append('<?%s>' % text) def output(self): '''Return processed HTML as a single string''' return ''.join(self.pieces)
[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.history_manager = managers.histories.HistoryManager(app) self.history_serializer = managers.histories.HistorySerializer(self.app) self.hda_manager = managers.hdas.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.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: user = trans.get_user() p_title = payload.get('title') p_slug = payload.get('slug') p_annotation = payload.get('annotation') if not p_title: return self.message_exception(trans, 'Please provide a page name is required.') elif not p_slug: return self.message_exception(trans, 'Please provide a unique identifier.') elif not self._is_valid_slug(p_slug): return self.message_exception(trans, 'Page identifier can only contain lowercase letters, numbers, and dashes (-).') elif trans.sa_session.query(model.Page).filter_by(user=user, slug=p_slug, deleted=False).first(): return self.message_exception(trans, 'Page id must be unique.') else: # Create the new stored page p = model.Page() p.title = p_title p.slug = p_slug p.user = user if p_annotation: p_annotation = sanitize_html(p_annotation) self.add_item_annotation(trans.sa_session, user, p, p_annotation) # And the first (empty) page revision p_revision = model.PageRevision() p_revision.title = p_title p_revision.page = p p.latest_revision = p_revision p_revision.content = "" # Persist trans.sa_session.add(p) trans.sa_session.flush() return {'message': 'Page \'%s\' successfully created.' % p.title, 'status': 'success'}
[docs] @web.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 content = page.latest_revision.content processor = _PageContentProcessor(trans, _placeholderRenderForEdit) processor.feed(content) content = unicodify(processor.output(), 'utf-8') return trans.fill_template("page/editor.mako", page=page, content=content)
[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, annotations): id = self.decode_id(id) page = trans.sa_session.query(model.Page).get(id) assert page.user == trans.user # Sanitize content content = sanitize_html(content) processor = _PageContentProcessor(trans, _placeholderRenderForSave) processor.feed(content) # Output is string, so convert to unicode for saving. content = unicodify(processor.output(), 'utf-8') # Add a new revision to the page with the provided content. page_revision = model.PageRevision() page_revision.title = page.title page_revision.page = page page.latest_revision = page_revision page_revision.content = content # Save annotations. annotations = loads(annotations) for annotation_dict in annotations: item_id = self.decode_id(annotation_dict['item_id']) item_class = self.get_class(annotation_dict['item_class']) item = trans.sa_session.query(item_class).filter_by(id=item_id).first() if not item: raise RuntimeError("cannot find annotated item") text = sanitize_html(annotation_dict['text']) # Add/update annotation. if item_id and item_class and text: # Get annotation association. annotation_assoc_class = eval("model.%sAnnotationAssociation" % item_class.__name__) annotation_assoc = trans.sa_session.query(annotation_assoc_class).filter_by(user=trans.get_user()) if item_class == model.History.__class__: annotation_assoc = annotation_assoc.filter_by(history=item) elif item_class == model.HistoryDatasetAssociation.__class__: annotation_assoc = annotation_assoc.filter_by(hda=item) elif item_class == model.StoredWorkflow.__class__: annotation_assoc = annotation_assoc.filter_by(stored_workflow=item) elif item_class == model.WorkflowStep.__class__: annotation_assoc = annotation_assoc.filter_by(workflow_step=item) annotation_assoc = annotation_assoc.first() if not annotation_assoc: # Create association. annotation_assoc = annotation_assoc_class() item.annotations.append(annotation_assoc) annotation_assoc.user = trans.get_user() # Set annotation user text. annotation_assoc.annotation = text trans.sa_session.flush()
[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
PLACEHOLDER_TEMPLATE = '''<div class="embedded-item {class_shorthand_lower} placeholder" id="{item_class}-{item_id}"><p class="title">Embedded Galaxy {class_shorthand} - '{item_name}'</p><p class="content">[Do not edit this block; Galaxy will fill it in with the annotated {class_shorthand} when it is displayed]</p></div>''' # This is a mapping of the id portion of page contents to the cssclass/shortname. PAGE_CLASS_MAPPING = { 'History': 'History', 'HistoryDatasetAssociation': 'Dataset', 'StoredWorkflow': 'Workflow', 'Visualization': 'Visualization' } def _placeholderRenderForEdit(trans, item_class, item_id): return _placeholderRenderForSave(trans, item_class, item_id, encode=True) def _placeholderRenderForSave(trans, item_class, item_id, encode=False): encoded_item_id, decoded_item_id = _get_page_identifiers(item_id, trans.app) item_name = '' if item_class == 'History': history = trans.sa_session.query(trans.model.History).get(decoded_item_id) history = managers.base.security_check(trans, history, False, True) item_name = history.name elif item_class == 'HistoryDatasetAssociation': hda = trans.sa_session.query(trans.model.HistoryDatasetAssociation).get(decoded_item_id) hda_manager = managers.hdas.HDAManager(trans.app) hda = hda_manager.get_accessible(decoded_item_id, trans.user) item_name = hda.name elif item_class == 'StoredWorkflow': wf = trans.sa_session.query(trans.model.StoredWorkflow).get(decoded_item_id) wf = managers.base.security_check(trans, wf, False, True) item_name = wf.name elif item_class == 'Visualization': visualization = trans.sa_session.query(trans.model.Visualization).get(decoded_item_id) visualization = managers.base.security_check(trans, visualization, False, True) item_name = visualization.title class_shorthand = PAGE_CLASS_MAPPING[item_class] if encode: item_id = encoded_item_id else: item_id = decoded_item_id return PLACEHOLDER_TEMPLATE.format( item_class=item_class, class_shorthand=class_shorthand, class_shorthand_lower=class_shorthand.lower(), item_id=item_id, item_name=item_name )