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Source code for galaxy.managers.visualizations

Manager and Serializers for Visualizations.

Visualizations are saved configurations/variables used to
reproduce a specific view in a Galaxy visualization.

import logging
from typing import (

from sqlalchemy import (
from sqlalchemy.orm import aliased

from galaxy import (
from galaxy.managers import (
from galaxy.managers.context import ProvidesUserContext
from galaxy.model.index_filter_util import (
from galaxy.schema.visualization import VisualizationIndexQueryPayload
from galaxy.structured_app import MinimalManagerApp
from galaxy.util.search import (

log = logging.getLogger(__name__)

    "title": "title",
    "slug": "slug",
    "tag": "tag",
    "user": "user",
    "u": "user",
    "s": "slug",
    "t": "tag",
    "is": "is",

[docs]class VisualizationManager(sharable.SharableModelManager): """ Handle operations outside and between visualizations and other models. """ # TODO: copy, revisions model_class = model.Visualization foreign_key_name = "visualization" user_share_model = model.VisualizationUserShareAssociation tag_assoc = model.VisualizationTagAssociation annotation_assoc = model.VisualizationAnnotationAssociation rating_assoc = model.VisualizationRatingAssociation
[docs] def index_query( self, trans: ProvidesUserContext, payload: VisualizationIndexQueryPayload, include_total_count: bool = False ) -> Tuple[List[model.Visualization], int]: show_deleted = payload.deleted show_own = payload.show_own show_published = payload.show_published show_shared = payload.show_shared is_admin = trans.user_is_admin user = trans.user if not user and not show_published: message = "Requires user to log in." raise exceptions.RequestParameterInvalidException(message) stmt = select(self.model_class) filters = [] if show_own or (not show_published and not show_shared and not is_admin): filters = [self.model_class.user == user] if show_published: filters.append(self.model_class.published == true()) if user and show_shared: filters.append(self.user_share_model.user == user) stmt = stmt.outerjoin(self.model_class.users_shared_with) stmt = stmt.where(or_(*filters)) if payload.user_id: stmt = stmt.where(self.model_class.user_id == payload.user_id) if payload.search: search_query = payload.search parsed_search = parse_filters_structured(search_query, INDEX_SEARCH_FILTERS) def p_tag_filter(term_text: str, quoted: bool): nonlocal stmt alias = aliased(model.VisualizationTagAssociation) stmt = stmt.outerjoin(self.model_class.tags.of_type(alias)) return tag_filter(alias, term_text, quoted) for term in parsed_search.terms: if isinstance(term, FilteredTerm): key = term.filter q = term.text if key == "tag": pg = p_tag_filter(term.text, term.quoted) stmt = stmt.where(pg) elif key == "title": stmt = stmt.where(text_column_filter(self.model_class.title, term)) elif key == "slug": stmt = stmt.where(text_column_filter(self.model_class.slug, term)) elif key == "user": stmt = append_user_filter(stmt, self.model_class, term) elif key == "is": if q == "deleted": show_deleted = True if q == "published": stmt = stmt.where(self.model_class.published == true()) if q == "importable": stmt = stmt.where(self.model_class.importable == true()) elif q == "shared_with_me": if not show_shared: message = "Can only use tag is:shared_with_me if show_shared parameter also true." raise exceptions.RequestParameterInvalidException(message) stmt = stmt.where(self.user_share_model.user == user) elif isinstance(term, RawTextTerm): tf = p_tag_filter(term.text, False) alias = aliased(model.User) stmt = stmt.outerjoin(self.model_class.user.of_type(alias)) stmt = stmt.where( raw_text_column_filter( [ self.model_class.title, self.model_class.slug, tf, alias.username, ], term, ) ) if (show_published or show_shared) and not is_admin: show_deleted = False stmt = stmt.where(self.model_class.deleted == (true() if show_deleted else false())).distinct() if include_total_count: total_matches = get_count(trans.sa_session, stmt) else: total_matches = None sort_column = getattr(model.Visualization, payload.sort_by) if payload.sort_desc: sort_column = sort_column.desc() stmt = stmt.order_by(sort_column) if payload.limit is not None: stmt = stmt.limit(payload.limit) if payload.offset is not None: stmt = stmt.offset(payload.offset) return trans.sa_session.scalars(stmt), total_matches # type:ignore[return-value]
[docs]class VisualizationSerializer(sharable.SharableModelSerializer): """ Interface/service object for serializing visualizations into dictionaries. """ model_manager_class = VisualizationManager SINGLE_CHAR_ABBR = "v"
[docs] def __init__(self, app: MinimalManagerApp): super().__init__(app) self.visualization_manager = self.manager self.default_view = "summary" self.add_view("summary", []) self.add_view("detailed", [])
[docs] def add_serializers(self): super().add_serializers() serializers: Dict[str, base.Serializer] = {} self.serializers.update(serializers)
[docs]class VisualizationDeserializer(sharable.SharableModelDeserializer): """ Interface/service object for validating and deserializing dictionaries into visualizations. """ model_manager_class = VisualizationManager
[docs] def __init__(self, app): super().__init__(app) self.visualization_manager = self.manager
[docs] def add_deserializers(self): super().add_deserializers() self.deserializers.update({}) self.deserializable_keyset.update(self.deserializers.keys())
[docs]def get_count(session, statement): stmt = select(func.count()).select_from(statement) return session.scalar(stmt)