diff --git a/lib/galaxy/webapps/galaxy/api/forms.py b/lib/galaxy/webapps/galaxy/api/forms.py index c3313fb46cce..3abb53bc5f8a 100644 --- a/lib/galaxy/webapps/galaxy/api/forms.py +++ b/lib/galaxy/webapps/galaxy/api/forms.py @@ -3,6 +3,8 @@ """ import logging +from sqlalchemy import select + from galaxy import web from galaxy.forms.forms import form_factory from galaxy.model.base import transaction @@ -23,9 +25,10 @@ def index(self, trans, **kwd): if not trans.user_is_admin: trans.response.status = 403 return "You are not authorized to view the list of forms." - query = trans.sa_session.query(trans.app.model.FormDefinition) + rval = [] - for form_definition in query: + form_defs = trans.sa_session.scalars(select(trans.app.model.FormDefinition)).all() + for form_definition in form_defs: item = form_definition.to_dict( value_mapper={"id": trans.security.encode_id, "form_definition_current_id": trans.security.encode_id} ) @@ -46,7 +49,7 @@ def show(self, trans, id, **kwd): trans.response.status = 400 return f"Malformed form definition id ( {str(form_definition_id)} ) specified, unable to decode." try: - form_definition = trans.sa_session.query(trans.app.model.FormDefinition).get(decoded_form_definition_id) + form_definition = trans.sa_session.get(trans.app.model.FormDefinition, decoded_form_definition_id) except Exception: form_definition = None if not form_definition or not trans.user_is_admin: diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py index e6ec29d640f9..67bffb2a9eae 100644 --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -126,7 +126,7 @@ def __authorize_job_access(self, trans, encoded_job_id, **kwargs): raise exceptions.ItemAccessibilityException("Invalid job_key supplied.") # Verify job is active. Don't update the contents of complete jobs. - job = trans.sa_session.query(model.Job).get(job_id) + job = trans.sa_session.get(model.Job, job_id) if job.finished: error_message = "Attempting to read or modify the files of a job that has already completed." raise exceptions.ItemAccessibilityException(error_message) diff --git a/lib/galaxy/webapps/galaxy/api/job_tokens.py b/lib/galaxy/webapps/galaxy/api/job_tokens.py index 7c654709ece7..1693b8eaf0ac 100644 --- a/lib/galaxy/webapps/galaxy/api/job_tokens.py +++ b/lib/galaxy/webapps/galaxy/api/job_tokens.py @@ -53,7 +53,7 @@ def get_token( def __authorize_job_access(self, trans, encoded_job_id, job_key): job_id = trans.security.decode_id(encoded_job_id) - job = trans.sa_session.query(model.Job).get(job_id) + job = trans.sa_session.get(model.Job, job_id) secret = job.destination_params.get("job_secret_base", "jobs_token") job_key_internal = trans.security.encode_id(job_id, kind=secret) @@ -61,7 +61,7 @@ def __authorize_job_access(self, trans, encoded_job_id, job_key): raise exceptions.AuthenticationFailed("Invalid job_key supplied.") # Verify job is active - job = trans.sa_session.query(model.Job).get(job_id) + job = trans.sa_session.get(model.Job, job_id) if job.finished: error_message = "Attempting to get oidc token for a job that has already completed." raise exceptions.ItemAccessibilityException(error_message) diff --git a/lib/galaxy/webapps/galaxy/api/library_contents.py b/lib/galaxy/webapps/galaxy/api/library_contents.py index c152759b66c4..cf70efe97cac 100644 --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -4,6 +4,7 @@ import logging from typing import Optional +from sqlalchemy import select from sqlalchemy.orm.exc import ( MultipleResultsFound, NoResultFound, @@ -103,11 +104,8 @@ def traverse(folder): decoded_library_id = self.decode_id(library_id) try: - library = ( - trans.sa_session.query(trans.app.model.Library) - .filter(trans.app.model.Library.table.c.id == decoded_library_id) - .one() - ) + stmt = select(trans.app.model.Library).filter(trans.app.model.Library.id == decoded_library_id) + library = trans.sa_session.execute(stmt).scalar_one() except MultipleResultsFound: raise exceptions.InconsistentDatabase("Multiple libraries found with the same id.") except NoResultFound: @@ -348,7 +346,7 @@ def _upload_library_dataset(self, trans, folder_id: int, **kwd): roles = kwd.get("roles", "") is_admin = trans.user_is_admin current_user_roles = trans.get_current_user_roles() - folder = trans.sa_session.query(trans.app.model.LibraryFolder).get(folder_id) + folder = trans.sa_session.get(trans.app.model.LibraryFolder, folder_id) self._check_access(trans, is_admin, folder, current_user_roles) self._check_add(trans, is_admin, folder, current_user_roles) library = folder.parent_library diff --git a/lib/galaxy/webapps/galaxy/api/page_revisions.py b/lib/galaxy/webapps/galaxy/api/page_revisions.py index 85121077e53f..d913a995eb69 100644 --- a/lib/galaxy/webapps/galaxy/api/page_revisions.py +++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py @@ -3,6 +3,8 @@ """ import logging +from sqlalchemy import select + from galaxy.managers.base import get_object from galaxy.managers.pages import PageManager from galaxy.web import expose_api @@ -30,7 +32,7 @@ def index(self, trans, page_id, **kwd): :returns: dictionaries containing different revisions of the page """ page = get_object(trans, page_id, "Page", check_ownership=False, check_accessible=True) - r = trans.sa_session.query(trans.app.model.PageRevision).filter_by(page_id=page.id) + r = trans.sa_session.scalars(select(trans.app.model.PageRevision).filter_by(page_id=page.id)) out = [] for page in r: as_dict = self.encode_all_ids(trans, page.to_dict(), True) diff --git a/lib/galaxy/webapps/galaxy/api/tool_entry_points.py b/lib/galaxy/webapps/galaxy/api/tool_entry_points.py index f6590ef07344..d2d43031dfb3 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_entry_points.py +++ b/lib/galaxy/webapps/galaxy/api/tool_entry_points.py @@ -51,7 +51,7 @@ def index(self, trans: ProvidesUserContext, running=False, job_id=None, **kwd): ) if job_id is not None: - job = trans.sa_session.query(Job).get(self.decode_id(job_id)) + job = trans.sa_session.get(Job, self.decode_id(job_id)) if not self.interactivetool_manager.can_access_job(trans, job): raise exceptions.ItemAccessibilityException() entry_points = job.interactivetool_entry_points @@ -94,7 +94,7 @@ def stop_entry_point(self, trans: ProvidesUserContext, id, **kwds): raise exceptions.RequestParameterMissingException("Must supply entry point id") try: entry_point_id = self.decode_id(id) - entry_point = trans.sa_session.query(InteractiveToolEntryPoint).get(entry_point_id) + entry_point = trans.sa_session.get(InteractiveToolEntryPoint, entry_point_id) except Exception: raise exceptions.RequestParameterInvalidException("entry point invalid") if self.app.interactivetool_manager.can_access_entry_point(trans, entry_point): diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py index f68f44eebd42..644aac3e00d5 100644 --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -21,6 +21,7 @@ from sqlalchemy import ( false, or_, + select, true, ) from typing_extensions import Literal @@ -292,31 +293,31 @@ def index(self, trans: ProvidesUserContext, deleted="False", f_email=None, f_nam :type f_any: str """ rval = [] - query = trans.sa_session.query(User) + stmt = select(User) deleted = util.string_as_bool(deleted) if f_email and (trans.user_is_admin or trans.app.config.expose_user_email): - query = query.filter(User.email.like(f"%{f_email}%")) + stmt = stmt.filter(User.email.like(f"%{f_email}%")) if f_name and (trans.user_is_admin or trans.app.config.expose_user_name): - query = query.filter(User.username.like(f"%{f_name}%")) + stmt = stmt.filter(User.username.like(f"%{f_name}%")) if f_any: if trans.user_is_admin: - query = query.filter(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%"))) + stmt = stmt.filter(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%"))) else: if trans.app.config.expose_user_email and trans.app.config.expose_user_name: - query = query.filter(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%"))) + stmt = stmt.filter(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%"))) elif trans.app.config.expose_user_email: - query = query.filter(User.email.like(f"%{f_any}%")) + stmt = stmt.filter(User.email.like(f"%{f_any}%")) elif trans.app.config.expose_user_name: - query = query.filter(User.username.like(f"%{f_any}%")) + stmt = stmt.filter(User.username.like(f"%{f_any}%")) if deleted: # only admins can see deleted users if not trans.user_is_admin: return [] - query = query.filter(User.table.c.deleted == true()) + stmt = stmt.filter(User.deleted == true()) else: # special case: user can see only their own user # special case2: if the galaxy admin has specified that other user email/names are @@ -328,8 +329,8 @@ def index(self, trans: ProvidesUserContext, deleted="False", f_email=None, f_nam ): item = trans.user.to_dict(value_mapper={"id": trans.security.encode_id}) return [item] - query = query.filter(User.table.c.deleted == false()) - for user in query: + stmt = stmt.filter(User.deleted == false()) + for user in trans.sa_session.scalars(stmt).all(): item = user.to_dict(value_mapper={"id": trans.security.encode_id}) # If NOT configured to expose_email, do not expose email UNLESS the user is self, or # the user is an admin @@ -699,8 +700,8 @@ def set_information(self, trans, id, payload=None, **kwd): user_info_form_id = payload.get("info|form_id") if user_info_form_id: prefix = "info|" - user_info_form = trans.sa_session.query(trans.app.model.FormDefinition).get( - trans.security.decode_id(user_info_form_id) + user_info_form = trans.sa_session.get( + trans.app.model.FormDefinition, trans.security.decode_id(user_info_form_id) ) user_info_values = {} for item in payload: @@ -752,7 +753,7 @@ def set_information(self, trans, id, payload=None, **kwd): d = address_dicts[index] if d.get("id"): try: - user_address = trans.sa_session.query(UserAddress).get(trans.security.decode_id(d["id"])) + user_address = trans.sa_session.get(UserAddress, trans.security.decode_id(d["id"])) except Exception as e: raise exceptions.ObjectNotFound(f"Failed to access user address ({d['id']}). {e}") else: @@ -921,9 +922,7 @@ def set_permissions(self, trans, id, payload=None, **kwd): permissions = {} for index, action in trans.app.model.Dataset.permitted_actions.items(): action_id = trans.app.security_agent.get_action(action.action).action - permissions[action_id] = [ - trans.sa_session.query(trans.app.model.Role).get(x) for x in (payload.get(index) or []) - ] + permissions[action_id] = [trans.sa_session.get(trans.app.model.Role, x) for x in (payload.get(index) or [])] trans.app.security_agent.user_set_default_permissions(user, permissions) return {"message": "Permissions have been saved."} @@ -1042,8 +1041,8 @@ def get_custom_builds(self, trans, id, payload=None, **kwd): update = False for key, dbkey in dbkeys.items(): if "count" not in dbkey and "linecount" in dbkey: - chrom_count_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get( - dbkey["linecount"] + chrom_count_dataset = trans.sa_session.get( + trans.app.model.HistoryDatasetAssociation, dbkey["linecount"] ) if ( chrom_count_dataset @@ -1139,7 +1138,7 @@ def add_custom_builds(self, trans, id, key, payload=None, **kwd): build_dict["count"] = counter else: build_dict["fasta"] = trans.security.decode_id(len_value) - dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(build_dict["fasta"]) + dataset = trans.sa_session.get(trans.app.model.HistoryDatasetAssociation, build_dict["fasta"]) try: new_len = dataset.get_converted_dataset(trans, "len") new_linecount = new_len.get_converted_dataset(trans, "linecount") diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index 8c99c6cb983e..11a0861bc443 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -23,6 +23,10 @@ from gxformat2._yaml import ordered_dump from markupsafe import escape from pydantic import Extra +from sqlalchemy import ( + func, + select, +) from starlette.responses import StreamingResponse from galaxy import ( @@ -162,7 +166,6 @@ def set_workflow_menu(self, trans: GalaxyWebTransaction, payload=None, **kwd): for m in user.stored_workflow_menu_entries: sess.delete(m) user.stored_workflow_menu_entries = [] - q = sess.query(model.StoredWorkflow) # To ensure id list is unique seen_workflow_ids = set() for wf_id in workflow_ids_decoded: @@ -171,7 +174,8 @@ def set_workflow_menu(self, trans: GalaxyWebTransaction, payload=None, **kwd): else: seen_workflow_ids.add(wf_id) m = model.StoredWorkflowMenuEntry() - m.stored_workflow = q.get(wf_id) + m.stored_workflow = sess.get(model.StoredWorkflow, wf_id) + user.stored_workflow_menu_entries.append(m) with transaction(sess): sess.commit() @@ -192,12 +196,11 @@ def show(self, trans: GalaxyWebTransaction, id, **kwd): """ stored_workflow = self.__get_stored_workflow(trans, id, **kwd) if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin: - if ( - trans.sa_session.query(model.StoredWorkflowUserShareAssociation) - .filter_by(user=trans.user, stored_workflow=stored_workflow) - .count() - == 0 - ): + stmt = select(model.StoredWorkflowUserShareAssociation).filter_by( + user=trans.user, stored_workflow=stored_workflow + ) + stmt = select(func.count()).select_from(stmt) + if trans.sa_session.scalar(stmt) == 0: message = "Workflow is neither importable, nor owned by or shared with current user" raise exceptions.ItemAccessibilityException(message) if kwd.get("legacy", False):