Fix SA2.0 (query->select) in galaxy.tools

Author: jdavcs

lib/galaxy/tools/__init__.py

@@ -30,6 +30,11 @@
 from lxml import etree
 from mako.template import Template
 from packaging.version import Version
+from sqlalchemy import (
+    delete,
+    func,
+    select,
+)
 
 from galaxy import (
     exceptions,
@@ -346,9 +351,9 @@ def __init__(self, app):
 
     def reset_tags(self):
         log.info(
-            f"removing all tool tag associations ({str(self.sa_session.query(self.app.model.ToolTagAssociation).count())})"
+            f"removing all tool tag associations ({str(self.sa_session.scalar(select(func.count(self.app.model.ToolTagAssociation))))})"
         )
-        self.sa_session.query(self.app.model.ToolTagAssociation).delete()
+        self.sa_session.execute(delete(self.app.model.ToolTagAssociation))
         with transaction(self.sa_session):
             self.sa_session.commit()
 
@@ -359,7 +364,8 @@ def handle_tags(self, tool_id, tool_definition_source):
             for tag_name in tag_names:
                 if tag_name == "":
                     continue
-                tag = self.sa_session.query(self.app.model.Tag).filter_by(name=tag_name).first()
+                stmt = select(self.app.model.Tag).filter_by(name=tag_name).limit(1)
+                tag = self.sa_session.scalars(stmt).first()
                 if not tag:
                     tag = self.app.model.Tag(name=tag_name)
                     self.sa_session.add(tag)
@@ -618,7 +624,7 @@ def _load_workflow(self, workflow_id):
         which is encoded in the tool panel.
         """
         id = self.app.security.decode_id(workflow_id)
-        stored = self.app.model.context.query(self.app.model.StoredWorkflow).get(id)
+        stored = self.app.model.context.get(self.app.model.StoredWorkflow, id)
         return stored.latest_workflow
 
     def __build_tool_version_select_field(self, tools, tool_id, set_selected):
@@ -3121,7 +3127,7 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
                 self.sa_session.commit()
 
     def job_failed(self, job_wrapper, message, exception=False):
-        job = job_wrapper.sa_session.query(model.Job).get(job_wrapper.job_id)
+        job = job_wrapper.sa_session.get(model.Job, job_wrapper.job_id)
         if job:
             inp_data = {}
             for dataset_assoc in job.input_datasets:
@@ -3168,7 +3174,7 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
 
     def job_failed(self, job_wrapper, message, exception=False):
         super().job_failed(job_wrapper, message, exception=exception)
-        job = job_wrapper.sa_session.query(model.Job).get(job_wrapper.job_id)
+        job = job_wrapper.sa_session.get(model.Job, job_wrapper.job_id)
         self.__remove_interactivetool_by_job(job)
 
 

lib/galaxy/tools/actions/__init__.py

@@ -481,7 +481,7 @@ def handle_output(name, output, hidden=None):
             if async_tool and name in incoming:
                 # HACK: output data has already been created as a result of the async controller
                 dataid = incoming[name]
-                data = trans.sa_session.query(app.model.HistoryDatasetAssociation).get(dataid)
+                data = trans.sa_session.get(app.model.HistoryDatasetAssociation, dataid)
                 assert data is not None
                 out_data[name] = data
             else:
@@ -745,7 +745,7 @@ def _remap_job_on_rerun(self, trans, galaxy_session, rerun_remap_job_id, current
         input datasets to be those of the job that is being rerun.
         """
         try:
-            old_job = trans.sa_session.query(trans.app.model.Job).get(rerun_remap_job_id)
+            old_job = trans.sa_session.get(trans.app.model.Job, rerun_remap_job_id)
             assert old_job is not None, f"({rerun_remap_job_id}/{current_job.id}): Old job id is invalid"
             assert (
                 old_job.tool_id == current_job.tool_id

lib/galaxy/tools/actions/upload_common.py

@@ -13,6 +13,7 @@
     Optional,
 )
 
+from sqlalchemy import select
 from sqlalchemy.orm import joinedload
 from webob.compat import cgi_FieldStorage
 
@@ -94,12 +95,12 @@ def handle_library_params(
     # See if we have any template field contents
     template_field_contents = {}
     template_id = params.get("template_id", None)
-    folder = trans.sa_session.query(LibraryFolder).get(folder_id)
+    folder = trans.sa_session.get(LibraryFolder, folder_id)
     # We are inheriting the folder's info_association, so we may have received inherited contents or we may have redirected
     # here after the user entered template contents ( due to errors ).
     template: Optional[FormDefinition] = None
     if template_id not in [None, "None"]:
-        template = trans.sa_session.query(FormDefinition).get(template_id)
+        template = trans.sa_session.get(FormDefinition, template_id)
         assert template
         for field in template.fields:
             field_name = field["name"]
@@ -108,7 +109,7 @@ def handle_library_params(
                 template_field_contents[field_name] = field_value
     roles: List[Role] = []
     for role_id in util.listify(params.get("roles", [])):
-        role = trans.sa_session.query(Role).get(role_id)
+        role = trans.sa_session.get(Role, role_id)
         roles.append(role)
     tags = params.get("tags", None)
     return LibraryParams(
@@ -436,10 +437,11 @@ def active_folders(trans, folder):
     # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues).
     # Much faster way of retrieving all active sub-folders within a given folder than the
     # performance of the mapper.  This query also eagerloads the permissions on each folder.
-    return (
-        trans.sa_session.query(LibraryFolder)
+    stmt = (
+        select(LibraryFolder)
         .filter_by(parent=folder, deleted=False)
         .options(joinedload(LibraryFolder.actions))
-        .order_by(LibraryFolder.table.c.name)
-        .all()
+        .unique()
+        .order_by(LibraryFolder.name)
     )
+    return trans.sa_session.scalars(stmt).all()

lib/galaxy/tools/errors.py

@@ -137,10 +137,10 @@ def __init__(self, hda, app):
         if not isinstance(hda, model.HistoryDatasetAssociation):
             hda_id = hda
             try:
-                hda = sa_session.query(model.HistoryDatasetAssociation).get(hda_id)
+                hda = sa_session.get(model.HistoryDatasetAssociation, hda_id)
                 assert hda is not None, ValueError("No HDA yet")
             except Exception:
-                hda = sa_session.query(model.HistoryDatasetAssociation).get(app.security.decode_id(hda_id))
+                hda = sa_session.get(model.HistoryDatasetAssociation, app.security.decode_id(hda_id))
         assert isinstance(hda, model.HistoryDatasetAssociation), ValueError(f"Bad value provided for HDA ({hda}).")
         self.hda = hda
         # Get the associated job

lib/galaxy/tools/imp_exp/__init__.py

@@ -4,6 +4,8 @@
 import shutil
 from typing import Optional
 
+from sqlalchemy import select
+
 from galaxy import model
 from galaxy.model import store
 from galaxy.model.base import transaction
@@ -49,7 +51,8 @@ def cleanup_after_job(self):
         # Import history.
         #
 
-        jiha = self.sa_session.query(model.JobImportHistoryArchive).filter_by(job_id=self.job_id).first()
+        stmt = select(model.JobImportHistoryArchive).filter_by(job_id=self.job_id).limit(1)
+        jiha = self.sa_session.scalars(stmt).first()
         if not jiha:
             return None
         user = jiha.job.user

lib/galaxy/tools/parameters/basic.py

@@ -1943,13 +1943,13 @@ def single_to_python(value):
             if isinstance(value, dict) and "src" in value:
                 id = value["id"] if isinstance(value["id"], int) else app.security.decode_id(value["id"])
                 if value["src"] == "dce":
-                    return app.model.context.query(DatasetCollectionElement).get(id)
+                    return app.model.context.get(DatasetCollectionElement, id)
                 elif value["src"] == "hdca":
-                    return app.model.context.query(HistoryDatasetCollectionAssociation).get(id)
+                    return app.model.context.get(HistoryDatasetCollectionAssociation, id)
                 elif value["src"] == "ldda":
-                    return app.model.context.query(LibraryDatasetDatasetAssociation).get(id)
+                    return app.model.context.get(LibraryDatasetDatasetAssociation, id)
                 else:
-                    return app.model.context.query(HistoryDatasetAssociation).get(id)
+                    return app.model.context.get(HistoryDatasetAssociation, id)
 
         if isinstance(value, dict) and "values" in value:
             if hasattr(self, "multiple") and self.multiple is True:
@@ -1963,21 +1963,21 @@ def single_to_python(value):
             return None
         if isinstance(value, str) and value.find(",") > -1:
             return [
-                app.model.context.query(HistoryDatasetAssociation).get(int(v))
+                app.model.context.get(HistoryDatasetAssociation, int(v))
                 for v in value.split(",")
                 if v not in none_values
             ]
         elif str(value).startswith("__collection_reduce__|"):
             decoded_id = str(value)[len("__collection_reduce__|") :]
             if not decoded_id.isdigit():
                 decoded_id = app.security.decode_id(decoded_id)
-            return app.model.context.query(HistoryDatasetCollectionAssociation).get(int(decoded_id))
+            return app.model.context.get(HistoryDatasetCollectionAssociation, int(decoded_id))
         elif str(value).startswith("dce:"):
-            return app.model.context.query(DatasetCollectionElement).get(int(value[len("dce:") :]))
+            return app.model.context.get(DatasetCollectionElement, int(value[len("dce:") :]))
         elif str(value).startswith("hdca:"):
-            return app.model.context.query(HistoryDatasetCollectionAssociation).get(int(value[len("hdca:") :]))
+            return app.model.context.get(HistoryDatasetCollectionAssociation, int(value[len("hdca:") :]))
         else:
-            return app.model.context.query(HistoryDatasetAssociation).get(int(value))
+            return app.model.context.get(HistoryDatasetAssociation, int(value))
 
     def validate(self, value, trans=None):
         def do_validate(v):
@@ -2097,17 +2097,17 @@ def from_json(self, value, trans, other_values=None):
                 if isinstance(single_value, dict) and "src" in single_value and "id" in single_value:
                     if single_value["src"] == "hda":
                         decoded_id = trans.security.decode_id(single_value["id"])
-                        rval.append(trans.sa_session.query(HistoryDatasetAssociation).get(decoded_id))
+                        rval.append(trans.sa_session.get(HistoryDatasetAssociation, decoded_id))
                     elif single_value["src"] == "hdca":
                         found_hdca = True
                         decoded_id = trans.security.decode_id(single_value["id"])
-                        rval.append(trans.sa_session.query(HistoryDatasetCollectionAssociation).get(decoded_id))
+                        rval.append(trans.sa_session.get(HistoryDatasetCollectionAssociation, decoded_id))
                     elif single_value["src"] == "ldda":
                         decoded_id = trans.security.decode_id(single_value["id"])
-                        rval.append(trans.sa_session.query(LibraryDatasetDatasetAssociation).get(decoded_id))
+                        rval.append(trans.sa_session.get(LibraryDatasetDatasetAssociation, decoded_id))
                     elif single_value["src"] == "dce":
                         decoded_id = trans.security.decode_id(single_value["id"])
-                        rval.append(trans.sa_session.query(DatasetCollectionElement).get(decoded_id))
+                        rval.append(trans.sa_session.get(DatasetCollectionElement, decoded_id))
                     else:
                         raise ValueError(f"Unknown input source {single_value['src']} passed to job submission API.")
                 elif isinstance(
@@ -2126,7 +2126,7 @@ def from_json(self, value, trans, other_values=None):
                         # support that for integer column types.
                         log.warning("Encoded ID where unencoded ID expected.")
                         single_value = trans.security.decode_id(single_value)
-                    rval.append(trans.sa_session.query(HistoryDatasetAssociation).get(single_value))
+                    rval.append(trans.sa_session.get(HistoryDatasetAssociation, single_value))
             if found_hdca:
                 for val in rval:
                     if not isinstance(val, HistoryDatasetCollectionAssociation):
@@ -2139,26 +2139,26 @@ def from_json(self, value, trans, other_values=None):
         elif isinstance(value, dict) and "src" in value and "id" in value:
             if value["src"] == "hda":
                 decoded_id = trans.security.decode_id(value["id"])
-                rval.append(trans.sa_session.query(HistoryDatasetAssociation).get(decoded_id))
+                rval.append(trans.sa_session.get(HistoryDatasetAssociation, decoded_id))
             elif value["src"] == "hdca":
                 decoded_id = trans.security.decode_id(value["id"])
-                rval.append(trans.sa_session.query(HistoryDatasetCollectionAssociation).get(decoded_id))
+                rval.append(trans.sa_session.get(HistoryDatasetCollectionAssociation, decoded_id))
             elif value["src"] == "dce":
                 decoded_id = trans.security.decode_id(value["id"])
-                rval.append(trans.sa_session.query(DatasetCollectionElement).get(decoded_id))
+                rval.append(trans.sa_session.get(DatasetCollectionElement, decoded_id))
             else:
                 raise ValueError(f"Unknown input source {value['src']} passed to job submission API.")
         elif str(value).startswith("__collection_reduce__|"):
             encoded_ids = [v[len("__collection_reduce__|") :] for v in str(value).split(",")]
             decoded_ids = map(trans.security.decode_id, encoded_ids)
             rval = []
             for decoded_id in decoded_ids:
-                hdca = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(decoded_id)
+                hdca = trans.sa_session.get(HistoryDatasetCollectionAssociation, decoded_id)
                 rval.append(hdca)
         elif isinstance(value, HistoryDatasetCollectionAssociation) or isinstance(value, DatasetCollectionElement):
             rval.append(value)
         else:
-            rval.append(trans.sa_session.query(HistoryDatasetAssociation).get(value))
+            rval.append(trans.sa_session.get(HistoryDatasetAssociation, value))
         dataset_matcher_factory = get_dataset_matcher_factory(trans)
         dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
         for v in rval:
@@ -2443,28 +2443,24 @@ def from_json(self, value, trans, other_values=None):
             rval = value
         elif isinstance(value, dict) and "src" in value and "id" in value:
             if value["src"] == "hdca":
-                rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(
-                    trans.security.decode_id(value["id"])
-                )
+                rval = trans.sa_session.get(HistoryDatasetCollectionAssociation, trans.security.decode_id(value["id"]))
         elif isinstance(value, list):
             if len(value) > 0:
                 value = value[0]
                 if isinstance(value, dict) and "src" in value and "id" in value:
                     if value["src"] == "hdca":
-                        rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(
-                            trans.security.decode_id(value["id"])
+                        rval = trans.sa_session.get(
+                            HistoryDatasetCollectionAssociation, trans.security.decode_id(value["id"])
                         )
                     elif value["src"] == "dce":
-                        rval = trans.sa_session.query(DatasetCollectionElement).get(
-                            trans.security.decode_id(value["id"])
-                        )
+                        rval = trans.sa_session.get(DatasetCollectionElement, trans.security.decode_id(value["id"]))
         elif isinstance(value, str):
             if value.startswith("dce:"):
-                rval = trans.sa_session.query(DatasetCollectionElement).get(value[len("dce:") :])
+                rval = trans.sa_session.get(DatasetCollectionElement, value[len("dce:") :])
             elif value.startswith("hdca:"):
-                rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(value[len("hdca:") :])
+                rval = trans.sa_session.get(HistoryDatasetCollectionAssociation, value[len("hdca:") :])
             else:
-                rval = trans.sa_session.query(HistoryDatasetCollectionAssociation).get(value)
+                rval = trans.sa_session.get(HistoryDatasetCollectionAssociation, value)
         if rval and isinstance(rval, HistoryDatasetCollectionAssociation):
             if rval.deleted:
                 raise ParameterValueError("the previously selected dataset collection has been deleted", self.name)
@@ -2634,8 +2630,9 @@ def to_python(self, value, app, other_values=None, validate=False):
                 else:
                     lst = []
                     break
-                lda = app.model.context.query(LibraryDatasetDatasetAssociation).get(
-                    lda_id if isinstance(lda_id, int) else app.security.decode_id(lda_id)
+                lda = app.model.context.get(
+                    LibraryDatasetDatasetAssociation,
+                    lda_id if isinstance(lda_id, int) else app.security.decode_id(lda_id),
                 )
                 if lda is not None:
                     lst.append(lda)

lib/galaxy/tools/parameters/meta.py

@@ -265,7 +265,7 @@ def __expand_collection_parameter(trans, input_key, incoming_val, collections_to
             encoded_hdc_id = incoming_val
             subcollection_type = None
     hdc_id = trans.app.security.decode_id(encoded_hdc_id)
-    hdc = trans.sa_session.query(model.HistoryDatasetCollectionAssociation).get(hdc_id)
+    hdc = trans.sa_session.get(model.HistoryDatasetCollectionAssociation, hdc_id)
     collections_to_match.add(input_key, hdc, subcollection_type=subcollection_type, linked=linked)
     if subcollection_type is not None:
         subcollection_elements = subcollections.split_dataset_collection_instance(hdc, subcollection_type)