nci-cidc-api-modules 1.0.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

cidc_api/models/models.py

@@ -28,9 +28,6 @@ from collections import defaultdict
 import re
 import hashlib
 import os
-import inspect
-
-os.environ["TZ"] = "UTC"
 from datetime import datetime, timedelta
 from enum import Enum as EnumBaseClass
 from functools import wraps
@@ -65,7 +62,6 @@ from sqlalchemy import (
     CheckConstraint,
     ForeignKey,
     ForeignKeyConstraint,
-    UniqueConstraint,
     PrimaryKeyConstraint,
     tuple_,
     asc,
@@ -80,27 +76,23 @@ from sqlalchemy import (
     Table,
     MetaData,
 )
-from sqlalchemy.orm import (
-    relationship,
-    validates,
-)
+from sqlalchemy.orm import relationship, validates
+from sqlalchemy.orm.attributes import flag_modified
+from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.orm.session import Session
+from sqlalchemy.orm.query import Query
 from sqlalchemy.sql import (
     # This is unfortunate but other code in this file relies on sqlalchemy.and_, or_, etc
     # instead of the sqlalchemy.sql versions we are importing here.  The solution is to
     # break up this giant file.
     and_ as sql_and,
-    or_ as sql_or,
-    select,
+    # or_ as sql_or, # NOT USED
+    # select, # ALREADY IMPORTED
     text,
 )
+from sqlalchemy.sql.functions import coalesce
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.ext.hybrid import hybrid_property
-from sqlalchemy.orm import validates
-from sqlalchemy.orm.attributes import flag_modified
-from sqlalchemy.orm.exc import NoResultFound
-from sqlalchemy.orm.session import Session
-from sqlalchemy.orm.query import Query
-from sqlalchemy.sql.functions import coalesce
 from sqlalchemy.dialects.postgresql import JSONB, UUID
 from sqlalchemy.engine import ResultProxy
 
@@ -137,6 +129,8 @@ from ..shared.gcloud_client import (
 )
 from ..config.logging import get_logger
 
+
+os.environ["TZ"] = "UTC"
 logger = get_logger(__name__)
 
 
@@ -185,7 +179,7 @@ class CommonColumns(BaseModel):  # type: ignore
             [s for c in cls.__bases__ for s in _all_bases(c)]
         )
 
-        columns_to_check = [c for c in type(self).__table__.columns]
+        columns_to_check = list(type(self).__table__.columns)
         for b in _all_bases(type(self)):
             if hasattr(b, "__table__"):
                 columns_to_check.extend(b.__table__.columns)
@@ -337,7 +331,6 @@ class CommonColumns(BaseModel):  # type: ignore
 
     def validate(self):
         """Run custom validations on attributes set on this instance."""
-        pass
 
     @classmethod
     def get_unique_columns(cls):
@@ -433,7 +426,7 @@ class Users(CommonColumns):
 
         user = Users.find_by_email(email)
         if not user:
-            logger.info(f"Creating new user with email {email}")
+            logger.info("Creating new user with email %s", email)
             user = Users(
                 email=email, contact_email=email, first_n=first_n, last_n=last_n
             )
@@ -456,7 +449,7 @@ class Users(CommonColumns):
             .values(disabled=True)
             .returning(Users.id)
         )
-        disabled_user_ids: List[int] = [uid for uid in session.execute(update_query)]
+        disabled_user_ids: List[int] = list(session.execute(update_query))
         if commit:
             session.commit()
 
@@ -659,7 +652,7 @@ class Permissions(CommonColumns):
             raise IntegrityError(
                 params=None,
                 statement=None,
-                orig=f"`granted_by_user` user must be given",
+                orig="`granted_by_user` user must be given",
             )
         if grantor is None:
             raise IntegrityError(
@@ -677,9 +670,8 @@ class Permissions(CommonColumns):
                     orig=f"`file_group` must exist, but none found with id {self.file_group_id}",
                 )
 
-        logger.info(
-            f"admin-action: {grantor.email} gave {grantee.email} the permission {self.upload_type or 'all assays'}{'(' + file_group.name + ')' if file_group else ''} on {self.trial_id or 'all trials'}"
-        )
+        info_message = f"admin-action: {grantor.email} gave {grantee.email} the permission {self.upload_type or 'all assays'}{'(' + file_group.name + ')' if file_group else ''} on {self.trial_id or 'all trials'}"
+        logger.info(info_message)
 
         if self.upload_type == "file_group":
             # Do not delete past-assigned file_group permissions for this user.
@@ -695,18 +687,22 @@ class Permissions(CommonColumns):
                     Permissions.granted_to_user == self.granted_to_user,
                     # If inserting a cross-trial perm, then select relevant
                     # trial-specific perms for deletion.
-                    Permissions.trial_id != self.EVERY
-                    if self.trial_id == self.EVERY
-                    else Permissions.trial_id == self.trial_id,
+                    (
+                        Permissions.trial_id != self.EVERY
+                        if self.trial_id == self.EVERY
+                        else Permissions.trial_id == self.trial_id
+                    ),
                     # If inserting a cross-upload type perm, then select relevant
                     # upload type-specific perms for deletion. This does NOT
                     # include clinical_data, just manifests/assays/analysis.
-                    and_(
-                        Permissions.upload_type != self.EVERY,
-                        Permissions.upload_type != "clinical_data",
-                    )
-                    if self.upload_type == self.EVERY
-                    else Permissions.upload_type == self.upload_type,
+                    (
+                        and_(
+                            Permissions.upload_type != self.EVERY,
+                            Permissions.upload_type != "clinical_data",
+                        )
+                        if self.upload_type == self.EVERY
+                        else Permissions.upload_type == self.upload_type
+                    ),
                 )
                 .all()
             )
@@ -784,7 +780,9 @@ class Permissions(CommonColumns):
                 revoke_download_access(grantee.email, self.trial_id, self.upload_type)
 
                 # If the permission to delete is the last one, also revoke Lister access
-                filter_ = lambda q: q.filter(Permissions.granted_to_user == grantee.id)
+                def filter_(q):
+                    return q.filter(Permissions.granted_to_user == grantee.id)
+
                 if Permissions.count(session=session, filter_=filter_) <= 1:
                     # this one hasn't been deleted yet, so 1 means this is the last one
                     revoke_lister_access(grantee.email)
@@ -794,9 +792,8 @@ class Permissions(CommonColumns):
                     "IAM revoke failed, and permission db record not removed."
                 ) from e
 
-        logger.info(
-            f"admin-action: {deleted_by_user.email} removed from {grantee.email} the permission {self.upload_type or 'all assays'} on {self.trial_id or 'all trials'}"
-        )
+        info_message = f"admin-action: {deleted_by_user.email} removed from {grantee.email} the permission {self.upload_type or 'all assays'} on {self.trial_id or 'all trials'}"
+        logger.info(info_message)
         super().delete(session=session, commit=True)
 
     @staticmethod
@@ -968,7 +965,7 @@ class Permissions(CommonColumns):
         # if they have any download permissions, they need the CIDC Lister role
         # If a Permission's FileGroup is None, that implies the Permission is a
         # trial/assay type and thus lister access is required.
-        if len(perms) and any([perm.file_group_id is None for perm in perms]):
+        if len(perms) and any(perm.file_group_id is None for perm in perms):
             grant_lister_access(user.email)
 
         # separate permissions by trial, as they are strictly non-overlapping
@@ -1071,9 +1068,9 @@ class Permissions(CommonColumns):
                 or user.email in user_email_list
             ):
                 continue
-            else:
-                user_email_list.append(user.email)
-                grant_lister_access(user.email)
+
+            user_email_list.append(user.email)
+            grant_lister_access(user.email)
 
         if upload.upload_type in prism.SUPPORTED_SHIPPING_MANIFESTS:
             # Passed with empty user email list because they will be queried for in CFn
@@ -1087,7 +1084,9 @@ class Permissions(CommonColumns):
         # grant to individual blobs rather than calling grant_download_access(grantee, trial, upload_type)
         blob_names: list[str] = [df.object_url for df in file_group.downloadable_files]
         logger.info(
-            f"Granting access to {user_email} for the following downloadables: {blob_names}"
+            "Granting access to %s for the following downloadables: %s",
+            user_email,
+            blob_names,
         )
         grant_download_access_to_blob_names([user_email], blob_names)
 
@@ -1095,8 +1094,6 @@ class Permissions(CommonColumns):
 class ValidationMultiError(Exception):
     """Holds multiple jsonschema.ValidationErrors"""
 
-    pass
-
 
 trial_metadata_validator: json_validation._Validator = (
     json_validation.load_and_validate_schema(
@@ -1230,7 +1227,7 @@ class TrialMetadata(CommonColumns):
         Create a new clinical trial metadata record.
         """
 
-        logger.info(f"Creating new trial metadata with id {trial_id}")
+        logger.info("Creating new trial metadata with id %s", trial_id)
         trial = TrialMetadata(trial_id=trial_id, metadata_json=metadata_json)
         trial.insert(session=session, commit=commit)
 
@@ -1422,7 +1419,10 @@ class TrialMetadata(CommonColumns):
             session.commit()
 
     @classmethod
-    def build_trial_filter(cls, user: Users, trial_ids: List[str] = []):
+    def build_trial_filter(cls, user: Users, trial_ids: List[str] = None):
+        if trial_ids is None:
+            trial_ids = []
+
         filters = []
         if trial_ids:
             filters.append(cls.trial_id.in_(trial_ids))
@@ -1683,7 +1683,7 @@ class TrialMetadata(CommonColumns):
                     trial_metadata,
                     jsonb_array_elements(metadata_json->'participants') participant,
                     jsonb_array_elements(participant->'samples') sample
-                
+
                 where
                         sample->>'processed_sample_derivative' = 'Tumor DNA'
                     or
@@ -1799,7 +1799,7 @@ class TrialMetadata(CommonColumns):
                 trial_id,
                 jsonb_object_agg(key, value) as value
             from (
-                select 
+                select
                     trial_id,
                     key,
                     jsonb_agg(sample) as value
@@ -2017,7 +2017,7 @@ class UploadJobs(CommonColumns):
     __tablename__ = "upload_jobs"
     # An upload job must contain a gcs_file_map is it isn't a manifest upload
     __table_args__ = (
-        CheckConstraint(f"multifile = true OR gcs_file_map != null"),
+        CheckConstraint("multifile = true OR gcs_file_map != null"),
         ForeignKeyConstraint(
             ["uploader_email"],
             ["users.email"],
@@ -2159,10 +2159,10 @@ class UploadJobs(CommonColumns):
         if job is None or job.status == UploadJobStatus.MERGE_COMPLETED.value:
             raise ValueError(f"Upload job {job_id} doesn't exist or is already merged")
 
-        logger.info(f"About to merge extra md to {job.id}/{job.status}")
+        logger.info("About to merge extra md to %s/%s", job.id, job.status)
 
         for uuid, file in files.items():
-            logger.info(f"About to parse/merge extra md on {uuid}")
+            logger.info("About to parse/merge extra md on %s", uuid)
             (
                 job.metadata_patch,
                 updated_artifact,
@@ -2170,14 +2170,14 @@ class UploadJobs(CommonColumns):
             ) = prism.merge_artifact_extra_metadata(
                 job.metadata_patch, uuid, job.upload_type, file
             )
-            logger.info(f"Updated md for {uuid}: {updated_artifact.keys()}")
+            logger.info("Updated md for %s: %s", uuid, updated_artifact.keys())
 
         # A workaround fix for JSON field modifications not being tracked
         # by SQLalchemy for some reason. Using MutableDict.as_mutable(JSON)
         # in the model doesn't seem to help.
         flag_modified(job, "metadata_patch")
 
-        logger.info(f"Updated {job.id}/{job.status} patch: {job.metadata_patch}")
+        logger.info("Updated %s/%s patch: %s", job.id, job.status, job.metadata_patch)
         session.commit()
 
     @classmethod
@@ -2323,15 +2323,15 @@ class DownloadableFiles(CommonColumns):
         return match.group(1) if match else None
 
     @file_ext.expression
-    def file_ext(cls):
-        return func.substring(cls.object_url, cls.FILE_EXT_REGEX)
+    def file_ext(self):
+        return func.substring(self.object_url, self.FILE_EXT_REGEX)
 
     @hybrid_property
     def data_category(self):
         return facet_groups_to_categories.get(self.facet_group)
 
     @data_category.expression
-    def data_category(cls):
+    def data_category(self):
         return DATA_CATEGORY_CASE_CLAUSE
 
     @hybrid_property
@@ -2345,7 +2345,7 @@ class DownloadableFiles(CommonColumns):
         return self.data_category.split(FACET_NAME_DELIM, 1)[0]
 
     @data_category_prefix.expression
-    def data_category_prefix(cls):
+    def data_category_prefix(self):
         return func.split_part(DATA_CATEGORY_CASE_CLAUSE, FACET_NAME_DELIM, 1)
 
     @hybrid_property
@@ -2353,7 +2353,7 @@ class DownloadableFiles(CommonColumns):
         return details_dict.get(self.facet_group).file_purpose
 
     @file_purpose.expression
-    def file_purpose(cls):
+    def file_purpose(self):
         return FILE_PURPOSE_CASE_CLAUSE
 
     @property
@@ -2388,7 +2388,7 @@ class DownloadableFiles(CommonColumns):
         # definitions in this class, but it seemed to be the only way to get the
         # SQLAlchemy Expression Language API to work.
         metadata = MetaData()
-        downloadableFiles_forQuery = Table(
+        downloadable_files_for_query = Table(
             "downloadable_files",
             metadata,
             Column("_created", BigInteger, nullable=False),
@@ -2415,24 +2415,20 @@ class DownloadableFiles(CommonColumns):
         # TODO(jcallaway): consider this reflection-based approach instead.  It doesn't
         # currently work because of the relationship()s and foreign keys, among other
         # problems.
-        """
-        columns = []
-        attributes = inspect.getmembers(CommonColumns, lambda x: not (inspect.isroutine(x)))
-        for k, v in attributes:
-            if not(k.startswith('__') and k.endswith('__')) and isinstance(v, Column):
-                v.name = k
-                columns.append(v)
-
-        attributes = inspect.getmembers(DownloadableFiles, lambda x: not (inspect.isroutine(x)))
-        for k, v in attributes:
-            if not (k.startswith('__') and k.endswith('__')) and isinstance(v, Column):
-                v.name = k
-                columns.append(v)
-
-        downloadableFiles_forQuery = Table("downloadable_files", metadata, *columns)
-        """
-
-        filesToFileGroups_forQuery = Table(
+        # columns = []
+        # attributes = inspect.getmembers(CommonColumns, lambda x: not (inspect.isroutine(x)))
+        # for k, v in attributes:
+        #     if not(k.startswith('__') and k.endswith('__')) and isinstance(v, Column):
+        #         v.name = k
+        #         columns.append(v)
+        # attributes = inspect.getmembers(DownloadableFiles, lambda x: not (inspect.isroutine(x)))
+        # for k, v in attributes:
+        #     if not (k.startswith('__') and k.endswith('__')) and isinstance(v, Column):
+        #         v.name = k
+        #         columns.append(v)
+        # downloadable_files_for_query = Table("downloadable_files", metadata, *columns)
+
+        files_to_file_groups_for_query = Table(
             "files_to_file_groups",
             metadata,
             Column("_created", BigInteger, nullable=False),
@@ -2443,11 +2439,11 @@ class DownloadableFiles(CommonColumns):
             Column("file_id", ForeignKey("downloadable_files.id")),
         )
 
-        return downloadableFiles_forQuery, filesToFileGroups_forQuery
+        return downloadable_files_for_query, files_to_file_groups_for_query
 
     @classmethod
     def _convert_list_results(
-        cls, downloadableFiles_forQuery: Table, query_files: List
+        cls, downloadable_files_for_query: Table, query_files: List
     ):
         """Converts the results of a SQLalchemy expression language query into actual DownloadableFiles
         objects.  This is necessary since the UI depends on some of the derived properties in
@@ -2456,7 +2452,7 @@ class DownloadableFiles(CommonColumns):
         results = []
         for query_file in query_files:
             args = {}
-            for column in downloadableFiles_forQuery.c:
+            for column in downloadable_files_for_query.c:
                 args[column.name] = getattr(query_file, column.name)
             results.append(DownloadableFiles(**args))
 
@@ -2465,8 +2461,8 @@ class DownloadableFiles(CommonColumns):
     @classmethod
     def _generate_where_clauses(
         cls,
-        downloadableFiles_forQuery: Table,
-        filesToFileGroups_forQuery: Table,
+        downloadable_files_for_query: Table,
+        files_to_file_groups_for_query: Table,
         trial_ids: List[str],
         facets: List[List[str]],
         user: Users,
@@ -2483,11 +2479,11 @@ class DownloadableFiles(CommonColumns):
 
         where_clauses = []
         if trial_ids:
-            where_clauses.append(downloadableFiles_forQuery.c.trial_id.in_(trial_ids))
+            where_clauses.append(downloadable_files_for_query.c.trial_id.in_(trial_ids))
         if facets:
             facet_groups = get_facet_groups_for_paths(facets)
             where_clauses.append(
-                downloadableFiles_forQuery.c.facet_group.in_(facet_groups)
+                downloadable_files_for_query.c.facet_group.in_(facet_groups)
             )
 
         if user and not is_admin:
@@ -2505,11 +2501,11 @@ class DownloadableFiles(CommonColumns):
                     where_clauses.append(
                         sql_and(
                             (
-                                downloadableFiles_forQuery.c.trial_id
+                                downloadable_files_for_query.c.trial_id
                                 == permission.trial_id
                             ),
                             (
-                                downloadableFiles_forQuery.c.upload_type
+                                downloadable_files_for_query.c.upload_type
                                 == permission.upload_type
                             ),
                         )
@@ -2518,11 +2514,11 @@ class DownloadableFiles(CommonColumns):
                     where_clauses.append(
                         sql_and(
                             (
-                                downloadableFiles_forQuery.c.trial_id
+                                downloadable_files_for_query.c.trial_id
                                 == permission.trial_id
                             ),
                             (
-                                filesToFileGroups_forQuery.c.file_group_id
+                                files_to_file_groups_for_query.c.file_group_id
                                 == permission.file_group_id
                             ),
                         )
@@ -2533,29 +2529,29 @@ class DownloadableFiles(CommonColumns):
                 # don't include clinical_data in cross-trial permission
                 where_clauses.append(
                     sql_and(
-                        downloadableFiles_forQuery.c.trial_id.in_(full_trial_perms),
-                        (downloadableFiles_forQuery.c.upload_type != "clinical_data"),
+                        downloadable_files_for_query.c.trial_id.in_(full_trial_perms),
+                        (downloadable_files_for_query.c.upload_type != "clinical_data"),
                     )
                 )
             if full_type_perms:
                 where_clauses.append(
-                    downloadableFiles_forQuery.c.upload_type.in_(full_type_perms)
+                    downloadable_files_for_query.c.upload_type.in_(full_type_perms)
                 )
 
         # Need to be careful about return logic.  Empty results could be because the user
         # is an admin, whereas None means the user has no permissions to view any files.
         if is_admin or where_clauses:
             return where_clauses
-        else:
-            return None
+
+        return None
 
     @classmethod
     @with_default_session
     def list_with_permissions(
         cls,
         session: Session,
-        trial_ids: List[str] = [],
-        facets: List[List[str]] = [],
+        trial_ids: List[str] = None,
+        facets: List[List[str]] = None,
         page_num: int = 0,
         page_size: int = PAGINATION_PAGE_SIZE,
         sort_field: Optional[str] = None,
@@ -2563,13 +2559,19 @@ class DownloadableFiles(CommonColumns):
         user: Users = None,
     ):
         """List records in this table, with pagination support."""
+        if trial_ids is None:
+            trial_ids = []
+
+        if facets is None:
+            facets = []
+
         (
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
         ) = DownloadableFiles._generate_query_objects()
         where_clauses = DownloadableFiles._generate_where_clauses(
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
             trial_ids,
             facets,
             user,
@@ -2579,19 +2581,21 @@ class DownloadableFiles(CommonColumns):
             # User doesn't have permissions to view any files; no need to issue a query.
             return {}
 
-        elif not len(where_clauses):
+        if where_clauses:
 
             # No where clause (the user is likely an admin).
-            statement = select([downloadableFiles_forQuery]).select_from(
-                downloadableFiles_forQuery
+            statement = select([downloadable_files_for_query]).select_from(
+                downloadable_files_for_query
             )
 
         else:
             statement = (
-                select([downloadableFiles_forQuery])
+                select([downloadable_files_for_query])
                 .where(sql_and(*where_clauses))
                 .select_from(
-                    downloadableFiles_forQuery.outerjoin(filesToFileGroups_forQuery)
+                    downloadable_files_for_query.outerjoin(
+                        files_to_file_groups_for_query
+                    )
                 )
             )
 
@@ -2610,7 +2614,7 @@ class DownloadableFiles(CommonColumns):
         statement = statement.limit(page_size).offset(page_num * page_size)
 
         return DownloadableFiles._convert_list_results(
-            downloadableFiles_forQuery, session.execute(statement).fetchall()
+            downloadable_files_for_query, session.execute(statement).fetchall()
         )
 
     @classmethod
@@ -2618,25 +2622,32 @@ class DownloadableFiles(CommonColumns):
     def count_with_permissions(
         cls,
         session: Session,
-        trial_ids: List[str] = [],
-        facets: List[List[str]] = [],
-        page_num: int = 0,
-        page_size: int = PAGINATION_PAGE_SIZE,
-        sort_field: Optional[str] = None,
-        sort_direction: Optional[str] = None,
+        trial_ids: List[str] = None,
+        facets: List[List[str]] = None,
+        # page_num: int = 0,
+        # page_size: int = PAGINATION_PAGE_SIZE,
+        # sort_field: Optional[str] = None,
+        # sort_direction: Optional[str] = None,
         user: Users = None,
     ):
         """
         Return the total number of records that would be returned by equivalent calls to
         list_with_permissions() (disregarding results paging).
         """
+
+        if trial_ids is None:
+            trial_ids = []
+
+        if facets is None:
+            facets = []
+
         (
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
         ) = DownloadableFiles._generate_query_objects()
         where_clauses = DownloadableFiles._generate_where_clauses(
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
             trial_ids,
             facets,
             user,
@@ -2646,19 +2657,21 @@ class DownloadableFiles(CommonColumns):
             # User doesn't have permissions to view any files; no need to issue a query.
             return 0
 
-        elif not len(where_clauses):
+        if where_clauses:
 
             # No where clause (the user is likely an admin).
             statement = select(
-                [func.count(downloadableFiles_forQuery.c.id)]
-            ).select_from(downloadableFiles_forQuery)
+                [func.count(downloadable_files_for_query.c.id)]
+            ).select_from(downloadable_files_for_query)
 
         else:
             statement = (
-                select([func.count(downloadableFiles_forQuery.c.id)])
+                select([func.count(downloadable_files_for_query.c.id)])
                 .where(sql_and(*where_clauses))
                 .select_from(
-                    downloadableFiles_forQuery.outerjoin(filesToFileGroups_forQuery)
+                    downloadable_files_for_query.outerjoin(
+                        files_to_file_groups_for_query
+                    )
                 )
             )
 
@@ -2667,19 +2680,23 @@ class DownloadableFiles(CommonColumns):
     @classmethod
     @with_default_session
     def count_by_facet_with_permissions(
-        cls, session: Session, trial_ids: List[str] = [], user: Users = None
+        cls, session: Session, trial_ids: List[str] = None, user: Users = None
     ):
         """
         Returns a map of facet_group to a count of the number of files that the given user
         has permissions to view.
         """
+
+        if trial_ids is None:
+            trial_ids = []
+
         (
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
         ) = DownloadableFiles._generate_query_objects()
         where_clauses = DownloadableFiles._generate_where_clauses(
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
             trial_ids,
             None,
             user,
@@ -2689,33 +2706,35 @@ class DownloadableFiles(CommonColumns):
             # User doesn't have permissions to view any files; no need to issue a query.
             return {}
 
-        elif not len(where_clauses):
+        if not where_clauses:
 
             # No where clause (the user is likely an admin).
             statement = select(
                 [
-                    downloadableFiles_forQuery.c.facet_group,
-                    func.count(downloadableFiles_forQuery.c.id),
+                    downloadable_files_for_query.c.facet_group,
+                    func.count(downloadable_files_for_query.c.id),
                 ]
-            ).select_from(downloadableFiles_forQuery)
+            ).select_from(downloadable_files_for_query)
 
         else:
             statement = (
                 select(
                     [
-                        downloadableFiles_forQuery.c.facet_group,
-                        func.count(downloadableFiles_forQuery.c.id),
+                        downloadable_files_for_query.c.facet_group,
+                        func.count(downloadable_files_for_query.c.id),
                     ]
                 )
                 .where(sql_and(*where_clauses))
                 .select_from(
-                    downloadableFiles_forQuery.outerjoin(filesToFileGroups_forQuery)
+                    downloadable_files_for_query.outerjoin(
+                        files_to_file_groups_for_query
+                    )
                 )
             )
 
-        statement = statement.group_by(downloadableFiles_forQuery.c.facet_group)
+        statement = statement.group_by(downloadable_files_for_query.c.facet_group)
         results = session.execute(statement).fetchall()
-        return {k: v for k, v in results}
+        return dict(results)
 
     @classmethod
     @with_default_session
@@ -2727,12 +2746,12 @@ class DownloadableFiles(CommonColumns):
         the object_urls for those the user has permission for.
         """
         (
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
         ) = DownloadableFiles._generate_query_objects()
         where_clauses = DownloadableFiles._generate_where_clauses(
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
             None,
             None,
             user,
@@ -2742,23 +2761,25 @@ class DownloadableFiles(CommonColumns):
             # User doesn't have permissions to view any files; no need to issue a query.
             return {}
 
-        elif not len(where_clauses):
+        if not where_clauses:
 
             # No where clause (the user is likely an admin).
             statement = (
-                select([downloadableFiles_forQuery.c.object_url])
-                .where(downloadableFiles_forQuery.c.id.in_(ids))
-                .select_from(downloadableFiles_forQuery)
+                select([downloadable_files_for_query.c.object_url])
+                .where(downloadable_files_for_query.c.id.in_(ids))
+                .select_from(downloadable_files_for_query)
             )
 
         else:
             statement = (
-                select([downloadableFiles_forQuery.c.object_url])
+                select([downloadable_files_for_query.c.object_url])
                 .where(
-                    sql_and(*where_clauses, downloadableFiles_forQuery.c.id.in_(ids))
+                    sql_and(*where_clauses, downloadable_files_for_query.c.id.in_(ids))
                 )
                 .select_from(
-                    downloadableFiles_forQuery.outerjoin(filesToFileGroups_forQuery)
+                    downloadable_files_for_query.outerjoin(
+                        files_to_file_groups_for_query
+                    )
                 )
             )
 
@@ -2786,12 +2807,12 @@ class DownloadableFiles(CommonColumns):
         Files with a non-true data_category property are not included in these counts.
         """
         (
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
         ) = DownloadableFiles._generate_query_objects()
         where_clauses = DownloadableFiles._generate_where_clauses(
-            downloadableFiles_forQuery,
-            filesToFileGroups_forQuery,
+            downloadable_files_for_query,
+            files_to_file_groups_for_query,
             None,
             facets,
             user,
@@ -2801,25 +2822,26 @@ class DownloadableFiles(CommonColumns):
             # User doesn't have permissions to view any files; no need to issue a query.
             return {}
 
-        elif not len(where_clauses):
+        if not where_clauses:
 
             # No where clause (the user is likely an admin).
-            statement = select([downloadableFiles_forQuery]).select_from(
-                downloadableFiles_forQuery
+            statement = select([downloadable_files_for_query]).select_from(
+                downloadable_files_for_query
             )
 
         else:
             statement = (
-                select([downloadableFiles_forQuery])
+                select([downloadable_files_for_query])
                 .where(sql_and(*where_clauses))
                 .select_from(
-                    downloadableFiles_forQuery.outerjoin(filesToFileGroups_forQuery)
+                    downloadable_files_for_query.outerjoin(
+                        files_to_file_groups_for_query
+                    )
                 )
             )
 
-        results = session.execute(statement).fetchall()
         downloadable_files = DownloadableFiles._convert_list_results(
-            downloadableFiles_forQuery, session.execute(statement).fetchall()
+            downloadable_files_for_query, session.execute(statement).fetchall()
         )
         trial_file_counts = DownloadableFiles._generate_trial_file_counts(
             downloadable_files
@@ -2872,7 +2894,7 @@ class DownloadableFiles(CommonColumns):
     # TODO use old serach code again
     @staticmethod
     def build_file_filter(
-        trial_ids: List[str] = [], facets: List[List[str]] = [], user: Users = None
+        trial_ids: List[str] = None, facets: List[List[str]] = None, user: Users = None
     ) -> Callable[[Query], Query]:
         """
         Build a file filter function based on the provided parameters. The resultant
@@ -2887,6 +2909,12 @@ class DownloadableFiles(CommonColumns):
         Returns:
             A function that adds filters to a query against the DownloadableFiles table.
         """
+        if trial_ids is None:
+            trial_ids = []
+
+        if facets is None:
+            facets = []
+
         file_filters = []
         if trial_ids:
             file_filters.append(DownloadableFiles.trial_id.in_(trial_ids))
@@ -2947,10 +2975,10 @@ class DownloadableFiles(CommonColumns):
             "additional_metadata": additional_metadata,
         }
 
+        # TODO maybe put non supported stuff from file_metadata to some misc jsonb column?
         for key, value in file_metadata.items():
             if key in supported_columns:
                 filtered_metadata[key] = value
-        # TODO maybe put non supported stuff from file_metadata to some misc jsonb column?
 
         etag = make_etag(filtered_metadata.values())