diff --git a/apiv2/database/migrations/versions/20241213_131118_autogenerated.py b/apiv2/database/migrations/versions/20241213_131118_autogenerated.py index 299fc6dab..7516b6ed6 100644 --- a/apiv2/database/migrations/versions/20241213_131118_autogenerated.py +++ b/apiv2/database/migrations/versions/20241213_131118_autogenerated.py @@ -3,27 +3,28 @@ Create Date: 2024-12-13 18:11:22.094904 """ + import sqlalchemy as sa from alembic import op # revision identifiers, used by Alembic. -revision = '20241213_131118' -down_revision = '20241010_153240' +revision = "20241213_131118" +down_revision = "20241010_153240" branch_labels = None depends_on = None def upgrade() -> None: # ### commands auto generated by Alembic - please adjust! ### - op.add_column('tiltseries', sa.Column('size_x', sa.Integer(), nullable=True)) - op.add_column('tiltseries', sa.Column('size_y', sa.Integer(), nullable=True)) - op.add_column('tiltseries', sa.Column('size_z', sa.Integer(), nullable=True)) + op.add_column("tiltseries", sa.Column("size_x", sa.Integer(), nullable=True)) + op.add_column("tiltseries", sa.Column("size_y", sa.Integer(), nullable=True)) + op.add_column("tiltseries", sa.Column("size_z", sa.Integer(), nullable=True)) # ### end Alembic commands ### def downgrade() -> None: # ### commands auto generated by Alembic - please adjust! ### - op.drop_column('tiltseries', 'size_z') - op.drop_column('tiltseries', 'size_y') - op.drop_column('tiltseries', 'size_x') + op.drop_column("tiltseries", "size_z") + op.drop_column("tiltseries", "size_y") + op.drop_column("tiltseries", "size_x") # ### end Alembic commands ### diff --git a/apiv2/database/migrations/versions/20250109_114311_autogenerated.py b/apiv2/database/migrations/versions/20250109_114311_autogenerated.py new file mode 100644 index 000000000..15c9fffa2 --- /dev/null +++ b/apiv2/database/migrations/versions/20250109_114311_autogenerated.py @@ -0,0 +1,38 @@ +"""autogenerated + +Create Date: 2025-01-09 16:43:14.268438 + +""" + +import sqlalchemy as sa +from alembic import op + +# revision identifiers, used by Alembic. +revision = "20250109_114311" +down_revision = "20241213_131118" +branch_labels = None +depends_on = None + + +def upgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.add_column("annotation_file", sa.Column("file_size", sa.Integer(), nullable=True)) + op.add_column("dataset", sa.Column("file_size", sa.Integer(), nullable=True)) + op.add_column("frame", sa.Column("file_size", sa.Integer(), nullable=True)) + op.add_column("tiltseries", sa.Column("file_size_omezarr", sa.Integer(), nullable=True)) + op.add_column("tiltseries", sa.Column("file_size_mrc", sa.Integer(), nullable=True)) + op.add_column("tomogram", sa.Column("file_size_omezarr", sa.Integer(), nullable=True)) + op.add_column("tomogram", sa.Column("file_size_mrc", sa.Integer(), nullable=True)) + # ### end Alembic commands ### + + +def downgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column("tomogram", "file_size_mrc") + op.drop_column("tomogram", "file_size_omezarr") + op.drop_column("tiltseries", "file_size_mrc") + op.drop_column("tiltseries", "file_size_omezarr") + op.drop_column("frame", "file_size") + op.drop_column("dataset", "file_size") + op.drop_column("annotation_file", "file_size") + # ### end Alembic commands ### diff --git a/apiv2/database/migrations/versions/20250110_181130_autogenerated.py b/apiv2/database/migrations/versions/20250110_181130_autogenerated.py new file mode 100644 index 000000000..9f0470e99 --- /dev/null +++ b/apiv2/database/migrations/versions/20250110_181130_autogenerated.py @@ -0,0 +1,701 @@ +"""autogenerated + +Create Date: 2025-01-10 23:11:33.018478 + +""" +import sqlalchemy as sa +from alembic import op + +# revision identifiers, used by Alembic. +revision = '20250110_181130' +down_revision = '20250109_114311' +branch_labels = None +depends_on = None + + +def upgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.alter_column('alignment', 'deposition_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('alignment', 'tiltseries_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('alignment', 'run_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('alignment', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('alignment_id_seq'::regclass)")) + op.alter_column('annotation', 'run_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation', 'deposition_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation', 'object_count', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('annotation_author', 'annotation_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation_author', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('annotation_author', 'author_list_order', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('annotation_file', 'alignment_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation_file', 'annotation_shape_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation_file', 'tomogram_voxel_spacing_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation_file', 'file_size', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation_file', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('annotation_method_link', 'annotation_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation_method_link', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('annotation_shape', 'annotation_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('annotation_shape', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('dataset', 'deposition_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('dataset', 'organism_taxid', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('dataset', 'file_size', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('dataset', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('dataset_author', 'dataset_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('dataset_author', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('dataset_author', 'author_list_order', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('dataset_funding', 'dataset_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('dataset_funding', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('deposition', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('deposition_id_seq'::regclass)")) + op.alter_column('deposition_author', 'deposition_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('deposition_author', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('deposition_author', 'author_list_order', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('deposition_type', 'deposition_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('deposition_type', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('frame', 'deposition_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('frame', 'run_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('frame', 'acquisition_order', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('frame', 'file_size', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('frame', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('frame_acquisition_file', 'run_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('frame_acquisition_file', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('gain_file', 'run_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('gain_file', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('per_section_alignment_parameters', 'alignment_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('per_section_alignment_parameters', 'z_index', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('per_section_alignment_parameters', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('run', 'dataset_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('run', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('run_id_seq'::regclass)")) + op.alter_column('tiltseries', 'run_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tiltseries', 'deposition_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tiltseries', 'file_size_omezarr', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tiltseries', 'file_size_mrc', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tiltseries', 'acceleration_voltage', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tiltseries', 'tilt_series_quality', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tiltseries', 'aligned_tiltseries_binning', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tiltseries', 'size_x', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tiltseries', 'size_y', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tiltseries', 'size_z', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tiltseries', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('tiltseries_id_seq'::regclass)")) + op.alter_column('tomogram', 'alignment_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tomogram', 'deposition_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tomogram', 'run_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tomogram', 'tomogram_voxel_spacing_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tomogram', 'size_x', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tomogram', 'size_y', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tomogram', 'size_z', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tomogram', 'file_size_omezarr', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tomogram', 'file_size_mrc', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tomogram', 'offset_x', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tomogram', 'offset_y', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tomogram', 'offset_z', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tomogram', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('tomogram_id_seq'::regclass)")) + op.alter_column('tomogram_author', 'tomogram_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tomogram_author', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True) + op.alter_column('tomogram_author', 'author_list_order', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False) + op.alter_column('tomogram_voxel_spacing', 'run_id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=True) + op.alter_column('tomogram_voxel_spacing', 'id', + existing_type=sa.INTEGER(), + type_=sa.BigInteger(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('tomogram_voxel_spacing_id_seq'::regclass)")) + # ### end Alembic commands ### + + +def downgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.alter_column('tomogram_voxel_spacing', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('tomogram_voxel_spacing_id_seq'::regclass)")) + op.alter_column('tomogram_voxel_spacing', 'run_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tomogram_author', 'author_list_order', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tomogram_author', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('tomogram_author', 'tomogram_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tomogram', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('tomogram_id_seq'::regclass)")) + op.alter_column('tomogram', 'offset_z', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tomogram', 'offset_y', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tomogram', 'offset_x', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tomogram', 'file_size_mrc', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tomogram', 'file_size_omezarr', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tomogram', 'size_z', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tomogram', 'size_y', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tomogram', 'size_x', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tomogram', 'tomogram_voxel_spacing_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tomogram', 'run_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tomogram', 'deposition_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tomogram', 'alignment_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tiltseries', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('tiltseries_id_seq'::regclass)")) + op.alter_column('tiltseries', 'size_z', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tiltseries', 'size_y', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tiltseries', 'size_x', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tiltseries', 'aligned_tiltseries_binning', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tiltseries', 'tilt_series_quality', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tiltseries', 'acceleration_voltage', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('tiltseries', 'file_size_mrc', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tiltseries', 'file_size_omezarr', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tiltseries', 'deposition_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('tiltseries', 'run_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('run', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('run_id_seq'::regclass)")) + op.alter_column('run', 'dataset_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('per_section_alignment_parameters', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('per_section_alignment_parameters', 'z_index', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('per_section_alignment_parameters', 'alignment_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('gain_file', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('gain_file', 'run_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('frame_acquisition_file', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('frame_acquisition_file', 'run_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('frame', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('frame', 'file_size', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('frame', 'acquisition_order', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('frame', 'run_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('frame', 'deposition_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('deposition_type', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('deposition_type', 'deposition_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('deposition_author', 'author_list_order', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('deposition_author', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('deposition_author', 'deposition_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('deposition', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('deposition_id_seq'::regclass)")) + op.alter_column('dataset_funding', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('dataset_funding', 'dataset_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('dataset_author', 'author_list_order', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('dataset_author', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('dataset_author', 'dataset_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('dataset', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('dataset', 'file_size', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('dataset', 'organism_taxid', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('dataset', 'deposition_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('annotation_shape', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('annotation_shape', 'annotation_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('annotation_method_link', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('annotation_method_link', 'annotation_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('annotation_file', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('annotation_file', 'file_size', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('annotation_file', 'tomogram_voxel_spacing_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('annotation_file', 'annotation_shape_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('annotation_file', 'alignment_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('annotation_author', 'author_list_order', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False) + op.alter_column('annotation_author', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('annotation_author', 'annotation_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('annotation', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True) + op.alter_column('annotation', 'object_count', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('annotation', 'deposition_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('annotation', 'run_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('alignment', 'id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=False, + autoincrement=True, + existing_server_default=sa.text("nextval('alignment_id_seq'::regclass)")) + op.alter_column('alignment', 'run_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('alignment', 'tiltseries_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + op.alter_column('alignment', 'deposition_id', + existing_type=sa.BigInteger(), + type_=sa.INTEGER(), + existing_nullable=True) + # ### end Alembic commands ### diff --git a/apiv2/database/models/alignment.py b/apiv2/database/models/alignment.py index a6e722c75..6dbe4a7ab 100644 --- a/apiv2/database/models/alignment.py +++ b/apiv2/database/models/alignment.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Boolean, Enum, Float, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, Enum, Float, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from support.enums import alignment_method_type_enum, alignment_type_enum @@ -54,13 +54,13 @@ class Alignment(Base): foreign_keys="PerSectionAlignmentParameters.alignment_id", cascade="all, delete-orphan", ) - deposition_id: Mapped[int] = mapped_column(Integer, ForeignKey("deposition.id"), nullable=True, index=True) + deposition_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("deposition.id"), nullable=True, index=True) deposition: Mapped["Deposition"] = relationship( "Deposition", foreign_keys=deposition_id, back_populates="alignments", ) - tiltseries_id: Mapped[int] = mapped_column(Integer, ForeignKey("tiltseries.id"), nullable=True, index=True) + tiltseries_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("tiltseries.id"), nullable=True, index=True) tiltseries: Mapped["Tiltseries"] = relationship( "Tiltseries", foreign_keys=tiltseries_id, @@ -73,7 +73,7 @@ class Alignment(Base): foreign_keys="Tomogram.alignment_id", cascade="all, delete-orphan", ) - run_id: Mapped[int] = mapped_column(Integer, ForeignKey("run.id"), nullable=True, index=True) + run_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("run.id"), nullable=True, index=True) run: Mapped["Run"] = relationship( "Run", foreign_keys=run_id, @@ -97,4 +97,4 @@ class Alignment(Base): s3_alignment_metadata: Mapped[str] = mapped_column(String, nullable=True) https_alignment_metadata: Mapped[str] = mapped_column(String, nullable=True) is_portal_standard: Mapped[bool] = mapped_column(Boolean, nullable=True) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/annotation.py b/apiv2/database/models/annotation.py index 60ce1a4c0..b3aab7abf 100644 --- a/apiv2/database/models/annotation.py +++ b/apiv2/database/models/annotation.py @@ -8,7 +8,7 @@ import datetime from typing import TYPE_CHECKING -from sqlalchemy import Boolean, DateTime, Enum, Float, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, DateTime, Enum, Float, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from support.enums import annotation_method_type_enum @@ -39,7 +39,7 @@ class Annotation(Base): __tablename__ = "annotation" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - run_id: Mapped[int] = mapped_column(Integer, ForeignKey("run.id"), nullable=True, index=True) + run_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("run.id"), nullable=True, index=True) run: Mapped["Run"] = relationship( "Run", foreign_keys=run_id, @@ -66,7 +66,7 @@ class Annotation(Base): foreign_keys="AnnotationAuthor.annotation_id", cascade="all, delete-orphan", ) - deposition_id: Mapped[int] = mapped_column(Integer, ForeignKey("deposition.id"), nullable=True, index=True) + deposition_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("deposition.id"), nullable=True, index=True) deposition: Mapped["Deposition"] = relationship( "Deposition", foreign_keys=deposition_id, @@ -81,7 +81,7 @@ class Annotation(Base): object_name: Mapped[str] = mapped_column(String, nullable=False) object_description: Mapped[str] = mapped_column(String, nullable=True) object_state: Mapped[str] = mapped_column(String, nullable=True) - object_count: Mapped[int] = mapped_column(Integer, nullable=True) + object_count: Mapped[int] = mapped_column(BigInteger, nullable=True) confidence_precision: Mapped[float] = mapped_column(Float, nullable=True) confidence_recall: Mapped[float] = mapped_column(Float, nullable=True) ground_truth_used: Mapped[str] = mapped_column(String, nullable=True) @@ -93,4 +93,4 @@ class Annotation(Base): deposition_date: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable=False) release_date: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable=False) last_modified_date: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable=False) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/annotation_author.py b/apiv2/database/models/annotation_author.py index 0eee45d9b..fbf5f1d7a 100644 --- a/apiv2/database/models/annotation_author.py +++ b/apiv2/database/models/annotation_author.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Boolean, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -29,14 +29,14 @@ class AnnotationAuthor(Base): __tablename__ = "annotation_author" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - annotation_id: Mapped[int] = mapped_column(Integer, ForeignKey("annotation.id"), nullable=True, index=True) + annotation_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("annotation.id"), nullable=True, index=True) annotation: Mapped["Annotation"] = relationship( "Annotation", foreign_keys=annotation_id, back_populates="authors", ) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) - author_list_order: Mapped[int] = mapped_column(Integer, nullable=False) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) + author_list_order: Mapped[int] = mapped_column(BigInteger, nullable=False) orcid: Mapped[str] = mapped_column(String, nullable=True) name: Mapped[str] = mapped_column(String, nullable=False) email: Mapped[str] = mapped_column(String, nullable=True) diff --git a/apiv2/database/models/annotation_file.py b/apiv2/database/models/annotation_file.py index 7c03ee90f..46424e118 100644 --- a/apiv2/database/models/annotation_file.py +++ b/apiv2/database/models/annotation_file.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Boolean, Enum, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, Enum, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from support.enums import annotation_file_source_enum @@ -34,14 +34,14 @@ class AnnotationFile(Base): __tablename__ = "annotation_file" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - alignment_id: Mapped[int] = mapped_column(Integer, ForeignKey("alignment.id"), nullable=True, index=True) + alignment_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("alignment.id"), nullable=True, index=True) alignment: Mapped["Alignment"] = relationship( "Alignment", foreign_keys=alignment_id, back_populates="annotation_files", ) annotation_shape_id: Mapped[int] = mapped_column( - Integer, ForeignKey("annotation_shape.id"), nullable=True, index=True, + BigInteger, ForeignKey("annotation_shape.id"), nullable=True, index=True, ) annotation_shape: Mapped["AnnotationShape"] = relationship( "AnnotationShape", @@ -49,7 +49,7 @@ class AnnotationFile(Base): back_populates="annotation_files", ) tomogram_voxel_spacing_id: Mapped[int] = mapped_column( - Integer, ForeignKey("tomogram_voxel_spacing.id"), nullable=True, index=True, + BigInteger, ForeignKey("tomogram_voxel_spacing.id"), nullable=True, index=True, ) tomogram_voxel_spacing: Mapped["TomogramVoxelSpacing"] = relationship( "TomogramVoxelSpacing", @@ -58,9 +58,10 @@ class AnnotationFile(Base): ) format: Mapped[str] = mapped_column(String, nullable=False) s3_path: Mapped[str] = mapped_column(String, nullable=False) + file_size: Mapped[int] = mapped_column(BigInteger, nullable=True) https_path: Mapped[str] = mapped_column(String, nullable=False) is_visualization_default: Mapped[bool] = mapped_column(Boolean, nullable=True) source: Mapped[annotation_file_source_enum] = mapped_column( Enum(annotation_file_source_enum, native_enum=False), nullable=True, ) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/annotation_method_link.py b/apiv2/database/models/annotation_method_link.py index 904600bb7..2bbfeffb7 100644 --- a/apiv2/database/models/annotation_method_link.py +++ b/apiv2/database/models/annotation_method_link.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Enum, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Enum, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from support.enums import annotation_method_link_type_enum @@ -30,7 +30,7 @@ class AnnotationMethodLink(Base): __tablename__ = "annotation_method_link" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - annotation_id: Mapped[int] = mapped_column(Integer, ForeignKey("annotation.id"), nullable=True, index=True) + annotation_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("annotation.id"), nullable=True, index=True) annotation: Mapped["Annotation"] = relationship( "Annotation", foreign_keys=annotation_id, @@ -41,4 +41,4 @@ class AnnotationMethodLink(Base): ) name: Mapped[str] = mapped_column(String, nullable=True) link: Mapped[str] = mapped_column(String, nullable=False) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/annotation_shape.py b/apiv2/database/models/annotation_shape.py index 4b0bba426..4e6228513 100644 --- a/apiv2/database/models/annotation_shape.py +++ b/apiv2/database/models/annotation_shape.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Enum, ForeignKey, Integer +from sqlalchemy import BigInteger, Enum, ForeignKey from sqlalchemy.orm import Mapped, mapped_column, relationship from support.enums import annotation_file_shape_type_enum @@ -32,7 +32,7 @@ class AnnotationShape(Base): __tablename__ = "annotation_shape" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - annotation_id: Mapped[int] = mapped_column(Integer, ForeignKey("annotation.id"), nullable=True, index=True) + annotation_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("annotation.id"), nullable=True, index=True) annotation: Mapped["Annotation"] = relationship( "Annotation", foreign_keys=annotation_id, @@ -48,4 +48,4 @@ class AnnotationShape(Base): shape_type: Mapped[annotation_file_shape_type_enum] = mapped_column( Enum(annotation_file_shape_type_enum, native_enum=False), nullable=True, ) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/dataset.py b/apiv2/database/models/dataset.py index 63f3ef380..258df245b 100644 --- a/apiv2/database/models/dataset.py +++ b/apiv2/database/models/dataset.py @@ -8,7 +8,7 @@ import datetime from typing import TYPE_CHECKING -from sqlalchemy import DateTime, Enum, ForeignKey, Integer, String +from sqlalchemy import BigInteger, DateTime, Enum, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from support.enums import sample_type_enum @@ -37,7 +37,7 @@ class Dataset(Base): __tablename__ = "dataset" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - deposition_id: Mapped[int] = mapped_column(Integer, ForeignKey("deposition.id"), nullable=False, index=True) + deposition_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("deposition.id"), nullable=False, index=True) deposition: Mapped["Deposition"] = relationship( "Deposition", foreign_keys=deposition_id, @@ -63,7 +63,7 @@ class Dataset(Base): title: Mapped[str] = mapped_column(String, nullable=False) description: Mapped[str] = mapped_column(String, nullable=False) organism_name: Mapped[str] = mapped_column(String, nullable=True) - organism_taxid: Mapped[int] = mapped_column(Integer, nullable=True) + organism_taxid: Mapped[int] = mapped_column(BigInteger, nullable=True) tissue_name: Mapped[str] = mapped_column(String, nullable=True) tissue_id: Mapped[str] = mapped_column(String, nullable=True) cell_name: Mapped[str] = mapped_column(String, nullable=True) @@ -85,4 +85,5 @@ class Dataset(Base): related_database_entries: Mapped[str] = mapped_column(String, nullable=True) s3_prefix: Mapped[str] = mapped_column(String, nullable=False) https_prefix: Mapped[str] = mapped_column(String, nullable=False) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, primary_key=True) + file_size: Mapped[int] = mapped_column(BigInteger, nullable=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, primary_key=True) diff --git a/apiv2/database/models/dataset_author.py b/apiv2/database/models/dataset_author.py index 388edd817..3a00e9d97 100644 --- a/apiv2/database/models/dataset_author.py +++ b/apiv2/database/models/dataset_author.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Boolean, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -29,14 +29,14 @@ class DatasetAuthor(Base): __tablename__ = "dataset_author" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - dataset_id: Mapped[int] = mapped_column(Integer, ForeignKey("dataset.id"), nullable=True, index=True) + dataset_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("dataset.id"), nullable=True, index=True) dataset: Mapped["Dataset"] = relationship( "Dataset", foreign_keys=dataset_id, back_populates="authors", ) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) - author_list_order: Mapped[int] = mapped_column(Integer, nullable=False) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) + author_list_order: Mapped[int] = mapped_column(BigInteger, nullable=False) orcid: Mapped[str] = mapped_column(String, nullable=True) name: Mapped[str] = mapped_column(String, nullable=False) email: Mapped[str] = mapped_column(String, nullable=True) diff --git a/apiv2/database/models/dataset_funding.py b/apiv2/database/models/dataset_funding.py index 86974cc60..f03fefe46 100644 --- a/apiv2/database/models/dataset_funding.py +++ b/apiv2/database/models/dataset_funding.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import ForeignKey, Integer, String +from sqlalchemy import BigInteger, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -29,7 +29,7 @@ class DatasetFunding(Base): __tablename__ = "dataset_funding" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - dataset_id: Mapped[int] = mapped_column(Integer, ForeignKey("dataset.id"), nullable=True, index=True) + dataset_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("dataset.id"), nullable=True, index=True) dataset: Mapped["Dataset"] = relationship( "Dataset", foreign_keys=dataset_id, @@ -37,4 +37,4 @@ class DatasetFunding(Base): ) funding_agency_name: Mapped[str] = mapped_column(String, nullable=True) grant_id: Mapped[str] = mapped_column(String, nullable=True) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/deposition.py b/apiv2/database/models/deposition.py index 75e59aa4d..cdd862b85 100644 --- a/apiv2/database/models/deposition.py +++ b/apiv2/database/models/deposition.py @@ -8,7 +8,7 @@ import datetime from typing import TYPE_CHECKING -from sqlalchemy import DateTime, Integer, String +from sqlalchemy import BigInteger, DateTime, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -109,4 +109,4 @@ class Deposition(Base): last_modified_date: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable=False) key_photo_url: Mapped[str] = mapped_column(String, nullable=True) key_photo_thumbnail_url: Mapped[str] = mapped_column(String, nullable=True) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/deposition_author.py b/apiv2/database/models/deposition_author.py index 6fc0bbf68..a42f4efe9 100644 --- a/apiv2/database/models/deposition_author.py +++ b/apiv2/database/models/deposition_author.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Boolean, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -29,14 +29,14 @@ class DepositionAuthor(Base): __tablename__ = "deposition_author" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - deposition_id: Mapped[int] = mapped_column(Integer, ForeignKey("deposition.id"), nullable=False, index=True) + deposition_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("deposition.id"), nullable=False, index=True) deposition: Mapped["Deposition"] = relationship( "Deposition", foreign_keys=deposition_id, back_populates="authors", ) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) - author_list_order: Mapped[int] = mapped_column(Integer, nullable=False) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) + author_list_order: Mapped[int] = mapped_column(BigInteger, nullable=False) orcid: Mapped[str] = mapped_column(String, nullable=True) name: Mapped[str] = mapped_column(String, nullable=False) email: Mapped[str] = mapped_column(String, nullable=True) diff --git a/apiv2/database/models/deposition_type.py b/apiv2/database/models/deposition_type.py index 84d78dcef..e1cd39e65 100644 --- a/apiv2/database/models/deposition_type.py +++ b/apiv2/database/models/deposition_type.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Enum, ForeignKey, Integer +from sqlalchemy import BigInteger, Enum, ForeignKey from sqlalchemy.orm import Mapped, mapped_column, relationship from support.enums import deposition_types_enum @@ -30,11 +30,11 @@ class DepositionType(Base): __tablename__ = "deposition_type" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - deposition_id: Mapped[int] = mapped_column(Integer, ForeignKey("deposition.id"), nullable=False, index=True) + deposition_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("deposition.id"), nullable=False, index=True) deposition: Mapped["Deposition"] = relationship( "Deposition", foreign_keys=deposition_id, back_populates="deposition_types", ) type: Mapped[deposition_types_enum] = mapped_column(Enum(deposition_types_enum, native_enum=False), nullable=True) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/frame.py b/apiv2/database/models/frame.py index a2a9b8a69..f03c4079a 100644 --- a/apiv2/database/models/frame.py +++ b/apiv2/database/models/frame.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Boolean, Float, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, Float, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -31,22 +31,23 @@ class Frame(Base): __tablename__ = "frame" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - deposition_id: Mapped[int] = mapped_column(Integer, ForeignKey("deposition.id"), nullable=False, index=True) + deposition_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("deposition.id"), nullable=False, index=True) deposition: Mapped["Deposition"] = relationship( "Deposition", foreign_keys=deposition_id, back_populates="frames", ) - run_id: Mapped[int] = mapped_column(Integer, ForeignKey("run.id"), nullable=False, index=True) + run_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("run.id"), nullable=False, index=True) run: Mapped["Run"] = relationship( "Run", foreign_keys=run_id, back_populates="frames", ) raw_angle: Mapped[float] = mapped_column(Float, nullable=True) - acquisition_order: Mapped[int] = mapped_column(Integer, nullable=True) + acquisition_order: Mapped[int] = mapped_column(BigInteger, nullable=True) dose: Mapped[float] = mapped_column(Float, nullable=True) is_gain_corrected: Mapped[bool] = mapped_column(Boolean, nullable=True) s3_frame_path: Mapped[str] = mapped_column(String, nullable=False) https_frame_path: Mapped[str] = mapped_column(String, nullable=False) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + file_size: Mapped[int] = mapped_column(BigInteger, nullable=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/frame_acquisition_file.py b/apiv2/database/models/frame_acquisition_file.py index d9bb01b98..ddad4d371 100644 --- a/apiv2/database/models/frame_acquisition_file.py +++ b/apiv2/database/models/frame_acquisition_file.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import ForeignKey, Integer, String +from sqlalchemy import BigInteger, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -29,7 +29,7 @@ class FrameAcquisitionFile(Base): __tablename__ = "frame_acquisition_file" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - run_id: Mapped[int] = mapped_column(Integer, ForeignKey("run.id"), nullable=True, index=True) + run_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("run.id"), nullable=True, index=True) run: Mapped["Run"] = relationship( "Run", foreign_keys=run_id, @@ -37,4 +37,4 @@ class FrameAcquisitionFile(Base): ) s3_mdoc_path: Mapped[str] = mapped_column(String, nullable=False) https_mdoc_path: Mapped[str] = mapped_column(String, nullable=False) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/gain_file.py b/apiv2/database/models/gain_file.py index 63448cc63..0485db259 100644 --- a/apiv2/database/models/gain_file.py +++ b/apiv2/database/models/gain_file.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import ForeignKey, Integer, String +from sqlalchemy import BigInteger, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -29,7 +29,7 @@ class GainFile(Base): __tablename__ = "gain_file" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - run_id: Mapped[int] = mapped_column(Integer, ForeignKey("run.id"), nullable=False, index=True) + run_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("run.id"), nullable=False, index=True) run: Mapped["Run"] = relationship( "Run", foreign_keys=run_id, @@ -37,4 +37,4 @@ class GainFile(Base): ) s3_file_path: Mapped[str] = mapped_column(String, nullable=False) https_file_path: Mapped[str] = mapped_column(String, nullable=False) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/per_section_alignment_parameters.py b/apiv2/database/models/per_section_alignment_parameters.py index 13a45d0ac..de940d298 100644 --- a/apiv2/database/models/per_section_alignment_parameters.py +++ b/apiv2/database/models/per_section_alignment_parameters.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Float, ForeignKey, Integer +from sqlalchemy import BigInteger, Float, ForeignKey from sqlalchemy.dialects.postgresql import JSONB from sqlalchemy.orm import Mapped, mapped_column, relationship @@ -30,16 +30,16 @@ class PerSectionAlignmentParameters(Base): __tablename__ = "per_section_alignment_parameters" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - alignment_id: Mapped[int] = mapped_column(Integer, ForeignKey("alignment.id"), nullable=False, index=True) + alignment_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("alignment.id"), nullable=False, index=True) alignment: Mapped["Alignment"] = relationship( "Alignment", foreign_keys=alignment_id, back_populates="per_section_alignments", ) - z_index: Mapped[int] = mapped_column(Integer, nullable=False) + z_index: Mapped[int] = mapped_column(BigInteger, nullable=False) x_offset: Mapped[float] = mapped_column(Float, nullable=True) y_offset: Mapped[float] = mapped_column(Float, nullable=True) volume_x_rotation: Mapped[float] = mapped_column(Float, nullable=True) in_plane_rotation: Mapped[JSONB] = mapped_column(JSONB, nullable=True) tilt_angle: Mapped[float] = mapped_column(Float, nullable=True) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/run.py b/apiv2/database/models/run.py index 347aa961f..24b191c1d 100644 --- a/apiv2/database/models/run.py +++ b/apiv2/database/models/run.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import ForeignKey, Integer, String +from sqlalchemy import BigInteger, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -51,7 +51,7 @@ class Run(Base): annotations: Mapped[list[Annotation]] = relationship( "Annotation", back_populates="run", uselist=True, foreign_keys="Annotation.run_id", cascade="all, delete-orphan", ) - dataset_id: Mapped[int] = mapped_column(Integer, ForeignKey("dataset.id"), nullable=False, index=True) + dataset_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("dataset.id"), nullable=False, index=True) dataset: Mapped["Dataset"] = relationship( "Dataset", foreign_keys=dataset_id, @@ -86,4 +86,4 @@ class Run(Base): name: Mapped[str] = mapped_column(String, nullable=False) s3_prefix: Mapped[str] = mapped_column(String, nullable=False) https_prefix: Mapped[str] = mapped_column(String, nullable=False) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/tiltseries.py b/apiv2/database/models/tiltseries.py index d7b21e514..7f7c29406 100644 --- a/apiv2/database/models/tiltseries.py +++ b/apiv2/database/models/tiltseries.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Boolean, Enum, Float, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, Enum, Float, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from support.enums import tiltseries_microscope_manufacturer_enum @@ -41,25 +41,27 @@ class Tiltseries(Base): foreign_keys="Alignment.tiltseries_id", cascade="all, delete-orphan", ) - run_id: Mapped[int] = mapped_column(Integer, ForeignKey("run.id"), nullable=False, index=True) + run_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("run.id"), nullable=False, index=True) run: Mapped["Run"] = relationship( "Run", foreign_keys=run_id, back_populates="tiltseries", ) - deposition_id: Mapped[int] = mapped_column(Integer, ForeignKey("deposition.id"), nullable=True, index=True) + deposition_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("deposition.id"), nullable=True, index=True) deposition: Mapped["Deposition"] = relationship( "Deposition", foreign_keys=deposition_id, back_populates="tiltseries", ) s3_omezarr_dir: Mapped[str] = mapped_column(String, nullable=True) + file_size_omezarr: Mapped[int] = mapped_column(BigInteger, nullable=True) s3_mrc_file: Mapped[str] = mapped_column(String, nullable=True) + file_size_mrc: Mapped[int] = mapped_column(BigInteger, nullable=True) https_omezarr_dir: Mapped[str] = mapped_column(String, nullable=True) https_mrc_file: Mapped[str] = mapped_column(String, nullable=True) s3_angle_list: Mapped[str] = mapped_column(String, nullable=True) https_angle_list: Mapped[str] = mapped_column(String, nullable=True) - acceleration_voltage: Mapped[int] = mapped_column(Integer, nullable=False) + acceleration_voltage: Mapped[int] = mapped_column(BigInteger, nullable=False) spherical_aberration_constant: Mapped[float] = mapped_column(Float, nullable=False) microscope_manufacturer: Mapped[tiltseries_microscope_manufacturer_enum] = mapped_column( Enum(tiltseries_microscope_manufacturer_enum, native_enum=False), nullable=False, @@ -81,11 +83,11 @@ class Tiltseries(Base): data_acquisition_software: Mapped[str] = mapped_column(String, nullable=False) related_empiar_entry: Mapped[str] = mapped_column(String, nullable=True) binning_from_frames: Mapped[float] = mapped_column(Float, nullable=True) - tilt_series_quality: Mapped[int] = mapped_column(Integer, nullable=False) + tilt_series_quality: Mapped[int] = mapped_column(BigInteger, nullable=False) is_aligned: Mapped[bool] = mapped_column(Boolean, nullable=False) pixel_spacing: Mapped[float] = mapped_column(Float, nullable=False) - aligned_tiltseries_binning: Mapped[int] = mapped_column(Integer, nullable=True) - size_x: Mapped[int] = mapped_column(Integer, nullable=True) - size_y: Mapped[int] = mapped_column(Integer, nullable=True) - size_z: Mapped[int] = mapped_column(Integer, nullable=True) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + aligned_tiltseries_binning: Mapped[int] = mapped_column(BigInteger, nullable=True) + size_x: Mapped[int] = mapped_column(BigInteger, nullable=True) + size_y: Mapped[int] = mapped_column(BigInteger, nullable=True) + size_z: Mapped[int] = mapped_column(BigInteger, nullable=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/database/models/tomogram.py b/apiv2/database/models/tomogram.py index 59b2c93cf..7581a4ed0 100644 --- a/apiv2/database/models/tomogram.py +++ b/apiv2/database/models/tomogram.py @@ -8,7 +8,7 @@ import datetime from typing import TYPE_CHECKING -from sqlalchemy import Boolean, DateTime, Enum, Float, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, DateTime, Enum, Float, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from support.enums import fiducial_alignment_status_enum, tomogram_processing_enum, tomogram_reconstruction_method_enum @@ -39,7 +39,7 @@ class Tomogram(Base): __tablename__ = "tomogram" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - alignment_id: Mapped[int] = mapped_column(Integer, ForeignKey("alignment.id"), nullable=True, index=True) + alignment_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("alignment.id"), nullable=True, index=True) alignment: Mapped["Alignment"] = relationship( "Alignment", foreign_keys=alignment_id, @@ -52,20 +52,20 @@ class Tomogram(Base): foreign_keys="TomogramAuthor.tomogram_id", cascade="all, delete-orphan", ) - deposition_id: Mapped[int] = mapped_column(Integer, ForeignKey("deposition.id"), nullable=False, index=True) + deposition_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("deposition.id"), nullable=False, index=True) deposition: Mapped["Deposition"] = relationship( "Deposition", foreign_keys=deposition_id, back_populates="tomograms", ) - run_id: Mapped[int] = mapped_column(Integer, ForeignKey("run.id"), nullable=True, index=True) + run_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("run.id"), nullable=True, index=True) run: Mapped["Run"] = relationship( "Run", foreign_keys=run_id, back_populates="tomograms", ) tomogram_voxel_spacing_id: Mapped[int] = mapped_column( - Integer, ForeignKey("tomogram_voxel_spacing.id"), nullable=True, index=True, + BigInteger, ForeignKey("tomogram_voxel_spacing.id"), nullable=True, index=True, ) tomogram_voxel_spacing: Mapped["TomogramVoxelSpacing"] = relationship( "TomogramVoxelSpacing", @@ -73,9 +73,9 @@ class Tomogram(Base): back_populates="tomograms", ) name: Mapped[str] = mapped_column(String, nullable=True) - size_x: Mapped[int] = mapped_column(Integer, nullable=False) - size_y: Mapped[int] = mapped_column(Integer, nullable=False) - size_z: Mapped[int] = mapped_column(Integer, nullable=False) + size_x: Mapped[int] = mapped_column(BigInteger, nullable=False) + size_y: Mapped[int] = mapped_column(BigInteger, nullable=False) + size_z: Mapped[int] = mapped_column(BigInteger, nullable=False) voxel_spacing: Mapped[float] = mapped_column(Float, nullable=False) fiducial_alignment_status: Mapped[fiducial_alignment_status_enum] = mapped_column( Enum(fiducial_alignment_status_enum, native_enum=False), nullable=False, @@ -94,21 +94,23 @@ class Tomogram(Base): is_visualization_default: Mapped[bool] = mapped_column(Boolean, nullable=True) s3_omezarr_dir: Mapped[str] = mapped_column(String, nullable=True) https_omezarr_dir: Mapped[str] = mapped_column(String, nullable=True) + file_size_omezarr: Mapped[int] = mapped_column(BigInteger, nullable=True) s3_mrc_file: Mapped[str] = mapped_column(String, nullable=True) https_mrc_file: Mapped[str] = mapped_column(String, nullable=True) + file_size_mrc: Mapped[int] = mapped_column(BigInteger, nullable=True) scale0_dimensions: Mapped[str] = mapped_column(String, nullable=True) scale1_dimensions: Mapped[str] = mapped_column(String, nullable=True) scale2_dimensions: Mapped[str] = mapped_column(String, nullable=True) ctf_corrected: Mapped[bool] = mapped_column(Boolean, nullable=True) - offset_x: Mapped[int] = mapped_column(Integer, nullable=False) - offset_y: Mapped[int] = mapped_column(Integer, nullable=False) - offset_z: Mapped[int] = mapped_column(Integer, nullable=False) + offset_x: Mapped[int] = mapped_column(BigInteger, nullable=False) + offset_y: Mapped[int] = mapped_column(BigInteger, nullable=False) + offset_z: Mapped[int] = mapped_column(BigInteger, nullable=False) key_photo_url: Mapped[str] = mapped_column(String, nullable=True) key_photo_thumbnail_url: Mapped[str] = mapped_column(String, nullable=True) neuroglancer_config: Mapped[str] = mapped_column(String, nullable=True) publications: Mapped[str] = mapped_column(String, nullable=True) related_database_entries: Mapped[str] = mapped_column(String, nullable=True) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) deposition_date: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable=True) release_date: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable=True) last_modified_date: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable=True) diff --git a/apiv2/database/models/tomogram_author.py b/apiv2/database/models/tomogram_author.py index 4586558ef..d37fcc494 100644 --- a/apiv2/database/models/tomogram_author.py +++ b/apiv2/database/models/tomogram_author.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Boolean, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Boolean, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -29,14 +29,14 @@ class TomogramAuthor(Base): __tablename__ = "tomogram_author" __mapper_args__ = {"polymorphic_identity": __tablename__, "polymorphic_load": "inline"} - tomogram_id: Mapped[int] = mapped_column(Integer, ForeignKey("tomogram.id"), nullable=True, index=True) + tomogram_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("tomogram.id"), nullable=True, index=True) tomogram: Mapped["Tomogram"] = relationship( "Tomogram", foreign_keys=tomogram_id, back_populates="authors", ) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) - author_list_order: Mapped[int] = mapped_column(Integer, nullable=False) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) + author_list_order: Mapped[int] = mapped_column(BigInteger, nullable=False) orcid: Mapped[str] = mapped_column(String, nullable=True) name: Mapped[str] = mapped_column(String, nullable=False) email: Mapped[str] = mapped_column(String, nullable=True) diff --git a/apiv2/database/models/tomogram_voxel_spacing.py b/apiv2/database/models/tomogram_voxel_spacing.py index 7e5c1f8b6..312dc9f11 100644 --- a/apiv2/database/models/tomogram_voxel_spacing.py +++ b/apiv2/database/models/tomogram_voxel_spacing.py @@ -7,7 +7,7 @@ from typing import TYPE_CHECKING -from sqlalchemy import Float, ForeignKey, Integer, String +from sqlalchemy import BigInteger, Float, ForeignKey, String from sqlalchemy.orm import Mapped, mapped_column, relationship from platformics.database.models.base import Base @@ -40,7 +40,7 @@ class TomogramVoxelSpacing(Base): foreign_keys="AnnotationFile.tomogram_voxel_spacing_id", cascade="all, delete-orphan", ) - run_id: Mapped[int] = mapped_column(Integer, ForeignKey("run.id"), nullable=True, index=True) + run_id: Mapped[int] = mapped_column(BigInteger, ForeignKey("run.id"), nullable=True, index=True) run: Mapped["Run"] = relationship( "Run", foreign_keys=run_id, @@ -56,4 +56,4 @@ class TomogramVoxelSpacing(Base): voxel_spacing: Mapped[float] = mapped_column(Float, nullable=False) s3_prefix: Mapped[str] = mapped_column(String, nullable=False) https_prefix: Mapped[str] = mapped_column(String, nullable=False) - id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True) + id: Mapped[int] = mapped_column(BigInteger, nullable=False, index=True, autoincrement=True, primary_key=True) diff --git a/apiv2/db_import/importers/annotation.py b/apiv2/db_import/importers/annotation.py index e343f4f98..754e7dd38 100644 --- a/apiv2/db_import/importers/annotation.py +++ b/apiv2/db_import/importers/annotation.py @@ -82,6 +82,7 @@ def load_computed_fields(self): self.model_args["source"] = self.calculate_source() self.model_args["s3_path"] = self.get_s3_url(self.input_data["path"]) self.model_args["https_path"] = self.get_https_url(self.input_data["path"]) + self.model_args["file_size"] = self.get_file_size(self.input_data["path"]) class AnnotationImporter(IntegratedDBImporter): diff --git a/apiv2/db_import/importers/base.py b/apiv2/db_import/importers/base.py index 42cf82a98..430169911 100644 --- a/apiv2/db_import/importers/base.py +++ b/apiv2/db_import/importers/base.py @@ -47,6 +47,27 @@ def get_s3_url(self, *input_path: tuple[str]) -> str: input_path = input_path[len(self.config.bucket_name) + 1 :] return os.path.join(self.config.s3_prefix, input_path) + def get_file_size(self, *input_path: tuple[str]) -> str: + input_path = os.path.join(*input_path) + if input_path.startswith(self.config.bucket_name): + input_path = input_path[len(self.config.bucket_name) + 1 :] + + total_size = 0 + try: + paginator = self.config.s3_client.get_paginator('list_objects_v2') + pages = paginator.paginate(Bucket=self.config.bucket_name, Prefix=input_path) + for page in pages: + if "Contents" in page: + for obj in page["Contents"]: + total_size += obj["Size"] + + + return total_size + except Exception as e: + print(f"Error retrieving folder size: {e}") + return None + + def _map_direct_fields(self): """Iterate over `self.direct_mapped_fields` and populate model args based on the data we find in the input dict.""" for db_key, _ in self.direct_mapped_fields.items(): diff --git a/apiv2/db_import/importers/base_importer.py b/apiv2/db_import/importers/base_importer.py index 8f3b051d1..f3f952dec 100644 --- a/apiv2/db_import/importers/base_importer.py +++ b/apiv2/db_import/importers/base_importer.py @@ -79,6 +79,26 @@ def get_s3_url(self, *input_path: tuple[str]) -> str: input_path = input_path[len(self.config.bucket_name) + 1 :] return os.path.join(self.config.s3_prefix, input_path) + def get_file_size(self, *input_path: tuple[str]) -> str: + input_path = os.path.join(*input_path) + if input_path.startswith(self.config.bucket_name): + input_path = input_path[len(self.config.bucket_name) + 1 :] + + total_size = 0 + try: + paginator = self.config.s3_client.get_paginator('list_objects_v2') + pages = paginator.paginate(Bucket=self.config.bucket_name, Prefix=input_path) + for page in pages: + if "Contents" in page: + for obj in page["Contents"]: + total_size += obj["Size"] + + + return total_size + except Exception as e: + print(f"Error retrieving folder size: {e}") + return None + class StaleDeletionDBImporter(BaseDBImporter): """ diff --git a/apiv2/db_import/importers/dataset.py b/apiv2/db_import/importers/dataset.py index 1a65ba57c..da26e1f72 100644 --- a/apiv2/db_import/importers/dataset.py +++ b/apiv2/db_import/importers/dataset.py @@ -64,6 +64,7 @@ def get_computed_fields(self) -> dict[str, Any]: extra_data = { "s3_prefix": self.get_s3_url(self.dir_prefix), "https_prefix": self.get_https_url(self.dir_prefix), + "file_size": self.get_file_size(self.dir_prefix), "key_photo_url": None, "key_photo_thumbnail_url": None, } diff --git a/apiv2/db_import/importers/frame.py b/apiv2/db_import/importers/frame.py index b6d881d81..a0bd2d941 100644 --- a/apiv2/db_import/importers/frame.py +++ b/apiv2/db_import/importers/frame.py @@ -24,6 +24,7 @@ class FrameItem(ItemDBImporter): def load_computed_fields(self): self.model_args["s3_frame_path"] = self.get_s3_url(self.input_data["file"]) self.model_args["https_frame_path"] = self.get_https_url(self.input_data["file"]) + self.model_args["file_size"] = self.get_file_size(self.input_data["file"]) self.model_args["run_id"] = self.input_data["run"].id self.model_args["deposition_id"] = self.input_data["deposition"].id diff --git a/apiv2/db_import/importers/tiltseries.py b/apiv2/db_import/importers/tiltseries.py index 4b34b8b38..b4e925c56 100644 --- a/apiv2/db_import/importers/tiltseries.py +++ b/apiv2/db_import/importers/tiltseries.py @@ -79,10 +79,12 @@ def get_computed_fields(self) -> dict[str, Any]: if mrc_path := self.metadata.get("mrc_file"): extra_data["s3_mrc_file"] = self.get_s3_url(mrc_path) extra_data["https_mrc_file"] = self.get_https_url(mrc_path) + extra_data["file_size_mrc"] = self.get_file_size(mrc_path) if omezarr_path := self.metadata.get("omezarr_dir"): extra_data["s3_omezarr_dir"] = self.get_s3_url(omezarr_path) extra_data["https_omezarr_dir"] = self.get_https_url(omezarr_path) + extra_data["file_size_omezarr"] = self.get_file_size(omezarr_path) if angle_list := self.get_first_match_file_name("*.rawtlt") or self.get_first_match_file_name("*.tlt"): extra_data["s3_angle_list"] = self.get_s3_url(angle_list) diff --git a/apiv2/db_import/tests/conftest.py b/apiv2/db_import/tests/conftest.py index a0896fea6..74852e3ca 100644 --- a/apiv2/db_import/tests/conftest.py +++ b/apiv2/db_import/tests/conftest.py @@ -127,4 +127,5 @@ def expected_dataset(http_prefix: str) -> dict[str, Any]: "key_photo_url": f"{http_prefix}/{DATASET_ID}/KeyPhoto/snapshot.png", "key_photo_thumbnail_url": f"{http_prefix}/{DATASET_ID}/KeyPhoto/thumbnail.png", "deposition_id": 300, + "file_size": 1373074, } diff --git a/apiv2/db_import/tests/test_db_annotation_import.py b/apiv2/db_import/tests/test_db_annotation_import.py index c40561e1b..283bf13d7 100644 --- a/apiv2/db_import/tests/test_db_annotation_import.py +++ b/apiv2/db_import/tests/test_db_annotation_import.py @@ -61,6 +61,7 @@ def expected_annotation_files(http_prefix: str) -> list[dict[str, Any]]: "source": "community", "format": "ndjson", "is_visualization_default": True, + "file_size": 0, }, { "tomogram_voxel_spacing_id": TOMOGRAM_VOXEL_ID1, @@ -69,6 +70,7 @@ def expected_annotation_files(http_prefix: str) -> list[dict[str, Any]]: "source": "community", "format": "mrc", "is_visualization_default": False, + "file_size": 0, }, { "tomogram_voxel_spacing_id": TOMOGRAM_VOXEL_ID1, @@ -77,6 +79,7 @@ def expected_annotation_files(http_prefix: str) -> list[dict[str, Any]]: "source": "community", "format": "zarr", "is_visualization_default": False, + "file_size": 0, }, ] diff --git a/apiv2/db_import/tests/test_db_tiltseries_import.py b/apiv2/db_import/tests/test_db_tiltseries_import.py index 41e9095ff..463035f42 100644 --- a/apiv2/db_import/tests/test_db_tiltseries_import.py +++ b/apiv2/db_import/tests/test_db_tiltseries_import.py @@ -55,6 +55,8 @@ def expected_tiltseries(http_prefix: str) -> list[dict[str, Any]]: "size_z": 31, "size_y": 3838, "size_x": 3708, + "file_size_omezarr": 0, + "file_size_mrc": 0, }, { "acceleration_voltage": 10000, @@ -82,6 +84,8 @@ def expected_tiltseries(http_prefix: str) -> list[dict[str, Any]]: "tilt_step": 3, "tilting_scheme": "min to max tilt", "total_flux": 12, + "file_size_omezarr": 0, + "file_size_mrc": 0, }, ] diff --git a/apiv2/db_import/tests/test_frame_import.py b/apiv2/db_import/tests/test_frame_import.py index ab2d0e909..90d13eb0d 100644 --- a/apiv2/db_import/tests/test_frame_import.py +++ b/apiv2/db_import/tests/test_frame_import.py @@ -20,10 +20,12 @@ def expected_frames(http_prefix: str) -> list[dict[str, Any]]: { "s3_frame_path": "s3://test-public-bucket/30001/RUN1/Frames/frame1", "https_frame_path": "https://foo.com/30001/RUN1/Frames/frame1", + "file_size": 0, }, { "s3_frame_path": "s3://test-public-bucket/30001/RUN1/Frames/frame2", "https_frame_path": "https://foo.com/30001/RUN1/Frames/frame2", + "file_size": 0, }, ] diff --git a/apiv2/graphql_api/helpers/annotation_file.py b/apiv2/graphql_api/helpers/annotation_file.py index 9b72e4dc4..267506cc2 100644 --- a/apiv2/graphql_api/helpers/annotation_file.py +++ b/apiv2/graphql_api/helpers/annotation_file.py @@ -40,6 +40,7 @@ class AnnotationFileGroupByOptions: ] = None format: Optional[str] = None s3_path: Optional[str] = None + file_size: Optional[int] = None https_path: Optional[str] = None is_visualization_default: Optional[bool] = None source: Optional[annotation_file_source_enum] = None diff --git a/apiv2/graphql_api/helpers/dataset.py b/apiv2/graphql_api/helpers/dataset.py index 867fc636d..63e83ba2b 100644 --- a/apiv2/graphql_api/helpers/dataset.py +++ b/apiv2/graphql_api/helpers/dataset.py @@ -70,6 +70,7 @@ class DatasetGroupByOptions: related_database_entries: Optional[str] = None s3_prefix: Optional[str] = None https_prefix: Optional[str] = None + file_size: Optional[int] = None id: Optional[int] = None diff --git a/apiv2/graphql_api/helpers/frame.py b/apiv2/graphql_api/helpers/frame.py index e0cbeb61d..e14feccf7 100644 --- a/apiv2/graphql_api/helpers/frame.py +++ b/apiv2/graphql_api/helpers/frame.py @@ -37,6 +37,7 @@ class FrameGroupByOptions: is_gain_corrected: Optional[bool] = None s3_frame_path: Optional[str] = None https_frame_path: Optional[str] = None + file_size: Optional[int] = None id: Optional[int] = None diff --git a/apiv2/graphql_api/helpers/tiltseries.py b/apiv2/graphql_api/helpers/tiltseries.py index b8e16504e..0d1f2bc79 100644 --- a/apiv2/graphql_api/helpers/tiltseries.py +++ b/apiv2/graphql_api/helpers/tiltseries.py @@ -37,7 +37,9 @@ class TiltseriesGroupByOptions: None ) s3_omezarr_dir: Optional[str] = None + file_size_omezarr: Optional[int] = None s3_mrc_file: Optional[str] = None + file_size_mrc: Optional[int] = None https_omezarr_dir: Optional[str] = None https_mrc_file: Optional[str] = None s3_angle_list: Optional[str] = None diff --git a/apiv2/graphql_api/helpers/tomogram.py b/apiv2/graphql_api/helpers/tomogram.py index a9e10de86..e20c80efd 100644 --- a/apiv2/graphql_api/helpers/tomogram.py +++ b/apiv2/graphql_api/helpers/tomogram.py @@ -65,8 +65,10 @@ class TomogramGroupByOptions: is_visualization_default: Optional[bool] = None s3_omezarr_dir: Optional[str] = None https_omezarr_dir: Optional[str] = None + file_size_omezarr: Optional[int] = None s3_mrc_file: Optional[str] = None https_mrc_file: Optional[str] = None + file_size_mrc: Optional[int] = None scale0_dimensions: Optional[str] = None scale1_dimensions: Optional[str] = None scale2_dimensions: Optional[str] = None diff --git a/apiv2/graphql_api/schema.graphql b/apiv2/graphql_api/schema.graphql index 9593a8c16..e02e3dd93 100644 --- a/apiv2/graphql_api/schema.graphql +++ b/apiv2/graphql_api/schema.graphql @@ -121,6 +121,17 @@ type AlignmentAggregateFunctions { count(distinct: Boolean = false, columns: AlignmentCountColumns = null): Int } +input AlignmentAggregateWhereClause { + count: AlignmentAggregateWhereClauseCount! +} + +input AlignmentAggregateWhereClauseCount { + arguments: AlignmentCountColumns + distinct: Boolean + filter: AlignmentWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type AlignmentConnection { """Pagination data for this connection""" @@ -131,12 +142,6 @@ type AlignmentConnection { } enum AlignmentCountColumns { - annotationFiles - perSectionAlignments - deposition - tiltseries - tomograms - run alignmentType alignmentMethod volumeXDimension @@ -339,12 +344,15 @@ input AlignmentUpdateInput { input AlignmentWhereClause { annotationFiles: AnnotationFileWhereClause + annotationFilesAggregate: AnnotationFileAggregateWhereClause perSectionAlignments: PerSectionAlignmentParametersWhereClause + perSectionAlignmentsAggregate: PerSectionAlignmentParametersAggregateWhereClause deposition: DepositionWhereClause depositionId: IntComparators tiltseries: TiltseriesWhereClause tiltseriesId: IntComparators tomograms: TomogramWhereClause + tomogramsAggregate: TomogramAggregateWhereClause run: RunWhereClause runId: IntComparators alignmentType: Alignment_type_enumEnumComparators @@ -548,6 +556,17 @@ type AnnotationAggregateFunctions { count(distinct: Boolean = false, columns: AnnotationCountColumns = null): Int } +input AnnotationAggregateWhereClause { + count: AnnotationAggregateWhereClauseCount! +} + +input AnnotationAggregateWhereClauseCount { + arguments: AnnotationCountColumns + distinct: Boolean + filter: AnnotationWhereClause + predicate: IntComparators +} + """Metadata for an annotation's authors""" type AnnotationAuthor implements EntityInterface & Node { """The Globally Unique ID of this object""" @@ -607,6 +626,17 @@ type AnnotationAuthorAggregateFunctions { count(distinct: Boolean = false, columns: AnnotationAuthorCountColumns = null): Int } +input AnnotationAuthorAggregateWhereClause { + count: AnnotationAuthorAggregateWhereClauseCount! +} + +input AnnotationAuthorAggregateWhereClauseCount { + arguments: AnnotationAuthorCountColumns + distinct: Boolean + filter: AnnotationAuthorWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type AnnotationAuthorConnection { """Pagination data for this connection""" @@ -617,7 +647,6 @@ type AnnotationAuthorConnection { } enum AnnotationAuthorCountColumns { - annotation id authorListOrder orcid @@ -794,11 +823,6 @@ type AnnotationConnection { } enum AnnotationCountColumns { - run - annotationShapes - methodLinks - authors - deposition s3MetadataPath httpsMetadataPath annotationPublication @@ -935,6 +959,9 @@ type AnnotationFile implements EntityInterface & Node { """s3 path of the annotation file""" s3Path: String! + """Size of the file in bytes""" + fileSize: Int + """HTTPS path for this annotation file""" httpsPath: String! @@ -964,6 +991,17 @@ type AnnotationFileAggregateFunctions { count(distinct: Boolean = false, columns: AnnotationFileCountColumns = null): Int } +input AnnotationFileAggregateWhereClause { + count: AnnotationFileAggregateWhereClauseCount! +} + +input AnnotationFileAggregateWhereClauseCount { + arguments: AnnotationFileCountColumns + distinct: Boolean + filter: AnnotationFileWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type AnnotationFileConnection { """Pagination data for this connection""" @@ -974,11 +1012,9 @@ type AnnotationFileConnection { } enum AnnotationFileCountColumns { - alignment - annotationShape - tomogramVoxelSpacing format s3Path + fileSize httpsPath isVisualizationDefault source @@ -1001,6 +1037,9 @@ input AnnotationFileCreateInput { """s3 path of the annotation file""" s3Path: String! + """Size of the file in bytes""" + fileSize: Int = null + """HTTPS path for this annotation file""" httpsPath: String! @@ -1033,6 +1072,7 @@ type AnnotationFileGroupByOptions { tomogramVoxelSpacing: TomogramVoxelSpacingGroupByOptions format: String s3Path: String + fileSize: Int httpsPath: String isVisualizationDefault: Boolean source: annotation_file_source_enum @@ -1042,11 +1082,13 @@ type AnnotationFileGroupByOptions { type AnnotationFileMinMaxColumns { format: String s3Path: String + fileSize: Int httpsPath: String id: Int } type AnnotationFileNumericalColumns { + fileSize: Int id: Int } @@ -1056,6 +1098,7 @@ input AnnotationFileOrderByClause { tomogramVoxelSpacing: TomogramVoxelSpacingOrderByClause format: orderBy s3Path: orderBy + fileSize: orderBy httpsPath: orderBy isVisualizationDefault: orderBy source: orderBy @@ -1078,6 +1121,9 @@ input AnnotationFileUpdateInput { """s3 path of the annotation file""" s3Path: String + """Size of the file in bytes""" + fileSize: Int = null + """HTTPS path for this annotation file""" httpsPath: String @@ -1104,6 +1150,7 @@ input AnnotationFileWhereClause { tomogramVoxelSpacingId: IntComparators format: StrComparators s3Path: StrComparators + fileSize: IntComparators httpsPath: StrComparators isVisualizationDefault: BoolComparators source: Annotation_file_source_enumEnumComparators @@ -1179,6 +1226,17 @@ type AnnotationMethodLinkAggregateFunctions { count(distinct: Boolean = false, columns: AnnotationMethodLinkCountColumns = null): Int } +input AnnotationMethodLinkAggregateWhereClause { + count: AnnotationMethodLinkAggregateWhereClauseCount! +} + +input AnnotationMethodLinkAggregateWhereClauseCount { + arguments: AnnotationMethodLinkCountColumns + distinct: Boolean + filter: AnnotationMethodLinkWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type AnnotationMethodLinkConnection { """Pagination data for this connection""" @@ -1189,7 +1247,6 @@ type AnnotationMethodLinkConnection { } enum AnnotationMethodLinkCountColumns { - annotation linkType name link @@ -1378,6 +1435,17 @@ type AnnotationShapeAggregateFunctions { count(distinct: Boolean = false, columns: AnnotationShapeCountColumns = null): Int } +input AnnotationShapeAggregateWhereClause { + count: AnnotationShapeAggregateWhereClauseCount! +} + +input AnnotationShapeAggregateWhereClauseCount { + arguments: AnnotationShapeCountColumns + distinct: Boolean + filter: AnnotationShapeWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type AnnotationShapeConnection { """Pagination data for this connection""" @@ -1388,8 +1456,6 @@ type AnnotationShapeConnection { } enum AnnotationShapeCountColumns { - annotation - annotationFiles shapeType id } @@ -1454,6 +1520,7 @@ input AnnotationShapeWhereClause { annotation: AnnotationWhereClause annotationId: IntComparators annotationFiles: AnnotationFileWhereClause + annotationFilesAggregate: AnnotationFileAggregateWhereClause shapeType: Annotation_file_shape_type_enumEnumComparators id: IntComparators } @@ -1551,8 +1618,11 @@ input AnnotationWhereClause { run: RunWhereClause runId: IntComparators annotationShapes: AnnotationShapeWhereClause + annotationShapesAggregate: AnnotationShapeAggregateWhereClause methodLinks: AnnotationMethodLinkWhereClause + methodLinksAggregate: AnnotationMethodLinkAggregateWhereClause authors: AnnotationAuthorWhereClause + authorsAggregate: AnnotationAuthorAggregateWhereClause deposition: DepositionWhereClause depositionId: IntComparators s3MetadataPath: StrComparators @@ -1792,6 +1862,9 @@ type Dataset implements EntityInterface & Node { """The https directory path where this dataset is contained""" httpsPrefix: String! + + """Size of the dataset in bytes""" + fileSize: Int } type DatasetAggregate { @@ -1809,6 +1882,17 @@ type DatasetAggregateFunctions { count(distinct: Boolean = false, columns: DatasetCountColumns = null): Int } +input DatasetAggregateWhereClause { + count: DatasetAggregateWhereClauseCount! +} + +input DatasetAggregateWhereClauseCount { + arguments: DatasetCountColumns + distinct: Boolean + filter: DatasetWhereClause + predicate: IntComparators +} + """An author of a dataset""" type DatasetAuthor implements EntityInterface & Node { """The Globally Unique ID of this object""" @@ -1866,6 +1950,17 @@ type DatasetAuthorAggregateFunctions { count(distinct: Boolean = false, columns: DatasetAuthorCountColumns = null): Int } +input DatasetAuthorAggregateWhereClause { + count: DatasetAuthorAggregateWhereClauseCount! +} + +input DatasetAuthorAggregateWhereClauseCount { + arguments: DatasetAuthorCountColumns + distinct: Boolean + filter: DatasetAuthorWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type DatasetAuthorConnection { """Pagination data for this connection""" @@ -1876,7 +1971,6 @@ type DatasetAuthorConnection { } enum DatasetAuthorCountColumns { - dataset id authorListOrder orcid @@ -2049,10 +2143,6 @@ type DatasetConnection { } enum DatasetCountColumns { - deposition - fundingSources - authors - runs title description organismName @@ -2078,6 +2168,7 @@ enum DatasetCountColumns { relatedDatabaseEntries s3Prefix httpsPrefix + fileSize id } @@ -2178,6 +2269,9 @@ input DatasetCreateInput { """The https directory path where this dataset is contained""" httpsPrefix: String! + """Size of the dataset in bytes""" + fileSize: Int = null + """ An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree """ @@ -2225,6 +2319,17 @@ type DatasetFundingAggregateFunctions { count(distinct: Boolean = false, columns: DatasetFundingCountColumns = null): Int } +input DatasetFundingAggregateWhereClause { + count: DatasetFundingAggregateWhereClauseCount! +} + +input DatasetFundingAggregateWhereClauseCount { + arguments: DatasetFundingCountColumns + distinct: Boolean + filter: DatasetFundingWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type DatasetFundingConnection { """Pagination data for this connection""" @@ -2235,7 +2340,6 @@ type DatasetFundingConnection { } enum DatasetFundingCountColumns { - dataset fundingAgencyName grantId id @@ -2344,6 +2448,7 @@ type DatasetGroupByOptions { relatedDatabaseEntries: String s3Prefix: String httpsPrefix: String + fileSize: Int id: Int } @@ -2372,11 +2477,13 @@ type DatasetMinMaxColumns { relatedDatabaseEntries: String s3Prefix: String httpsPrefix: String + fileSize: Int id: Int } type DatasetNumericalColumns { organismTaxid: Int + fileSize: Int id: Int } @@ -2407,6 +2514,7 @@ input DatasetOrderByClause { relatedDatabaseEntries: orderBy s3Prefix: orderBy httpsPrefix: orderBy + fileSize: orderBy id: orderBy } @@ -2507,6 +2615,9 @@ input DatasetUpdateInput { """The https directory path where this dataset is contained""" httpsPrefix: String + """Size of the dataset in bytes""" + fileSize: Int = null + """ An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree """ @@ -2517,8 +2628,11 @@ input DatasetWhereClause { deposition: DepositionWhereClause depositionId: IntComparators fundingSources: DatasetFundingWhereClause + fundingSourcesAggregate: DatasetFundingAggregateWhereClause authors: DatasetAuthorWhereClause + authorsAggregate: DatasetAuthorAggregateWhereClause runs: RunWhereClause + runsAggregate: RunAggregateWhereClause title: StrComparators description: StrComparators organismName: StrComparators @@ -2544,6 +2658,7 @@ input DatasetWhereClause { relatedDatabaseEntries: StrComparators s3Prefix: StrComparators httpsPrefix: StrComparators + fileSize: IntComparators id: IntComparators } @@ -2808,6 +2923,17 @@ type DepositionAuthorAggregateFunctions { count(distinct: Boolean = false, columns: DepositionAuthorCountColumns = null): Int } +input DepositionAuthorAggregateWhereClause { + count: DepositionAuthorAggregateWhereClauseCount! +} + +input DepositionAuthorAggregateWhereClauseCount { + arguments: DepositionAuthorCountColumns + distinct: Boolean + filter: DepositionAuthorWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type DepositionAuthorConnection { """Pagination data for this connection""" @@ -2818,7 +2944,6 @@ type DepositionAuthorConnection { } enum DepositionAuthorCountColumns { - deposition id authorListOrder orcid @@ -2976,16 +3101,8 @@ input DepositionAuthorWhereClauseMutations { } enum DepositionCountColumns { - authors - alignments - annotations - datasets - frames - tiltseries - tomograms title description - depositionTypes depositionPublications relatedDatabaseEntries depositionDate @@ -3109,6 +3226,17 @@ type DepositionTypeAggregateFunctions { count(distinct: Boolean = false, columns: DepositionTypeCountColumns = null): Int } +input DepositionTypeAggregateWhereClause { + count: DepositionTypeAggregateWhereClauseCount! +} + +input DepositionTypeAggregateWhereClauseCount { + arguments: DepositionTypeCountColumns + distinct: Boolean + filter: DepositionTypeWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type DepositionTypeConnection { """Pagination data for this connection""" @@ -3119,7 +3247,6 @@ type DepositionTypeConnection { } enum DepositionTypeCountColumns { - deposition type id } @@ -3222,15 +3349,23 @@ input DepositionUpdateInput { input DepositionWhereClause { authors: DepositionAuthorWhereClause + authorsAggregate: DepositionAuthorAggregateWhereClause alignments: AlignmentWhereClause + alignmentsAggregate: AlignmentAggregateWhereClause annotations: AnnotationWhereClause + annotationsAggregate: AnnotationAggregateWhereClause datasets: DatasetWhereClause + datasetsAggregate: DatasetAggregateWhereClause frames: FrameWhereClause + framesAggregate: FrameAggregateWhereClause tiltseries: TiltseriesWhereClause + tiltseriesAggregate: TiltseriesAggregateWhereClause tomograms: TomogramWhereClause + tomogramsAggregate: TomogramAggregateWhereClause title: StrComparators description: StrComparators depositionTypes: DepositionTypeWhereClause + depositionTypesAggregate: DepositionTypeAggregateWhereClause depositionPublications: StrComparators relatedDatabaseEntries: StrComparators depositionDate: DatetimeComparators @@ -3314,6 +3449,9 @@ type Frame implements EntityInterface & Node { """HTTPS path to the frame file""" httpsFramePath: String! + + """Size of the frame file in bytes""" + fileSize: Int } """ @@ -3350,6 +3488,17 @@ type FrameAcquisitionFileAggregateFunctions { count(distinct: Boolean = false, columns: FrameAcquisitionFileCountColumns = null): Int } +input FrameAcquisitionFileAggregateWhereClause { + count: FrameAcquisitionFileAggregateWhereClauseCount! +} + +input FrameAcquisitionFileAggregateWhereClauseCount { + arguments: FrameAcquisitionFileCountColumns + distinct: Boolean + filter: FrameAcquisitionFileWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type FrameAcquisitionFileConnection { """Pagination data for this connection""" @@ -3360,7 +3509,6 @@ type FrameAcquisitionFileConnection { } enum FrameAcquisitionFileCountColumns { - run s3MdocPath httpsMdocPath id @@ -3452,6 +3600,17 @@ type FrameAggregateFunctions { count(distinct: Boolean = false, columns: FrameCountColumns = null): Int } +input FrameAggregateWhereClause { + count: FrameAggregateWhereClauseCount! +} + +input FrameAggregateWhereClauseCount { + arguments: FrameCountColumns + distinct: Boolean + filter: FrameWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type FrameConnection { """Pagination data for this connection""" @@ -3462,14 +3621,13 @@ type FrameConnection { } enum FrameCountColumns { - deposition - run rawAngle acquisitionOrder dose isGainCorrected s3FramePath httpsFramePath + fileSize id } @@ -3495,6 +3653,9 @@ input FrameCreateInput { """HTTPS path to the frame file""" httpsFramePath: String! + """Size of the frame file in bytes""" + fileSize: Int = null + """Numeric identifier (May change!)""" id: Int! } @@ -3517,6 +3678,7 @@ type FrameGroupByOptions { isGainCorrected: Boolean s3FramePath: String httpsFramePath: String + fileSize: Int id: Int } @@ -3526,6 +3688,7 @@ type FrameMinMaxColumns { dose: Float s3FramePath: String httpsFramePath: String + fileSize: Int id: Int } @@ -3533,6 +3696,7 @@ type FrameNumericalColumns { rawAngle: Float acquisitionOrder: Int dose: Float + fileSize: Int id: Int } @@ -3545,6 +3709,7 @@ input FrameOrderByClause { isGainCorrected: orderBy s3FramePath: orderBy httpsFramePath: orderBy + fileSize: orderBy id: orderBy } @@ -3570,6 +3735,9 @@ input FrameUpdateInput { """HTTPS path to the frame file""" httpsFramePath: String + """Size of the frame file in bytes""" + fileSize: Int = null + """Numeric identifier (May change!)""" id: Int } @@ -3585,6 +3753,7 @@ input FrameWhereClause { isGainCorrected: BoolComparators s3FramePath: StrComparators httpsFramePath: StrComparators + fileSize: IntComparators id: IntComparators } @@ -3624,6 +3793,17 @@ type GainFileAggregateFunctions { count(distinct: Boolean = false, columns: GainFileCountColumns = null): Int } +input GainFileAggregateWhereClause { + count: GainFileAggregateWhereClauseCount! +} + +input GainFileAggregateWhereClauseCount { + arguments: GainFileCountColumns + distinct: Boolean + filter: GainFileWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type GainFileConnection { """Pagination data for this connection""" @@ -3634,7 +3814,6 @@ type GainFileConnection { } enum GainFileCountColumns { - run s3FilePath httpsFilePath id @@ -3864,6 +4043,17 @@ type PerSectionAlignmentParametersAggregateFunctions { count(distinct: Boolean = false, columns: PerSectionAlignmentParametersCountColumns = null): Int } +input PerSectionAlignmentParametersAggregateWhereClause { + count: PerSectionAlignmentParametersAggregateWhereClauseCount! +} + +input PerSectionAlignmentParametersAggregateWhereClauseCount { + arguments: PerSectionAlignmentParametersCountColumns + distinct: Boolean + filter: PerSectionAlignmentParametersWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type PerSectionAlignmentParametersConnection { """Pagination data for this connection""" @@ -3874,7 +4064,6 @@ type PerSectionAlignmentParametersConnection { } enum PerSectionAlignmentParametersCountColumns { - alignment zIndex xOffset yOffset @@ -4215,6 +4404,17 @@ type RunAggregateFunctions { count(distinct: Boolean = false, columns: RunCountColumns = null): Int } +input RunAggregateWhereClause { + count: RunAggregateWhereClauseCount! +} + +input RunAggregateWhereClauseCount { + arguments: RunCountColumns + distinct: Boolean + filter: RunWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type RunConnection { """Pagination data for this connection""" @@ -4225,15 +4425,6 @@ type RunConnection { } enum RunCountColumns { - alignments - annotations - dataset - frames - gainFiles - frameAcquisitionFiles - tiltseries - tomogramVoxelSpacings - tomograms name s3Prefix httpsPrefix @@ -4320,15 +4511,23 @@ input RunUpdateInput { input RunWhereClause { alignments: AlignmentWhereClause + alignmentsAggregate: AlignmentAggregateWhereClause annotations: AnnotationWhereClause + annotationsAggregate: AnnotationAggregateWhereClause dataset: DatasetWhereClause datasetId: IntComparators frames: FrameWhereClause + framesAggregate: FrameAggregateWhereClause gainFiles: GainFileWhereClause + gainFilesAggregate: GainFileAggregateWhereClause frameAcquisitionFiles: FrameAcquisitionFileWhereClause + frameAcquisitionFilesAggregate: FrameAcquisitionFileAggregateWhereClause tiltseries: TiltseriesWhereClause + tiltseriesAggregate: TiltseriesAggregateWhereClause tomogramVoxelSpacings: TomogramVoxelSpacingWhereClause + tomogramVoxelSpacingsAggregate: TomogramVoxelSpacingAggregateWhereClause tomograms: TomogramWhereClause + tomogramsAggregate: TomogramAggregateWhereClause name: StrComparators s3Prefix: StrComparators httpsPrefix: StrComparators @@ -4402,9 +4601,15 @@ type Tiltseries implements EntityInterface & Node { """S3 path to this tiltseries in multiscale OME-Zarr format""" s3OmezarrDir: String + """Size of the OME-Zarr file in bytes""" + fileSizeOmezarr: Int + """S3 path to this tiltseries in MRC format (no scaling)""" s3MrcFile: String + """Size of the MRC file in bytes""" + fileSizeMrc: Int + """HTTPS path to this tiltseries in multiscale OME-Zarr format""" httpsOmezarrDir: String @@ -4522,6 +4727,17 @@ type TiltseriesAggregateFunctions { count(distinct: Boolean = false, columns: TiltseriesCountColumns = null): Int } +input TiltseriesAggregateWhereClause { + count: TiltseriesAggregateWhereClauseCount! +} + +input TiltseriesAggregateWhereClauseCount { + arguments: TiltseriesCountColumns + distinct: Boolean + filter: TiltseriesWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type TiltseriesConnection { """Pagination data for this connection""" @@ -4532,11 +4748,10 @@ type TiltseriesConnection { } enum TiltseriesCountColumns { - alignments - run - deposition s3OmezarrDir + fileSizeOmezarr s3MrcFile + fileSizeMrc httpsOmezarrDir httpsMrcFile s3AngleList @@ -4578,9 +4793,15 @@ input TiltseriesCreateInput { """S3 path to this tiltseries in multiscale OME-Zarr format""" s3OmezarrDir: String = null + """Size of the OME-Zarr file in bytes""" + fileSizeOmezarr: Int = null + """S3 path to this tiltseries in MRC format (no scaling)""" s3MrcFile: String = null + """Size of the MRC file in bytes""" + fileSizeMrc: Int = null + """HTTPS path to this tiltseries in multiscale OME-Zarr format""" httpsOmezarrDir: String = null @@ -4700,7 +4921,9 @@ type TiltseriesGroupByOptions { run: RunGroupByOptions deposition: DepositionGroupByOptions s3OmezarrDir: String + fileSizeOmezarr: Int s3MrcFile: String + fileSizeMrc: Int httpsOmezarrDir: String httpsMrcFile: String s3AngleList: String @@ -4737,7 +4960,9 @@ type TiltseriesGroupByOptions { type TiltseriesMinMaxColumns { s3OmezarrDir: String + fileSizeOmezarr: Int s3MrcFile: String + fileSizeMrc: Int httpsOmezarrDir: String httpsMrcFile: String s3AngleList: String @@ -4771,6 +4996,8 @@ type TiltseriesMinMaxColumns { } type TiltseriesNumericalColumns { + fileSizeOmezarr: Int + fileSizeMrc: Int accelerationVoltage: Int sphericalAberrationConstant: Float tiltMin: Float @@ -4793,7 +5020,9 @@ input TiltseriesOrderByClause { run: RunOrderByClause deposition: DepositionOrderByClause s3OmezarrDir: orderBy + fileSizeOmezarr: orderBy s3MrcFile: orderBy + fileSizeMrc: orderBy httpsOmezarrDir: orderBy httpsMrcFile: orderBy s3AngleList: orderBy @@ -4835,9 +5064,15 @@ input TiltseriesUpdateInput { """S3 path to this tiltseries in multiscale OME-Zarr format""" s3OmezarrDir: String = null + """Size of the OME-Zarr file in bytes""" + fileSizeOmezarr: Int = null + """S3 path to this tiltseries in MRC format (no scaling)""" s3MrcFile: String = null + """Size of the MRC file in bytes""" + fileSizeMrc: Int = null + """HTTPS path to this tiltseries in multiscale OME-Zarr format""" httpsOmezarrDir: String = null @@ -4945,12 +5180,15 @@ input TiltseriesUpdateInput { input TiltseriesWhereClause { alignments: AlignmentWhereClause + alignmentsAggregate: AlignmentAggregateWhereClause run: RunWhereClause runId: IntComparators deposition: DepositionWhereClause depositionId: IntComparators s3OmezarrDir: StrComparators + fileSizeOmezarr: IntComparators s3MrcFile: StrComparators + fileSizeMrc: IntComparators httpsOmezarrDir: StrComparators httpsMrcFile: StrComparators s3AngleList: StrComparators @@ -5090,12 +5328,18 @@ type Tomogram implements EntityInterface & Node { """HTTPS path to this tomogram in multiscale OME-Zarr format""" httpsOmezarrDir: String + """Size of the OME-Zarr file in bytes""" + fileSizeOmezarr: Int + """S3 path to this tomogram in MRC format (no scaling)""" s3MrcFile: String """HTTPS path to this tomogram in MRC format (no scaling)""" httpsMrcFile: String + """Size of the MRC file in bytes""" + fileSizeMrc: Int + """comma separated x,y,z dimensions of the unscaled tomogram""" scale0Dimensions: String @@ -5161,6 +5405,17 @@ type TomogramAggregateFunctions { count(distinct: Boolean = false, columns: TomogramCountColumns = null): Int } +input TomogramAggregateWhereClause { + count: TomogramAggregateWhereClauseCount! +} + +input TomogramAggregateWhereClauseCount { + arguments: TomogramCountColumns + distinct: Boolean + filter: TomogramWhereClause + predicate: IntComparators +} + """Author of a tomogram""" type TomogramAuthor implements EntityInterface & Node { """The Globally Unique ID of this object""" @@ -5216,6 +5471,17 @@ type TomogramAuthorAggregateFunctions { count(distinct: Boolean = false, columns: TomogramAuthorCountColumns = null): Int } +input TomogramAuthorAggregateWhereClause { + count: TomogramAuthorAggregateWhereClauseCount! +} + +input TomogramAuthorAggregateWhereClauseCount { + arguments: TomogramAuthorCountColumns + distinct: Boolean + filter: TomogramAuthorWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type TomogramAuthorConnection { """Pagination data for this connection""" @@ -5226,7 +5492,6 @@ type TomogramAuthorConnection { } enum TomogramAuthorCountColumns { - tomogram id authorListOrder orcid @@ -5395,11 +5660,6 @@ type TomogramConnection { } enum TomogramCountColumns { - alignment - authors - deposition - run - tomogramVoxelSpacing name sizeX sizeY @@ -5416,8 +5676,10 @@ enum TomogramCountColumns { isVisualizationDefault s3OmezarrDir httpsOmezarrDir + fileSizeOmezarr s3MrcFile httpsMrcFile + fileSizeMrc scale0Dimensions scale1Dimensions scale2Dimensions @@ -5503,12 +5765,18 @@ input TomogramCreateInput { """HTTPS path to this tomogram in multiscale OME-Zarr format""" httpsOmezarrDir: String = null + """Size of the OME-Zarr file in bytes""" + fileSizeOmezarr: Int = null + """S3 path to this tomogram in MRC format (no scaling)""" s3MrcFile: String = null """HTTPS path to this tomogram in MRC format (no scaling)""" httpsMrcFile: String = null + """Size of the MRC file in bytes""" + fileSizeMrc: Int = null + """comma separated x,y,z dimensions of the unscaled tomogram""" scale0Dimensions: String = null @@ -5593,8 +5861,10 @@ type TomogramGroupByOptions { isVisualizationDefault: Boolean s3OmezarrDir: String httpsOmezarrDir: String + fileSizeOmezarr: Int s3MrcFile: String httpsMrcFile: String + fileSizeMrc: Int scale0Dimensions: String scale1Dimensions: String scale2Dimensions: String @@ -5624,8 +5894,10 @@ type TomogramMinMaxColumns { reconstructionSoftware: String s3OmezarrDir: String httpsOmezarrDir: String + fileSizeOmezarr: Int s3MrcFile: String httpsMrcFile: String + fileSizeMrc: Int scale0Dimensions: String scale1Dimensions: String scale2Dimensions: String @@ -5649,6 +5921,8 @@ type TomogramNumericalColumns { sizeZ: Int voxelSpacing: Float tomogramVersion: Float + fileSizeOmezarr: Int + fileSizeMrc: Int offsetX: Int offsetY: Int offsetZ: Int @@ -5676,8 +5950,10 @@ input TomogramOrderByClause { isVisualizationDefault: orderBy s3OmezarrDir: orderBy httpsOmezarrDir: orderBy + fileSizeOmezarr: orderBy s3MrcFile: orderBy httpsMrcFile: orderBy + fileSizeMrc: orderBy scale0Dimensions: orderBy scale1Dimensions: orderBy scale2Dimensions: orderBy @@ -5763,12 +6039,18 @@ input TomogramUpdateInput { """HTTPS path to this tomogram in multiscale OME-Zarr format""" httpsOmezarrDir: String = null + """Size of the OME-Zarr file in bytes""" + fileSizeOmezarr: Int = null + """S3 path to this tomogram in MRC format (no scaling)""" s3MrcFile: String = null """HTTPS path to this tomogram in MRC format (no scaling)""" httpsMrcFile: String = null + """Size of the MRC file in bytes""" + fileSizeMrc: Int = null + """comma separated x,y,z dimensions of the unscaled tomogram""" scale0Dimensions: String = null @@ -5895,6 +6177,17 @@ type TomogramVoxelSpacingAggregateFunctions { count(distinct: Boolean = false, columns: TomogramVoxelSpacingCountColumns = null): Int } +input TomogramVoxelSpacingAggregateWhereClause { + count: TomogramVoxelSpacingAggregateWhereClauseCount! +} + +input TomogramVoxelSpacingAggregateWhereClauseCount { + arguments: TomogramVoxelSpacingCountColumns + distinct: Boolean + filter: TomogramVoxelSpacingWhereClause + predicate: IntComparators +} + """A connection to a list of items.""" type TomogramVoxelSpacingConnection { """Pagination data for this connection""" @@ -5905,9 +6198,6 @@ type TomogramVoxelSpacingConnection { } enum TomogramVoxelSpacingCountColumns { - annotationFiles - run - tomograms voxelSpacing s3Prefix httpsPrefix @@ -5997,9 +6287,11 @@ input TomogramVoxelSpacingUpdateInput { input TomogramVoxelSpacingWhereClause { annotationFiles: AnnotationFileWhereClause + annotationFilesAggregate: AnnotationFileAggregateWhereClause run: RunWhereClause runId: IntComparators tomograms: TomogramWhereClause + tomogramsAggregate: TomogramAggregateWhereClause voxelSpacing: FloatComparators s3Prefix: StrComparators httpsPrefix: StrComparators @@ -6014,6 +6306,7 @@ input TomogramWhereClause { alignment: AlignmentWhereClause alignmentId: IntComparators authors: TomogramAuthorWhereClause + authorsAggregate: TomogramAuthorAggregateWhereClause deposition: DepositionWhereClause depositionId: IntComparators run: RunWhereClause @@ -6036,8 +6329,10 @@ input TomogramWhereClause { isVisualizationDefault: BoolComparators s3OmezarrDir: StrComparators httpsOmezarrDir: StrComparators + fileSizeOmezarr: IntComparators s3MrcFile: StrComparators httpsMrcFile: StrComparators + fileSizeMrc: IntComparators scale0Dimensions: StrComparators scale1Dimensions: StrComparators scale2Dimensions: StrComparators diff --git a/apiv2/graphql_api/schema.json b/apiv2/graphql_api/schema.json index 6ec3c6736..02bf71166 100644 --- a/apiv2/graphql_api/schema.json +++ b/apiv2/graphql_api/schema.json @@ -4102,6 +4102,15 @@ } } }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "httpsPath", @@ -4164,6 +4173,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "annotationFilesAggregate", + "type": { + "kind": "INPUT_OBJECT", + "name": "AnnotationFileAggregateWhereClause", + "ofType": null + } + }, { "defaultValue": null, "name": "perSectionAlignments", @@ -4173,6 +4191,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "perSectionAlignmentsAggregate", + "type": { + "kind": "INPUT_OBJECT", + "name": "PerSectionAlignmentParametersAggregateWhereClause", + "ofType": null + } + }, { "defaultValue": null, "name": "deposition", @@ -4218,6 +4245,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "tomogramsAggregate", + "type": { + "kind": "INPUT_OBJECT", + "name": "TomogramAggregateWhereClause", + "ofType": null + } + }, { "defaultValue": null, "name": "run", @@ -4453,6 +4489,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "fileSize", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, { "defaultValue": null, "name": "httpsPath", @@ -4633,6 +4678,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "annotationFilesAggregate", + "type": { + "kind": "INPUT_OBJECT", + "name": "AnnotationFileAggregateWhereClause", + "ofType": null + } + }, { "defaultValue": null, "name": "shapeType", @@ -4688,6 +4742,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "annotationShapesAggregate", + "type": { + "kind": "INPUT_OBJECT", + "name": "AnnotationShapeAggregateWhereClause", + "ofType": null + } + }, { "defaultValue": null, "name": "methodLinks", @@ -4697,6 +4760,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "methodLinksAggregate", + "type": { + "kind": "INPUT_OBJECT", + "name": "AnnotationMethodLinkAggregateWhereClause", + "ofType": null + } + }, { "defaultValue": null, "name": "authors", @@ -4706,6 +4778,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "authorsAggregate", + "type": { + "kind": "INPUT_OBJECT", + "name": "AnnotationAuthorAggregateWhereClause", + "ofType": null + } + }, { "defaultValue": null, "name": "deposition", @@ -4925,179 +5006,160 @@ }, { "defaultValue": null, - "name": "annotations", + "name": "alignmentsAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "AnnotationWhereClause", + "name": "AlignmentAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "dataset", + "name": "annotations", "type": { "kind": "INPUT_OBJECT", - "name": "DatasetWhereClause", + "name": "AnnotationWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "datasetId", + "name": "annotationsAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "AnnotationAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "frames", + "name": "dataset", "type": { "kind": "INPUT_OBJECT", - "name": "FrameWhereClause", + "name": "DatasetWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "gainFiles", + "name": "datasetId", "type": { "kind": "INPUT_OBJECT", - "name": "GainFileWhereClause", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "frameAcquisitionFiles", + "name": "frames", "type": { "kind": "INPUT_OBJECT", - "name": "FrameAcquisitionFileWhereClause", + "name": "FrameWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "tiltseries", + "name": "framesAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "TiltseriesWhereClause", + "name": "FrameAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "tomogramVoxelSpacings", + "name": "gainFiles", "type": { "kind": "INPUT_OBJECT", - "name": "TomogramVoxelSpacingWhereClause", + "name": "GainFileWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "tomograms", + "name": "gainFilesAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "TomogramWhereClause", + "name": "GainFileAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "name", + "name": "frameAcquisitionFiles", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "FrameAcquisitionFileWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "s3Prefix", + "name": "frameAcquisitionFilesAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "FrameAcquisitionFileAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "httpsPrefix", + "name": "tiltseries", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "TiltseriesWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "id", - "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null - } - } - ], - "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "RunWhereClause", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": [ - { - "defaultValue": null, - "name": "deposition", + "name": "tiltseriesAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "DepositionWhereClause", + "name": "TiltseriesAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "depositionId", + "name": "tomogramVoxelSpacings", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "TomogramVoxelSpacingWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "fundingSources", + "name": "tomogramVoxelSpacingsAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "DatasetFundingWhereClause", + "name": "TomogramVoxelSpacingAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "authors", + "name": "tomograms", "type": { "kind": "INPUT_OBJECT", - "name": "DatasetAuthorWhereClause", + "name": "TomogramWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "runs", + "name": "tomogramsAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "RunWhereClause", + "name": "TomogramAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "title", + "name": "name", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5106,7 +5168,7 @@ }, { "defaultValue": null, - "name": "description", + "name": "s3Prefix", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5115,7 +5177,7 @@ }, { "defaultValue": null, - "name": "organismName", + "name": "httpsPrefix", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5124,287 +5186,415 @@ }, { "defaultValue": null, - "name": "organismTaxid", + "name": "id", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", "ofType": null } - }, + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "RunWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "tissueName", + "name": "count", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "AlignmentAggregateWhereClauseCount", + "ofType": null + } } - }, + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "AlignmentAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "tissueId", + "name": "arguments", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "ENUM", + "name": "AlignmentCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "cellName", + "name": "distinct", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "cellTypeId", + "name": "filter", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "AlignmentWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "cellStrainName", + "name": "predicate", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "IntComparators", "ofType": null } - }, + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "AlignmentAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ { - "defaultValue": null, - "name": "cellStrainId", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } + "name": "alignmentType" }, { - "defaultValue": null, - "name": "sampleType", - "type": { - "kind": "INPUT_OBJECT", - "name": "Sample_type_enumEnumComparators", - "ofType": null - } + "name": "alignmentMethod" }, { - "defaultValue": null, - "name": "samplePreparation", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } + "name": "volumeXDimension" }, { - "defaultValue": null, - "name": "gridPreparation", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } + "name": "volumeYDimension" }, { - "defaultValue": null, - "name": "otherSetup", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } + "name": "volumeZDimension" }, + { + "name": "volumeXOffset" + }, + { + "name": "volumeYOffset" + }, + { + "name": "volumeZOffset" + }, + { + "name": "xRotationOffset" + }, + { + "name": "tiltOffset" + }, + { + "name": "affineTransformationMatrix" + }, + { + "name": "s3AlignmentMetadata" + }, + { + "name": "httpsAlignmentMetadata" + }, + { + "name": "isPortalStandard" + }, + { + "name": "id" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "AlignmentCountColumns", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "keyPhotoUrl", + "name": "count", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + 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"defaultValue": null, - "name": "s3Prefix", + "name": "authors", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "DatasetAuthorWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "httpsPrefix", + "name": "authorsAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "DatasetAuthorAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "id", + "name": "runs", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "RunWhereClause", "ofType": null } - } - ], - "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "DatasetWhereClause", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": [ + }, { "defaultValue": null, - "name": "authors", + "name": "runsAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "DepositionAuthorWhereClause", + "name": "RunAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "alignments", + "name": "title", "type": { "kind": "INPUT_OBJECT", - "name": "AlignmentWhereClause", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "annotations", + "name": "description", "type": { "kind": "INPUT_OBJECT", - "name": "AnnotationWhereClause", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "datasets", + "name": "organismName", "type": { "kind": "INPUT_OBJECT", - "name": "DatasetWhereClause", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "frames", + "name": "organismTaxid", "type": { "kind": "INPUT_OBJECT", - "name": "FrameWhereClause", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "tiltseries", + "name": "tissueName", "type": { "kind": "INPUT_OBJECT", - "name": "TiltseriesWhereClause", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "tomograms", + "name": "tissueId", "type": { "kind": "INPUT_OBJECT", - "name": "TomogramWhereClause", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "title", + "name": "cellName", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5413,7 +5603,7 @@ }, { "defaultValue": null, - "name": "description", + "name": "cellTypeId", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5422,16 +5612,16 @@ }, { "defaultValue": null, - "name": "depositionTypes", + "name": "cellStrainName", "type": { "kind": "INPUT_OBJECT", - "name": "DepositionTypeWhereClause", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "depositionPublications", + "name": "cellStrainId", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5440,37 +5630,37 @@ }, { "defaultValue": null, - "name": "relatedDatabaseEntries", + "name": "sampleType", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "Sample_type_enumEnumComparators", "ofType": null } }, { "defaultValue": null, - "name": "depositionDate", + "name": "samplePreparation", "type": { "kind": "INPUT_OBJECT", - "name": "DatetimeComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "releaseDate", + "name": "gridPreparation", "type": { "kind": "INPUT_OBJECT", - "name": "DatetimeComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "lastModifiedDate", + "name": "otherSetup", "type": { "kind": "INPUT_OBJECT", - "name": "DatetimeComparators", + "name": "StrComparators", "ofType": null } }, @@ -5494,80 +5684,52 @@ }, { "defaultValue": null, - "name": "id", + "name": "cellComponentName", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null - } - } - ], - "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "DepositionWhereClause", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": [ - { - "defaultValue": null, - "name": "deposition", - "type": { - "kind": "INPUT_OBJECT", - "name": "DepositionWhereClause", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "depositionId", - "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "id", + "name": "cellComponentId", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "authorListOrder", + "name": "depositionDate", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "DatetimeComparators", "ofType": null } }, { "defaultValue": null, - "name": "orcid", + "name": "releaseDate", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "DatetimeComparators", "ofType": null } }, { "defaultValue": null, - "name": "name", + "name": "lastModifiedDate", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "DatetimeComparators", "ofType": null } }, { "defaultValue": null, - "name": "email", + "name": "datasetPublications", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5576,7 +5738,7 @@ }, { "defaultValue": null, - "name": "affiliationName", + "name": "relatedDatabaseEntries", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5585,7 +5747,7 @@ }, { "defaultValue": null, - "name": "affiliationAddress", + "name": "s3Prefix", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5594,7 +5756,7 @@ }, { "defaultValue": null, - "name": "affiliationIdentifier", + "name": "httpsPrefix", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5603,26 +5765,26 @@ }, { "defaultValue": null, - "name": "correspondingAuthorStatus", + "name": "fileSize", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "primaryAuthorStatus", + "name": "id", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", + "name": "IntComparators", "ofType": null } } ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "DepositionAuthorWhereClause", + "name": "DatasetWhereClause", "possibleTypes": null }, { @@ -5631,302 +5793,269 @@ "inputFields": [ { "defaultValue": null, - "name": "_eq", + "name": "authors", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "DepositionAuthorWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_neq", + "name": "authorsAggregate", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "DepositionAuthorAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_in", + "name": "alignments", "type": { - "kind": "LIST", - "name": null, - "ofType": { - "kind": "NON_NULL", - "name": null, - "ofType": { - "kind": "SCALAR", - "name": "String", - "ofType": null - } - } + "kind": "INPUT_OBJECT", + "name": "AlignmentWhereClause", + "ofType": null } }, { "defaultValue": null, - "name": "_nin", + "name": "alignmentsAggregate", "type": { - "kind": "LIST", - "name": null, - "ofType": { - "kind": "NON_NULL", - "name": null, - "ofType": { - "kind": "SCALAR", - "name": "String", - "ofType": null - } - } + "kind": "INPUT_OBJECT", + "name": "AlignmentAggregateWhereClause", + "ofType": null } }, { "defaultValue": null, - "name": "_is_null", + "name": "annotations", "type": { - "kind": "SCALAR", - "name": "Boolean", + "kind": "INPUT_OBJECT", + "name": "AnnotationWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_gt", + "name": "annotationsAggregate", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "AnnotationAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_gte", + "name": "datasets", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "DatasetWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_lt", + "name": "datasetsAggregate", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "DatasetAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_lte", + "name": "frames", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "FrameWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_like", + "name": "framesAggregate", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "FrameAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_nlike", + "name": "tiltseries", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "TiltseriesWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_ilike", + "name": "tiltseriesAggregate", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "TiltseriesAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_nilike", + "name": "tomograms", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "TomogramWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_regex", + "name": "tomogramsAggregate", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "TomogramAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_nregex", + "name": "title", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "_iregex", + "name": "description", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "_niregex", + "name": "depositionTypes", "type": { - "kind": "SCALAR", - "name": "String", + "kind": "INPUT_OBJECT", + "name": "DepositionTypeWhereClause", "ofType": null } - } - ], - "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": [ + }, { "defaultValue": null, - "name": "_eq", + "name": "depositionTypesAggregate", "type": { - "kind": "SCALAR", - "name": "Boolean", + "kind": "INPUT_OBJECT", + "name": "DepositionTypeAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_neq", + "name": "depositionPublications", "type": { - "kind": "SCALAR", - "name": "Boolean", + "kind": "INPUT_OBJECT", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "_in", + "name": "relatedDatabaseEntries", "type": { - "kind": "LIST", - "name": null, - "ofType": { - "kind": "NON_NULL", - "name": null, - "ofType": { - "kind": "SCALAR", - "name": "Boolean", - "ofType": null - } - } + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null } }, { "defaultValue": null, - "name": "_nin", + "name": "depositionDate", "type": { - "kind": "LIST", - "name": null, - "ofType": { - "kind": "NON_NULL", - "name": null, - "ofType": { - "kind": "SCALAR", - "name": "Boolean", - "ofType": null - } - } + "kind": "INPUT_OBJECT", + "name": "DatetimeComparators", + "ofType": null } }, { "defaultValue": null, - "name": "_is_null", + "name": "releaseDate", "type": { - "kind": "SCALAR", - "name": "Boolean", + "kind": "INPUT_OBJECT", + "name": "DatetimeComparators", "ofType": null } - } - ], - "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "BoolComparators", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": [ + }, { "defaultValue": null, - "name": "deposition", + "name": "lastModifiedDate", "type": { "kind": "INPUT_OBJECT", - "name": "DepositionWhereClause", + "name": "DatetimeComparators", "ofType": null } }, { "defaultValue": null, - "name": "depositionId", + "name": "keyPhotoUrl", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "run", + "name": "keyPhotoThumbnailUrl", "type": { "kind": "INPUT_OBJECT", - "name": "RunWhereClause", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "runId", + "name": "id", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", "ofType": null } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "DepositionWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "deposition", + "type": { + "kind": "INPUT_OBJECT", + "name": "DepositionWhereClause", + "ofType": null + } }, { "defaultValue": null, - "name": "rawAngle", + "name": "depositionId", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "acquisitionOrder", + "name": "id", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -5935,25 +6064,25 @@ }, { "defaultValue": null, - "name": "dose", + "name": "authorListOrder", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "isGainCorrected", + "name": "orcid", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "s3FramePath", + "name": "name", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5962,7 +6091,7 @@ }, { "defaultValue": null, - "name": "httpsFramePath", + "name": "email", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -5971,17 +6100,53 @@ }, { "defaultValue": null, - "name": "id", + "name": "affiliationName", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "affiliationAddress", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "affiliationIdentifier", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "correspondingAuthorStatus", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "primaryAuthorStatus", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", "ofType": null } } ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "FrameWhereClause", + "name": "DepositionAuthorWhereClause", "possibleTypes": null }, { @@ -5993,7 +6158,7 @@ "name": "_eq", "type": { "kind": "SCALAR", - "name": "Float", + "name": "String", "ofType": null } }, @@ -6002,7 +6167,7 @@ "name": "_neq", "type": { "kind": "SCALAR", - "name": "Float", + "name": "String", "ofType": null } }, @@ -6017,7 +6182,7 @@ "name": null, "ofType": { "kind": "SCALAR", - "name": "Float", + "name": "String", "ofType": null } } @@ -6034,7 +6199,7 @@ "name": null, "ofType": { "kind": "SCALAR", - "name": "Float", + "name": "String", "ofType": null } } @@ -6042,314 +6207,528 @@ }, { "defaultValue": null, - "name": "_gt", + "name": "_is_null", "type": { "kind": "SCALAR", - "name": "Float", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "_gte", + "name": "_gt", "type": { "kind": "SCALAR", - "name": "Float", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "_lt", + "name": "_gte", "type": { "kind": "SCALAR", - "name": "Float", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "_lte", + "name": "_lt", "type": { "kind": "SCALAR", - "name": "Float", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "_is_null", + "name": "_lte", "type": { "kind": "SCALAR", - "name": "Boolean", + "name": "String", "ofType": null } - } - ], - "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "FloatComparators", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "SCALAR", - "name": "Float", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": [ + }, { "defaultValue": null, - "name": "alignments", + "name": "_like", "type": { - "kind": "INPUT_OBJECT", - "name": "AlignmentWhereClause", + "kind": "SCALAR", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "run", + "name": "_nlike", "type": { - "kind": "INPUT_OBJECT", - "name": "RunWhereClause", + "kind": "SCALAR", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "runId", + "name": "_ilike", "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", + "kind": "SCALAR", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "deposition", + "name": "_nilike", "type": { - "kind": "INPUT_OBJECT", - "name": "DepositionWhereClause", + "kind": "SCALAR", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "depositionId", + "name": "_regex", "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", + "kind": "SCALAR", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "s3OmezarrDir", + "name": "_nregex", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "SCALAR", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "s3MrcFile", + "name": "_iregex", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "SCALAR", + "name": "String", "ofType": null } }, { "defaultValue": null, - "name": "httpsOmezarrDir", + "name": "_niregex", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "SCALAR", + "name": "String", "ofType": null } - }, + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "httpsMrcFile", + "name": "_eq", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "s3AngleList", + "name": "_neq", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "httpsAngleList", + "name": "_in", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null + "kind": "LIST", + "name": null, + "ofType": { + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "SCALAR", + "name": "Boolean", + "ofType": null + } + } } }, { "defaultValue": null, - "name": "accelerationVoltage", + "name": "_nin", "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null + "kind": "LIST", + "name": null, + "ofType": { + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "SCALAR", + "name": "Boolean", + "ofType": null + } + } } }, { "defaultValue": null, - "name": "sphericalAberrationConstant", + "name": "_is_null", "type": { - "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } - }, + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "microscopeManufacturer", + "name": "count", "type": { - "kind": "INPUT_OBJECT", - "name": "Tiltseries_microscope_manufacturer_enumEnumComparators", + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "DepositionAuthorAggregateWhereClauseCount", + "ofType": null + } + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "DepositionAuthorAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "arguments", + "type": { + "kind": "ENUM", + "name": "DepositionAuthorCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "microscopeModel", + "name": "distinct", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "microscopeEnergyFilter", + "name": "filter", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "DepositionAuthorWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "microscopePhasePlate", + "name": "predicate", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "IntComparators", "ofType": null } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "DepositionAuthorAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ + { + "name": "id" + }, + { + "name": "authorListOrder" + }, + { + "name": "orcid" + }, + { + "name": "name" + }, + { + "name": "email" + }, + { + "name": "affiliationName" + }, + { + "name": "affiliationAddress" + }, + { + "name": "affiliationIdentifier" + }, + { + "name": "correspondingAuthorStatus" }, + { + "name": "primaryAuthorStatus" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "DepositionAuthorCountColumns", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "microscopeImageCorrector", + "name": "count", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "DatasetAggregateWhereClauseCount", + "ofType": null + } + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "DatasetAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "arguments", + "type": { + "kind": "ENUM", + "name": "DatasetCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "microscopeAdditionalInfo", + "name": "distinct", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "cameraManufacturer", + "name": "filter", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "DatasetWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "cameraModel", + "name": "predicate", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "IntComparators", "ofType": null } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "DatasetAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ + { + "name": "title" + }, + { + "name": "description" + }, + { + "name": "organismName" + }, + { + "name": "organismTaxid" + }, + { + "name": "tissueName" + }, + { + "name": "tissueId" + }, + { + "name": "cellName" + }, + { + "name": "cellTypeId" + }, + { + "name": "cellStrainName" + }, + { + "name": "cellStrainId" + }, + { + "name": "sampleType" + }, + { + "name": "samplePreparation" + }, + { + "name": "gridPreparation" + }, + { + "name": "otherSetup" + }, + { + "name": "keyPhotoUrl" + }, + { + "name": "keyPhotoThumbnailUrl" + }, + { + "name": "cellComponentName" + }, + { + "name": "cellComponentId" + }, + { + "name": "depositionDate" + }, + { + "name": "releaseDate" + }, + { + "name": "lastModifiedDate" + }, + { + "name": "datasetPublications" + }, + { + "name": "relatedDatabaseEntries" }, + { + "name": "s3Prefix" + }, + { + "name": "httpsPrefix" + }, + { + "name": "fileSize" + }, + { + "name": "id" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "DatasetCountColumns", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "tiltMin", + "name": "deposition", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "DepositionWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "tiltMax", + "name": "depositionId", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "tiltRange", + "name": "run", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "RunWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "tiltStep", + "name": "runId", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "tiltingScheme", + "name": "rawAngle", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "tiltAxis", + "name": "acquisitionOrder", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "totalFlux", + "name": "dose", "type": { "kind": "INPUT_OBJECT", "name": "FloatComparators", @@ -6358,16 +6737,16 @@ }, { "defaultValue": null, - "name": "dataAcquisitionSoftware", + "name": "isGainCorrected", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "BoolComparators", "ofType": null } }, { "defaultValue": null, - "name": "relatedEmpiarEntry", + "name": "s3FramePath", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6376,16 +6755,16 @@ }, { "defaultValue": null, - "name": "binningFromFrames", + "name": "httpsFramePath", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "tiltSeriesQuality", + "name": "fileSize", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -6394,71 +6773,17 @@ }, { "defaultValue": null, - "name": "isAligned", + "name": "id", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "pixelSpacing", - "type": { - "kind": "INPUT_OBJECT", - "name": "FloatComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "alignedTiltseriesBinning", - "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "sizeX", - "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "sizeY", - "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "sizeZ", - "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "id", - "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "IntComparators", "ofType": null } } ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "TiltseriesWhereClause", + "name": "FrameWhereClause", "possibleTypes": null }, { @@ -6469,8 +6794,8 @@ "defaultValue": null, "name": "_eq", "type": { - "kind": "ENUM", - "name": "tiltseries_microscope_manufacturer_enum", + "kind": "SCALAR", + "name": "Float", "ofType": null } }, @@ -6478,8 +6803,8 @@ "defaultValue": null, "name": "_neq", "type": { - "kind": "ENUM", - "name": "tiltseries_microscope_manufacturer_enum", + "kind": "SCALAR", + "name": "Float", "ofType": null } }, @@ -6493,8 +6818,8 @@ "kind": "NON_NULL", "name": null, "ofType": { - "kind": "ENUM", - "name": "tiltseries_microscope_manufacturer_enum", + "kind": "SCALAR", + "name": "Float", "ofType": null } } @@ -6510,8 +6835,8 @@ "kind": "NON_NULL", "name": null, "ofType": { - "kind": "ENUM", - "name": "tiltseries_microscope_manufacturer_enum", + "kind": "SCALAR", + "name": "Float", "ofType": null } } @@ -6521,8 +6846,8 @@ "defaultValue": null, "name": "_gt", "type": { - "kind": "ENUM", - "name": "tiltseries_microscope_manufacturer_enum", + "kind": "SCALAR", + "name": "Float", "ofType": null } }, @@ -6530,8 +6855,8 @@ "defaultValue": null, "name": "_gte", "type": { - "kind": "ENUM", - "name": "tiltseries_microscope_manufacturer_enum", + "kind": "SCALAR", + "name": "Float", "ofType": null } }, @@ -6539,8 +6864,8 @@ "defaultValue": null, "name": "_lt", "type": { - "kind": "ENUM", - "name": "tiltseries_microscope_manufacturer_enum", + "kind": "SCALAR", + "name": "Float", "ofType": null } }, @@ -6548,8 +6873,8 @@ "defaultValue": null, "name": "_lte", "type": { - "kind": "ENUM", - "name": "tiltseries_microscope_manufacturer_enum", + "kind": "SCALAR", + "name": "Float", "ofType": null } }, @@ -6565,29 +6890,16 @@ ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "Tiltseries_microscope_manufacturer_enumEnumComparators", + "name": "FloatComparators", "possibleTypes": null }, { - "enumValues": [ - { - "name": "FEI" - }, - { - "name": "TFS" - }, - { - "name": "JEOL" - }, - { - "name": "SIMULATED" - } - ], + "enumValues": null, "fields": null, "inputFields": null, "interfaces": null, - "kind": "ENUM", - "name": "tiltseries_microscope_manufacturer_enum", + "kind": "SCALAR", + "name": "Float", "possibleTypes": null }, { @@ -6596,79 +6908,137 @@ "inputFields": [ { "defaultValue": null, - "name": "alignment", + "name": "count", "type": { - "kind": "INPUT_OBJECT", - "name": "AlignmentWhereClause", - "ofType": null + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "FrameAggregateWhereClauseCount", + "ofType": null + } } - }, + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "FrameAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "alignmentId", + "name": "arguments", "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", + "kind": "ENUM", + "name": "FrameCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "authors", + "name": "distinct", "type": { - "kind": "INPUT_OBJECT", - "name": "TomogramAuthorWhereClause", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "deposition", + "name": "filter", "type": { "kind": "INPUT_OBJECT", - "name": "DepositionWhereClause", + "name": "FrameWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "depositionId", + "name": "predicate", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", "ofType": null } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "FrameAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ + { + "name": "rawAngle" + }, + { + "name": "acquisitionOrder" + }, + { + "name": "dose" + }, + { + "name": "isGainCorrected" + }, + { + "name": "s3FramePath" + }, + { + "name": "httpsFramePath" }, + { + "name": "fileSize" + }, + { + "name": "id" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "FrameCountColumns", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "run", + "name": "alignments", "type": { "kind": "INPUT_OBJECT", - "name": "RunWhereClause", + "name": "AlignmentWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "runId", + "name": "alignmentsAggregate", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "AlignmentAggregateWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "tomogramVoxelSpacing", + "name": "run", "type": { "kind": "INPUT_OBJECT", - "name": "TomogramVoxelSpacingWhereClause", + "name": "RunWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "tomogramVoxelSpacingId", + "name": "runId", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -6677,16 +7047,16 @@ }, { "defaultValue": null, - "name": "name", + "name": "deposition", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "DepositionWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "sizeX", + "name": "depositionId", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -6695,16 +7065,16 @@ }, { "defaultValue": null, - "name": "sizeY", + "name": "s3OmezarrDir", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "sizeZ", + "name": "fileSizeOmezarr", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -6713,52 +7083,52 @@ }, { "defaultValue": null, - "name": "voxelSpacing", + "name": "s3MrcFile", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "fiducialAlignmentStatus", + "name": "fileSizeMrc", "type": { "kind": "INPUT_OBJECT", - "name": "Fiducial_alignment_status_enumEnumComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "reconstructionMethod", + "name": "httpsOmezarrDir", "type": { "kind": "INPUT_OBJECT", - "name": "Tomogram_reconstruction_method_enumEnumComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "processing", + "name": "httpsMrcFile", "type": { "kind": "INPUT_OBJECT", - "name": "Tomogram_processing_enumEnumComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "tomogramVersion", + "name": "s3AngleList", "type": { "kind": "INPUT_OBJECT", - "name": "FloatComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "processingSoftware", + "name": "httpsAngleList", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6767,43 +7137,43 @@ }, { "defaultValue": null, - "name": "reconstructionSoftware", + "name": "accelerationVoltage", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "isPortalStandard", + "name": "sphericalAberrationConstant", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "isAuthorSubmitted", + "name": "microscopeManufacturer", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", + "name": "Tiltseries_microscope_manufacturer_enumEnumComparators", "ofType": null } }, { "defaultValue": null, - "name": "isVisualizationDefault", + "name": "microscopeModel", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "s3OmezarrDir", + "name": "microscopeEnergyFilter", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6812,7 +7182,7 @@ }, { "defaultValue": null, - "name": "httpsOmezarrDir", + "name": "microscopePhasePlate", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6821,7 +7191,7 @@ }, { "defaultValue": null, - "name": "s3MrcFile", + "name": "microscopeImageCorrector", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6830,7 +7200,7 @@ }, { "defaultValue": null, - "name": "httpsMrcFile", + "name": "microscopeAdditionalInfo", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6839,7 +7209,7 @@ }, { "defaultValue": null, - "name": "scale0Dimensions", + "name": "cameraManufacturer", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6848,16 +7218,7 @@ }, { "defaultValue": null, - "name": "scale1Dimensions", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "scale2Dimensions", + "name": "cameraModel", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6866,43 +7227,43 @@ }, { "defaultValue": null, - "name": "ctfCorrected", + "name": "tiltMin", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "offsetX", + "name": "tiltMax", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "offsetY", + "name": "tiltRange", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "offsetZ", + "name": "tiltStep", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "keyPhotoUrl", + "name": "tiltingScheme", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6911,25 +7272,25 @@ }, { "defaultValue": null, - "name": "keyPhotoThumbnailUrl", + "name": "tiltAxis", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "neuroglancerConfig", + "name": "totalFlux", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "publications", + "name": "dataAcquisitionSoftware", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6938,7 +7299,7 @@ }, { "defaultValue": null, - "name": "relatedDatabaseEntries", + "name": "relatedEmpiarEntry", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -6947,62 +7308,43 @@ }, { "defaultValue": null, - "name": "id", + "name": "binningFromFrames", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "depositionDate", + "name": "tiltSeriesQuality", "type": { "kind": "INPUT_OBJECT", - "name": "DatetimeComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "releaseDate", + "name": "isAligned", "type": { "kind": "INPUT_OBJECT", - "name": "DatetimeComparators", + "name": "BoolComparators", "ofType": null } }, { "defaultValue": null, - "name": "lastModifiedDate", - "type": { - "kind": "INPUT_OBJECT", - "name": "DatetimeComparators", - "ofType": null - } - } - ], - "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "TomogramWhereClause", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": [ - { - "defaultValue": null, - "name": "tomogram", + "name": "pixelSpacing", "type": { "kind": "INPUT_OBJECT", - "name": "TomogramWhereClause", + "name": "FloatComparators", "ofType": null } }, { "defaultValue": null, - "name": "tomogramId", + "name": "alignedTiltseriesBinning", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -7011,7 +7353,7 @@ }, { "defaultValue": null, - "name": "id", + "name": "sizeX", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -7020,7 +7362,7 @@ }, { "defaultValue": null, - "name": "authorListOrder", + "name": "sizeY", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -7029,149 +7371,13 @@ }, { "defaultValue": null, - "name": "orcid", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "name", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "email", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "affiliationName", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "affiliationAddress", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "affiliationIdentifier", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "correspondingAuthorStatus", - "type": { - "kind": "INPUT_OBJECT", - "name": "BoolComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "primaryAuthorStatus", - "type": { - "kind": "INPUT_OBJECT", - "name": "BoolComparators", - "ofType": null - } - } - ], - "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "TomogramAuthorWhereClause", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": [ - { - "defaultValue": null, - "name": "annotationFiles", - "type": { - "kind": "INPUT_OBJECT", - "name": "AnnotationFileWhereClause", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "run", - "type": { - "kind": "INPUT_OBJECT", - "name": "RunWhereClause", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "runId", + "name": "sizeZ", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", "ofType": null } }, - { - "defaultValue": null, - "name": "tomograms", - "type": { - "kind": "INPUT_OBJECT", - "name": "TomogramWhereClause", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "voxelSpacing", - "type": { - "kind": "INPUT_OBJECT", - "name": "FloatComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "s3Prefix", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "httpsPrefix", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, { "defaultValue": null, "name": "id", @@ -7184,7 +7390,7 @@ ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "TomogramVoxelSpacingWhereClause", + "name": "TiltseriesWhereClause", "possibleTypes": null }, { @@ -7196,7 +7402,7 @@ "name": "_eq", "type": { "kind": "ENUM", - "name": "fiducial_alignment_status_enum", + "name": "tiltseries_microscope_manufacturer_enum", "ofType": null } }, @@ -7205,7 +7411,7 @@ "name": "_neq", "type": { "kind": "ENUM", - "name": "fiducial_alignment_status_enum", + "name": "tiltseries_microscope_manufacturer_enum", "ofType": null } }, @@ -7220,7 +7426,7 @@ "name": null, "ofType": { "kind": "ENUM", - "name": "fiducial_alignment_status_enum", + "name": "tiltseries_microscope_manufacturer_enum", "ofType": null } } @@ -7237,7 +7443,7 @@ "name": null, "ofType": { "kind": "ENUM", - "name": "fiducial_alignment_status_enum", + "name": "tiltseries_microscope_manufacturer_enum", "ofType": null } } @@ -7248,7 +7454,7 @@ "name": "_gt", "type": { "kind": "ENUM", - "name": "fiducial_alignment_status_enum", + "name": "tiltseries_microscope_manufacturer_enum", "ofType": null } }, @@ -7257,7 +7463,7 @@ "name": "_gte", "type": { "kind": "ENUM", - "name": "fiducial_alignment_status_enum", + "name": "tiltseries_microscope_manufacturer_enum", "ofType": null } }, @@ -7266,7 +7472,7 @@ "name": "_lt", "type": { "kind": "ENUM", - "name": "fiducial_alignment_status_enum", + "name": "tiltseries_microscope_manufacturer_enum", "ofType": null } }, @@ -7275,7 +7481,7 @@ "name": "_lte", "type": { "kind": "ENUM", - "name": "fiducial_alignment_status_enum", + "name": "tiltseries_microscope_manufacturer_enum", "ofType": null } }, @@ -7291,23 +7497,29 @@ ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "Fiducial_alignment_status_enumEnumComparators", + "name": "Tiltseries_microscope_manufacturer_enumEnumComparators", "possibleTypes": null }, { "enumValues": [ { - "name": "FIDUCIAL" + "name": "FEI" }, { - "name": "NON_FIDUCIAL" + "name": "TFS" + }, + { + "name": "JEOL" + }, + { + "name": "SIMULATED" } ], "fields": null, "inputFields": null, "interfaces": null, "kind": "ENUM", - "name": "fiducial_alignment_status_enum", + "name": "tiltseries_microscope_manufacturer_enum", "possibleTypes": null }, { @@ -7316,130 +7528,2120 @@ "inputFields": [ { "defaultValue": null, - "name": "_eq", + "name": "count", "type": { - "kind": "ENUM", - "name": "tomogram_reconstruction_method_enum", + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "TiltseriesAggregateWhereClauseCount", + "ofType": null + } + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "TiltseriesAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "arguments", + "type": { + "kind": "ENUM", + "name": "TiltseriesCountColumns", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "distinct", + "type": { + "kind": "SCALAR", + "name": "Boolean", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "filter", + "type": { + "kind": "INPUT_OBJECT", + "name": "TiltseriesWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "predicate", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "TiltseriesAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ + { + "name": "s3OmezarrDir" + }, + { + "name": "fileSizeOmezarr" + }, + { + "name": "s3MrcFile" + }, + { + "name": "fileSizeMrc" + }, + { + "name": "httpsOmezarrDir" + }, + { + "name": "httpsMrcFile" + }, + { + "name": "s3AngleList" + }, + { + "name": "httpsAngleList" + }, + { + "name": "accelerationVoltage" + }, + { + "name": "sphericalAberrationConstant" + }, + { + "name": "microscopeManufacturer" + }, + { + "name": "microscopeModel" + }, + { + "name": "microscopeEnergyFilter" + }, + { + "name": "microscopePhasePlate" + }, + { + "name": "microscopeImageCorrector" + }, + { + "name": "microscopeAdditionalInfo" + }, + { + "name": "cameraManufacturer" + }, + { + "name": "cameraModel" + }, + { + "name": "tiltMin" + }, + { + "name": "tiltMax" + }, + { + "name": "tiltRange" + }, + { + "name": "tiltStep" + }, + { + "name": "tiltingScheme" + }, + { + "name": "tiltAxis" + }, + { + "name": "totalFlux" + }, + { + "name": "dataAcquisitionSoftware" + }, + { + "name": "relatedEmpiarEntry" + }, + { + "name": "binningFromFrames" + }, + { + "name": "tiltSeriesQuality" + }, + { + "name": "isAligned" + }, + { + "name": "pixelSpacing" + }, + { + "name": "alignedTiltseriesBinning" + }, + { + "name": "sizeX" + }, + { + "name": "sizeY" + }, + { + "name": "sizeZ" + }, + { + "name": "id" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "TiltseriesCountColumns", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "alignment", + "type": { + "kind": "INPUT_OBJECT", + "name": "AlignmentWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "alignmentId", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "authors", + "type": { + "kind": "INPUT_OBJECT", + "name": "TomogramAuthorWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "authorsAggregate", + "type": { + "kind": "INPUT_OBJECT", + "name": "TomogramAuthorAggregateWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "deposition", + "type": { + "kind": "INPUT_OBJECT", + "name": "DepositionWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "depositionId", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "run", + "type": { + "kind": "INPUT_OBJECT", + "name": "RunWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "runId", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "tomogramVoxelSpacing", + "type": { + "kind": "INPUT_OBJECT", + "name": "TomogramVoxelSpacingWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "tomogramVoxelSpacingId", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "name", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "sizeX", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "sizeY", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "sizeZ", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "voxelSpacing", + "type": { + "kind": "INPUT_OBJECT", + "name": "FloatComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "fiducialAlignmentStatus", + "type": { + "kind": "INPUT_OBJECT", + "name": "Fiducial_alignment_status_enumEnumComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "reconstructionMethod", + "type": { + "kind": "INPUT_OBJECT", + "name": "Tomogram_reconstruction_method_enumEnumComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "processing", + "type": { + "kind": "INPUT_OBJECT", + "name": "Tomogram_processing_enumEnumComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "tomogramVersion", + "type": { + "kind": "INPUT_OBJECT", + "name": "FloatComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "processingSoftware", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "reconstructionSoftware", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "isPortalStandard", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "isAuthorSubmitted", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "isVisualizationDefault", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "s3OmezarrDir", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "httpsOmezarrDir", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "fileSizeOmezarr", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "s3MrcFile", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "httpsMrcFile", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "fileSizeMrc", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "scale0Dimensions", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "scale1Dimensions", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "scale2Dimensions", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "ctfCorrected", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "offsetX", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "offsetY", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "offsetZ", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "keyPhotoUrl", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "keyPhotoThumbnailUrl", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "neuroglancerConfig", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "publications", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "relatedDatabaseEntries", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "id", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "depositionDate", + "type": { + "kind": "INPUT_OBJECT", + "name": "DatetimeComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "releaseDate", + "type": { + "kind": "INPUT_OBJECT", + "name": "DatetimeComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "lastModifiedDate", + "type": { + "kind": "INPUT_OBJECT", + "name": "DatetimeComparators", + "ofType": null + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "TomogramWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "tomogram", + "type": { + "kind": "INPUT_OBJECT", + "name": "TomogramWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "tomogramId", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "id", + "type": { + "kind": "INPUT_OBJECT", + "name": 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"INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "correspondingAuthorStatus", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "primaryAuthorStatus", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "TomogramAuthorWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "count", + "type": { + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "TomogramAuthorAggregateWhereClauseCount", + "ofType": null + } + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "TomogramAuthorAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": 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"name": "affiliationAddress", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "affiliationIdentifier", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "correspondingAuthorStatus", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", "ofType": null } }, { "defaultValue": null, - "name": "_gte", + "name": "primaryAuthorStatus", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "DatasetAuthorWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "count", + "type": { + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "DatasetAuthorAggregateWhereClauseCount", + "ofType": null + } + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "DatasetAuthorAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "arguments", "type": { "kind": "ENUM", - "name": "tomogram_processing_enum", + "name": "DatasetAuthorCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "_lt", + "name": "distinct", "type": { - "kind": "ENUM", - "name": "tomogram_processing_enum", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "_lte", + "name": "filter", "type": { - "kind": "ENUM", - "name": "tomogram_processing_enum", + "kind": "INPUT_OBJECT", + "name": "DatasetAuthorWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_is_null", + "name": "predicate", "type": { - "kind": "SCALAR", - "name": "Boolean", + "kind": "INPUT_OBJECT", + "name": "IntComparators", "ofType": null } } ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "Tomogram_processing_enumEnumComparators", + "name": "DatasetAuthorAggregateWhereClauseCount", "possibleTypes": null }, { "enumValues": [ { - "name": "denoised" + "name": "id" }, { - "name": "filtered" + "name": "authorListOrder" }, { - "name": "raw" + "name": "orcid" + }, + { + "name": "name" + }, + { + "name": "email" + }, + { + "name": "affiliationName" + }, + { + "name": "affiliationAddress" + }, + { + "name": "affiliationIdentifier" + }, + { + "name": "correspondingAuthorStatus" + }, + { + "name": "primaryAuthorStatus" } ], "fields": null, "inputFields": null, "interfaces": null, "kind": "ENUM", - "name": "tomogram_processing_enum", + "name": "DatasetAuthorCountColumns", "possibleTypes": null }, { @@ -7574,160 +9877,89 @@ "inputFields": [ { "defaultValue": null, - "name": "_eq", - "type": { - "kind": "SCALAR", - "name": "DateTime", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "_neq", - "type": { - "kind": "SCALAR", - "name": "DateTime", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "_in", - "type": { - "kind": "LIST", - "name": null, - "ofType": { - "kind": "NON_NULL", - "name": null, - "ofType": { - "kind": "SCALAR", - "name": "DateTime", - "ofType": null - } - } - } - }, - { - "defaultValue": null, - "name": "_nin", + "name": "count", "type": { - "kind": "LIST", + "kind": "NON_NULL", "name": null, "ofType": { - "kind": "NON_NULL", - "name": null, - "ofType": { - "kind": "SCALAR", - "name": "DateTime", - "ofType": null - } + "kind": "INPUT_OBJECT", + "name": "RunAggregateWhereClauseCount", + "ofType": null } } - }, - { - "defaultValue": null, - "name": "_gt", - "type": { - "kind": "SCALAR", - "name": "DateTime", - "ofType": null - } - }, + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "RunAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "_gte", + "name": "arguments", "type": { - "kind": "SCALAR", - "name": "DateTime", + "kind": "ENUM", + "name": "RunCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "_lt", + "name": "distinct", "type": { "kind": "SCALAR", - "name": "DateTime", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "_lte", + "name": "filter", "type": { - "kind": "SCALAR", - "name": "DateTime", + "kind": "INPUT_OBJECT", + "name": "RunWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_is_null", + "name": "predicate", "type": { - "kind": "SCALAR", - "name": "Boolean", + "kind": "INPUT_OBJECT", + "name": "IntComparators", "ofType": null } } ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "DatetimeComparators", - "possibleTypes": null - }, - { - "enumValues": null, - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "SCALAR", - "name": "DateTime", + "name": "RunAggregateWhereClauseCount", "possibleTypes": null }, { - "enumValues": null, - "fields": null, - "inputFields": [ + "enumValues": [ { - "defaultValue": null, - "name": "deposition", - "type": { - "kind": "INPUT_OBJECT", - "name": "DepositionWhereClause", - "ofType": null - } + "name": "name" }, { - "defaultValue": null, - "name": "depositionId", - "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null - } + "name": "s3Prefix" }, { - "defaultValue": null, - "name": "type", - "type": { - "kind": "INPUT_OBJECT", - "name": "Deposition_types_enumEnumComparators", - "ofType": null - } + "name": "httpsPrefix" }, { - "defaultValue": null, - "name": "id", - "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null - } + "name": "id" } ], + "fields": null, + "inputFields": null, "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "DepositionTypeWhereClause", + "kind": "ENUM", + "name": "RunCountColumns", "possibleTypes": null }, { @@ -7739,7 +9971,7 @@ "name": "_eq", "type": { "kind": "ENUM", - "name": "deposition_types_enum", + "name": "sample_type_enum", "ofType": null } }, @@ -7748,7 +9980,7 @@ "name": "_neq", "type": { "kind": "ENUM", - "name": "deposition_types_enum", + "name": "sample_type_enum", "ofType": null } }, @@ -7763,7 +9995,7 @@ "name": null, "ofType": { "kind": "ENUM", - "name": "deposition_types_enum", + "name": "sample_type_enum", "ofType": null } } @@ -7780,7 +10012,7 @@ "name": null, "ofType": { "kind": "ENUM", - "name": "deposition_types_enum", + "name": "sample_type_enum", "ofType": null } } @@ -7791,7 +10023,7 @@ "name": "_gt", "type": { "kind": "ENUM", - "name": "deposition_types_enum", + "name": "sample_type_enum", "ofType": null } }, @@ -7800,7 +10032,7 @@ "name": "_gte", "type": { "kind": "ENUM", - "name": "deposition_types_enum", + "name": "sample_type_enum", "ofType": null } }, @@ -7809,7 +10041,7 @@ "name": "_lt", "type": { "kind": "ENUM", - "name": "deposition_types_enum", + "name": "sample_type_enum", "ofType": null } }, @@ -7818,7 +10050,7 @@ "name": "_lte", "type": { "kind": "ENUM", - "name": "deposition_types_enum", + "name": "sample_type_enum", "ofType": null } }, @@ -7834,26 +10066,41 @@ ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "Deposition_types_enumEnumComparators", + "name": "Sample_type_enumEnumComparators", "possibleTypes": null }, { "enumValues": [ { - "name": "annotation" + "name": "cell" }, { - "name": "dataset" + "name": "tissue" }, { - "name": "tomogram" + "name": "organism" + }, + { + "name": "organelle" + }, + { + "name": "virus" + }, + { + "name": "in_vitro" + }, + { + "name": "in_silico" + }, + { + "name": "other" } ], "fields": null, "inputFields": null, "interfaces": null, "kind": "ENUM", - "name": "deposition_types_enum", + "name": "sample_type_enum", "possibleTypes": null }, { @@ -7862,16 +10109,16 @@ "inputFields": [ { "defaultValue": null, - "name": "dataset", + "name": "run", "type": { "kind": "INPUT_OBJECT", - "name": "DatasetWhereClause", + "name": "RunWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "datasetId", + "name": "runId", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -7880,7 +10127,7 @@ }, { "defaultValue": null, - "name": "fundingAgencyName", + "name": "s3FilePath", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -7889,7 +10136,7 @@ }, { "defaultValue": null, - "name": "grantId", + "name": "httpsFilePath", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -7900,15 +10147,38 @@ "defaultValue": null, "name": "id", "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "GainFileWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "count", + "type": { + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "GainFileAggregateWhereClauseCount", + "ofType": null + } } } ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "DatasetFundingWhereClause", + "name": "GainFileAggregateWhereClause", "possibleTypes": null }, { @@ -7917,88 +10187,90 @@ "inputFields": [ { "defaultValue": null, - "name": "dataset", + "name": "arguments", "type": { - "kind": "INPUT_OBJECT", - "name": "DatasetWhereClause", + "kind": "ENUM", + "name": "GainFileCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "datasetId", + "name": "distinct", "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "id", + "name": "filter", "type": { "kind": "INPUT_OBJECT", - "name": "IntComparators", + "name": "GainFileWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "authorListOrder", + "name": "predicate", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", "ofType": null } - }, + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "GainFileAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ { - "defaultValue": null, - "name": "orcid", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } + "name": "s3FilePath" }, { - "defaultValue": null, - "name": "name", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } + "name": "httpsFilePath" }, { - "defaultValue": null, - "name": "email", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } - }, + "name": "id" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "GainFileCountColumns", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "affiliationName", + "name": "run", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "RunWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "affiliationAddress", + "name": "runId", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "IntComparators", "ofType": null } }, { "defaultValue": null, - "name": "affiliationIdentifier", + "name": "s3MdocPath", "type": { "kind": "INPUT_OBJECT", "name": "StrComparators", @@ -8007,26 +10279,26 @@ }, { "defaultValue": null, - "name": "correspondingAuthorStatus", + "name": "httpsMdocPath", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", + "name": "StrComparators", "ofType": null } }, { "defaultValue": null, - "name": "primaryAuthorStatus", + "name": "id", "type": { "kind": "INPUT_OBJECT", - "name": "BoolComparators", + "name": "IntComparators", "ofType": null } } ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "DatasetAuthorWhereClause", + "name": "FrameAcquisitionFileWhereClause", "possibleTypes": null }, { @@ -8035,139 +10307,86 @@ "inputFields": [ { "defaultValue": null, - "name": "_eq", - "type": { - "kind": "ENUM", - "name": "sample_type_enum", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "_neq", - "type": { - "kind": "ENUM", - "name": "sample_type_enum", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "_in", - "type": { - "kind": "LIST", - "name": null, - "ofType": { - "kind": "NON_NULL", - "name": null, - "ofType": { - "kind": "ENUM", - "name": "sample_type_enum", - "ofType": null - } - } - } - }, - { - "defaultValue": null, - "name": "_nin", + "name": "count", "type": { - "kind": "LIST", + "kind": "NON_NULL", "name": null, "ofType": { - "kind": "NON_NULL", - "name": null, - "ofType": { - "kind": "ENUM", - "name": "sample_type_enum", - "ofType": null - } + "kind": "INPUT_OBJECT", + "name": "FrameAcquisitionFileAggregateWhereClauseCount", + "ofType": null } } - }, - { - "defaultValue": null, - "name": "_gt", - "type": { - "kind": "ENUM", - "name": "sample_type_enum", - "ofType": null - } - }, + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "FrameAcquisitionFileAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "_gte", + "name": "arguments", "type": { "kind": "ENUM", - "name": "sample_type_enum", + "name": "FrameAcquisitionFileCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "_lt", + "name": "distinct", "type": { - "kind": "ENUM", - "name": "sample_type_enum", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "_lte", + "name": "filter", "type": { - "kind": "ENUM", - "name": "sample_type_enum", + "kind": "INPUT_OBJECT", + "name": "FrameAcquisitionFileWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "_is_null", + "name": "predicate", "type": { - "kind": "SCALAR", - "name": "Boolean", + "kind": "INPUT_OBJECT", + "name": "IntComparators", "ofType": null } } ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "Sample_type_enumEnumComparators", + "name": "FrameAcquisitionFileAggregateWhereClauseCount", "possibleTypes": null }, { "enumValues": [ { - "name": "cell" - }, - { - "name": "tissue" - }, - { - "name": "organism" - }, - { - "name": "organelle" - }, - { - "name": "virus" - }, - { - "name": "in_vitro" + "name": "s3MdocPath" }, { - "name": "in_silico" + "name": "httpsMdocPath" }, { - "name": "other" + "name": "id" } ], "fields": null, "inputFields": null, "interfaces": null, "kind": "ENUM", - "name": "sample_type_enum", + "name": "FrameAcquisitionFileCountColumns", "possibleTypes": null }, { @@ -8176,53 +10395,112 @@ "inputFields": [ { "defaultValue": null, - "name": "run", + "name": "count", "type": { - "kind": "INPUT_OBJECT", - "name": "RunWhereClause", + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "TomogramVoxelSpacingAggregateWhereClauseCount", + "ofType": null + } + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "TomogramVoxelSpacingAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "arguments", + "type": { + "kind": "ENUM", + "name": "TomogramVoxelSpacingCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "runId", + "name": "distinct", "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "s3FilePath", + "name": "filter", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "TomogramVoxelSpacingWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "httpsFilePath", + "name": "predicate", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "IntComparators", "ofType": null } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "TomogramVoxelSpacingAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ + { + "name": "voxelSpacing" + }, + { + "name": "s3Prefix" + }, + { + "name": "httpsPrefix" }, + { + "name": "id" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "TomogramVoxelSpacingCountColumns", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ { "defaultValue": null, - "name": "id", + "name": "count", "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", - "ofType": null + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "AnnotationShapeAggregateWhereClauseCount", + "ofType": null + } } } ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "GainFileWhereClause", + "name": "AnnotationShapeAggregateWhereClause", "possibleTypes": null }, { @@ -8231,43 +10509,34 @@ "inputFields": [ { "defaultValue": null, - "name": "run", - "type": { - "kind": "INPUT_OBJECT", - "name": "RunWhereClause", - "ofType": null - } - }, - { - "defaultValue": null, - "name": "runId", + "name": "arguments", "type": { - "kind": "INPUT_OBJECT", - "name": "IntComparators", + "kind": "ENUM", + "name": "AnnotationShapeCountColumns", "ofType": null } }, { "defaultValue": null, - "name": "s3MdocPath", + "name": "distinct", "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", + "kind": "SCALAR", + "name": "Boolean", "ofType": null } }, { "defaultValue": null, - "name": "httpsMdocPath", + "name": "filter", "type": { "kind": "INPUT_OBJECT", - "name": "StrComparators", + "name": "AnnotationShapeWhereClause", "ofType": null } }, { "defaultValue": null, - "name": "id", + "name": "predicate", "type": { "kind": "INPUT_OBJECT", "name": "IntComparators", @@ -8277,7 +10546,23 @@ ], "interfaces": null, "kind": "INPUT_OBJECT", - "name": "FrameAcquisitionFileWhereClause", + "name": "AnnotationShapeAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ + { + "name": "shapeType" + }, + { + "name": "id" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "AnnotationShapeCountColumns", "possibleTypes": null }, { @@ -8476,6 +10761,97 @@ "name": "annotation_method_link_type_enum", "possibleTypes": null }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "count", + "type": { + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "AnnotationMethodLinkAggregateWhereClauseCount", + "ofType": null + } + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "AnnotationMethodLinkAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "arguments", + "type": { + "kind": "ENUM", + "name": "AnnotationMethodLinkCountColumns", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "distinct", + "type": { + "kind": "SCALAR", + "name": "Boolean", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "filter", + "type": { + "kind": "INPUT_OBJECT", + "name": "AnnotationMethodLinkWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "predicate", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "AnnotationMethodLinkAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ + { + "name": "linkType" + }, + { + "name": "name" + }, + { + "name": "link" + }, + { + "name": "id" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "AnnotationMethodLinkCountColumns", + "possibleTypes": null + }, { "enumValues": null, "fields": null, @@ -8562,36 +10938,145 @@ } }, { - "defaultValue": null, - "name": "affiliationIdentifier", - "type": { - "kind": "INPUT_OBJECT", - "name": "StrComparators", - "ofType": null - } + "defaultValue": null, + "name": "affiliationIdentifier", + "type": { + "kind": "INPUT_OBJECT", + "name": "StrComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "correspondingAuthorStatus", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "primaryAuthorStatus", + "type": { + "kind": "INPUT_OBJECT", + "name": "BoolComparators", + "ofType": null + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "AnnotationAuthorWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "count", + "type": { + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "AnnotationAuthorAggregateWhereClauseCount", + "ofType": null + } + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "AnnotationAuthorAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "arguments", + "type": { + "kind": "ENUM", + "name": "AnnotationAuthorCountColumns", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "distinct", + "type": { + "kind": "SCALAR", + "name": "Boolean", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "filter", + "type": { + "kind": "INPUT_OBJECT", + "name": "AnnotationAuthorWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "predicate", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "AnnotationAuthorAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ + { + "name": "id" + }, + { + "name": "authorListOrder" + }, + { + "name": "orcid" + }, + { + "name": "name" + }, + { + "name": "email" + }, + { + "name": "affiliationName" + }, + { + "name": "affiliationAddress" + }, + { + "name": "affiliationIdentifier" }, { - "defaultValue": null, - "name": "correspondingAuthorStatus", - "type": { - "kind": "INPUT_OBJECT", - "name": "BoolComparators", - "ofType": null - } + "name": "correspondingAuthorStatus" }, { - "defaultValue": null, - "name": "primaryAuthorStatus", - "type": { - "kind": "INPUT_OBJECT", - "name": "BoolComparators", - "ofType": null - } + "name": "primaryAuthorStatus" } ], + "fields": null, + "inputFields": null, "interfaces": null, - "kind": "INPUT_OBJECT", - "name": "AnnotationAuthorWhereClause", + "kind": "ENUM", + "name": "AnnotationAuthorCountColumns", "possibleTypes": null }, { @@ -9063,6 +11548,106 @@ "name": "PerSectionAlignmentParametersWhereClause", "possibleTypes": null }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "count", + "type": { + "kind": "NON_NULL", + "name": null, + "ofType": { + "kind": "INPUT_OBJECT", + "name": "PerSectionAlignmentParametersAggregateWhereClauseCount", + "ofType": null + } + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "PerSectionAlignmentParametersAggregateWhereClause", + "possibleTypes": null + }, + { + "enumValues": null, + "fields": null, + "inputFields": [ + { + "defaultValue": null, + "name": "arguments", + "type": { + "kind": "ENUM", + "name": "PerSectionAlignmentParametersCountColumns", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "distinct", + "type": { + "kind": "SCALAR", + "name": "Boolean", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "filter", + "type": { + "kind": "INPUT_OBJECT", + "name": "PerSectionAlignmentParametersWhereClause", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "predicate", + "type": { + "kind": "INPUT_OBJECT", + "name": "IntComparators", + "ofType": null + } + } + ], + "interfaces": null, + "kind": "INPUT_OBJECT", + "name": "PerSectionAlignmentParametersAggregateWhereClauseCount", + "possibleTypes": null + }, + { + "enumValues": [ + { + "name": "zIndex" + }, + { + "name": "xOffset" + }, + { + "name": "yOffset" + }, + { + "name": "volumeXRotation" + }, + { + "name": "inPlaneRotation" + }, + { + "name": "tiltAngle" + }, + { + "name": "id" + } + ], + "fields": null, + "inputFields": null, + "interfaces": null, + "kind": "ENUM", + "name": "PerSectionAlignmentParametersCountColumns", + "possibleTypes": null + }, { "enumValues": null, "fields": null, @@ -9643,6 +12228,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "fileSizeOmezarr", + "type": { + "kind": "ENUM", + "name": "orderBy", + "ofType": null + } + }, { "defaultValue": null, "name": "s3MrcFile", @@ -9652,6 +12246,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "fileSizeMrc", + "type": { + "kind": "ENUM", + "name": "orderBy", + "ofType": null + } + }, { "defaultValue": null, "name": "httpsOmezarrDir", @@ -10239,6 +12842,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "fileSize", + "type": { + "kind": "ENUM", + "name": "orderBy", + "ofType": null + } + }, { "defaultValue": null, "name": "id", @@ -12225,6 +14837,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "httpsPath", @@ -12533,6 +15154,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "s3MrcFile", @@ -12551,6 +15181,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "scale0Dimensions", @@ -13356,6 +15995,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "id", @@ -13602,6 +16250,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "id", @@ -13657,6 +16314,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "s3MrcFile", @@ -13666,6 +16332,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "httpsOmezarrDir", @@ -14352,28 +17027,6 @@ "name": "AnnotationAuthorGroupByOptions", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "annotation" - }, - { - "name": "annotationFiles" - }, - { - "name": "shapeType" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "AnnotationShapeCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -14799,50 +17452,25 @@ "args": [], "name": "link", "type": { - "kind": "SCALAR", - "name": "String", - "ofType": null - } - }, - { - "args": [], - "name": "id", - "type": { - "kind": "SCALAR", - "name": "Int", - "ofType": null - } - } - ], - "inputFields": null, - "interfaces": [], - "kind": "OBJECT", - "name": "AnnotationMethodLinkMinMaxColumns", - "possibleTypes": null - }, - { - "enumValues": [ - { - "name": "annotation" - }, - { - "name": "linkType" - }, - { - "name": "name" - }, - { - "name": "link" + "kind": "SCALAR", + "name": "String", + "ofType": null + } }, { - "name": "id" + "args": [], + "name": "id", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } } ], - "fields": null, "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "AnnotationMethodLinkCountColumns", + "interfaces": [], + "kind": "OBJECT", + "name": "AnnotationMethodLinkMinMaxColumns", "possibleTypes": null }, { @@ -15453,49 +18081,6 @@ "name": "AnnotationAuthorMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "annotation" - }, - { - "name": "id" - }, - { - "name": "authorListOrder" - }, - { - "name": "orcid" - }, - { - "name": "name" - }, - { - "name": "email" - }, - { - "name": "affiliationName" - }, - { - "name": "affiliationAddress" - }, - { - "name": "affiliationIdentifier" - }, - { - "name": "correspondingAuthorStatus" - }, - { - "name": "primaryAuthorStatus" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "AnnotationAuthorCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -17016,49 +19601,6 @@ "name": "DepositionAuthorMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "deposition" - }, - { - "name": "id" - }, - { - "name": "authorListOrder" - }, - { - "name": "orcid" - }, - { - "name": "name" - }, - { - "name": "email" - }, - { - "name": "affiliationName" - }, - { - "name": "affiliationAddress" - }, - { - "name": "affiliationIdentifier" - }, - { - "name": "correspondingAuthorStatus" - }, - { - "name": "primaryAuthorStatus" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "DepositionAuthorCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -17396,79 +19938,6 @@ "name": "AlignmentMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "annotationFiles" - }, - { - "name": "perSectionAlignments" - }, - { - "name": "deposition" - }, - { - "name": "tiltseries" - }, - { - "name": "tomograms" - }, - { - "name": "run" - }, - { - "name": "alignmentType" - }, - { - "name": "alignmentMethod" - }, - { - "name": "volumeXDimension" - }, - { - "name": "volumeYDimension" - }, - { - "name": "volumeZDimension" - }, - { - "name": "volumeXOffset" - }, - { - "name": "volumeYOffset" - }, - { - "name": "volumeZOffset" - }, - { - "name": "xRotationOffset" - }, - { - "name": "tiltOffset" - }, - { - "name": "affineTransformationMatrix" - }, - { - "name": "s3AlignmentMetadata" - }, - { - "name": "httpsAlignmentMetadata" - }, - { - "name": "isPortalStandard" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "AlignmentCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -17872,103 +20341,18 @@ }, { "args": [], - "name": "id", - "type": { - "kind": "SCALAR", - "name": "Int", - "ofType": null - } - } - ], - "inputFields": null, - "interfaces": [], - "kind": "OBJECT", - "name": "AnnotationMinMaxColumns", - "possibleTypes": null - }, - { - "enumValues": [ - { - "name": "run" - }, - { - "name": "annotationShapes" - }, - { - "name": "methodLinks" - }, - { - "name": "authors" - }, - { - "name": "deposition" - }, - { - "name": "s3MetadataPath" - }, - { - "name": "httpsMetadataPath" - }, - { - "name": "annotationPublication" - }, - { - "name": "annotationMethod" - }, - { - "name": "groundTruthStatus" - }, - { - "name": "objectId" - }, - { - "name": "objectName" - }, - { - "name": "objectDescription" - }, - { - "name": "objectState" - }, - { - "name": "objectCount" - }, - { - "name": "confidencePrecision" - }, - { - "name": "confidenceRecall" - }, - { - "name": "groundTruthUsed" - }, - { - "name": "annotationSoftware" - }, - { - "name": "isCuratorRecommended" - }, - { - "name": "methodType" - }, - { - "name": "depositionDate" - }, - { - "name": "releaseDate" - }, - { - "name": "lastModifiedDate" - }, - { - "name": "id" + "name": "id", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } } ], - "fields": null, "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "AnnotationCountColumns", + "interfaces": [], + "kind": "OBJECT", + "name": "AnnotationMinMaxColumns", "possibleTypes": null }, { @@ -18666,6 +21050,15 @@ "ofType": null } } + }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } } ], "inputFields": null, @@ -19105,28 +21498,6 @@ "name": "DatasetFundingMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "dataset" - }, - { - "name": "fundingAgencyName" - }, - { - "name": "grantId" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "DatasetFundingCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -19735,49 +22106,6 @@ "name": "DatasetAuthorMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "dataset" - }, - { - "name": "id" - }, - { - "name": "authorListOrder" - }, - { - "name": "orcid" - }, - { - "name": "name" - }, - { - "name": "email" - }, - { - "name": "affiliationName" - }, - { - "name": "affiliationAddress" - }, - { - "name": "affiliationIdentifier" - }, - { - "name": "correspondingAuthorStatus" - }, - { - "name": "primaryAuthorStatus" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "DatasetAuthorCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -20051,55 +22379,6 @@ "name": "RunMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "alignments" - }, - { - "name": "annotations" - }, - { - "name": "dataset" - }, - { - "name": "frames" - }, - { - "name": "gainFiles" - }, - { - "name": "frameAcquisitionFiles" - }, - { - "name": "tiltseries" - }, - { - "name": "tomogramVoxelSpacings" - }, - { - "name": "tomograms" - }, - { - "name": "name" - }, - { - "name": "s3Prefix" - }, - { - "name": "httpsPrefix" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "RunCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -20240,6 +22519,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "id", @@ -20475,6 +22763,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "id", @@ -20491,106 +22788,6 @@ "name": "DatasetMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "deposition" - }, - { - "name": "fundingSources" - }, - { - "name": "authors" - }, - { - "name": "runs" - }, - { - "name": "title" - }, - { - "name": "description" - }, - { - "name": "organismName" - }, - { - "name": "organismTaxid" - }, - { - "name": "tissueName" - }, - { - "name": "tissueId" - }, - { - "name": "cellName" - }, - { - "name": "cellTypeId" - }, - { - "name": "cellStrainName" - }, - { - "name": "cellStrainId" - }, - { - "name": "sampleType" - }, - { - "name": "samplePreparation" - }, - { - "name": "gridPreparation" - }, - { - "name": "otherSetup" - }, - { - "name": "keyPhotoUrl" - }, - { - "name": "keyPhotoThumbnailUrl" - }, - { - "name": "cellComponentName" - }, - { - "name": "cellComponentId" - }, - { - "name": "depositionDate" - }, - { - "name": "releaseDate" - }, - { - "name": "lastModifiedDate" - }, - { - "name": "datasetPublications" - }, - { - "name": "relatedDatabaseEntries" - }, - { - "name": "s3Prefix" - }, - { - "name": "httpsPrefix" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "DatasetCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -20859,6 +23056,15 @@ "ofType": null } } + }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } } ], "inputFields": null, @@ -20920,7 +23126,16 @@ }, { "defaultValue": null, - "name": "dose", + "name": "dose", + "type": { + "kind": "ENUM", + "name": "orderBy", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "isGainCorrected", "type": { "kind": "ENUM", "name": "orderBy", @@ -20929,7 +23144,7 @@ }, { "defaultValue": null, - "name": "isGainCorrected", + "name": "s3FramePath", "type": { "kind": "ENUM", "name": "orderBy", @@ -20938,7 +23153,7 @@ }, { "defaultValue": null, - "name": "s3FramePath", + "name": "httpsFramePath", "type": { "kind": "ENUM", "name": "orderBy", @@ -20947,7 +23162,7 @@ }, { "defaultValue": null, - "name": "httpsFramePath", + "name": "fileSize", "type": { "kind": "ENUM", "name": "orderBy", @@ -21127,6 +23342,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "id", @@ -21191,6 +23415,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "id", @@ -21207,43 +23440,6 @@ "name": "FrameMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "deposition" - }, - { - "name": "run" - }, - { - "name": "rawAngle" - }, - { - "name": "acquisitionOrder" - }, - { - "name": "dose" - }, - { - "name": "isGainCorrected" - }, - { - "name": "s3FramePath" - }, - { - "name": "httpsFramePath" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "FrameCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -21551,6 +23747,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "s3MrcFile", @@ -21560,6 +23765,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "httpsOmezarrDir", @@ -22060,6 +24274,24 @@ { "enumValues": null, "fields": [ + { + "args": [], + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, + { + "args": [], + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "accelerationVoltage", @@ -22223,6 +24455,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "s3MrcFile", @@ -22232,6 +24473,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "httpsOmezarrDir", @@ -22509,127 +24759,6 @@ "name": "TiltseriesMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "alignments" - }, - { - "name": "run" - }, - { - "name": "deposition" - }, - { - "name": "s3OmezarrDir" - }, - { - "name": "s3MrcFile" - }, - { - "name": "httpsOmezarrDir" - }, - { - "name": "httpsMrcFile" - }, - { - "name": "s3AngleList" - }, - { - "name": "httpsAngleList" - }, - { - "name": "accelerationVoltage" - }, - { - "name": "sphericalAberrationConstant" - }, - { - "name": "microscopeManufacturer" - }, - { - "name": "microscopeModel" - }, - { - "name": "microscopeEnergyFilter" - }, - { - "name": "microscopePhasePlate" - }, - { - "name": "microscopeImageCorrector" - }, - { - "name": "microscopeAdditionalInfo" - }, - { - "name": "cameraManufacturer" - }, - { - "name": "cameraModel" - }, - { - "name": "tiltMin" - }, - { - "name": "tiltMax" - }, - { - "name": "tiltRange" - }, - { - "name": "tiltStep" - }, - { - "name": "tiltingScheme" - }, - { - "name": "tiltAxis" - }, - { - "name": "totalFlux" - }, - { - "name": "dataAcquisitionSoftware" - }, - { - "name": "relatedEmpiarEntry" - }, - { - "name": "binningFromFrames" - }, - { - "name": "tiltSeriesQuality" - }, - { - "name": "isAligned" - }, - { - "name": "pixelSpacing" - }, - { - "name": "alignedTiltseriesBinning" - }, - { - "name": "sizeX" - }, - { - "name": "sizeY" - }, - { - "name": "sizeZ" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "TiltseriesCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -23194,6 +25323,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "s3MrcFile", @@ -23212,6 +25350,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "scale0Dimensions", @@ -23822,6 +25969,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "fileSizeOmezarr", + "type": { + "kind": "ENUM", + "name": "orderBy", + "ofType": null + } + }, { "defaultValue": null, "name": "s3MrcFile", @@ -23833,7 +25989,16 @@ }, { "defaultValue": null, - "name": "httpsMrcFile", + "name": "httpsMrcFile", + "type": { + "kind": "ENUM", + "name": "orderBy", + "ofType": null + } + }, + { + "defaultValue": null, + "name": "fileSizeMrc", "type": { "kind": "ENUM", "name": "orderBy", @@ -24392,49 +26557,6 @@ "name": "TomogramAuthorMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "tomogram" - }, - { - "name": "id" - }, - { - "name": "authorListOrder" - }, - { - "name": "orcid" - }, - { - "name": "name" - }, - { - "name": "email" - }, - { - "name": "affiliationName" - }, - { - "name": "affiliationAddress" - }, - { - "name": "affiliationIdentifier" - }, - { - "name": "correspondingAuthorStatus" - }, - { - "name": "primaryAuthorStatus" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "TomogramAuthorCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -24805,6 +26927,15 @@ "ofType": null } }, + { + "defaultValue": null, + "name": "fileSize", + "type": { + "kind": "ENUM", + "name": "orderBy", + "ofType": null + } + }, { "defaultValue": null, "name": "httpsPath", @@ -24978,6 +27109,15 @@ { "enumValues": null, "fields": [ + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "id", @@ -25015,6 +27155,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "httpsPath", @@ -25040,43 +27189,6 @@ "name": "AnnotationFileMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "alignment" - }, - { - "name": "annotationShape" - }, - { - "name": "tomogramVoxelSpacing" - }, - { - "name": "format" - }, - { - "name": "s3Path" - }, - { - "name": "httpsPath" - }, - { - "name": "isVisualizationDefault" - }, - { - "name": "source" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "AnnotationFileCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -25253,6 +27365,24 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, + { + "args": [], + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "offsetX", @@ -25389,6 +27519,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "s3MrcFile", @@ -25407,6 +27546,15 @@ "ofType": null } }, + { + "args": [], + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "args": [], "name": "scale0Dimensions", @@ -25544,136 +27692,9 @@ } ], "inputFields": null, - "interfaces": [], - "kind": "OBJECT", - "name": "TomogramMinMaxColumns", - "possibleTypes": null - }, - { - "enumValues": [ - { - "name": "alignment" - }, - { - "name": "authors" - }, - { - "name": "deposition" - }, - { - "name": "run" - }, - { - "name": "tomogramVoxelSpacing" - }, - { - "name": "name" - }, - { - "name": "sizeX" - }, - { - "name": "sizeY" - }, - { - "name": "sizeZ" - }, - { - "name": "voxelSpacing" - }, - { - "name": "fiducialAlignmentStatus" - }, - { - "name": "reconstructionMethod" - }, - { - "name": "processing" - }, - { - "name": "tomogramVersion" - }, - { - "name": "processingSoftware" - }, - { - "name": "reconstructionSoftware" - }, - { - "name": "isPortalStandard" - }, - { - "name": "isAuthorSubmitted" - }, - { - "name": "isVisualizationDefault" - }, - { - "name": "s3OmezarrDir" - }, - { - "name": "httpsOmezarrDir" - }, - { - "name": "s3MrcFile" - }, - { - "name": "httpsMrcFile" - }, - { - "name": "scale0Dimensions" - }, - { - "name": "scale1Dimensions" - }, - { - "name": "scale2Dimensions" - }, - { - "name": "ctfCorrected" - }, - { - "name": "offsetX" - }, - { - "name": "offsetY" - }, - { - "name": "offsetZ" - }, - { - "name": "keyPhotoUrl" - }, - { - "name": "keyPhotoThumbnailUrl" - }, - { - "name": "neuroglancerConfig" - }, - { - "name": "publications" - }, - { - "name": "relatedDatabaseEntries" - }, - { - "name": "id" - }, - { - "name": "depositionDate" - }, - { - "name": "releaseDate" - }, - { - "name": "lastModifiedDate" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "TomogramCountColumns", + "interfaces": [], + "kind": "OBJECT", + "name": "TomogramMinMaxColumns", "possibleTypes": null }, { @@ -26064,25 +28085,6 @@ "name": "DepositionTypeMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "deposition" - }, - { - "name": "type" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "DepositionTypeCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -26671,40 +28673,6 @@ "name": "PerSectionAlignmentParametersMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "alignment" - }, - { - "name": "zIndex" - }, - { - "name": "xOffset" - }, - { - "name": "yOffset" - }, - { - "name": "volumeXRotation" - }, - { - "name": "inPlaneRotation" - }, - { - "name": "tiltAngle" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "PerSectionAlignmentParametersCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -27015,28 +28983,6 @@ "name": "GainFileMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "run" - }, - { - "name": "s3FilePath" - }, - { - "name": "httpsFilePath" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "GainFileCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -27465,28 +29411,6 @@ "name": "FrameAcquisitionFileMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "run" - }, - { - "name": "s3MdocPath" - }, - { - "name": "httpsMdocPath" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "FrameAcquisitionFileCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": [ @@ -27769,37 +29693,6 @@ "name": "TomogramVoxelSpacingMinMaxColumns", "possibleTypes": null }, - { - "enumValues": [ - { - "name": "annotationFiles" - }, - { - "name": "run" - }, - { - "name": "tomograms" - }, - { - "name": "voxelSpacing" - }, - { - "name": "s3Prefix" - }, - { - "name": "httpsPrefix" - }, - { - "name": "id" - } - ], - "fields": null, - "inputFields": null, - "interfaces": null, - "kind": "ENUM", - "name": "TomogramVoxelSpacingCountColumns", - "possibleTypes": null - }, { "enumValues": null, "fields": null, @@ -28077,36 +29970,12 @@ }, { "enumValues": [ - { - "name": "authors" - }, - { - "name": "alignments" - }, - { - "name": "annotations" - }, - { - "name": "datasets" - }, - { - "name": "frames" - }, - { - "name": "tiltseries" - }, - { - "name": "tomograms" - }, { "name": "title" }, { "name": "description" }, - { - "name": "depositionTypes" - }, { "name": "depositionPublications" }, @@ -31391,6 +33260,15 @@ } } }, + { + "defaultValue": "null", + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": null, "name": "httpsPath", @@ -31490,6 +33368,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": null, "name": "httpsPath", @@ -32757,6 +34644,15 @@ } } }, + { + "defaultValue": "null", + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": null, "name": "id", @@ -33014,6 +34910,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": null, "name": "id", @@ -33737,6 +35642,15 @@ } } }, + { + "defaultValue": "null", + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": null, "name": "id", @@ -33832,6 +35746,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSize", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": null, "name": "id", @@ -34277,6 +36200,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": "null", "name": "s3MrcFile", @@ -34286,6 +36218,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": "null", "name": "httpsOmezarrDir", @@ -34687,6 +36628,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": "null", "name": "s3MrcFile", @@ -34696,6 +36646,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": "null", "name": "httpsOmezarrDir", @@ -35623,6 +37582,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": "null", "name": "s3MrcFile", @@ -35641,6 +37609,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": "null", "name": "scale0Dimensions", @@ -35991,6 +37968,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSizeOmezarr", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": "null", "name": "s3MrcFile", @@ -36009,6 +37995,15 @@ "ofType": null } }, + { + "defaultValue": "null", + "name": "fileSizeMrc", + "type": { + "kind": "SCALAR", + "name": "Int", + "ofType": null + } + }, { "defaultValue": "null", "name": "scale0Dimensions", diff --git a/apiv2/graphql_api/types/annotation_file.py b/apiv2/graphql_api/types/annotation_file.py index f0511993c..df6110b9f 100644 --- a/apiv2/graphql_api/types/annotation_file.py +++ b/apiv2/graphql_api/types/annotation_file.py @@ -179,6 +179,7 @@ class AnnotationFileWhereClause(TypedDict): tomogram_voxel_spacing_id: Optional[IntComparators] | None format: Optional[StrComparators] | None s3_path: Optional[StrComparators] | None + file_size: Optional[IntComparators] | None https_path: Optional[StrComparators] | None is_visualization_default: Optional[BoolComparators] | None source: Optional[EnumComparators[annotation_file_source_enum]] | None @@ -205,6 +206,7 @@ class AnnotationFileOrderByClause(TypedDict): ) format: Optional[orderBy] | None s3_path: Optional[orderBy] | None + file_size: Optional[orderBy] | None https_path: Optional[orderBy] | None is_visualization_default: Optional[orderBy] | None source: Optional[orderBy] | None @@ -232,6 +234,7 @@ class AnnotationFile(EntityInterface): tomogram_voxel_spacing_id: Optional[int] format: str = strawberry.field(description="File format for this file") s3_path: str = strawberry.field(description="s3 path of the annotation file") + file_size: Optional[int] = strawberry.field(description="Size of the file in bytes", default=None) https_path: str = strawberry.field(description="HTTPS path for this annotation file") is_visualization_default: Optional[bool] = strawberry.field( description="Data curator’s subjective choice of default annotation to display in visualization for an object", @@ -264,6 +267,7 @@ class AnnotationFile(EntityInterface): @strawberry.type class AnnotationFileNumericalColumns: + file_size: Optional[int] = None id: Optional[int] = None @@ -276,6 +280,7 @@ class AnnotationFileNumericalColumns: class AnnotationFileMinMaxColumns: format: Optional[str] = None s3_path: Optional[str] = None + file_size: Optional[int] = None https_path: Optional[str] = None id: Optional[int] = None @@ -289,6 +294,7 @@ class AnnotationFileMinMaxColumns: class AnnotationFileCountColumns(enum.Enum): format = "format" s3Path = "s3_path" + fileSize = "file_size" httpsPath = "https_path" isVisualizationDefault = "is_visualization_default" source = "source" @@ -365,6 +371,7 @@ class AnnotationFileCreateInput: ) format: str = strawberry.field(description="File format for this file") s3_path: str = strawberry.field(description="s3 path of the annotation file") + file_size: Optional[int] = strawberry.field(description="Size of the file in bytes", default=None) https_path: str = strawberry.field(description="HTTPS path for this annotation file") is_visualization_default: Optional[bool] = strawberry.field( description="Data curator’s subjective choice of default annotation to display in visualization for an object", @@ -388,6 +395,7 @@ class AnnotationFileUpdateInput: ) format: Optional[str] = strawberry.field(description="File format for this file") s3_path: Optional[str] = strawberry.field(description="s3 path of the annotation file") + file_size: Optional[int] = strawberry.field(description="Size of the file in bytes", default=None) https_path: Optional[str] = strawberry.field(description="HTTPS path for this annotation file") is_visualization_default: Optional[bool] = strawberry.field( description="Data curator’s subjective choice of default annotation to display in visualization for an object", diff --git a/apiv2/graphql_api/types/dataset.py b/apiv2/graphql_api/types/dataset.py index 819c29f0a..a6435bf68 100644 --- a/apiv2/graphql_api/types/dataset.py +++ b/apiv2/graphql_api/types/dataset.py @@ -276,6 +276,7 @@ class DatasetWhereClause(TypedDict): related_database_entries: Optional[StrComparators] | None s3_prefix: Optional[StrComparators] | None https_prefix: Optional[StrComparators] | None + file_size: Optional[IntComparators] | None id: Optional[IntComparators] | None @@ -312,6 +313,7 @@ class DatasetOrderByClause(TypedDict): related_database_entries: Optional[orderBy] | None s3_prefix: Optional[orderBy] | None https_prefix: Optional[orderBy] | None + file_size: Optional[orderBy] | None id: Optional[orderBy] | None @@ -407,6 +409,7 @@ class Dataset(EntityInterface): ) s3_prefix: str = strawberry.field(description="The S3 public bucket path where this dataset is contained") https_prefix: str = strawberry.field(description="The https directory path where this dataset is contained") + file_size: Optional[int] = strawberry.field(description="Size of the dataset in bytes", default=None) id: int = strawberry.field( description="An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree", ) @@ -433,6 +436,7 @@ class Dataset(EntityInterface): @strawberry.type class DatasetNumericalColumns: organism_taxid: Optional[int] = None + file_size: Optional[int] = None id: Optional[int] = None @@ -467,6 +471,7 @@ class DatasetMinMaxColumns: related_database_entries: Optional[str] = None s3_prefix: Optional[str] = None https_prefix: Optional[str] = None + file_size: Optional[int] = None id: Optional[int] = None @@ -502,6 +507,7 @@ class DatasetCountColumns(enum.Enum): relatedDatabaseEntries = "related_database_entries" s3Prefix = "s3_prefix" httpsPrefix = "https_prefix" + fileSize = "file_size" id = "id" @@ -632,6 +638,7 @@ class DatasetCreateInput: ) s3_prefix: str = strawberry.field(description="The S3 public bucket path where this dataset is contained") https_prefix: str = strawberry.field(description="The https directory path where this dataset is contained") + file_size: Optional[int] = strawberry.field(description="Size of the dataset in bytes", default=None) id: int = strawberry.field( description="An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree", ) @@ -709,6 +716,7 @@ class DatasetUpdateInput: https_prefix: Optional[str] = strawberry.field( description="The https directory path where this dataset is contained", ) + file_size: Optional[int] = strawberry.field(description="Size of the dataset in bytes", default=None) id: Optional[int] = strawberry.field( description="An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree", ) diff --git a/apiv2/graphql_api/types/frame.py b/apiv2/graphql_api/types/frame.py index 445a1ab08..0835eccad 100644 --- a/apiv2/graphql_api/types/frame.py +++ b/apiv2/graphql_api/types/frame.py @@ -137,6 +137,7 @@ class FrameWhereClause(TypedDict): is_gain_corrected: Optional[BoolComparators] | None s3_frame_path: Optional[StrComparators] | None https_frame_path: Optional[StrComparators] | None + file_size: Optional[IntComparators] | None id: Optional[IntComparators] | None @@ -155,6 +156,7 @@ class FrameOrderByClause(TypedDict): is_gain_corrected: Optional[orderBy] | None s3_frame_path: Optional[orderBy] | None https_frame_path: Optional[orderBy] | None + file_size: Optional[orderBy] | None id: Optional[orderBy] | None @@ -181,6 +183,7 @@ class Frame(EntityInterface): ) s3_frame_path: str = strawberry.field(description="S3 path to the frame file") https_frame_path: str = strawberry.field(description="HTTPS path to the frame file") + file_size: Optional[int] = strawberry.field(description="Size of the frame file in bytes", default=None) id: int = strawberry.field(description="Numeric identifier (May change!)") @@ -207,6 +210,7 @@ class FrameNumericalColumns: raw_angle: Optional[float] = None acquisition_order: Optional[int] = None dose: Optional[float] = None + file_size: Optional[int] = None id: Optional[int] = None @@ -222,6 +226,7 @@ class FrameMinMaxColumns: dose: Optional[float] = None s3_frame_path: Optional[str] = None https_frame_path: Optional[str] = None + file_size: Optional[int] = None id: Optional[int] = None @@ -238,6 +243,7 @@ class FrameCountColumns(enum.Enum): isGainCorrected = "is_gain_corrected" s3FramePath = "s3_frame_path" httpsFramePath = "https_frame_path" + fileSize = "file_size" id = "id" @@ -312,6 +318,7 @@ class FrameCreateInput: ) s3_frame_path: str = strawberry.field(description="S3 path to the frame file") https_frame_path: str = strawberry.field(description="HTTPS path to the frame file") + file_size: Optional[int] = strawberry.field(description="Size of the frame file in bytes", default=None) id: int = strawberry.field(description="Numeric identifier (May change!)") @@ -329,6 +336,7 @@ class FrameUpdateInput: ) s3_frame_path: Optional[str] = strawberry.field(description="S3 path to the frame file") https_frame_path: Optional[str] = strawberry.field(description="HTTPS path to the frame file") + file_size: Optional[int] = strawberry.field(description="Size of the frame file in bytes", default=None) id: Optional[int] = strawberry.field(description="Numeric identifier (May change!)") diff --git a/apiv2/graphql_api/types/tiltseries.py b/apiv2/graphql_api/types/tiltseries.py index a77739bc2..bbff6739c 100644 --- a/apiv2/graphql_api/types/tiltseries.py +++ b/apiv2/graphql_api/types/tiltseries.py @@ -180,7 +180,9 @@ class TiltseriesWhereClause(TypedDict): deposition: Optional[Annotated["DepositionWhereClause", strawberry.lazy("graphql_api.types.deposition")]] | None deposition_id: Optional[IntComparators] | None s3_omezarr_dir: Optional[StrComparators] | None + file_size_omezarr: Optional[IntComparators] | None s3_mrc_file: Optional[StrComparators] | None + file_size_mrc: Optional[IntComparators] | None https_omezarr_dir: Optional[StrComparators] | None https_mrc_file: Optional[StrComparators] | None s3_angle_list: Optional[StrComparators] | None @@ -225,7 +227,9 @@ class TiltseriesOrderByClause(TypedDict): run: Optional[Annotated["RunOrderByClause", strawberry.lazy("graphql_api.types.run")]] | None deposition: Optional[Annotated["DepositionOrderByClause", strawberry.lazy("graphql_api.types.deposition")]] | None s3_omezarr_dir: Optional[orderBy] | None + file_size_omezarr: Optional[orderBy] | None s3_mrc_file: Optional[orderBy] | None + file_size_mrc: Optional[orderBy] | None https_omezarr_dir: Optional[orderBy] | None https_mrc_file: Optional[orderBy] | None s3_angle_list: Optional[orderBy] | None @@ -282,9 +286,11 @@ class Tiltseries(EntityInterface): s3_omezarr_dir: Optional[str] = strawberry.field( description="S3 path to this tiltseries in multiscale OME-Zarr format", default=None, ) + file_size_omezarr: Optional[int] = strawberry.field(description="Size of the OME-Zarr file in bytes", default=None) s3_mrc_file: Optional[str] = strawberry.field( description="S3 path to this tiltseries in MRC format (no scaling)", default=None, ) + file_size_mrc: Optional[int] = strawberry.field(description="Size of the MRC file in bytes", default=None) https_omezarr_dir: Optional[str] = strawberry.field( description="HTTPS path to this tiltseries in multiscale OME-Zarr format", default=None, ) @@ -364,6 +370,8 @@ class Tiltseries(EntityInterface): @strawberry.type class TiltseriesNumericalColumns: + file_size_omezarr: Optional[int] = None + file_size_mrc: Optional[int] = None acceleration_voltage: Optional[int] = None spherical_aberration_constant: Optional[float] = None tilt_min: Optional[float] = None @@ -390,7 +398,9 @@ class TiltseriesNumericalColumns: @strawberry.type class TiltseriesMinMaxColumns: s3_omezarr_dir: Optional[str] = None + file_size_omezarr: Optional[int] = None s3_mrc_file: Optional[str] = None + file_size_mrc: Optional[int] = None https_omezarr_dir: Optional[str] = None https_mrc_file: Optional[str] = None s3_angle_list: Optional[str] = None @@ -431,7 +441,9 @@ class TiltseriesMinMaxColumns: @strawberry.enum class TiltseriesCountColumns(enum.Enum): s3OmezarrDir = "s3_omezarr_dir" + fileSizeOmezarr = "file_size_omezarr" s3MrcFile = "s3_mrc_file" + fileSizeMrc = "file_size_mrc" httpsOmezarrDir = "https_omezarr_dir" httpsMrcFile = "https_mrc_file" s3AngleList = "s3_angle_list" @@ -532,9 +544,11 @@ class TiltseriesCreateInput: s3_omezarr_dir: Optional[str] = strawberry.field( description="S3 path to this tiltseries in multiscale OME-Zarr format", default=None, ) + file_size_omezarr: Optional[int] = strawberry.field(description="Size of the OME-Zarr file in bytes", default=None) s3_mrc_file: Optional[str] = strawberry.field( description="S3 path to this tiltseries in MRC format (no scaling)", default=None, ) + file_size_mrc: Optional[int] = strawberry.field(description="Size of the MRC file in bytes", default=None) https_omezarr_dir: Optional[str] = strawberry.field( description="HTTPS path to this tiltseries in multiscale OME-Zarr format", default=None, ) @@ -601,9 +615,11 @@ class TiltseriesUpdateInput: s3_omezarr_dir: Optional[str] = strawberry.field( description="S3 path to this tiltseries in multiscale OME-Zarr format", default=None, ) + file_size_omezarr: Optional[int] = strawberry.field(description="Size of the OME-Zarr file in bytes", default=None) s3_mrc_file: Optional[str] = strawberry.field( description="S3 path to this tiltseries in MRC format (no scaling)", default=None, ) + file_size_mrc: Optional[int] = strawberry.field(description="Size of the MRC file in bytes", default=None) https_omezarr_dir: Optional[str] = strawberry.field( description="HTTPS path to this tiltseries in multiscale OME-Zarr format", default=None, ) diff --git a/apiv2/graphql_api/types/tomogram.py b/apiv2/graphql_api/types/tomogram.py index 2fcd5b781..cd8d60928 100644 --- a/apiv2/graphql_api/types/tomogram.py +++ b/apiv2/graphql_api/types/tomogram.py @@ -266,8 +266,10 @@ class TomogramWhereClause(TypedDict): is_visualization_default: Optional[BoolComparators] | None s3_omezarr_dir: Optional[StrComparators] | None https_omezarr_dir: Optional[StrComparators] | None + file_size_omezarr: Optional[IntComparators] | None s3_mrc_file: Optional[StrComparators] | None https_mrc_file: Optional[StrComparators] | None + file_size_mrc: Optional[IntComparators] | None scale0_dimensions: Optional[StrComparators] | None scale1_dimensions: Optional[StrComparators] | None scale2_dimensions: Optional[StrComparators] | None @@ -318,8 +320,10 @@ class TomogramOrderByClause(TypedDict): is_visualization_default: Optional[orderBy] | None s3_omezarr_dir: Optional[orderBy] | None https_omezarr_dir: Optional[orderBy] | None + file_size_omezarr: Optional[orderBy] | None s3_mrc_file: Optional[orderBy] | None https_mrc_file: Optional[orderBy] | None + file_size_mrc: Optional[orderBy] | None scale0_dimensions: Optional[orderBy] | None scale1_dimensions: Optional[orderBy] | None scale2_dimensions: Optional[orderBy] | None @@ -402,12 +406,14 @@ class Tomogram(EntityInterface): https_omezarr_dir: Optional[str] = strawberry.field( description="HTTPS path to this tomogram in multiscale OME-Zarr format", default=None, ) + file_size_omezarr: Optional[int] = strawberry.field(description="Size of the OME-Zarr file in bytes", default=None) s3_mrc_file: Optional[str] = strawberry.field( description="S3 path to this tomogram in MRC format (no scaling)", default=None, ) https_mrc_file: Optional[str] = strawberry.field( description="HTTPS path to this tomogram in MRC format (no scaling)", default=None, ) + file_size_mrc: Optional[int] = strawberry.field(description="Size of the MRC file in bytes", default=None) scale0_dimensions: Optional[str] = strawberry.field( description="comma separated x,y,z dimensions of the unscaled tomogram", default=None, ) @@ -472,6 +478,8 @@ class TomogramNumericalColumns: size_z: Optional[int] = None voxel_spacing: Optional[float] = None tomogram_version: Optional[float] = None + file_size_omezarr: Optional[int] = None + file_size_mrc: Optional[int] = None offset_x: Optional[int] = None offset_y: Optional[int] = None offset_z: Optional[int] = None @@ -495,8 +503,10 @@ class TomogramMinMaxColumns: reconstruction_software: Optional[str] = None s3_omezarr_dir: Optional[str] = None https_omezarr_dir: Optional[str] = None + file_size_omezarr: Optional[int] = None s3_mrc_file: Optional[str] = None https_mrc_file: Optional[str] = None + file_size_mrc: Optional[int] = None scale0_dimensions: Optional[str] = None scale1_dimensions: Optional[str] = None scale2_dimensions: Optional[str] = None @@ -537,8 +547,10 @@ class TomogramCountColumns(enum.Enum): isVisualizationDefault = "is_visualization_default" s3OmezarrDir = "s3_omezarr_dir" httpsOmezarrDir = "https_omezarr_dir" + fileSizeOmezarr = "file_size_omezarr" s3MrcFile = "s3_mrc_file" httpsMrcFile = "https_mrc_file" + fileSizeMrc = "file_size_mrc" scale0Dimensions = "scale0_dimensions" scale1Dimensions = "scale1_dimensions" scale2Dimensions = "scale2_dimensions" @@ -661,12 +673,14 @@ class TomogramCreateInput: https_omezarr_dir: Optional[str] = strawberry.field( description="HTTPS path to this tomogram in multiscale OME-Zarr format", default=None, ) + file_size_omezarr: Optional[int] = strawberry.field(description="Size of the OME-Zarr file in bytes", default=None) s3_mrc_file: Optional[str] = strawberry.field( description="S3 path to this tomogram in MRC format (no scaling)", default=None, ) https_mrc_file: Optional[str] = strawberry.field( description="HTTPS path to this tomogram in MRC format (no scaling)", default=None, ) + file_size_mrc: Optional[int] = strawberry.field(description="Size of the MRC file in bytes", default=None) scale0_dimensions: Optional[str] = strawberry.field( description="comma separated x,y,z dimensions of the unscaled tomogram", default=None, ) @@ -753,12 +767,14 @@ class TomogramUpdateInput: https_omezarr_dir: Optional[str] = strawberry.field( description="HTTPS path to this tomogram in multiscale OME-Zarr format", default=None, ) + file_size_omezarr: Optional[int] = strawberry.field(description="Size of the OME-Zarr file in bytes", default=None) s3_mrc_file: Optional[str] = strawberry.field( description="S3 path to this tomogram in MRC format (no scaling)", default=None, ) https_mrc_file: Optional[str] = strawberry.field( description="HTTPS path to this tomogram in MRC format (no scaling)", default=None, ) + file_size_mrc: Optional[int] = strawberry.field(description="Size of the MRC file in bytes", default=None) scale0_dimensions: Optional[str] = strawberry.field( description="comma separated x,y,z dimensions of the unscaled tomogram", default=None, ) diff --git a/apiv2/platformics/codegen/templates/database/models/class_name.py.j2 b/apiv2/platformics/codegen/templates/database/models/class_name.py.j2 index 1e51fe170..d44a8afae 100644 --- a/apiv2/platformics/codegen/templates/database/models/class_name.py.j2 +++ b/apiv2/platformics/codegen/templates/database/models/class_name.py.j2 @@ -14,7 +14,7 @@ import datetime from typing import TYPE_CHECKING from platformics.database.models.base import Base -from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime +from sqlalchemy import ForeignKey, String, Float, BigInteger, Enum, Boolean, DateTime from sqlalchemy.dialects.postgresql import UUID, JSONB from sqlalchemy.orm import Mapped, mapped_column, relationship from sqlalchemy.sql import func @@ -68,7 +68,7 @@ class {{cls.name}}({%- if cls.is_a %}{{cls.is_a}}{%- else %}Base{%- endif %}): "uuid": ("UUID", "uuid.UUID"), "string": ("String", "str"), "Array2dFloat": ("JSONB", "JSONB"), - "integer": ("Integer", "int"), + "integer": ("BigInteger", "int"), "float": ("Float", "float"), "boolean": ("Boolean", "bool"), "date": ("DateTime(timezone=True)", "datetime.datetime"), diff --git a/apiv2/schema/README.md b/apiv2/schema/README.md index a317774d1..97947cece 100644 --- a/apiv2/schema/README.md +++ b/apiv2/schema/README.md @@ -17,8 +17,10 @@ Tomogram { boolean is_visualization_default string s3_omezarr_dir string https_omezarr_dir + integer file_size_omezarr string s3_mrc_file string https_mrc_file + integer file_size_mrc string scale0_dimensions string scale1_dimensions string scale2_dimensions @@ -56,7 +58,9 @@ TomogramAuthor { } Tiltseries { string s3_omezarr_dir + integer file_size_omezarr string s3_mrc_file + integer file_size_mrc string https_omezarr_dir string https_mrc_file string s3_angle_list @@ -128,6 +132,7 @@ Frame { boolean is_gain_corrected string s3_frame_path string https_frame_path + integer file_size integer id } Deposition { @@ -180,6 +185,7 @@ Dataset { string related_database_entries string s3_prefix string https_prefix + integer file_size integer id } DatasetFunding { @@ -228,6 +234,7 @@ AnnotationShape { AnnotationFile { string format string s3_path + integer file_size string https_path boolean is_visualization_default annotation_file_source_enum source diff --git a/apiv2/schema/schema.yaml b/apiv2/schema/schema.yaml index c050707c4..0598eab89 100644 --- a/apiv2/schema/schema.yaml +++ b/apiv2/schema/schema.yaml @@ -841,6 +841,17 @@ classes: - api_s3_path range: string required: true + file_size: + name: file_size + description: Size of the file in bytes + from_schema: cdp-dataset-config + exact_mappings: + - api_file_size + range: integer + minimum_value: 0 + unit: + symbol: B + descriptive_name: bytes https_path: name: https_path description: HTTPS path for this annotation file @@ -1410,6 +1421,17 @@ classes: - api_https_prefix range: string required: true + file_size: + name: file_size + description: Size of the dataset in bytes + from_schema: cdp-dataset-config + exact_mappings: + - api_file_size + range: integer + minimum_value: 0 + unit: + symbol: B + descriptive_name: bytes slot_usage: id: description: An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree @@ -1666,6 +1688,17 @@ classes: description: HTTPS path to the frame file range: string required: true + file_size: + name: file_size + description: Size of the frame file in bytes + from_schema: cdp-dataset-config + exact_mappings: + - api_frame_file_size + range: integer + minimum_value: 0 + unit: + symbol: B + descriptive_name: bytes PerSectionAlignmentParameters: name: PerSectionAlignmentParameters annotations: @@ -1876,6 +1909,17 @@ classes: exact_mappings: - tiltseries_s3_omezarr_dir range: string + file_size_omezarr: + name: file_size_omezarr + description: Size of the OME-Zarr file in bytes + from_schema: cdp-dataset-config + exact_mappings: + - tiltseries_file_size_omezarr + range: integer + minimum_value: 0 + unit: + symbol: B + descriptive_name: bytes s3_mrc_file: name: s3_mrc_file description: S3 path to this tiltseries in MRC format (no scaling) @@ -1883,6 +1927,17 @@ classes: exact_mappings: - tiltseries_s3_mrc_file range: string + file_size_mrc: + name: file_size_mrc + description: Size of the MRC file in bytes + from_schema: cdp-dataset-config + exact_mappings: + - tiltseries_file_size_mrc + range: integer + minimum_value: 0 + unit: + symbol: B + descriptive_name: bytes https_omezarr_dir: name: https_omezarr_dir description: HTTPS path to this tiltseries in multiscale OME-Zarr format @@ -2432,6 +2487,16 @@ classes: exact_mappings: - tomogram_https_omezarr_dir range: string + file_size_omezarr: + name: file_size_omezarr + description: Size of the OME-Zarr file in bytes + from_schema: cdp-dataset-config + exact_mappings: + - tomogram_file_size_omezarr + range: integer + unit: + symbol: B + descriptive_name: bytes s3_mrc_file: name: s3_mrc_file description: S3 path to this tomogram in MRC format (no scaling) @@ -2446,6 +2511,16 @@ classes: exact_mappings: - tomogram_https_mrc_file range: string + file_size_mrc: + name: file_size_mrc + description: Size of the MRC file in bytes + from_schema: cdp-dataset-config + exact_mappings: + - tomogram_file_size_mrc + range: integer + unit: + symbol: B + descriptive_name: bytes scale0_dimensions: name: scale0_dimensions description: comma separated x,y,z dimensions of the unscaled tomogram diff --git a/apiv2/scripts/scrape.py b/apiv2/scripts/scrape.py index 560234fa2..4f40f29f3 100644 --- a/apiv2/scripts/scrape.py +++ b/apiv2/scripts/scrape.py @@ -367,13 +367,16 @@ def fetch_method_links(client_url, annotation): headers = { "Content-type": "application/json", } - query = """ + query = ( + """ query MyQuery { annotations(where: {id: {_eq: %d }}) { method_links } } - """ % annotation.id + """ + % annotation.id + ) payload = json.dumps({"query": query, "variables": None, "operationName": "MyQuery"}) res = requests.post(client_url, headers=headers, data=payload) data = res.json() diff --git a/apiv2/test_infra/factories/annotation_file.py b/apiv2/test_infra/factories/annotation_file.py index 4163bd3f3..13fea981e 100644 --- a/apiv2/test_infra/factories/annotation_file.py +++ b/apiv2/test_infra/factories/annotation_file.py @@ -42,6 +42,7 @@ class Meta: ) format = fuzzy.FuzzyText() s3_path = fuzzy.FuzzyText() + file_size = fuzzy.FuzzyInteger(1, 1000) https_path = fuzzy.FuzzyText() is_visualization_default = factory.Faker("boolean") source = fuzzy.FuzzyChoice(["dataset_author", "community", "portal_standard"]) diff --git a/apiv2/test_infra/factories/dataset.py b/apiv2/test_infra/factories/dataset.py index f5648e8e6..1f6fa80b7 100644 --- a/apiv2/test_infra/factories/dataset.py +++ b/apiv2/test_infra/factories/dataset.py @@ -61,6 +61,6 @@ class Meta: related_database_entries = fuzzy.FuzzyText() s3_prefix = fuzzy.FuzzyText() https_prefix = fuzzy.FuzzyText() - + file_size = fuzzy.FuzzyInteger(1, 1000) # Auto increment integer identifiers starting with 1 id = factory.Sequence(lambda n: n + 1) diff --git a/apiv2/test_infra/factories/frame.py b/apiv2/test_infra/factories/frame.py index 99816aabd..18c989cc7 100644 --- a/apiv2/test_infra/factories/frame.py +++ b/apiv2/test_infra/factories/frame.py @@ -44,6 +44,6 @@ class Meta: is_gain_corrected = factory.Faker("boolean") s3_frame_path = fuzzy.FuzzyText() https_frame_path = fuzzy.FuzzyText() - + file_size = fuzzy.FuzzyInteger(1, 1000) # Auto increment integer identifiers starting with 1 id = factory.Sequence(lambda n: n + 1) diff --git a/apiv2/test_infra/factories/tiltseries.py b/apiv2/test_infra/factories/tiltseries.py index 3513b4fcd..f0172807e 100644 --- a/apiv2/test_infra/factories/tiltseries.py +++ b/apiv2/test_infra/factories/tiltseries.py @@ -37,7 +37,9 @@ class Meta: DepositionFactory, ) s3_omezarr_dir = fuzzy.FuzzyText() + file_size_omezarr = fuzzy.FuzzyInteger(1, 1000) s3_mrc_file = fuzzy.FuzzyText() + file_size_mrc = fuzzy.FuzzyInteger(1, 1000) https_omezarr_dir = fuzzy.FuzzyText() https_mrc_file = fuzzy.FuzzyText() s3_angle_list = fuzzy.FuzzyText() diff --git a/apiv2/test_infra/factories/tomogram.py b/apiv2/test_infra/factories/tomogram.py index 026504a08..c2c953c85 100644 --- a/apiv2/test_infra/factories/tomogram.py +++ b/apiv2/test_infra/factories/tomogram.py @@ -64,8 +64,10 @@ class Meta: is_visualization_default = factory.Faker("boolean") s3_omezarr_dir = fuzzy.FuzzyText() https_omezarr_dir = fuzzy.FuzzyText() + file_size_omezarr = fuzzy.FuzzyInteger(1, 1000) s3_mrc_file = fuzzy.FuzzyText() https_mrc_file = fuzzy.FuzzyText() + file_size_mrc = fuzzy.FuzzyInteger(1, 1000) scale0_dimensions = fuzzy.FuzzyText() scale1_dimensions = fuzzy.FuzzyText() scale2_dimensions = fuzzy.FuzzyText() diff --git a/apiv2/validators/annotation_file.py b/apiv2/validators/annotation_file.py index f24891fb0..65f7de4f8 100644 --- a/apiv2/validators/annotation_file.py +++ b/apiv2/validators/annotation_file.py @@ -33,6 +33,12 @@ class AnnotationFileCreateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size: Annotated[ + int | None, + Field( + ge=0, + ), + ] https_path: Annotated[ str, StringConstraints( @@ -62,6 +68,12 @@ class AnnotationFileUpdateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size: Annotated[ + int | None, + Field( + ge=0, + ), + ] https_path: Annotated[ str | None, StringConstraints( diff --git a/apiv2/validators/dataset.py b/apiv2/validators/dataset.py index 17b393d2d..f029e9435 100644 --- a/apiv2/validators/dataset.py +++ b/apiv2/validators/dataset.py @@ -156,6 +156,12 @@ class DatasetCreateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size: Annotated[ + int | None, + Field( + ge=0, + ), + ] id: Annotated[int, Field()] @@ -299,4 +305,10 @@ class DatasetUpdateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size: Annotated[ + int | None, + Field( + ge=0, + ), + ] id: Annotated[int | None, Field()] diff --git a/apiv2/validators/frame.py b/apiv2/validators/frame.py index ea027d317..d753877ac 100644 --- a/apiv2/validators/frame.py +++ b/apiv2/validators/frame.py @@ -41,6 +41,12 @@ class FrameCreateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size: Annotated[ + int | None, + Field( + ge=0, + ), + ] id: Annotated[int, Field()] @@ -71,4 +77,10 @@ class FrameUpdateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size: Annotated[ + int | None, + Field( + ge=0, + ), + ] id: Annotated[int | None, Field()] diff --git a/apiv2/validators/tiltseries.py b/apiv2/validators/tiltseries.py index cc3cc8a48..06c9fbfce 100644 --- a/apiv2/validators/tiltseries.py +++ b/apiv2/validators/tiltseries.py @@ -26,12 +26,24 @@ class TiltseriesCreateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size_omezarr: Annotated[ + int | None, + Field( + ge=0, + ), + ] s3_mrc_file: Annotated[ str | None, StringConstraints( strip_whitespace=True, ), ] + file_size_mrc: Annotated[ + int | None, + Field( + ge=0, + ), + ] https_omezarr_dir: Annotated[ str | None, StringConstraints( @@ -229,12 +241,24 @@ class TiltseriesUpdateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size_omezarr: Annotated[ + int | None, + Field( + ge=0, + ), + ] s3_mrc_file: Annotated[ str | None, StringConstraints( strip_whitespace=True, ), ] + file_size_mrc: Annotated[ + int | None, + Field( + ge=0, + ), + ] https_omezarr_dir: Annotated[ str | None, StringConstraints( diff --git a/apiv2/validators/tomogram.py b/apiv2/validators/tomogram.py index a30f3f138..60f7167cf 100644 --- a/apiv2/validators/tomogram.py +++ b/apiv2/validators/tomogram.py @@ -84,6 +84,7 @@ class TomogramCreateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size_omezarr: Annotated[int | None, Field()] s3_mrc_file: Annotated[ str | None, StringConstraints( @@ -96,6 +97,7 @@ class TomogramCreateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size_mrc: Annotated[int | None, Field()] scale0_dimensions: Annotated[ str | None, StringConstraints( @@ -224,6 +226,7 @@ class TomogramUpdateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size_omezarr: Annotated[int | None, Field()] s3_mrc_file: Annotated[ str | None, StringConstraints( @@ -236,6 +239,7 @@ class TomogramUpdateInputValidator(BaseModel): strip_whitespace=True, ), ] + file_size_mrc: Annotated[int | None, Field()] scale0_dimensions: Annotated[ str | None, StringConstraints( diff --git a/docker-compose.yml b/docker-compose.yml index 7cc0c64c8..35a512ded 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -6,7 +6,7 @@ services: volumes: - ./test_infra/test_files:/usr/share/nginx/html motoserver: - image: motoserver/moto:4.1.0 + image: motoserver/moto:5.0.26 ports: - "5566:5566" environment: @@ -17,7 +17,7 @@ services: db: image: postgres:14.2 healthcheck: - test: ['CMD', 'pg_isready', '-d', 'cryoet', '-U', 'postgres'] + test: ["CMD", "pg_isready", "-d", "cryoet", "-U", "postgres"] environment: POSTGRES_INITDB_ARGS: --data-checksums POSTGRES_DB: cryoet @@ -32,7 +32,7 @@ services: volumes: - ./test_infra:/test_infra ports: - - '5432:5432' + - "5432:5432" cryoet-api: platform: linux/arm64 profiles: ["api", "apiv1"] @@ -49,12 +49,12 @@ services: db: condition: service_healthy environment: - HASURA_GRAPHQL_ENABLE_CONSOLE: 'false' + HASURA_GRAPHQL_ENABLE_CONSOLE: "false" HASURA_GRAPHQL_DATABASE_URL: postgresql://postgres:postgres@db:5432/cryoet HASURA_GRAPHQL_ADMIN_SECRET: secret HASURA_GRAPHQL_UNAUTHORIZED_ROLE: anonymous ports: - - '8080:8080' + - "8080:8080" hasura-console: platform: linux/arm64 profiles: ["api", "apiv1"] @@ -76,8 +76,8 @@ services: --api-port 9693 --console-hge-endpoint http://localhost:8080 ports: - - '9695:9695' - - '9693:9693' + - "9695:9695" + - "9693:9693" depends_on: cryoet-api: condition: service_healthy @@ -91,8 +91,7 @@ services: - "3693:3693" volumes: - ./apiv2/cerbos:/var/policies/cerbos/ - command: - ["server", "--config", "/var/policies/cerbos/config.yaml"] + command: ["server", "--config", "/var/policies/cerbos/config.yaml"] graphql-api: image: "graphql-api" profiles: ["api", "apiv2"] diff --git a/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Tomograms/100/tomogram_metadata.json b/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Tomograms/100/tomogram_metadata.json index f33a80553..b6f3f2eb5 100644 --- a/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Tomograms/100/tomogram_metadata.json +++ b/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Tomograms/100/tomogram_metadata.json @@ -85,8 +85,8 @@ "mrc_file": "30001/RUN1/Reconstructions/VoxelSpacing12.300/Tomograms/100/RUN1.mrc", "run_name": "RUN1", "key_photo": { - "snapshot": "30001/RUN1/Reconstructions/VoxelSpacing12.300/Images/key-photo-snapshot.png", - "thumbnail": "30001/RUN1/Reconstructions/VoxelSpacing12.300/Images/key-photo-thumbnail.png" + "thumbnail": "30001/RUN1/Reconstructions/VoxelSpacing12.300/Images/key-photo-thumbnail.png", + "snapshot": "30001/RUN1/Reconstructions/VoxelSpacing12.300/Images/key-photo-snapshot.png" }, "deposition_id": 300, "dates": {