Merge pull request #13315 from mvdbeek/restore_metadata_size_limit (d27ded4d) · Commits · NDIP / Galaxy

lib/galaxy/model/mapping.py

+4 −3

Original line number	Diff line number	Diff line
		@@ -43,6 +43,7 @@ from galaxy import model
		from galaxy.model.base import SharedModelMapping
		from galaxy.model.custom_types import (
		JSONType,
		MetadataType,
		MutableJSONType,
		TrimmedString,
		UUIDType,
		@@ -248,7 +249,7 @@ model.HistoryDatasetAssociation.table = Table(
		Column("peek", TEXT, key="_peek"),
		Column("tool_version", TEXT),
		Column("extension", TrimmedString(64)),
		Column("metadata", JSONType, key="_metadata"),
		Column("metadata", MetadataType, key="_metadata"),
		Column("parent_id", Integer, ForeignKey("history_dataset_association.id"), nullable=True),
		Column("designation", TrimmedString(255)),
		Column("deleted", Boolean, index=True, default=False),
		@@ -271,7 +272,7 @@ model.HistoryDatasetAssociationHistory.table = Table(
		Column("version", Integer),
		Column("name", TrimmedString(255)),
		Column("extension", TrimmedString(64)),
		Column("metadata", JSONType, key="_metadata"),
		Column("metadata", MetadataType, key="_metadata"),
		Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True),
		)

		@@ -527,7 +528,7 @@ model.LibraryDatasetDatasetAssociation.table = Table(
		Column("peek", TEXT, key="_peek"),
		Column("tool_version", TEXT),
		Column("extension", TrimmedString(64)),
		Column("metadata", JSONType, key="_metadata"),
		Column("metadata", MetadataType, key="_metadata"),
		Column("parent_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
		Column("designation", TrimmedString(255)),
		Column("deleted", Boolean, index=True, default=False),

test/unit/data/test_metadata_limit.py

0 → 100644

+44 −0

Original line number	Diff line number	Diff line
		import pytest

		import galaxy.datatypes.registry as registry
		import galaxy.model.mapping as mapping
		from galaxy.model import (
		custom_types,
		HistoryDatasetAssociation,
		set_datatypes_registry,
		)

		METADATA_LIMIT = 500


		@pytest.fixture(scope="module")
		def datatypes_registry():
		r = registry.Registry()
		r.load_datatypes()
		set_datatypes_registry(r)


		@pytest.fixture
		def sa_session(datatypes_registry):
		custom_types.MAX_METADATA_VALUE_SIZE = METADATA_LIMIT
		return mapping.init("/tmp", "sqlite:///:memory:", create_tables=True).session


		def create_bed_data(sa_session, string_size):
		hda = HistoryDatasetAssociation(extension="bed")
		big_string = "0" * string_size
		sa_session.add(hda)
		hda.metadata.column_names = [big_string]
		assert hda.metadata.column_names
		sa_session.flush()
		return hda


		def test_hda_below_limit(sa_session):
		hda = create_bed_data(sa_session=sa_session, string_size=1)
		assert len(hda.metadata.column_names[0]) == 1


		def test_hda_above_limit(sa_session):
		hda = create_bed_data(sa_session=sa_session, string_size=1000)
		assert not hda.metadata.column_names