diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 6aaef2f2544..df31d6c44f3 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -25,6 +25,7 @@ from galaxy.datatypes import metadata from galaxy.datatypes.data import ( DatatypeValidation, get_file_peek, +) from galaxy.datatypes.metadata import DictParameter, ListParameter, MetadataElement, MetadataParameter from galaxy.util import nice_size, sqlite from galaxy.util.checkers import is_bz2, is_gzip diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py index 0013823bbc1..c5f5095a92b 100644 --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -286,7 +286,7 @@ class Interval(Tabular): try: next(reader) except ParseError as e: - return DatatypeValidation.invalid(unicodify(e)) + return DatatypeValidation.invalid(util.unicodify(e)) except StopIteration: return DatatypeValidation.valid() diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index b306ab5f15d..90c04a9713d 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -732,12 +732,6 @@ class BaseVcf(Tabular): raise Exception("Error merging VCF files: %s" % stderr) def validate(self, dataset, **kwd): - # with tempfile.NamedTemporaryFile() as t: - # try: - # pysam.tabix_index(dataset.file_name, index=t.name, preset='vcf', force=False, keep_original=True) - # except Exception as e: - # data.DatatypeValidation.invalid("Failed to generate index [%s]" % e) - # return data.DatatypeValidation.validated() def validate_row(row): if len(row) < 8: raise Exception("Not enough columns in row %s" % row.join("\t")) diff --git a/lib/galaxy/model/migrate/versions/0156_rework_dataset_validation.py b/lib/galaxy/model/migrate/versions/0157_rework_dataset_validation.py similarity index 94% rename from lib/galaxy/model/migrate/versions/0156_rework_dataset_validation.py rename to lib/galaxy/model/migrate/versions/0157_rework_dataset_validation.py index 4b6c76808eb..f315961a724 100644 --- a/lib/galaxy/model/migrate/versions/0156_rework_dataset_validation.py +++ b/lib/galaxy/model/migrate/versions/0157_rework_dataset_validation.py @@ -39,10 +39,10 @@ def upgrade(migrate_engine): library_dataset_dataset_association_table = Table("library_dataset_dataset_association", metadata, autoload=True) for dataset_instance_table in [history_dataset_association_table, library_dataset_dataset_association_table]: validated_state_column = Column('validated_state', TrimmedString(64), default='unknown', server_default="unknown", nullable=False) - add_column(validated_state_column, dataset_instance_table) + add_column(validated_state_column, dataset_instance_table, metadata) validated_state_message_column = Column('validated_state_message', TEXT) - add_column(validated_state_message_column, dataset_instance_table) + add_column(validated_state_message_column, dataset_instance_table, metadata) def downgrade(migrate_engine): @@ -54,5 +54,5 @@ def downgrade(migrate_engine): history_dataset_association_table = Table("history_dataset_association", metadata, autoload=True) library_dataset_dataset_association_table = Table("library_dataset_dataset_association", metadata, autoload=True) for dataset_instance_table in [history_dataset_association_table, library_dataset_dataset_association_table]: - drop_column('validated_state', dataset_instance_table) - drop_column('validated_state_message', dataset_instance_table) + drop_column('validated_state', dataset_instance_table, metadata) + drop_column('validated_state_message', dataset_instance_table, metadata) diff --git a/test/unit/tool_util/test_parsing.py b/test/unit/tool_util/test_parsing.py index d94571d4d96..434e631ecf4 100644 --- a/test/unit/tool_util/test_parsing.py +++ b/test/unit/tool_util/test_parsing.py @@ -632,7 +632,7 @@ class ExpectationsTestCase(BaseLoaderTestCase): class QcStdioTestCase(BaseLoaderTestCase): - source_file_name = os.path.join(os.getcwd(), "test/functional/tools/qc_stdout.xml") + source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/qc_stdout.xml") source_contents = None def test_tests(self):