Cleanup of validation PR.

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

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()
 

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"))

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)

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):