diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 9fca963bc96..73e3b4b6dc0 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1298,11 +1298,10 @@ class JobWrapper( object ):
dataset.set_peek( is_multi_byte=True )
else:
dataset.set_peek()
- try:
- # set the name if provided by the tool
- dataset.name = context['name']
- except:
- pass
+ for context_key in ['name', 'info', 'dbkey']:
+ if context_key in context:
+ context_value = context[context_key]
+ setattr(dataset, context_key, context_value)
else:
dataset.blurb = "empty"
if dataset.ext == 'auto':
diff --git a/lib/galaxy/tools/parameters/output_collect.py b/lib/galaxy/tools/parameters/output_collect.py
index 1fb52296c77..6dff4027022 100644
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -314,6 +314,8 @@ def collect_primary_datasets( tool, output, job_working_directory, input_ext, in
)
metadata_dict = new_primary_datasets_attributes.get( 'metadata', None )
if metadata_dict:
+ if "dbkey" in new_primary_datasets_attributes:
+ metadata_dict["dbkey"] = new_primary_datasets_attributes["dbkey"]
primary_data.metadata.from_JSON_dict( json_dict=metadata_dict )
else:
primary_data.set_meta()
diff --git a/lib/galaxy/tools/parser/xml.py b/lib/galaxy/tools/parser/xml.py
index 178cf6a3f46..47b990901c1 100644
--- a/lib/galaxy/tools/parser/xml.py
+++ b/lib/galaxy/tools/parser/xml.py
@@ -391,15 +391,7 @@ def __parse_output_elem( output_elem ):
if name is None:
raise Exception( "Test output does not have a 'name'" )
- file, attributes = __parse_test_attributes( output_elem, attrib )
- primary_datasets = {}
- for primary_elem in ( output_elem.findall( "discovered_dataset" ) or [] ):
- primary_attrib = dict( primary_elem.attrib )
- designation = primary_attrib.pop( 'designation', None )
- if designation is None:
- raise Exception( "Test primary dataset does not have a 'designation'" )
- primary_datasets[ designation ] = __parse_test_attributes( primary_elem, primary_attrib )
- attributes[ "primary_datasets" ] = primary_datasets
+ file, attributes = __parse_test_attributes( output_elem, attrib, parse_discovered_datasets=True )
return name, file, attributes
@@ -436,7 +428,7 @@ def __parse_element_tests( parent_element ):
return element_tests
-def __parse_test_attributes( output_elem, attrib, parse_elements=False ):
+def __parse_test_attributes( output_elem, attrib, parse_elements=False, parse_discovered_datasets=False ):
assert_list = __parse_assert_list( output_elem )
# Allow either file or value to specify a target file to compare result with
@@ -466,8 +458,18 @@ def __parse_test_attributes( output_elem, attrib, parse_elements=False ):
if parse_elements:
element_tests = __parse_element_tests( output_elem )
+ primary_datasets = {}
+ if parse_discovered_datasets:
+ for primary_elem in ( output_elem.findall( "discovered_dataset" ) or [] ):
+ primary_attrib = dict( primary_elem.attrib )
+ designation = primary_attrib.pop( 'designation', None )
+ if designation is None:
+ raise Exception( "Test primary dataset does not have a 'designation'" )
+ primary_datasets[ designation ] = __parse_test_attributes( primary_elem, primary_attrib )
+
has_checksum = md5sum or checksum
- if not (assert_list or file or extra_files or metadata or has_checksum or element_tests):
+ has_nested_tests = extra_files or element_tests or primary_datasets
+ if not (assert_list or file or metadata or has_checksum or has_nested_tests):
raise Exception( "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or checksum tests, etc...)")
attributes['assert_list'] = assert_list
attributes['extra_files'] = extra_files
@@ -475,6 +477,7 @@ def __parse_test_attributes( output_elem, attrib, parse_elements=False ):
attributes['md5'] = md5sum
attributes['checksum'] = checksum
attributes['elements'] = element_tests
+ attributes['primary_datasets'] = primary_datasets
return file, attributes
diff --git a/lib/galaxy_ext/metadata/set_metadata.py b/lib/galaxy_ext/metadata/set_metadata.py
index a540ff36df5..6f70a9d0f63 100644
--- a/lib/galaxy_ext/metadata/set_metadata.py
+++ b/lib/galaxy_ext/metadata/set_metadata.py
@@ -141,10 +141,11 @@ def set_metadata():
json.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) # setting metadata has failed somehow
for i, ( filename, file_dict ) in enumerate( new_job_metadata_dict.iteritems(), start=1 ):
- new_dataset = galaxy.model.Dataset( id=-i, external_filename=os.path.join( tool_job_working_directory, file_dict[ 'filename' ] ) )
+ new_dataset_filename = os.path.join( tool_job_working_directory, "working", file_dict[ 'filename' ] )
+ new_dataset = galaxy.model.Dataset( id=-i, external_filename=new_dataset_filename )
extra_files = file_dict.get( 'extra_files', None )
if extra_files is not None:
- new_dataset._extra_files_path = os.path.join( tool_job_working_directory, extra_files )
+ new_dataset._extra_files_path = os.path.join( tool_job_working_directory, "working", extra_files )
new_dataset.state = new_dataset.states.OK
new_dataset_instance = galaxy.model.HistoryDatasetAssociation( id=-i, dataset=new_dataset, extension=file_dict.get( 'ext', 'data' ) )
set_meta_with_tool_provided( new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry )
diff --git a/test/base/interactor.py b/test/base/interactor.py
index 69e32f1b1a0..04a115a5d59 100644
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -7,6 +7,7 @@ from logging import getLogger
from requests import get, post, delete, patch
from six import StringIO
+from six import text_type
from galaxy import util
from galaxy.tools.parser.interface import TestCollectionDef
@@ -87,27 +88,45 @@ class GalaxyInteractorApi( object ):
def verify_output_dataset( self, history_id, hda_id, outfile, attributes, shed_tool_id ):
fetcher = self.__dataset_fetcher( history_id )
- self.twill_test_case.verify_hid( outfile, hda_id=hda_id, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id )
+ self.twill_test_case.verify_hid(
+ outfile,
+ hda_id=hda_id,
+ attributes=attributes,
+ dataset_fetcher=fetcher,
+ shed_tool_id=shed_tool_id
+ )
self._verify_metadata( history_id, hda_id, attributes )
def _verify_metadata( self, history_id, hid, attributes ):
+ """Check dataset metadata.
+
+ ftype on output maps to `file_ext` on the hda's API description, `name`, `info`,
+ and `dbkey` all map to the API description directly. Other metadata attributes
+ are assumed to be datatype-specific and mapped with a prefix of `metadata_`.
+ """
metadata = attributes.get( 'metadata', {} ).copy()
for key, value in metadata.copy().items():
- new_key = "metadata_%s" % key
- metadata[ new_key ] = metadata[ key ]
- del metadata[ key ]
+ if key not in ['name', 'info']:
+ new_key = "metadata_%s" % key
+ metadata[ new_key ] = metadata[ key ]
+ del metadata[ key ]
+ elif key == "info":
+ metadata[ "misc_info" ] = metadata[ "info" ]
+ del metadata[ "info" ]
expected_file_type = attributes.get( 'ftype', None )
if expected_file_type:
metadata[ "file_ext" ] = expected_file_type
if metadata:
+ import time
+ time.sleep(5)
dataset = self._get( "histories/%s/contents/%s" % ( history_id, hid ) ).json()
for key, value in metadata.items():
try:
dataset_value = dataset.get( key, None )
- if dataset_value != value:
- msg = "Dataset metadata verification for [%s] failed, expected [%s] but found [%s]."
- msg_params = ( key, value, dataset_value )
+ if text_type(dataset_value) != text_type(value):
+ msg = "Dataset metadata verification for [%s] failed, expected [%s] but found [%s]. Dataset API value was [%s]."
+ msg_params = ( key, value, dataset_value, dataset )
msg = msg % msg_params
raise Exception( msg )
except KeyError:
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 67ee93e5112..ef44e49a456 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -15,6 +15,9 @@
+
+
+
diff --git a/test/functional/tools/tool_provided_metadata_1.xml b/test/functional/tools/tool_provided_metadata_1.xml
new file mode 100644
index 00000000000..02d971a85f4
--- /dev/null
+++ b/test/functional/tools/tool_provided_metadata_1.xml
@@ -0,0 +1,29 @@
+
+
+ echo "This is a line of text." > $out1;
+ cp $c1 galaxy.json;
+
+
+ {"type": "dataset", "dataset_id": $out1.dataset.dataset.id, "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/functional/tools/tool_provided_metadata_2.xml b/test/functional/tools/tool_provided_metadata_2.xml
new file mode 100644
index 00000000000..8879d0f62af
--- /dev/null
+++ b/test/functional/tools/tool_provided_metadata_2.xml
@@ -0,0 +1,38 @@
+
+
+ echo "1" > sample1.report.tsv;
+ echo "2" > sample2.report.tsv;
+ cp $c1 galaxy.json;
+
+
+ {"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19"}
+{"type": "new_primary_dataset", "filename": "sample2.report.tsv", "name": "cool name 2", "ext": "txt", "info": "cool 2 info", "dbkey": "hg19"}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/functional/tools/tool_provided_metadata_3.xml b/test/functional/tools/tool_provided_metadata_3.xml
new file mode 100644
index 00000000000..a9a64f6ee82
--- /dev/null
+++ b/test/functional/tools/tool_provided_metadata_3.xml
@@ -0,0 +1,43 @@
+
+
+ echo "1" > sample1.report.tsv;
+ echo "2" > sample2.report.tsv;
+ cp $c1 galaxy.json;
+
+
+ {"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "metadata": {"data_lines": 10, "foo": "bar"}}
+{"type": "new_primary_dataset", "filename": "sample2.report.tsv", "name": "cool name 2", "ext": "txt", "info": "cool 2 info", "dbkey": "hg19", "metadata": {"data_lines": 20, "foo": "bar"}}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+