Refactor get_metadata_compute_strategy to not depend on `app`.

This allows me to claim galaxy-job-execution doesn't depend on ``app``.
This commit is contained in:
John Chilton
2019-06-12 14:43:45 -04:00
parent b4a1c21456
commit 7b6d06bd4e
5 changed files with 6 additions and 6 deletions
+1 -1
View File
@@ -875,7 +875,7 @@ class JobWrapper(HasResourceParameters):
self.output_hdas_and_paths = None
self.tool_provided_job_metadata = None
# Wrapper holding the info required to restore and clean up from files used for setting metadata externally
self.external_output_metadata = get_metadata_compute_strategy(self.app, job.id)
self.external_output_metadata = get_metadata_compute_strategy(self.app.config, job.id)
self.job_runner_mapper = JobRunnerMapper(self, queue.dispatcher.url_to_destination, self.app.job_config)
self.params = None
if job.params:
+2 -2
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@@ -20,8 +20,8 @@ log = getLogger(__name__)
SET_METADATA_SCRIPT = 'from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()'
def get_metadata_compute_strategy(app, job_id):
metadata_strategy = app.config.metadata_strategy
def get_metadata_compute_strategy(config, job_id):
metadata_strategy = config.metadata_strategy
if metadata_strategy == "legacy":
return JobExternalOutputMetadataWrapper(job_id)
else:
+1 -1
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@@ -2394,7 +2394,7 @@ class SetMetadataTool(Tool):
job, base_dir='job_work', dir_only=True, obj_dir=True
)
for name, dataset in inp_data.items():
external_metadata = get_metadata_compute_strategy(app, job.id)
external_metadata = get_metadata_compute_strategy(app.config, job.id)
sa_session = app.model.context
if external_metadata.external_metadata_set_successfully(dataset, name, sa_session, working_directory=working_directory):
external_metadata.load_metadata(dataset, name, sa_session, working_directory=working_directory)
+1 -1
View File
@@ -78,7 +78,7 @@ class SetMetadataToolAction(ToolAction):
job_working_dir = app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
datatypes_config = os.path.join(job_working_dir, 'registry.xml')
app.datatypes_registry.to_xml_file(path=datatypes_config)
external_metadata_wrapper = get_metadata_compute_strategy(app, job.id)
external_metadata_wrapper = get_metadata_compute_strategy(app.config, job.id)
output_datatasets_dict = {
dataset_name: dataset,
}
+1 -1
View File
@@ -143,7 +143,7 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesApp, tools_support.U
f.write(contents)
def metadata_command(self, output_datasets):
metadata_compute_strategy = get_metadata_compute_strategy(self.app, self.job.id)
metadata_compute_strategy = get_metadata_compute_strategy(self.app.config, self.job.id)
self.metadata_compute_strategy = metadata_compute_strategy
exec_dir = None