diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index db4384ddac44..dd28c0af0c68 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -1005,9 +1005,9 @@ def export_invocation_bco(self, trans, invocation_id, **kwd): # may want to extend this to have more reviewers. reviewing_users = [stored_workflow.user] - workflow_encoded_id = trans.security.encode_id(stored_workflow.id) - history_encoded_id = trans.security.encode_id(history.id) - dict_workflow = json.loads(self.workflow_dict(trans, workflow_encoded_id)) + encoded_workflow_id = trans.security.encode_id(stored_workflow.id) + encoded_history_id = trans.security.encode_id(history.id) + dict_workflow = json.loads(self.workflow_dict(trans, encoded_workflow_id)) # h_contents = self.history_contents_manager.contained(history) @@ -1016,7 +1016,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd): # listing the versions of the workflow for 'version' and 'derived_from' versions = [] - workflow_versions = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_encoded_id) + workflow_versions = self.workflow_manager.get_stored_accessible_workflow(trans, encoded_workflow_id) for i, w in enumerate(reversed(workflow_versions.workflows)): version = { 'version': i, @@ -1059,7 +1059,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd): 'name': workflow.name, 'version': current_version, 'review': reviewers, - 'derived_from': url_for('workflow', id=workflow_encoded_id, qualified=True), + 'derived_from': url_for('workflow', id=encoded_workflow_id, qualified=True), 'created': workflow_invocation.create_time.isoformat(), 'modified': workflow_invocation.update_time.isoformat(), 'contributors': contributors, @@ -1073,10 +1073,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd): if tag.user_tname not in keywords: keywords.append(tag.user_tname) - host = 'https://localhost:8080' input_subdomain, output_subdomain, pipeline_steps, software_prerequisites = [], [], [], [] - # Which `url_for` function option would generate this format below? - url_format = '{}/api/histories/{}/contents/{}' for i, step in enumerate(workflow_invocation.steps): current_tool = dict_workflow['steps'][str(i)] if step.workflow_step.type == 'tool': @@ -1086,20 +1083,20 @@ def export_invocation_bco(self, trans, invocation_id, **kwd): for job in step.jobs: for job_input in job.input_datasets: if hasattr(job_input.dataset, 'dataset_id'): - inputobj = trans.security.encode_id(job_input.dataset.dataset_id) + encoded_dataset_id = trans.security.encode_id(job_input.dataset.dataset_id) input_obj = { 'filename': job_input.dataset.name, - 'uri': url_format.format(host, history_encoded_id, inputobj), + 'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True), 'access_time': job_input.dataset.create_time.isoformat(), } input_list.append(input_obj) for job_output in job.output_datasets: if hasattr(job_output.dataset, 'dataset_id'): - outobj = trans.security.encode_id(job_output.dataset.dataset_id) + encoded_dataset_id = trans.security.encode_id(job_output.dataset.dataset_id) output_obj = { 'filename': job_output.dataset.name, - 'uri': url_format.format(host, history_encoded_id, outobj), + 'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True), 'access_time': job_output.dataset.create_time.isoformat(), } output_list.append(output_obj) @@ -1109,7 +1106,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd): 'mediatype': job_output.dataset.extension, 'uri': { 'filename': job_output.dataset.name, - 'uri': url_format.format(host, history_encoded_id, outobj) , + 'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True), 'access_time': job_output.dataset.create_time.isoformat(), } } @@ -1158,7 +1155,7 @@ def export_invocation_bco(self, trans, invocation_id, **kwd): execution_domain = { 'script_access_type': 'a_galaxy_workflow', - 'script': [url_for('workflows', encoded_workflow_id=workflow_encoded_id)], + 'script': [url_for('workflows', encoded_workflow_id=encoded_workflow_id)], 'script_driver': 'Galaxy', 'software_prerequisites': software_prerequisites, 'external_data_endpoints': [],