# Nov 28, 2017 (only in py file) # Adding a new command into Qiita/Alpha: delete_analysis from qiita_db.software import Software, Command from qiita_db.sql_connection import TRN # Create the delete study command Command.create(Software.from_name_and_version('Qiita', 'alpha'), 'delete_analysis', 'Deletes a full analysis', {'analysis_id': ['integer', None]}) # Make sure that all validate commands have the "analysis" parameter with TRN: # Get all validate commands that are missing the analysis parameter sql = """SELECT command_id FROM qiita.software_command sc WHERE name = 'Validate' AND NOT ( SELECT EXISTS(SELECT * FROM qiita.command_parameter WHERE parameter_name = 'analysis' AND command_id = sc.command_id));""" TRN.add(sql) sql = """INSERT INTO qiita.command_parameter (command_id, parameter_name, parameter_type, required, default_value, name_order, check_biom_merge) VALUES (6, 'analysis', 'analysis', false, NULL, NULL, false)""" sql_params = [[cmd_id, 'analysis', 'analysis', False, None, None, False] for cmd_id in TRN.execute_fetchflatten()] TRN.add(sql, sql_params, many=True) TRN.execute()
job = ProcessingJob.create(user, params) job._set_error(info['message']) payload = {'job_id': job.id} r_client.set(key, dumps(payload)) else: # The key doesn't contain any information. Delete the key r_client.delete(key) with TRN: # Retrieve the Qiita plugin qiita_plugin = Software.from_name_and_version('Qiita', 'alpha') # Create the submit command for VAMPS command parameters = {'artifact': ['integer', None]} Command.create(qiita_plugin, "submit_to_VAMPS", "submits an artifact to VAMPS", parameters) # Create the copy artifact command parameters = { 'artifact': ['integer', None], 'prep_template': ['prep_template', None] } Command.create(qiita_plugin, "copy_artifact", "Creates a copy of an artifact", parameters) # Create the submit command for EBI command parameters = { 'artifact': ['integer', None], 'submission_type': ['choice:["ADD", "MODIFY"]', 'ADD'] } Command.create(qiita_plugin, "submit_to_EBI", "submits an artifact to EBI",