# 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",
