def test_get_task(self):
from xssp_api.tasks import get_task
task = get_task('pdb_id', 'dssp')
eq_(task.__name__, 'get_dssp')
task = get_task('pdb_id', 'hssp_hssp')
eq_(task.__name__, 'get_hssp')
task = get_task('pdb_id', 'hssp_stockholm')
eq_(task.__name__, 'get_hssp')
task = get_task('pdb_redo_id', 'dssp')
eq_(task.__name__, 'get_dssp_redo')
task = get_task('pdb_file', 'dssp')
eq_(task.__name__, 'mkdssp_from_pdb')
task = get_task('pdb_file', 'hssp_hssp')
eq_(task.__name__, 'mkhssp_from_pdb')
task = get_task('pdb_file', 'hssp_stockholm')
eq_(task.__name__, 'mkhssp_from_pdb')
task = get_task('sequence', 'hssp_hssp')
eq_(task.__name__, 'mkhssp_from_sequence')
task = get_task('sequence', 'hssp_stockholm')
eq_(task.__name__, 'mkhssp_from_sequence')
task = get_task('sequence', 'hg_hssp')
eq_(task.__name__, 'get_hg_hssp')
def test_get_task(self):
from xssp_api.tasks import get_task
task = get_task('pdb_id', 'dssp')
eq_(task.__name__, 'get_dssp')
task = get_task('pdb_id', 'hssp_hssp')
eq_(task.__name__, 'get_hssp')
task = get_task('pdb_id', 'hssp_stockholm')
eq_(task.__name__, 'get_hssp')
task = get_task('pdb_redo_id', 'dssp')
eq_(task.__name__, 'get_dssp_redo')
task = get_task('pdb_file', 'dssp')
eq_(task.__name__, 'mkdssp_from_pdb')
task = get_task('pdb_file', 'hssp_hssp')
eq_(task.__name__, 'mkhssp_from_pdb')
task = get_task('pdb_file', 'hssp_stockholm')
eq_(task.__name__, 'mkhssp_from_pdb')
task = get_task('sequence', 'hssp_hssp')
eq_(task.__name__, 'mkhssp_from_sequence')
task = get_task('sequence', 'hssp_stockholm')
eq_(task.__name__, 'mkhssp_from_sequence')
task = get_task('sequence', 'hg_hssp')
eq_(task.__name__, 'get_hg_hssp')
def get_xssp_result(input_type, output_type, id):
"""
Get the result of a previous job submission.
:param input_type:
Either 'pdb_id', 'pdb_redo_id', 'pdb_file' or 'sequence'.
:param output_type: Either 'hssp_hssp', 'hssp_stockholm', or 'dssp'.
:param id: The id returned by a call to the create method.
:return: The output of the job. If the job status is not SUCCESS, this
method returns an error.
"""
from xssp_api.tasks import get_task
task = get_task(input_type, output_type)
_log.debug("task is {}".format(task.__name__))
async_result = task.AsyncResult(id)
if async_result.status != 'SUCCESS':
return jsonify({'error': 'job status is {}'.format(async_result.status)}), 500
result = async_result.get()
if len(result) <= 0:
return jsonify({'error': 'empty result'}), 500
response = {'result': result}
return jsonify(response)
def __call__(self):
from xssp_api.tasks import get_task
task = get_task('pdb_redo_id', self.output_format)
_log.debug("Calling task '{}'".format(task.__name__))
if self.output_format == 'dssp':
result = task.delay(self.pdb_redo_id)
return result.id
def __call__(self):
from xssp_api.tasks import get_task
task = get_task('sequence', self.output_format)
_log.debug("Calling task '{}'".format(task.__name__))
if 'hg_hssp' in self.output_format:
result = task.delay(self.sequence)
elif 'hssp' in self.output_format:
result = task.delay(self.sequence, self.output_format)
return result.id
def __call__(self):
from xssp_api.tasks import get_task
task = get_task('pdb_file', self.output_format)
_log.debug("Calling task '{}'".format(task.__name__))
if 'hssp' in self.output_format:
result = task.delay(self.pdb_file_path, self.output_format)
else:
result = task.delay(self.pdb_file_path)
return result.id
def get_queued():
res = storage.find('tasks', {})
from xssp_api.tasks import get_task
tasks = []
for t in res:
task = get_task(t['input_type'], t['output_type'])
async_result = task.AsyncResult(t['task_id'])
tasks.append({'task_id': t['task_id'],
'input_type': t['input_type'],
'output_type': t['output_type'],
'status': async_result.status})
return jsonify({ 'tasks': tasks })
def get_queued():
res = storage.find('tasks', {})
from xssp_api.tasks import get_task
tasks = []
for t in res:
task = get_task(t['input_type'], t['output_type'])
async_result = task.AsyncResult(t['task_id'])
tasks.append({'task_id': t['task_id'],
'input_type': t['input_type'],
'output_type': t['output_type'],
'status': async_result.status})
return jsonify({ 'tasks': tasks })
def get_xssp_result(input_type, output_type, id):
"""
Get the result of a previous job submission.
:param input_type:
Either 'pdb_id', 'pdb_redo_id', 'pdb_file' or 'sequence'.
:param output_type: Either 'hssp_hssp', 'hssp_stockholm', or 'dssp'.
:param id: The id returned by a call to the create method.
:return: The output of the job. If the job status is not SUCCESS, this
method returns an error.
"""
from xssp_api.tasks import get_task
task = get_task(input_type, output_type)
_log.debug("task is {}".format(task.__name__))
response = {'result': task.AsyncResult(id).get()}
return jsonify(response)
def get_xssp_status(input_type, output_type, id):
"""
Get the status of a previous job submission.
:param input_type:
Either 'pdb_id', 'pdb_redo_id', 'pdb_file' or 'sequence'.
:param output_type: Either 'hssp_hssp', 'hssp_stockholm', or 'dssp'.
:param id: The id returned by a call to the create method.
:return: Either PENDING, STARTED, SUCCESS, FAILURE, RETRY, or REVOKED.
"""
from xssp_api.tasks import get_task
task = get_task(input_type, output_type)
async_result = task.AsyncResult(id)
response = {'status': async_result.status}
if async_result.failed():
response.update({'message': async_result.traceback})
return jsonify(response)
def get_xssp_status(input_type, output_type, id):
"""
Get the status of a previous job submission.
:param input_type:
Either 'pdb_id', 'pdb_redo_id', 'pdb_file' or 'sequence'.
:param output_type: Either 'hssp_hssp', 'hssp_stockholm', or 'dssp'.
:param id: The id returned by a call to the create method.
:return: Either PENDING, STARTED, SUCCESS, FAILURE, RETRY, or REVOKED.
"""
from xssp_api.tasks import get_task
task = get_task(input_type, output_type)
async_result = task.AsyncResult(id)
response = {'status': async_result.status}
if async_result.failed():
response.update({'message': async_result.traceback})
return jsonify(response)
def test_get_task_invalid_combination_sequence_dssp(self):
from xssp_api.tasks import get_task
get_task('pdb_redo_id', 'hssp_stockholm')
def test_get_task_unexpected_input_type(self):
from xssp_api.tasks import get_task
get_task('unexpected', 'hssp_stockholm')
def test_get_task_invalid_combination_sequence_dssp(self):
from xssp_api.tasks import get_task
get_task('pdb_redo_id', 'hssp_stockholm')
def test_get_task_invalid_combination_pdb_redo_id_hssp_stockholm(self):
from xssp_api.tasks import get_task
get_task('sequence', 'dssp')
def test_get_task_invalid_combination_pdb_redo_id_hssp(self):
from xssp_api.tasks import get_task
get_task('pdb_redo_id', 'hssp')
def test_get_task_unexpected_input_type(self):
from xssp_api.tasks import get_task
get_task('unexpected', 'hssp_stockholm')
def test_get_task_invalid_combination_pdb_redo_id_hssp_stockholm(self):
from xssp_api.tasks import get_task
get_task('sequence', 'dssp')
def test_get_task_invalid_combination_pdb_redo_id_hssp(self):
from xssp_api.tasks import get_task
get_task('pdb_redo_id', 'hssp')