def galaxy_isa_upload_datalib_task(self, pks, param_pk, galaxy_pass, user_id):
"""
"""
tt = TrackTasks(taskid=self.request.id,
state='RUNNING',
name='Uploading ISA projects to Galaxy',
user_id=user_id)
tt.save()
self.update_state(state='RUNNING',
meta={
'current': 0.1,
'total': 100,
'status': 'Uploading ISA projects to Galaxy'
})
galaxy_isa_upload_param = FilesToGalaxyDataLibraryParam.objects.get(
pk=param_pk)
result_out = galaxy_isa_uplofad_datalib(pks, galaxy_isa_upload_param,
galaxy_pass, user_id, self)
if result_out:
self.update_state(state='SUCCESS',
meta={
'current': 100,
'total': 100,
'status': 'completed'
})
# save successful result
tt.result = reverse('galaxy_summary')
tt.state = 'SUCCESS'
tt.save()
def search_nm_task(self, sp, userid):
# track tasks in db
tt = TrackTasks(taskid=self.request.id,
state='RUNNING',
name='Search nm values',
user_id=userid)
tt.save()
search_nm(sp, self)
# save successful result
tt.result = reverse('search_nm_result')
tt.state = 'SUCCESS'
tt.save()
def download_cannotations_task(self, pk, userid):
# track tasks in db
tt = TrackTasks(taskid=self.request.id,
state='RUNNING',
name='Downloading LC-MSMS annotations',
user_id=userid)
tt.save()
# perform function
dam = DownloadAnnotations()
dam.download_cannotations(pk, self)
# save successful result
tt.result = reverse('canns_download_result')
tt.state = 'SUCCESS'
tt.save()
def save_lcms_data_task(self, pk, userid):
# track tasks in db
tt = TrackTasks(taskid=self.request.id,
state='RUNNING',
name='LC-MSMS data upload',
user_id=userid)
tt.save()
# run function
print('SAVE LCMS DATA')
lcms_data_transfer = LcmsDataTransfer(pk, None)
lcms_data_transfer.transfer(celery_obj=self)
# save successful result
tt.result = reverse('cpeakgroupmeta_summary')
tt.state = 'SUCCESS'
tt.save()
def upload_assay_data_files_dir_task(self, filelist, username, mapping_l,
assayid, save_as_link,
create_assay_details):
"""
"""
tt = TrackTasks(taskid=self.request.id,
state='RUNNING',
name='Upload assay data file',
user=User.objects.filter(username=username)[0])
tt.save()
upload_assay_data_files_dir(filelist, username, mapping_l, assayid,
create_assay_details, save_as_link, self)
tt.result = reverse('assayfile_summary', kwargs={'assayid': assayid})
tt.state = 'SUCCESS'
tt.save()
def upload_assay_data_files_dir_task(self, filelist, user_id, mapping_l,
assayid, save_as_link,
create_assay_details):
"""
"""
users = get_user_model()
tt = TrackTasks(taskid=self.request.id,
state='RUNNING',
name='Upload assay data file',
user=users.objects.get(pk=user_id))
tt.save()
upload_assay_data_files_dir(filelist, user_id, mapping_l, assayid,
create_assay_details, save_as_link, self)
tt.result = reverse('assayfile_summary', kwargs={'assayid': assayid})
tt.state = 'SUCCESS'
tt.save()
def upload_metab_results_task(self, pk, userid):
# track tasks in db
tt = TrackTasks(taskid=self.request.id,
state='RUNNING',
name='Data upload',
user_id=userid)
tt.save()
# upload file
results = UploadResults(pk, None)
# run function
results.upload(celery_obj=self)
# save successful result
tt.result = reverse('metabinputdata_summary')
tt.state = 'SUCCESS'
tt.save()
def upload_metab_results_galaxy_task(self, userid, galaxy_name, galaxy_data_id,
galaxy_history_id, investigation_name):
tt = TrackTasks(taskid=self.request.id,
state='RUNNING',
name='Data upload',
user_id=userid)
tt.save()
md = setup_results_file_from_galaxy(userid, galaxy_name, galaxy_data_id,
galaxy_history_id, investigation_name,
self)
print('MD {}'.format(md))
if not md:
tt.result = reverse('metabinputdata_summary')
tt.state = 'FAILURE'
tt.save()
return 0
results = UploadResults(md.id, None)
results.upload(celery_obj=self)
# save successful result
tt.result = reverse('metabinputdata_summary')
tt.state = 'SUCCESS'
tt.save()