def new_search(dataset_pk):
''' Perform a new database search
'''
current_dataset = models.Dataset.query.get_or_404(dataset_pk)
ms2_files = current_dataset.ms2files.all()
if not ms2_files:
abort(404)
params_form = forms.SearchParamsForm()
if params_form.validate_on_submit():
params = json.loads(json.dumps(dict(params_form.data.items()), default=lambda x: float(x) if isinstance(x, decimal.Decimal) else x))
##### clean and edit params #####
params = views_helpers.clean_params(params)
# Save new DBSearch record (including params_dict) in database
new_dbsearch_id = views_helpers.save_new_dbsearch(dataset_pk, params=params)
params['dbsearch_id'] = new_dbsearch_id
remote_host = 'admin@wolanlab'
remote_filepaths = [ms2file.file_path for ms2file in ms2_files]
# hard-coded for now... remove later! (once on production server)
if 'production' not in app.config['CONFIG_CLASS']:
remote_filepaths = ['/home/admin/test_files/121614_SC_sampleH1sol_25ug_pepstd_HCD_FTMS_MS2_07_11.ms2',
'/home/admin/test_files/121614_SC_sampleH1sol_25ug_pepstd_HCD_FTMS_MS2_07_11_duplicate.ms2']
remote_directory = str(uuid4()) # random 36-character hash
rsync_task = tasks.rsync_file.s(remote_host, remote_filepaths, new_local_directory=remote_directory).set(queue='sandip')
split_and_create_jobs_task = tasks.split_ms2_and_make_jobs.s(params).set(queue='sandip')
launch_submission_tasks = tasks.launch_submission_tasks.s().set(queue='sandip')
chained_tasks = rsync_task | split_and_create_jobs_task | launch_submission_tasks
task = chained_tasks.apply_async()
# save task ID to local database
current_dbsearch = models.DBSearch.query.get(new_dbsearch_id)
current_dbsearch.celery_id = str(task)
current_dbsearch.status = 'submitted'
current_dbsearch.remote_directory = remote_directory
db.session.commit()
print(task.children) # this GroupResult ID won't be available until a few moments after launching
app.logger.info('Launched Celery task {}'.format(task))
return jsonify(params)
return render_template( 'data/newsearch.html',
params_form=params_form,
current_dataset=current_dataset,
ms2_files=ms2_files,
)
def document_index():
''' View function for "index" page for all document types (including file uploader interface)
'''
upload_form = forms.DatasetUploadForm()
recent_five_datasets = views_helpers.get_recent_records(models.Dataset, models.Dataset.uploaded_time)
if upload_form.validate_on_submit():
files = request.files.getlist('data_file')
filenames = [file_obj.filename for file_obj in files]
app.logger.info('User trying to upload files {}'.format(', '.join(filenames)))
if not check_file_types(filenames):
return 'Can\'t upload all of those file types... {}'.format(', '.join(filenames)) # this should return a redirect to a different view/AJAX response
# save new uploaded file data
try:
ms1_file_paths = [save_new_file(file_obj) for file_obj in files if file_obj.filename.endswith('.ms1')]
ms2_file_paths = [save_new_file(file_obj) for file_obj in files if file_obj.filename.endswith('.ms2')]
sqt_file_paths = [save_new_file(file_obj) for file_obj in files if file_obj.filename.endswith('.sqt')]
dta_file_paths = [save_new_file(file_obj) for file_obj in files if file_obj.filename.endswith('.txt')]
except:
app.logger.error('Error saving new files')
return 'Error saving new files'
dataset_id = None
dbsearch_id = None
ms1_data_ids = None
ms2_data_ids = None
sqt_data_ids = None
dta_data_ids = None
# save new dataset in database
dataset_name = upload_form.dataset_name.data
dataset_description = upload_form.dataset_desc.data
try:
dataset_id = views_helpers.save_new_dataset(dataset_name, dataset_description)
except:
app.logger.error('Error creating new dataset {}'.format(dataset_name))
raise
return None
if ms1_file_paths:
try:
# save MS1 records to database
ms1_data_ids = [views_helpers.save_new_ms1_record(dataset_id, ms1_file_path, original_filename) for ms1_file_path, original_filename in ms1_file_paths]
except:
# log database error and return
app.logger.error('Error saving new MS1 file info to database')
raise
return None
if ms2_file_paths:
try:
# save MS2 records to database
ms2_data_ids = [views_helpers.save_new_ms2_record(dataset_id, ms2_file_path, original_filename) for ms2_file_path, original_filename in ms2_file_paths]
except:
# log database error and return
app.logger.error('Error saving new MS2 file info to database')
raise
return None
if sqt_file_paths or dta_file_paths:
try:
dbsearch_id = views_helpers.save_new_dbsearch(dataset_id) # create DBSearch
except:
# log DB error and return
app.logger.error('Error saving new Database Search to database')
raise
return None
if sqt_file_paths:
try:
# save SQT records to database
sqt_data_ids = [views_helpers.save_new_sqt_record(dbsearch_id, sqt_file_path, original_filename) for sqt_file_path, original_filename in sqt_file_paths]
for sqt_data_id in sqt_data_ids:
views_helpers.count_scans_in_file(sqt_data_id, 'sqt')
except:
app.logger.error('Error saving new SQT file info to database')
raise
return None
if dta_file_paths:
try:
# save DTA records to database
dta_data_ids = [views_helpers.save_new_dta_record(dbsearch_id, dta_file_path, original_filename) for dta_file_path, original_filename in dta_file_paths]
except:
app.logger.error('Error saving new DTA file info to database')
raise
return None
return jsonify({'dataset_id': dataset_id,
'dataset_name': dataset_name,
'dataset_description': dataset_description,
'dbsearch_id': dbsearch_id,
'ms1_data_ids': ms1_data_ids,
'ms2_data_ids': ms2_data_ids,
'sqt_data_ids': sqt_data_ids,
'dta_data_ids': dta_data_ids,
})
return render_template('data/document_index.html', upload_form=upload_form, recent_five_datasets=recent_five_datasets)
