def analyze():
sessionid = request.cookies.get('sessionid')
networkingpreset = request.form["networkingpreset"]
email = request.form["email"]
if len(email) < 1 or len(email) > 100:
email = "*****@*****.**"
present_folders = util.check_ftp_folders(sessionid)
if not "G1" in present_folders:
content = {'status': 'Group 1 files required but not selected'}
return json.dumps(content), 417
gnps_username = credentials.USERNAME
gnps_password = credentials.PASSWORD
try:
if len(request.form["username"]) > 3 and len(request.form["password"]):
gnps_username = request.form["username"]
gnps_password = request.form["password"]
except:
gnps_username = credentials.USERNAME
gnps_password = credentials.PASSWORD
remote_dir = os.path.join(credentials.USERNAME, sessionid)
task_id = util.launch_GNPS_workflow(
remote_dir, "GNPS Quickstart Molecular Networking Analysis ",
gnps_username, gnps_password, present_folders, email, networkingpreset)
content = {'status': 'Success', 'task_id': task_id}
return json.dumps(content), 200
def datasetsubmit():
sessionid = request.cookies.get('sessionid')
present_folders = util.check_ftp_folders(sessionid)
massive_preset_url = "https://massive.ucsd.edu/ProteoSAFe/index.jsp"
parameters = {
"workflow": "MASSIVE-COMPLETE",
"desc": "GNPS - Dataset Created via Quickstart"
}
one_category_present = False
if "raw" in present_folders:
one_category_present = True
parameters["raw_list_files"] = "d.%s/%s/raw" % (credentials.USERNAME,
sessionid)
if "peak" in present_folders:
one_category_present = True
parameters["peak_list_files"] = "d.%s/%s/peak" % (credentials.USERNAME,
sessionid)
if "supplementary" in present_folders:
one_category_present = True
parameters["other_files"] = "d.%s/%s/supplementary" % (
credentials.USERNAME, sessionid)
url = massive_preset_url + "#" + json.dumps(parameters)
return url, 200
def analyzefeaturenetworking():
sessionid = request.cookies.get('sessionid')
print(sessionid)
email = request.form["email"]
networkingpreset = request.form["networkingpreset"]
featuretool = request.form["featuretool"]
if len(email) < 1 or len(email) > 100:
email = "*****@*****.**"
present_folders = util.check_ftp_folders(sessionid)
if not "featurequantification" in present_folders:
content = {'status': 'featurequantification required but not selected'}
return json.dumps(present_folders), 417
if not "featurems2" in present_folders:
content = {'status': 'featurems2 required but not selected'}
return json.dumps(present_folders), 417
gnps_username = credentials.USERNAME
gnps_password = credentials.PASSWORD
try:
if len(request.form["username"]) > 3 and len(request.form["password"]):
gnps_username = request.form["username"]
gnps_password = request.form["password"]
except:
gnps_username = credentials.USERNAME
gnps_password = credentials.PASSWORD
remote_dir = os.path.join(credentials.USERNAME, sessionid)
task_id = util.launch_GNPS_featurenetworking_workflow(
remote_dir, "GNPS Quickstart Molecular Networking Analysis ",
gnps_username, gnps_password, email, featuretool, present_folders,
networkingpreset)
#Error
if len(task_id) != 32:
content = {'status': 'Error'}
return json.dumps(content), 500
content = {
'status': 'Success',
'task_id': task_id,
'url':
"https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=%s" % (task_id)
}
return json.dumps(content), 200
def uploadanalyzefeaturenetworking():
sessionid = str(uuid.uuid4())
upload_string = util.upload_single_file(request, "featurequantification")
networkingpreset = "LOWRES"
if "networkingpreset" in request.form:
networkingpreset = request.form["networkingpreset"]
#Performing Data Upload
util.upload_single_file_push(request.files["featurequantification"],
sessionid, "featurequantification")
util.upload_single_file_push(request.files["featurems2"], sessionid,
"featurems2")
if "samplemetadata" in request.files:
util.upload_single_file_push(request.files["samplemetadata"],
sessionid, "samplemetadata")
if "additionalpairs" in request.files:
util.upload_single_file_push(request.files["additionalpairs"],
sessionid, "additionalpairs")
email = ""
try:
email = request.form["email"]
except:
email = ""
if len(email) < 1 or len(email) > 100:
email = "*****@*****.**"
featuretool = request.form["featuretool"]
present_folders = util.check_ftp_folders(sessionid)
if not "featurequantification" in present_folders:
content = {'status': 'featurequantification required but not selected'}
return json.dumps(present_folders), 417
if not "featurems2" in present_folders:
content = {'status': 'featurems2 required but not selected'}
return json.dumps(present_folders), 417
gnps_username = credentials.USERNAME
gnps_password = credentials.PASSWORD
try:
if len(request.form["username"]) > 3 and len(request.form["password"]):
gnps_username = request.form["username"]
gnps_password = request.form["password"]
except:
gnps_username = credentials.USERNAME
gnps_password = credentials.PASSWORD
task_description = "GNPS Quickstart Molecular Networking Analysis from MZmine2"
if "description" in request.form:
if len(request.form["description"]) > 1:
task_description = request.form["description"]
remote_dir = os.path.join(credentials.USERNAME, sessionid)
task_id = util.launch_GNPS_featurenetworking_workflow(
remote_dir, task_description, gnps_username, gnps_password, email,
featuretool, present_folders, networkingpreset)
#Error
if len(task_id) != 32:
content = {'status': 'Error'}
return json.dumps(content), 500
content = {
'status': 'Success',
'task_id': task_id,
'url':
"https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=%s" % (task_id)
}
return json.dumps(content), 200