def plain_parse_xtandem_combine_with_mgf():
xml_read_path = request.form['xmlReadPath']
log_error_threshold = request.form['logErrorThreshold']
geneFile = request.form['geneFile']
should_use_unacceptable = request.form['assignUnacceptableModifications']
unacceptable_mods = request.form.getlist('unacceptableMods[]')
timestamp = request.form['timestamp']
mgf_txt_foldername = makeFolderNames.construct_plain_parse_reporter_folder_path(
request.form)
mgf_read_dir_path = request.form['mgfReadDirPath']
mgf_list = ",".join(
utility.get_mgf_files_given_directory(mgf_read_dir_path))
a = call_xml_parser.plain_parse_xtandem_combine_with_mgf(
xml_read_path, log_error_threshold, geneFile, mgf_txt_foldername,
unacceptable_mods, timestamp, mgf_list)
if a:
print("Error in tab 4. Trying cleanup now, either way returning error")
try:
clean_up_after_tab_2()
finally: #In case it breaks
return a, 500
else:
return "Looks good"
def getMGFFiles():
try:
mgf_read_dir_path = str(request.form['mgfReadDirPath'])
files = utility.get_mgf_files_given_directory(mgf_read_dir_path)
text = json.dumps(files)
return text
except:
return "Error selecting mgf files, make sure you have a proper mgf directory name", 500
def getMGFFiles():
try:
mgf_read_dir_path = str(request.form['mgfReadDirPath'])
if utility.check_if_summary_exists(mgf_read_dir_path):
return "Temp summary file still exists, remove and rerun", 500
files = utility.get_mgf_files_given_directory(mgf_read_dir_path)
text = json.dumps(files)
return text
except:
return "Error selecting mgf files, make sure you have a proper mgf directory name", 500
def tab_2_helper_function():
valid, validation_error = validation.validate_tab_2(request.form)
if not valid:
return validation_error, 500
xml_read_path = request.form['xmlReadPath']
log_error_threshold = request.form['logErrorThreshold']
reporter_type = request.form['reporterIonType']
geneFile = request.form['geneFile']
should_use_unacceptable = request.form['assignUnacceptableModifications']
unacceptable_mods = request.form.getlist('unacceptableMods[]')
normalize_intensities = request.form.getlist('normalizeIntensities')
timestamp = request.form['timestamp']
keep_na = request.form['writeAllSpectra']
if request.form['mgfOperationToPerform'] == '1':
mgf_txt_foldername = makeFolderNames.construct_reporter_folder_path(
request.form)
else:
mgf_txt_foldername = request.form["mgfTxtReadDirPath"]
previous_ion_type = check_if_previous_summary_exists_and_get_reporter_type(
mgf_txt_foldername)
if not previous_ion_type:
return "No previous summary found. Please reselect reporters and keep the summary.", 500
if previous_ion_type != reporter_type:
return "Ion type from summary does not match current selection.", 500
mgf_read_dir_path = request.form['mgfReadDirPath']
mgf_list = ",".join(
utility.get_mgf_files_given_directory(mgf_read_dir_path))
if should_use_unacceptable == "1":
unacceptable_mods = []
a = call_xml_parser.parse_xtandem_combine_with_mgf(
xml_read_path, log_error_threshold, reporter_type, geneFile,
mgf_txt_foldername, unacceptable_mods, normalize_intensities,
timestamp, keep_na, mgf_list)
if a:
print("Error in tab 2. Cleaning up.")
try:
clean_up_after_tab_2()
finally: #In case it breaks
return a, 500
else:
return "Looks good"
