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added changes from template
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@Arslan-Siraj
Arslan-Siraj committed Oct 16, 2023
1 parent 7d40b6b commit f715ced
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92 changes: 46 additions & 46 deletions pages/1_⚙️_Analyze.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,64 +20,64 @@

### main content of page

#title of page
# title of page
st.title("⚙️ Run Analysis")

#make sure "selected-mzML-files" is in session state
# make sure "selected-mzML-files" is in session state
if "selected-mzML-files" not in st.session_state:
st.session_state["selected-mzML-files"] = params.get("selected-mzML-files", [])

#make sure "selected-fasta-files" is in session state
# make sure "selected-fasta-files" is in session state
if "selected-fasta-files" not in st.session_state:
st.session_state["selected-fasta-files"] = params.get("selected-fasta-files", [])

#make sure mzML example files in current session state
# make sure mzML example files in current session state
load_example_mzML_files()

#take mzML files from current session file
# take mzML files from current session file
mzML_files_ = [f.name for f in Path(st.session_state.workspace, "mzML-files").iterdir()]

#selecte mzML file from mzML files list
# selected mzML file from mzML files list
selected_mzML_file = st.selectbox(
"choose mzML file",
[item for item in mzML_files_ if not item.endswith(".csv")]
,
help="If file not here, please upload at File Upload"
)

#make sure fasta example files in current session state
# make sure fasta example files in current session state
load_example_fasta_files()

#take fasta files from current session file
# take fasta files from current session file
fasta_files = [f.name for f in Path(st.session_state.workspace,"fasta-files").iterdir()]

#select fasta file from mzML files list
# select fasta file from mzML files list
selected_fasta_file = st.selectbox(
"choose fasta file",
[f.name for f in Path(st.session_state.workspace,
"fasta-files").iterdir()],
help="If file not here, please upload at File Upload"
)

#take full path of mzML file
# take full path of mzML file
if selected_mzML_file:
mzML_file_path = str(Path(st.session_state.workspace, "mzML-files", selected_mzML_file))

#take full path of fasta file
# take full path of fasta file
if selected_fasta_file:
database_file_path = str(Path(st.session_state.workspace, "fasta-files", selected_fasta_file))

#out file path
# out file path
result_dir: Path = Path(st.session_state.workspace, "result-files")

#create same output file path name as input file path
# create same output file path name as input file path
mzML_file_name = os.path.basename(mzML_file_path)
protocol_name = os.path.splitext(mzML_file_name)[0]
result_path = os.path.join(result_dir, protocol_name + ".idXML")

######################## Take NuXL configurations ini read #################################
# Define the sections you want to extract
#will capture automaticaly if add new section as decoy_factor
# will capture automaticaly if add new section as decoy_factor
sections = [
"fixed",
"variable",
Expand All @@ -93,11 +93,11 @@
"missed_cleavages"
]

#current directory
# current directory
current_dir = os.getcwd()
#take .ini config path
# take .ini config path
config_path = os.path.join(current_dir, 'assets', 'OpenMS_NuXL.ini')
#take NuXL config dictionary
# take NuXL config dictionary
# (will give every section as 1 entry:
# entry = {
#"name": node_name,
Expand All @@ -107,7 +107,7 @@
# })
NuXL_config=ini2dict(config_path, sections)

#take all variables settings from config dictionary/ take all user configuration
# take all variables settings from config dictionary/ take all user configuration
cols=st.columns(2)
with cols[0]:
cols_=st.columns(2)
Expand Down Expand Up @@ -180,16 +180,16 @@

##################################### NuXL command (subprocess) ############################

#result dictionary to capture ooutput of subprocess
# result dictionary to capture ooutput of subprocess
result_dict = {}
result_dict["success"] = False
result_dict["log"] = " "

#create terminate flag from even function
# create terminate flag from even function
terminate_flag = threading.Event()
terminate_flag.set()

#terminate subprocess by terminate flag
# terminate subprocess by terminate flag
def terminate_subprocess():
global terminate_flag
terminate_flag.set()
Expand All @@ -205,12 +205,12 @@ def terminate_subprocess():
#clear form
st.experimental_rerun()

#with st.spinner("Running analysis... Please wait until analysis done 😑"): #without status/ just spinner button
# with st.spinner("Running analysis... Please wait until analysis done 😑"): #without status/ just spinner button
with st.status("Running analysis... Please wait until analysis done 😑"):
#If session state is local
# If session state is local
if st.session_state.location == "local":

#If local in current directory of app like bin and percolator folder
# If local in current directory of app like bin and percolator folder
OpenNuXL_exec = os.path.join(os.getcwd(),'bin', 'OpenNuXL')
perc_exec = os.path.join(os.getcwd(), 'Percolator', 'percolator.exe')

Expand All @@ -223,80 +223,80 @@ def terminate_subprocess():

args.extend(["-percolator_executable", perc_exec])

#If session state is online/docker
# If session state is online/docker
else:

#In docker it executable on path
# In docker it executable on path
args = ["OpenNuXL", "-in", mzML_file_path, "-database", database_file_path, "-out", result_path, "-NuXL:presets", preset,
"-NuXL:length", length, "-NuXL:scoring", scoring, "-precursor:mass_tolerance", Precursor_MT, "-precursor:mass_tolerance_unit", Precursor_MT_unit,
"-fragment:mass_tolerance", Fragment_MT, "-fragment:mass_tolerance_unit", Fragment_MT_unit,
"-peptide:min_size", peptide_min, "-peptide:max_size",peptide_max, "-peptide:missed_cleavages",Missed_cleavages, "-peptide:enzyme", Enzyme,
"-modifications:variable_max_per_peptide", Variable_max_per_peptide
]

#If variable modification provided
# If variable modification provided
if variable_modification:
args.extend(["-modifications:variable"])
args.extend(variable_modification)

#If fixed modification provided
# If fixed modification provided
if fixed_modification:
args.extend(["-modifications:fixed"])
args.extend(fixed_modification)

# Add any additional variables needed for the subprocess (if any)
variables = []

#want to see the command values and argues
#message = f"Running '{' '.join(args)}'"
#st.code(message)
# want to see the command values and argues
# message = f"Running '{' '.join(args)}'"
# st.code(message)

#run subprocess command
# run subprocess command
run_subprocess(args, variables, result_dict)


# Use st.experimental_thread to run the subprocess asynchronously
#terminate_flag = threading.Event()
#thread = threading.Thread(target=run_subprocess, args=(args, variables, result_dict))
#thread.start()
#thread.join()
# terminate_flag = threading.Event()
# thread = threading.Thread(target=run_subprocess, args=(args, variables, result_dict))
# thread.start()
# thread.join()

#if run_subprocess success (no need if not success because error will show/display in run_subprocess command)
# if run_subprocess success (no need if not success because error will show/display in run_subprocess command)
if result_dict["success"]:

#add .mzML.ambigious_masses.csv in result directory
# add .mzML.ambigious_masses.csv in result directory
add_this_result_file(f"{protocol_name}.mzML.ambigious_masses.csv", Path(st.session_state.workspace, "mzML-files"))

#remove .mzML.ambigious_masses.csv from mzML directory
# remove .mzML.ambigious_masses.csv from mzML directory
remove_this_mzML_file(f"{protocol_name}.mzML.ambigious_masses.csv")

# Save the log to a text file in the result_dir
log_file_path = result_dir / f"{protocol_name}_log.txt"
with open(log_file_path, "w") as log_file:
log_file.write(result_dict["log"])

#all result files in result-dir
# all result files in result-dir
All_files = [f.name for f in sorted(result_dir.iterdir())]

#filtered out all current run file from all resul-dir files
# filtered out all current run file from all resul-dir files
current_analysis_files = [s for s in All_files if protocol_name in s]

#add list of files to dataframe
# add list of files to dataframe
df = pd.DataFrame({"output files ": current_analysis_files})

#show table of all list files of current protocol
# show table of all list files of current protocol
show_table(df)

#check if perc files availabe in some cases could not run percolator e-g if identification hits are so less
# check if perc files availabe in some cases could not run percolator e-g if identification hits are so less
perc_exec = any("_perc_" in string for string in current_analysis_files)

#just show and download the identification_files of XLs PSMs/PRTs if perc_XLs available otherwise without the percolator identification file
# just show and download the identification_files of XLs PSMs/PRTs if perc_XLs available otherwise without the percolator identification file
if perc_exec :
identification_files = [string for string in current_analysis_files if "_perc_0.0100_XLs" in string or "_perc_0.1000_XLs" in string or "_perc_1.0000_XLs" in string or "_perc_proteins" in string]
else:
identification_files = [string for string in current_analysis_files if "_XLs" in string or "_proteins" in string]

#then download link for identification file of above criteria
# then download link for identification file of above criteria
download_selected_result_files(identification_files, f":arrow_down: {protocol_name}_XL_identification_files")

save_params(params)
68 changes: 30 additions & 38 deletions src/captcha_.py
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@@ -1,4 +1,3 @@
import os
from pathlib import Path
import streamlit as st
from streamlit.source_util import (
Expand All @@ -7,9 +6,11 @@
get_pages,
_on_pages_changed
)
import os

from captcha.image import ImageCaptcha
import random, string
from src.common import *

def delete_all_pages(main_script_path_str: str) -> None:
"""
Expand Down Expand Up @@ -172,51 +173,42 @@ def add_page(main_script_path_str: str, page_name: str) -> None:
height = 180

# define the function for the captcha control
def captcha_control() -> None:
"""
Captcha control function to verify if the user is not a robot.
This function displays a captcha image and allows the user to enter the captcha text.
It verifies whether the entered captcha text matches the generated captcha.
Returns:
None
"""
def captcha_control():
#control if the captcha is correct
if 'controllo' not in st.session_state or st.session_state['controllo'] == False:
st.title("Makesure you are not a robot🤖")
st.title("Make sure you are not a robot🤖")

# define the session state for control if the captcha is correct
st.session_state['controllo'] = False
col1, col2 = st.columns(2)

# define the session state for the captcha text because it doesn't change during refreshes
if 'Captcha' not in st.session_state:
st.session_state['Captcha'] = ''.join(random.choices(string.ascii_uppercase + string.digits, k=length_captcha))

#setup the captcha widget
image = ImageCaptcha(width=width, height=height)
data = image.generate(st.session_state['Captcha'])
col1.image(data)
capta2_text = col2.text_area('Enter captcha text', height=20)


if st.button("Verify the code"):
capta2_text = capta2_text.replace(" ", "")
# if the captcha is correct, the controllo session state is set to True
if st.session_state['Captcha'].lower() == capta2_text.lower().strip():
del st.session_state['Captcha']
col1.empty()
col2.empty()
st.session_state['controllo'] = True
st.rerun()
col1, _ = st.columns(2)
with col1.form("captcha-form"):
#setup the captcha widget
st.info("Please enter the captcha as text. Note: If your captcha is not accepted, you might need to disable your ad blocker.")
image = ImageCaptcha(width=width, height=height)
data = image.generate(st.session_state['Captcha'])
st.image(data)
c1, c2 = st.columns([70, 30])
capta2_text = c1.text_input('Enter captcha text', max_chars=5)
c2.markdown("##")
if c2.form_submit_button("Verify the code", type="primary"):
capta2_text = capta2_text.replace(" ", "")
# if the captcha is correct, the controllo session state is set to True
if st.session_state['Captcha'].lower() == capta2_text.lower().strip():
del st.session_state['Captcha']
col1.empty()
st.session_state['controllo'] = True
st.rerun()
else:
# if the captcha is wrong, the controllo session state is set to False and the captcha is regenerated
st.error("🚨 Captch is wrong")
del st.session_state['Captcha']
del st.session_state['controllo']
st.rerun()
else:
# if the captcha is wrong, the controllo session state is set to False and the captcha is regenerated
st.error("🚨 Captch is wrong")
del st.session_state['Captcha']
del st.session_state['controllo']
st.rerun()
else:
#wait for the button click
st.stop()

#wait for the button click
st.stop()
2 changes: 1 addition & 1 deletion src/common.py
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Expand Up @@ -10,7 +10,7 @@
import pandas as pd

# set these variables according to your project
APP_NAME = "OpenMS App Template"
APP_NAME = "OpenMS NuXL Streamlit App"
REPOSITORY_NAME = "streamlit-template"


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