refactoring some files

pegasus/run_sequentially.py

@@ -7,6 +7,12 @@
 import sys
 from enum import Enum
 from string import Template
+from configobj import ConfigObj
+
+config = ConfigObj()
+
+config = ConfigObj('/home/punit/github/GSOC/tvb-recon/web/TVB_patients/TVB1/configs/patient_flow.properties')
+print(config['parcelation.atlas'])
 
 PATH_TO_INPUT_SUBJ_FOLDERS = "/home/submitter/data"
 PATH_TO_SUBJ_CONFIG_FOLDERS = "/home/submitter/data"
@@ -16,7 +22,6 @@
 
 SUBJECTS_TO_BE_PROCESSED = [24]
 
-ATLASES = ["default", "a2009s"]
 
 OS = "LINUX"
 
@@ -29,7 +34,6 @@
 
 class configs(Enum):
  ENVIRON_CONFIGS = "environment_config.sh"
- PATIENT_PROPS = "patient_flow.properties"
  PEGASUS_PROPS = "pegasus.properties"
  SITES = "sites.xml"
  RC = "rc.txt"
@@ -46,14 +50,6 @@ def create_config_files_for_subj(current_subject, current_atlas):
  with open(subj_pegasus_props_path, "w+") as subj_pegasus_props_file:
  subj_pegasus_props_file.write(pegasus_props)
 
- default_patient_props_path = os.path.join(PATH_TO_DEFAULT_PEGASUS_CONFIGURATION, configs.PATIENT_PROPS.value)
- with open(default_patient_props_path) as default_patient_props_file:
- template = Template(default_patient_props_file.read())
- patient_props = template.substitute(subject=current_subject, atlas=current_atlas, os=OS)
- subj_patient_props = os.path.join(current_dir, configs.PATIENT_PROPS.value)
- with open(subj_patient_props, "w+") as subj_patient_props_file:
- subj_patient_props_file.write(patient_props)
-
  default_environ_config_path = os.path.join(PATH_TO_DEFAULT_PEGASUS_CONFIGURATION, configs.ENVIRON_CONFIGS.value)
  with open(default_environ_config_path) as default_environ_config_file:
  template = Template(default_environ_config_file.read())
@@ -88,25 +84,7 @@ def create_config_files_for_subj(current_subject, current_atlas):
  print("Configuration files for subject %s are ready!" % current_subject)
 
 
-def prepare_config_for_new_atlas(current_dir, current_atlas):
- atlas_exists_in_config = False
- atlas_config_name = "parcelation.atlas"
- atlas_config = atlas_config_name + "=" + current_atlas + "\n"
 
- current_patient_props_path = os.path.join(current_dir, configs.PATIENT_PROPS.value)
- with open(current_patient_props_path, "r") as current_patient_props_file:
- text = current_patient_props_file.readlines()
- for idx, line in enumerate(text):
- if line.startswith(atlas_config_name):
- text[idx] = atlas_config
- atlas_exists_in_config = True
- break
- if not atlas_exists_in_config:
- text.insert(len(text), atlas_config)
- print "Configured atlas %s for patient inside folder %s" % (current_atlas, current_dir)
- os.remove(current_patient_props_path)
- with open(current_patient_props_path, "w") as new_patient_props_file:
- new_patient_props_file.writelines(text)
 
 
 def get_currently_running_job_ids():
@@ -161,41 +139,45 @@ def get_specified_submit_folder(current_dir):
  print "Starting to process the subject: %s" % current_subject
 
  current_dir = os.path.join(PATH_TO_SUBJ_CONFIG_FOLDERS, current_subject, "configs")
- for atlas in ATLASES:
- if not os.path.exists(current_dir):
- os.mkdir(current_dir)
- print "Folder %s has been created..." % current_dir
+ if not os.path.exists(current_dir):
+ os.mkdir(current_dir)
+ print "Folder %s has been created..." % current_dir
 
-  create_config_files_for_subj(current_subject, atlas)
+ create_config_files_for_subj(current_subject, atlas)
 
- else:
- prepare_config_for_new_atlas(current_dir, atlas)
+
+ elif os.path.exists(current_dir):
+ print "Files are adding in the existing configs Folder"
+
+ create_config_files_for_subj(current_subject, atlas)
+ else:
+ prepare_config_for_new_atlas(current_dir, atlas)
 
-  existent_job_ids = get_currently_running_job_ids()
+ existent_job_ids = get_currently_running_job_ids()
 
-  print "Starting pegasus run for subject: " + current_subject + "with atlas: " + atlas
-  current_dax_dir = os.path.join(current_dir, "dax")
-  p = subprocess.call(["sh", "main_pegasus.sh", current_dir, current_dax_dir])
+ print "Starting pegasus run for subject: " + current_subject + "with atlas: " + atlas
+ current_dax_dir = os.path.join(current_dir, "dax")
+ p = subprocess.call(["sh", "main_pegasus.sh", current_dir, current_dax_dir])
 
-  new_job_ids = get_currently_running_job_ids()
+ new_job_ids = get_currently_running_job_ids()
 
-  for job in existent_job_ids:
-  new_job_ids.remove(job)
+ for job in existent_job_ids:
+ new_job_ids.remove(job)
 
-  current_job_id = new_job_ids[0]
-  print "The job that has been started has the id: %s" % current_job_id
+ current_job_id = new_job_ids[0]
+ print "The job that has been started has the id: %s" % current_job_id
 
-  submit_dir = os.path.join(get_specified_submit_folder(current_dir), getpass.getuser(), "pegasus",
+ submit_dir = os.path.join(get_specified_submit_folder(current_dir), getpass.getuser(), "pegasus",
  "TVB-PIPELINE", PREFIX_JOB_ID + current_job_id)
 
-  print("Starting to monitor the submit folder: %s ..." % submit_dir)
+ print("Starting to monitor the submit folder: %s ..." % submit_dir)
 
-  while True:
-  if MONITORED_FILE in os.listdir(submit_dir):
-  break
-  else:
-  print("Checked at %s and %s file was not generated yet!" % (
+ while True:
+ if MONITORED_FILE in os.listdir(submit_dir):
+ break
+ else:
+ print("Checked at %s and %s file was not generated yet!" % (
  str(time.strftime("%a, %d %b %Y %H:%M:%S", time.gmtime())), MONITORED_FILE))
-  time.sleep(600)
+ time.sleep(600)
 
-  print("The run has finished for job with id: %s" % current_job_id)
+ print("The run has finished for job with id: %s" % current_job_id)

web/package.json

@@ -14,6 +14,7 @@
  "font-awesome": "^4.7.0",
  "multer": "^1.4.2",
  "nodemon": "^2.0.4",
+ "properties-file": "^1.0.0",
  "react": "^16.13.1",
  "react-dom": "^16.13.1",
  "react-router": "^5.2.0",

web/server.js

@@ -7,6 +7,7 @@ app.use(cors())
 var bodyParser = require('body-parser');
 app.use(bodyParser.urlencoded({extended: true}));
 app.use(express.json())
+var parser = require("properties-file");
 
 //For Patient 1
 var storage = multer.diskStorage({
@@ -20,7 +21,7 @@ var storage = multer.diskStorage({
  }
  })
 
- var upload1 = multer({ storage: storage }).single('file')
+ var upload1 = multer({ storage: storage }).array('file')
 
 app.get('/',function(req,res){
  return res.send('Hello Server')
@@ -52,7 +53,7 @@ var storage = multer.diskStorage({
  }
 })
 
-var upload2 = multer({ storage: storage }).single('file')
+var upload2 = multer({ storage: storage }).array('file')
 
 app.post('/upload2',function(req, res) {
 
@@ -82,7 +83,7 @@ var storage = multer.diskStorage({
  }
 })
 
-var upload3 = multer({ storage: storage }).single('file')
+var upload3 = multer({ storage: storage }).array('file')
 
 app.post('/upload3',function(req, res) {
 
@@ -112,7 +113,7 @@ filename: function (req, file, cb) {
 }
 })
 
-var upload4 = multer({ storage: storage }).single('file')
+var upload4 = multer({ storage: storage }).array('file')
 
 app.post('/upload4',function(req, res) {
 
@@ -153,7 +154,7 @@ app.post("/input1",function(req,res){
  "decim.factor":req.body.label4,
  os:"LINUX"
  }
- fs.writeFile(file1,JSON.stringify(data,null,2) ,'utf-8',
+ fs.writeFile(file1,parser.stringify(data) ,'utf-8',
  (err) => {
  if(err) {
  return console.log(err);
@@ -185,7 +186,7 @@ app.post("/input2",function(req,res){
  "decim.factor":req.body.label4,
  os:"LINUX"
  }
- fs.writeFile(file2,JSON.stringify(data,null,2) ,'utf-8',
+ fs.writeFile(file2,parser.stringify(data) ,'utf-8',
  (err) => {
  if(err) {
  return console.log(err);
@@ -217,7 +218,7 @@ app.post("/input3",function(req,res){
  "decim.factor":req.body.label4,
  os:"LINUX"
  }
- fs.writeFile(file3,JSON.stringify(data,null,2) ,'utf-8',
+ fs.writeFile(file3,parser.stringify(data) ,'utf-8',
  (err) => {
  if(err) {
  return console.log(err);
@@ -249,13 +250,31 @@ app.post("/input4",function(req,res){
  "decim.factor":req.body.label4,
  os:"LINUX"
  }
- fs.writeFile(file4,JSON.stringify(data,null,2) ,'utf-8',
+ fs.writeFile(file4,parser.stringify(data) ,'utf-8',
  (err) => {
  if(err) {
  return console.log(err);
  }
 })
 })
+
+
+//Start docker
+const { exec } = require("child_process");
+const { cwd } = require('process');
+app.post("/start",function(req,res){
+exec("sudo docker run -it -v "+ (cwd())+"/TVB_patients/:/home/submitter/data thevirtualbrain/tvb-recon /bin/bash", (error, stdout, stderr) => {
+ if (error) {
+ console.log(`error: ${error.message}`);
+ return;
+ }
+ if (stderr) {
+ console.log(`stderr: ${stderr}`);
+ return;
+ }
+ console.log(`stdout: ${stdout}`);
+})
+})
 app.listen(8000, function() {
  console.log('App running on port 8000');
 });

web/src/App.js

@@ -1,7 +1,7 @@
 import React, { Component } from "react";
 import { BrowserRouter as Router,Switch,Route } from "react-router-dom";
 import Home from "./components/Home/Home";
-import Input from './components/Input/Patient';
+import Input from './components/Input/Input';
 import Configuration from './components/Configuration/Configuration'
 import WorkflowList from './components/WorkflowList/WorkflowList';
 import NewWorkflow from './components/NewWorkflow/NewWorkflow';

web/src/components/Configuration/Configuration.js

@@ -1,15 +1,17 @@
 import React, { Component } from 'react';
 import Header from '../Home/Header/Header';
-import Configuration1 from './Configuration1';
-import Configuration2 from './Configuration2';
-import Configuration3 from './Configuration3';
-import Configuration4 from './Configuration4';
+import InputConfiguration from './InputConfiguration'
 import Slider from "react-slick";
 import "slick-carousel/slick/slick.css"; 
 import "slick-carousel/slick/slick-theme.css";
-import './Configuration.css'
+import './Configuration.css';
+import axios from 'axios'
 class Configuration extends Component{
-
+ handleClick=()=>{
+ alert("Docker started on server")
+ axios.post('http:https://localhost:8000/start')
+
+ }
  render(){
  const settings = {
  dots: true,
@@ -22,12 +24,12 @@ class Configuration extends Component{
  <div>
  <Header/>
  <Slider {...settings}>
- <Configuration1/>
- <Configuration2/>
- <Configuration3/>
- <Configuration4/>
+ <InputConfiguration no="1"/>
+ <InputConfiguration no="2"/>
+ <InputConfiguration no="3"/>
+ <InputConfiguration no="4"/>
  </Slider>
- <button type="submit" className="proceed_btn" onClick={this.handleClick}>Click Here To Proceed >>></button>
+ <button className="proceed_btn" onClick={this.handleClick}>Start the Docker Container</button>
 
 
  </div>