moveConverted.js

	
const fs = require('fs');
const Promise = require('bluebird');
const path = require('path');
const argv = require('minimist')(process.argv.slice(2));
const _ = require('underscore');
const os = require('os');
const xnat = require("./index.js");


const help = function(){
	console.error("Change converted files from one location to another");
	console.error("Usage: node", process.argv[1],"-p <project id>");
	console.error("Options:");
	console.error("-p <project id>, project id in XNAT to upload the files.");
	console.error("--out_files <filename to write found files>");
	console.error("--in_files <filename to load input files instead of searching>");
	console.error("--move , move the found files.");
	console.error("--prompt , If set, forces prompt for login information again. It will use the previous server URL saved in the configuration file");
}


if(!argv["p"] || argv["h"] || argv["help"]){
	help();
	process.exit(1);
}

var projectid = argv["p"];
var promptlogin = argv["prompt"];
var outfiles = argv["out_files"];
var infiles = argv["in_files"];
var move = argv["move"];

xnat.start()
.then(function(res){
	return xnat.getSubjects(projectid);
})
.then(function(res){
	if(!infiles){
		return Promise.map(_.pluck(res, "ID"), function(subjectid){
			return xnat.getSubjectExperiments(projectid, subjectid)
			.then(function(experiments){
				return Promise.map(experiments.ResultSet.Result, function(exp){
					return xnat.getScans(projectid, subjectid, exp.ID)
					.then(function(subjectExperiments){
						return Promise.map(subjectExperiments, function(scans){
							return xnat.getScanFiles(projectid, subjectid, exp.ID, scans.ID)
							.then(function(scanfiles){
								var scanfilesfound = _.map(scanfiles, function(sfile){
									return {
										subjectid: subjectid,
										experimentid: exp.ID,
										scanid: scans.ID, 
										resourceid: sfile.cat_ID, 
										name: sfile.Name,
										uri: sfile.URI,
										collection: sfile.collection
									}
								});
								return _.filter(scanfilesfound, function(sfile){
									return (sfile.collection.indexOf("NRRD") == -1 && (sfile.name.indexOf(".nrrd") != -1 || sfile.name.indexOf(".nii.gz") != -1 || sfile.name.indexOf(".nii") != -1 || sfile.name.indexOf(".png") != -1 || sfile.name.indexOf(".txt") != -1 || sfile.name.indexOf(".bvals") != -1 || sfile.name.indexOf(".bvecs") != -1))
								});
							})
							.catch(function(e){
								console.error("getScanFiles", projectid, subjectid, exp.ID, scans.ID);
								console.error(e);
								return null;
							});
						}, {
							concurrency: 1
						});
					})
					.catch(function(e){
						console.error("getScans", projectid, subjectid, exp.ID);
						console.error(e);
						return null;
					});;
				}, {
					concurrency: 1
				})
			})
			.catch(function(e){
				console.error("getSubjectExperiments", projectid, subjectid);
				console.error(e);
				return null;
			});
		}, {
			concurrency: 1
		})
		.then(function(allexperiments){
			allexperiments = _.compact(_.flatten(allexperiments));
			if(outfiles){
				console.log("Writting file", outfiles);
				fs.writeFileSync(outfiles, JSON.stringify(allexperiments));
			}
			return allexperiments;
		})
		.catch(function(e){
			console.error("map ids");
			console.error(e);
			return null;
		});
	}else{
		return JSON.parse(fs.readFileSync(infiles));
	}
})
.then(function(allconvertedfiles){
	if(move){
		var uniqresource = _.uniq(_.map(allconvertedfiles, function(convfile){
			return {
				subjectid: convfile.subjectid,
			    experimentid: convfile.experimentid,
			    scanid: convfile.scanid
			}
		}), function(el, ind, l){
			return el.subjectid + el.experimentid + el.scanid;
		});

		return Promise.map(uniqresource, function(ur){
			return xnat.createResources(projectid, ur.subjectid, ur.experimentid, ur.scanid, "NRRD")
			.then(function(res){
				console.log("Resource created!", projectid, ur.subjectid, ur.experimentid, ur.scanid, "NRRD");
			})
			.catch(function(err){
				console.error(err);
			});
		}, {
				concurrency: 1
		})
		.then(function(){
			return Promise.map(allconvertedfiles, function(convfile){
				return xnat.moveResource(projectid, convfile.subjectid, convfile.experimentid, convfile.scanid, convfile.resourceid, convfile.name, convfile.subjectid, convfile.experimentid, convfile.scanid, "NRRD", convfile.name)
				.then(function(res){
					console.log("File Moved!", projectid, convfile.subjectid, convfile.experimentid, convfile.scanid, convfile.resourceid, convfile.name);
					return res;
				})
				.catch(function(err){
					console.error(err);
					return err;
				});
			}, {
				concurrency: 1
			});
		});
	}
	
})
.then(function(){
	return xnat.logout();
})
.catch(function(e){
	console.error(e);
	return xnat.logout();
})