From 92b3768b6f297cda1308c9d03fa4f6d772c897fe Mon Sep 17 00:00:00 2001
From: root <root@dheeraj-dev.js2local>
Date: Mon, 21 Aug 2023 20:09:18 +0000
Subject: [PATCH 1/3] added phenotype data to dataset -> file names and
 combined json data

---
 bids-walker.js | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/bids-walker.js b/bids-walker.js
index 91dabb8..79e6d62 100644
--- a/bids-walker.js
+++ b/bids-walker.js
@@ -55,6 +55,7 @@ exports.walk = (root, cb)=>{
         participants: [], //from participants.tsv
         participants_json: null, //from participants.json
         datasets: [], //{dataset, files} ... you have to do dataset.dataset.meta... maybe I should rename it to items"
+        phenotypes_json: {},
     }
 
     let tsv = null;
@@ -83,6 +84,29 @@ exports.walk = (root, cb)=>{
         ///mnt/datalad/datasets.datalad.org/openfmri/ds000201 contains participants.json that's basically the participants.tsv
     }
 
+    if(exists(root+"/phenotype")) {
+        console.log("phenotype directory found.. loading");
+        let files = fs.readdirSync(root+"/phenotype");
+        
+        // If there are files in the directory, set the phenotype_folder
+        if (files.length > 0) {
+            bids.phenotype_files = files;
+        }    
+        
+        //just load and combine json files 
+        bids.phenotypes_json = {};
+        files.forEach(file=>{
+            if(file.startsWith(".")) return;
+            if(!file.endsWith(".json")) return;
+            let json = fs.readFileSync(root+"/phenotype/"+file, "utf8");
+            let obj = JSON.parse(json);
+            for(let key in obj) {
+                bids.phenotypes_json[key] = obj[key];
+            }
+        });
+    }
+    
+
     //TODO - should I create a default participants.json if it's missing so that brainlife UI will at least show each columns?
 
     if(exists(root+"/README")) {
@@ -1277,4 +1301,4 @@ exports.walk = (root, cb)=>{
         bids.datasets.push({dataset, files});
         cb();
      }
-}
+}
\ No newline at end of file

From 96acabbda699f25f84ce38962992a19a10976b7a Mon Sep 17 00:00:00 2001
From: bhatiadheeraj <dheerajbhatia2010@gmail.com>
Date: Wed, 23 Aug 2023 20:00:09 +0000
Subject: [PATCH 2/3] groups json and .tsv file

---
 bids-walker.js | 57 ++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 44 insertions(+), 13 deletions(-)

diff --git a/bids-walker.js b/bids-walker.js
index 79e6d62..435417b 100644
--- a/bids-walker.js
+++ b/bids-walker.js
@@ -88,22 +88,53 @@ exports.walk = (root, cb)=>{
         console.log("phenotype directory found.. loading");
         let files = fs.readdirSync(root+"/phenotype");
         
-        // If there are files in the directory, set the phenotype_folder
-        if (files.length > 0) {
-            bids.phenotype_files = files;
-        }    
-        
-        //just load and combine json files 
-        bids.phenotypes_json = {};
+        bids.phenotypes = [];
+        // needs fix to group them to just one entry for file with same name but different extension
+
+        //group files with same name but different extensios
+        let groups = {};
         files.forEach(file=>{
             if(file.startsWith(".")) return;
-            if(!file.endsWith(".json")) return;
-            let json = fs.readFileSync(root+"/phenotype/"+file, "utf8");
-            let obj = JSON.parse(json);
-            for(let key in obj) {
-                bids.phenotypes_json[key] = obj[key];
-            }
+            let key = file.split(".")[0];
+            if(!groups[key]) groups[key] = [];
+            groups[key].push(file);
         });
+        for(let key in groups) {
+            let entry = {
+                //set the name to the file name without the extension
+                name: key,
+                //tsv file name
+                file: "phenotype/"+key+".tsv",
+                sidecar: null,
+                columns: {},
+                data: [],
+            }
+            if(groups[key].includes(key+".json")) {
+                //sidecar
+                entry.sidecar = "phenotype/"+key+".json";
+                let json = fs.readFileSync(root+"/phenotype/"+key+".json", "utf8");
+                let obj = JSON.parse(json);
+                entry.columns = obj
+            }
+
+            //load tsv
+            let tsv = fs.readFileSync(root+"/phenotype/"+key+".tsv", "utf8").trim().split("\n");
+            let header = tsv.shift().split("\t");
+            tsv.forEach((line, lineNumber) => {
+                try {
+                    let obj = {};
+                    let tokens = line.split("\t");
+                    header.forEach((key, idx) => {
+                        obj[key] = tokens[idx];
+                    });
+                    entry.data.push(obj);
+                } catch (error) {
+                    console.error(`Error parsing line ${lineNumber} of ${file}: ${error.message}`);
+                    console.error(`Line content: ${line}`);
+                }
+            });
+            bids.phenotypes.push(entry);
+        }
     }
     
 

From ca20ec53a80c677fbf43d0ddb7298152448ec1dd Mon Sep 17 00:00:00 2001
From: bhatiadheeraj <dheerajbhatia2010@gmail.com>
Date: Wed, 30 Aug 2023 20:35:27 +0000
Subject: [PATCH 3/3] removed comment and whitespace

---
 bids-walker.js | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/bids-walker.js b/bids-walker.js
index 435417b..45c2a82 100644
--- a/bids-walker.js
+++ b/bids-walker.js
@@ -87,9 +87,7 @@ exports.walk = (root, cb)=>{
     if(exists(root+"/phenotype")) {
         console.log("phenotype directory found.. loading");
         let files = fs.readdirSync(root+"/phenotype");
-        
         bids.phenotypes = [];
-        // needs fix to group them to just one entry for file with same name but different extension
 
         //group files with same name but different extensios
         let groups = {};
@@ -1332,4 +1330,4 @@ exports.walk = (root, cb)=>{
         bids.datasets.push({dataset, files});
         cb();
      }
-}
\ No newline at end of file
+}