From cb3085964ddf349d5eb90d6f8720812ca6d30bf4 Mon Sep 17 00:00:00 2001
From: Monica Keith <monicagiraldochica@gmail.com>
Date: Wed, 7 Jan 2026 11:52:26 -0600
Subject: [PATCH 01/22] remove (Something wrong) default script content. Since
 we will not re-write the content, this wouldnt be removed

---
 lib/history.rb | 4 +---
 views/form.erb | 4 +---
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/lib/history.rb b/lib/history.rb
index 8fc7ad7..2a9590d 100644
--- a/lib/history.rb
+++ b/lib/history.rb
@@ -39,9 +39,7 @@ def output_action_modal(action)
     <div class="modal" id="#{id}" aria-hidden="true" tabindex="-1">
       <div class="modal-dialog modal-dialog-scrollable">
         <div class="modal-content">
-          <div class="modal-body" id="#{id}Body">
-            (Something wrong)
-          </div>
+          <div class="modal-body" id="#{id}Body"></div>
           <div class="modal-footer">
             <form action="#{form_action}" method="post" id="#{id}Form">
               <input type="hidden" name="action" value="#{action}">
diff --git a/views/form.erb b/views/form.erb
index d0d817b..3a73964 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -54,9 +54,7 @@
     <!-- Script Content Section -->
     <div class="col py-3 d-flex flex-column">
       <label id="label_<%= OC_SCRIPT_CONTENT %>" class="fw-semibold" for="<%= OC_SCRIPT_CONTENT %>"><%= @script_label %></label>
-      <textarea id="<%= OC_SCRIPT_CONTENT %>" name="<%= OC_SCRIPT_CONTENT %>" class="form-control mt-1 mb-3 flex-grow-1" tabindex="<%= @table_index %>" accesskey="s" oninput="ocForm.updateHeight(ocForm.scriptArea)" required>
-        (Something wrong)
-      </textarea>
+      <textarea id="<%= OC_SCRIPT_CONTENT %>" name="<%= OC_SCRIPT_CONTENT %>" class="form-control mt-1 mb-3 flex-grow-1" tabindex="<%= @table_index %>" accesskey="s" oninput="ocForm.updateHeight(ocForm.scriptArea)" required></textarea>
       <!-- Submit Button -->
       <% if @form_action == "confirm" || @form_action == "confirm-save" %>
       <button class="btn btn-primary d-block w-100" id="<%= SUBMIT_BUTTON %>" type="button" data-bs-toggle="modal" data-bs-target="#modal-<%= SUBMIT_CONFIRM %>" tabindex="<%= @table_index + 1 %>">

From 9469f7af86b31dfe9d4429ee4e7865c17301f5f4 Mon Sep 17 00:00:00 2001
From: Monica Keith <monicagiraldochica@gmail.com>
Date: Wed, 7 Jan 2026 13:20:56 -0600
Subject: [PATCH 02/22] created helper function to re-write only the lines that
 start with SBATCH (the heather) and not the other lines

---
 views/form.erb | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/views/form.erb b/views/form.erb
index 3a73964..7842875 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -155,6 +155,56 @@ document.addEventListener('keydown', function(event) {
   }
 });
 
+// Header helper: rewrite ONLY lines that start with "#SBATCH"
+function rebuildWithSbatchHeader(currentText, headerText) {
+  const current = (currentText ?? '').toString();
+  const lines = current.split('\n');
+  const hasShebang = lines.length > 0 && lines[0].startsWith('#!');
+
+  const header = (headerText ?? '').toString();
+  const headerLines = header.split('\n');
+  const headerShebang = headerLines.find(l => l.startsWith('#!')) || '';
+  const headerSbatch  = headerLines.filter(l => l.trim().startsWith('#SBATCH'));
+  const cleanHeader = headerSbatch.join('\n');
+
+  // Find indices of all existing #SBATCH lines
+  const sbatchIdxs = [];
+  for (let i=0; i<lines.length; i++) {
+    if (lines[i].trim().startsWith('#SBATCH')) sbatchIdxs.push(i);
+  }
+
+  // Case A: Existing #SBATCH lines found — replace them with the new header
+  if (sbatchIdxs.length > 0) {
+    const firstIdx = Math.min(...sbatchIdxs);
+    // Prefix: everything before the first #SBATCH line (kept as-is)
+    const prefix = lines.slice(0, firstIdx).join('\n').replace(/\n+$/, '');
+    // Body: every line EXCEPT those starting with #SBATCH (kept as-is and in original order
+    const bodyLines = lines.filter(l => !l.trim().startsWith('#SBATCH'));
+    // Remove the prefix portion from bodyLines to avoid duplication
+    const prefixLineCount = prefix ? prefix.split('\n').length : 0;
+    const suffix = bodyLines.slice(prefixLineCount).join('\n').replace(/^\n+/, '');
+
+    const parts = [];
+    if (prefix) parts.push(prefix);
+    parts.push(cleanHeader);
+    if (suffix) parts.push(suffix);
+
+    return parts.join('\n\n').replace(/\n{3,}/g, '\n\n');
+  }
+
+  // Case B: No #SBATCH lines — insert header near shebang or at the top
+  if (hasShebang) {
+    const shebang = lines[0];
+    const rest = lines.slice(1).join('\n').trim();
+    return [shebang, cleanHeader, rest].filter(s => s && s !== '').join('\n\n').replace(/\n{3,}/g, '\n\n');
+  }
+
+  // No shebang: put header at top and keep all user text below
+  const shebangToUse = headerShebang || '';
+  const body = current.trim();
+  return [shebangToUse, cleanHeader, body].filter(s => s && s !== '').join('\n\n');
+}
+
 ocForm.isFirst = true;
 ocForm.multiSelectDisabledIndexes = {};
 ocForm.updateValues = function(fromId) {

From cd370fdbfd98f0d73b3dcd3801be60cfb2e921bc Mon Sep 17 00:00:00 2001
From: Monica Keith <monicagiraldochica@gmail.com>
Date: Wed, 7 Jan 2026 13:26:39 -0600
Subject: [PATCH 03/22] add comments in updateValues to make it clear where the
 script area is being overwritten in first and subsequent runs

---
 views/form.erb | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/views/form.erb b/views/form.erb
index 7842875..4de15bf 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -218,13 +218,22 @@ ocForm.updateValues = function(fromId) {
     ocForm.onceExec();
     ocForm.updateScriptContents(scriptValues);
     ocForm.updateSubmitContents(submitValues);
+
+    // Overwrite of script textarea (first run)
     ocForm.scriptArea.value = ocForm.isScriptCache() ? ocForm.loadScriptCache() : Object.values(scriptValues).join('\n');
+
+    // Overwrite of submit textarea (first run)
     ocForm.submitArea.value = ocForm.isSubmitCache() ? ocForm.loadSubmitCache() : Object.values(submitValues).join('\n');
   }
+
   else {
     ocForm.updateScriptContents(scriptValues);
     ocForm.updateSubmitContents(submitValues);
+
+    // Overwrite of script textarea (subsequent runs)
     ocForm.scriptArea.value = Object.values(scriptValues).join('\n');
+
+    // Overwrite of submit textarea (subsequent runs)
     ocForm.submitArea.value = Object.values(submitValues).join('\n')
   }
 

From 878ba73ca06a040fc2bd9f9224c9542273a805df Mon Sep 17 00:00:00 2001
From: Monica Keith <monicagiraldochica@gmail.com>
Date: Wed, 7 Jan 2026 13:35:01 -0600
Subject: [PATCH 04/22] fix script area issue that replaces all content instead
 of only the heather

---
 views/form.erb | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 4de15bf..1b26ad2 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -220,7 +220,10 @@ ocForm.updateValues = function(fromId) {
     ocForm.updateSubmitContents(submitValues);
 
     // Overwrite of script textarea (first run)
-    ocForm.scriptArea.value = ocForm.isScriptCache() ? ocForm.loadScriptCache() : Object.values(scriptValues).join('\n');
+    //ocForm.scriptArea.value = ocForm.isScriptCache() ? ocForm.loadScriptCache() : Object.values(scriptValues).join('\n');
+    const newHeaderFirst = Object.values(scriptValues).join('\n');
+    const baseTextFirst = ocForm.isScriptCache() ? ocForm.loadScriptCache() : (ocForm.scriptArea.value || '');
+    ocForm.scriptArea.value = rebuildWithSbatchHeader(baseTextFirst, newHeaderFirst);
 
     // Overwrite of submit textarea (first run)
     ocForm.submitArea.value = ocForm.isSubmitCache() ? ocForm.loadSubmitCache() : Object.values(submitValues).join('\n');
@@ -231,7 +234,9 @@ ocForm.updateValues = function(fromId) {
     ocForm.updateSubmitContents(submitValues);
 
     // Overwrite of script textarea (subsequent runs)
-    ocForm.scriptArea.value = Object.values(scriptValues).join('\n');
+    //ocForm.scriptArea.value = Object.values(scriptValues).join('\n');
+    const newHeaderNext = Object.values(scriptValues).join('\n');
+    ocForm.scriptArea.value = rebuildWithSbatchHeader(ocForm.scriptArea.value || '', newHeaderNext);
 
     // Overwrite of submit textarea (subsequent runs)
     ocForm.submitArea.value = Object.values(submitValues).join('\n')
@@ -244,6 +249,8 @@ ocForm.updateValues = function(fromId) {
   //if (!ocForm.submitArea.value.endsWith('\n')){
   //  ocForm.submitArea.value += '\n';
   //}
+
+  // Height adjustments
   ocForm.updateHeight(ocForm.scriptArea);
   ocForm.updateHeight(ocForm.submitArea);
 };

From 72bfb2bae852fd11beb537e2b179f25621b591d4 Mon Sep 17 00:00:00 2001
From: Monica Keith <monicagiraldochica@gmail.com>
Date: Wed, 7 Jan 2026 14:55:18 -0600
Subject: [PATCH 05/22] the space after the schebang is fixed for subsequent
 runs but not the first run

---
 views/form.erb | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 1b26ad2..1cc112e 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -185,8 +185,7 @@ function rebuildWithSbatchHeader(currentText, headerText) {
     const suffix = bodyLines.slice(prefixLineCount).join('\n').replace(/^\n+/, '');
 
     const parts = [];
-    if (prefix) parts.push(prefix);
-    parts.push(cleanHeader);
+    parts.push(prefix ? prefix + '\n' + cleanHeader : cleanHeader);
     if (suffix) parts.push(suffix);
 
     return parts.join('\n\n').replace(/\n{3,}/g, '\n\n');
@@ -196,7 +195,7 @@ function rebuildWithSbatchHeader(currentText, headerText) {
   if (hasShebang) {
     const shebang = lines[0];
     const rest = lines.slice(1).join('\n').trim();
-    return [shebang, cleanHeader, rest].filter(s => s && s !== '').join('\n\n').replace(/\n{3,}/g, '\n\n');
+    return [shebang + '\n' + cleanHeader, rest].filter(s => s && s !== '').join('\n\n').replace(/\n{3,}/g, '\n\n');
   }
 
   // No shebang: put header at top and keep all user text below

From 1f2c978193bf910a48d80134ef6b829efac876de Mon Sep 17 00:00:00 2001
From: Monica Keith <monicagiraldochica@gmail.com>
Date: Wed, 7 Jan 2026 15:21:04 -0600
Subject: [PATCH 06/22] fixed space after schebang in first run

---
 views/form.erb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 1cc112e..22da165 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -159,7 +159,7 @@ document.addEventListener('keydown', function(event) {
 function rebuildWithSbatchHeader(currentText, headerText) {
   const current = (currentText ?? '').toString();
   const lines = current.split('\n');
-  const hasShebang = lines.length > 0 && lines[0].startsWith('#!');
+  const hasShebang = lines.length>0 && lines[0].startsWith('#!');
 
   const header = (headerText ?? '').toString();
   const headerLines = header.split('\n');
@@ -201,7 +201,8 @@ function rebuildWithSbatchHeader(currentText, headerText) {
   // No shebang: put header at top and keep all user text below
   const shebangToUse = headerShebang || '';
   const body = current.trim();
-  return [shebangToUse, cleanHeader, body].filter(s => s && s !== '').join('\n\n');
+  if (shebangToUse) return [shebangToUse + '\n' + cleanHeader, body].filter(s => s && s !== '').join('\n\n');
+  return [cleanHeader, body].filter(s => s && s !== '').join('\n\n');
 }
 
 ocForm.isFirst = true;

From d12dad5ab07f2ec461a5ffd0fbf37a5148a4732c Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Fri, 16 Jan 2026 12:43:07 -0600
Subject: [PATCH 07/22] form.erb edits

added a test function to replace the current rebuildWithSbatchHeader with a much simpler function that does the same.
---
 .vscode/settings.json | 12 ++++++++++++
 views/form.erb        | 28 ++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+)
 create mode 100644 .vscode/settings.json

diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..161f38d
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,12 @@
+{
+    "cSpell.words": [
+        "accesskey",
+        "Idxs",
+        "oninput",
+        "onsubmit",
+        "sbatch",
+        "Sbatch",
+        "SBATCH",
+        "tabindex"
+    ]
+}
\ No newline at end of file
diff --git a/views/form.erb b/views/form.erb
index 22da165..66cc6e1 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -155,6 +155,32 @@ document.addEventListener('keydown', function(event) {
   }
 });
 
+// Split text into shebang, header (SBATCH lines) and body
+function splitText(text){
+    text = (text ?? '').toString();
+    const lines = text.split('\n');
+    let shebang = '';
+    const header = [];
+    const body = [];
+
+    for (const line of lines) {
+      const trimmed = line.trim();
+      if (!shebang && trimmed.startsWith("#!")) { shebang = trimmed; }
+      else if (trimmed.startsWith("#SBATCH")) { header.push(line); }
+      else { body.push(line); }
+    }
+
+    return { shebang, header, body }
+}
+
+// Temporary function to test changes
+function rebuildWithSbatchHeader2(currentText, headerText) {
+      console.group("test function")
+      const currentBody = splitText(currentText).body;
+      console.log("currentBody",currentBody)
+      console.groupEnd();
+}
+
 // Header helper: rewrite ONLY lines that start with "#SBATCH"
 function rebuildWithSbatchHeader(currentText, headerText) {
   const current = (currentText ?? '').toString();
@@ -224,6 +250,7 @@ ocForm.updateValues = function(fromId) {
     const newHeaderFirst = Object.values(scriptValues).join('\n');
     const baseTextFirst = ocForm.isScriptCache() ? ocForm.loadScriptCache() : (ocForm.scriptArea.value || '');
     ocForm.scriptArea.value = rebuildWithSbatchHeader(baseTextFirst, newHeaderFirst);
+    rebuildWithSbatchHeader2(baseTextFirst, newHeaderFirst);
 
     // Overwrite of submit textarea (first run)
     ocForm.submitArea.value = ocForm.isSubmitCache() ? ocForm.loadSubmitCache() : Object.values(submitValues).join('\n');
@@ -237,6 +264,7 @@ ocForm.updateValues = function(fromId) {
     //ocForm.scriptArea.value = Object.values(scriptValues).join('\n');
     const newHeaderNext = Object.values(scriptValues).join('\n');
     ocForm.scriptArea.value = rebuildWithSbatchHeader(ocForm.scriptArea.value || '', newHeaderNext);
+    rebuildWithSbatchHeader2(ocForm.scriptArea.value || '', newHeaderNext);
 
     // Overwrite of submit textarea (subsequent runs)
     ocForm.submitArea.value = Object.values(submitValues).join('\n')

From cb945275bf207ec1bd2377fafe28e7aba6e3409e Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Fri, 16 Jan 2026 13:57:21 -0600
Subject: [PATCH 08/22] Update form.erb

continue working on the test function
---
 views/form.erb | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 66cc6e1..c66153b 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -175,9 +175,19 @@ function splitText(text){
 
 // Temporary function to test changes
 function rebuildWithSbatchHeader2(currentText, headerText) {
-      console.group("test function")
-      const currentBody = splitText(currentText).body;
-      console.log("currentBody",currentBody)
+      console.group("test function");
+
+      const { shebang: currentShebang, header: currentHeader, body: currentBody } = splitText(currentText);
+      const { shebang: renderedShebang, header: renderedHeader, body: renderedBody } = splitText(headerText);
+
+      const finalShebang = renderedShebang?.trim() ? renderedShebang : currentShebang?.trim() || '';
+      const finalHeader = renderedHeader?.length>0 ? renderedHeader : currentHeader?.length>0 ? currentHeader : [];
+      const finalBody = (renderedBody.length===0 && currentBody.length===0) ? [] : [...renderedBody, ...(renderedBody.length>0 && currentBody.length>0 ? [""] : []), ...currentBody];
+
+      console.log("finalShebang",finalShebang);
+      console.log("finalHeader",finalHeader);
+      console.log("finalBody",finalBody);
+
       console.groupEnd();
 }
 

From 8efcd5af601bbeee9a44ef09699277f20e9baaff Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Mon, 19 Jan 2026 15:09:29 -0600
Subject: [PATCH 09/22] Update form.erb

Edit temporary function to print in the console what the final text to print in the script area would be
---
 views/form.erb | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index c66153b..4c51b31 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -183,11 +183,17 @@ function rebuildWithSbatchHeader2(currentText, headerText) {
       const finalShebang = renderedShebang?.trim() ? renderedShebang : currentShebang?.trim() || '';
       const finalHeader = renderedHeader?.length>0 ? renderedHeader : currentHeader?.length>0 ? currentHeader : [];
       const finalBody = (renderedBody.length===0 && currentBody.length===0) ? [] : [...renderedBody, ...(renderedBody.length>0 && currentBody.length>0 ? [""] : []), ...currentBody];
-
-      console.log("finalShebang",finalShebang);
-      console.log("finalHeader",finalHeader);
-      console.log("finalBody",finalBody);
-
+      
+      const hasTopSection = (finalShebang?.trim() !== '') || (finalHeader.length > 0);
+      const combined = [
+        ...(finalShebang ? [finalShebang] : []),
+        ...finalHeader,
+        ...(hasTopSection && (finalBody.length>0) ? [""] : []),
+        ...finalBody
+      ];
+      const finalText = combined.join("\n").replace(/\n{2,}/g, "\n").trim();
+
+      console.log(finalText);
       console.groupEnd();
 }
 

From b9c278f1a8ddb90e770c8e7a89c749489bd0f76a Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Tue, 20 Jan 2026 09:57:36 -0600
Subject: [PATCH 10/22] Change form.erb and .gitignore

Trim only the ends on finalText so that the empty line between the top section and the body is not removed.
---
 .gitignore     | 3 ++-
 views/form.erb | 6 +++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index 3cb7175..4f9cced 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,8 @@
 # General
 .DS_Store
+.swp
 
 # bundle
 Gemfile.lock
 vendor/
-.bundle
+.bundle
\ No newline at end of file
diff --git a/views/form.erb b/views/form.erb
index 4c51b31..9a2ccf4 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -184,16 +184,16 @@ function rebuildWithSbatchHeader2(currentText, headerText) {
       const finalHeader = renderedHeader?.length>0 ? renderedHeader : currentHeader?.length>0 ? currentHeader : [];
       const finalBody = (renderedBody.length===0 && currentBody.length===0) ? [] : [...renderedBody, ...(renderedBody.length>0 && currentBody.length>0 ? [""] : []), ...currentBody];
       
-      const hasTopSection = (finalShebang?.trim() !== '') || (finalHeader.length > 0);
+      const hasTopSection = (finalShebang?.trim()!=='') || (finalHeader.length>0);
       const combined = [
         ...(finalShebang ? [finalShebang] : []),
         ...finalHeader,
         ...(hasTopSection && (finalBody.length>0) ? [""] : []),
         ...finalBody
       ];
-      const finalText = combined.join("\n").replace(/\n{2,}/g, "\n").trim();
+      const finalText = combined.join("\n").replace(/\n{2,}/g, "\n").trimEnd();
 
-      console.log(finalText);
+      console.log("finalText", finalText);
       console.groupEnd();
 }
 

From 789477402f384f9d37a7b67148830ab79eee42a2 Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Tue, 20 Jan 2026 10:06:54 -0600
Subject: [PATCH 11/22] Update form.erb

---
 views/form.erb | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 9a2ccf4..6e0add7 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -166,8 +166,8 @@ function splitText(text){
     for (const line of lines) {
       const trimmed = line.trim();
       if (!shebang && trimmed.startsWith("#!")) { shebang = trimmed; }
-      else if (trimmed.startsWith("#SBATCH")) { header.push(line); }
-      else { body.push(line); }
+      else if (trimmed.startsWith("#SBATCH")) { header.push(trimmed); }
+      else { body.push(trimmed); }
     }
 
     return { shebang, header, body }
@@ -191,8 +191,12 @@ function rebuildWithSbatchHeader2(currentText, headerText) {
         ...(hasTopSection && (finalBody.length>0) ? [""] : []),
         ...finalBody
       ];
-      const finalText = combined.join("\n").replace(/\n{2,}/g, "\n").trimEnd();
+      const finalText = combined.join("\n").replace(/\n{2,}/g, "\n");
 
+      console.log("finalShebang", finalShebang)
+      console.log("finalHeader",finalHeader)
+      console.log("finalBody",finalBody)
+      console.log("combined",combined)
       console.log("finalText", finalText);
       console.groupEnd();
 }

From bd29972eaebac08772fbbf0d37ed51c33b45ca15 Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Tue, 20 Jan 2026 10:32:05 -0600
Subject: [PATCH 12/22] Update form.erb, do the trimming in splitText

---
 views/form.erb | 65 ++++++++++++++++++++++++++++----------------------
 1 file changed, 36 insertions(+), 29 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 6e0add7..26ec0e0 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -167,7 +167,7 @@ function splitText(text){
       const trimmed = line.trim();
       if (!shebang && trimmed.startsWith("#!")) { shebang = trimmed; }
       else if (trimmed.startsWith("#SBATCH")) { header.push(trimmed); }
-      else { body.push(trimmed); }
+      else if (body.at(-1)!="" || trimmed!="") { body.push(trimmed); }
     }
 
     return { shebang, header, body }
@@ -175,30 +175,37 @@ function splitText(text){
 
 // Temporary function to test changes
 function rebuildWithSbatchHeader2(currentText, headerText) {
-      console.group("test function");
-
-      const { shebang: currentShebang, header: currentHeader, body: currentBody } = splitText(currentText);
-      const { shebang: renderedShebang, header: renderedHeader, body: renderedBody } = splitText(headerText);
-
-      const finalShebang = renderedShebang?.trim() ? renderedShebang : currentShebang?.trim() || '';
-      const finalHeader = renderedHeader?.length>0 ? renderedHeader : currentHeader?.length>0 ? currentHeader : [];
-      const finalBody = (renderedBody.length===0 && currentBody.length===0) ? [] : [...renderedBody, ...(renderedBody.length>0 && currentBody.length>0 ? [""] : []), ...currentBody];
-      
-      const hasTopSection = (finalShebang?.trim()!=='') || (finalHeader.length>0);
-      const combined = [
-        ...(finalShebang ? [finalShebang] : []),
-        ...finalHeader,
-        ...(hasTopSection && (finalBody.length>0) ? [""] : []),
-        ...finalBody
-      ];
-      const finalText = combined.join("\n").replace(/\n{2,}/g, "\n");
-
-      console.log("finalShebang", finalShebang)
-      console.log("finalHeader",finalHeader)
-      console.log("finalBody",finalBody)
-      console.log("combined",combined)
-      console.log("finalText", finalText);
-      console.groupEnd();
+  console.group("test function");
+  
+  const { shebang: currentShebang, header: currentHeader, body: currentBody } = splitText(currentText);
+  const { shebang: renderedShebang, header: renderedHeader, body: renderedBody } = splitText(headerText);
+
+  const finalShebang = renderedShebang ? renderedShebang : currentShebang || '';
+  const finalHeader = renderedHeader?.length>0 ? renderedHeader : currentHeader?.length>0 ? currentHeader : [];
+
+  const filteredRenderedBody = renderedBody.filter(item => item.trim() !== "");
+  const filteredCurrentBody  = currentBody.filter(item => item.trim() !== "");
+  let finalBody;
+  if (filteredRenderedBody.length === 0 && filteredCurrentBody.length === 0) { finalBody = []; }
+  else if (filteredRenderedBody.length === 0) { finalBody = currentBody; }
+  else if (filteredCurrentBody.length === 0) { finalBody = renderedBody; }
+  else { finalBody = [...renderedBody, "", ...currentBody]; }
+  if (finalBody[0] === "") { finalBody.shift(); }
+  if (finalBody.at(-1) === "") { finalBody.pop(); }
+
+  const hasTopSection = (finalShebang?.trim()!=='') || (finalHeader.length>0);
+  const combined = [
+    ...(finalShebang ? [finalShebang] : []),
+    ...finalHeader,
+    ...(hasTopSection && finalBody.length>0 ? [""] : []),
+    ...finalBody
+  ];
+  const finalText = combined.join("\n");
+
+  console.log("finalText", finalText)
+  console.groupEnd();
+
+  return finalText;
 }
 
 // Header helper: rewrite ONLY lines that start with "#SBATCH"
@@ -269,8 +276,8 @@ ocForm.updateValues = function(fromId) {
     //ocForm.scriptArea.value = ocForm.isScriptCache() ? ocForm.loadScriptCache() : Object.values(scriptValues).join('\n');
     const newHeaderFirst = Object.values(scriptValues).join('\n');
     const baseTextFirst = ocForm.isScriptCache() ? ocForm.loadScriptCache() : (ocForm.scriptArea.value || '');
-    ocForm.scriptArea.value = rebuildWithSbatchHeader(baseTextFirst, newHeaderFirst);
-    rebuildWithSbatchHeader2(baseTextFirst, newHeaderFirst);
+    //ocForm.scriptArea.value = rebuildWithSbatchHeader(baseTextFirst, newHeaderFirst);
+    ocForm.scriptArea.value = rebuildWithSbatchHeader2(baseTextFirst, newHeaderFirst);
 
     // Overwrite of submit textarea (first run)
     ocForm.submitArea.value = ocForm.isSubmitCache() ? ocForm.loadSubmitCache() : Object.values(submitValues).join('\n');
@@ -283,8 +290,8 @@ ocForm.updateValues = function(fromId) {
     // Overwrite of script textarea (subsequent runs)
     //ocForm.scriptArea.value = Object.values(scriptValues).join('\n');
     const newHeaderNext = Object.values(scriptValues).join('\n');
-    ocForm.scriptArea.value = rebuildWithSbatchHeader(ocForm.scriptArea.value || '', newHeaderNext);
-    rebuildWithSbatchHeader2(ocForm.scriptArea.value || '', newHeaderNext);
+    //ocForm.scriptArea.value = rebuildWithSbatchHeader(ocForm.scriptArea.value || '', newHeaderNext);
+    ocForm.scriptArea.value = rebuildWithSbatchHeader2(ocForm.scriptArea.value || '', newHeaderNext);
 
     // Overwrite of submit textarea (subsequent runs)
     ocForm.submitArea.value = Object.values(submitValues).join('\n')

From ea119ea5f177f87b9c3b99d29ce0be7d5a3fbc35 Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Tue, 20 Jan 2026 13:18:32 -0600
Subject: [PATCH 13/22] Replace old rebuildwithSbatchHeader with the new

---
 views/form.erb | 57 ++++----------------------------------------------
 1 file changed, 4 insertions(+), 53 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 26ec0e0..67cdba5 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -174,7 +174,7 @@ function splitText(text){
 }
 
 // Temporary function to test changes
-function rebuildWithSbatchHeader2(currentText, headerText) {
+function rebuildWithSbatchHeader(currentText, headerText) {
   console.group("test function");
   
   const { shebang: currentShebang, header: currentHeader, body: currentBody } = splitText(currentText);
@@ -208,59 +208,10 @@ function rebuildWithSbatchHeader2(currentText, headerText) {
   return finalText;
 }
 
-// Header helper: rewrite ONLY lines that start with "#SBATCH"
-function rebuildWithSbatchHeader(currentText, headerText) {
-  const current = (currentText ?? '').toString();
-  const lines = current.split('\n');
-  const hasShebang = lines.length>0 && lines[0].startsWith('#!');
-
-  const header = (headerText ?? '').toString();
-  const headerLines = header.split('\n');
-  const headerShebang = headerLines.find(l => l.startsWith('#!')) || '';
-  const headerSbatch  = headerLines.filter(l => l.trim().startsWith('#SBATCH'));
-  const cleanHeader = headerSbatch.join('\n');
-
-  // Find indices of all existing #SBATCH lines
-  const sbatchIdxs = [];
-  for (let i=0; i<lines.length; i++) {
-    if (lines[i].trim().startsWith('#SBATCH')) sbatchIdxs.push(i);
-  }
-
-  // Case A: Existing #SBATCH lines found — replace them with the new header
-  if (sbatchIdxs.length > 0) {
-    const firstIdx = Math.min(...sbatchIdxs);
-    // Prefix: everything before the first #SBATCH line (kept as-is)
-    const prefix = lines.slice(0, firstIdx).join('\n').replace(/\n+$/, '');
-    // Body: every line EXCEPT those starting with #SBATCH (kept as-is and in original order
-    const bodyLines = lines.filter(l => !l.trim().startsWith('#SBATCH'));
-    // Remove the prefix portion from bodyLines to avoid duplication
-    const prefixLineCount = prefix ? prefix.split('\n').length : 0;
-    const suffix = bodyLines.slice(prefixLineCount).join('\n').replace(/^\n+/, '');
-
-    const parts = [];
-    parts.push(prefix ? prefix + '\n' + cleanHeader : cleanHeader);
-    if (suffix) parts.push(suffix);
-
-    return parts.join('\n\n').replace(/\n{3,}/g, '\n\n');
-  }
-
-  // Case B: No #SBATCH lines — insert header near shebang or at the top
-  if (hasShebang) {
-    const shebang = lines[0];
-    const rest = lines.slice(1).join('\n').trim();
-    return [shebang + '\n' + cleanHeader, rest].filter(s => s && s !== '').join('\n\n').replace(/\n{3,}/g, '\n\n');
-  }
-
-  // No shebang: put header at top and keep all user text below
-  const shebangToUse = headerShebang || '';
-  const body = current.trim();
-  if (shebangToUse) return [shebangToUse + '\n' + cleanHeader, body].filter(s => s && s !== '').join('\n\n');
-  return [cleanHeader, body].filter(s => s && s !== '').join('\n\n');
-}
-
 ocForm.isFirst = true;
 ocForm.multiSelectDisabledIndexes = {};
 ocForm.updateValues = function(fromId) {
+  console.group("updateValues");
   let scriptValues = [];
   let submitValues = [];
   ocForm.initDynamicWidget(fromId);
@@ -276,8 +227,7 @@ ocForm.updateValues = function(fromId) {
     //ocForm.scriptArea.value = ocForm.isScriptCache() ? ocForm.loadScriptCache() : Object.values(scriptValues).join('\n');
     const newHeaderFirst = Object.values(scriptValues).join('\n');
     const baseTextFirst = ocForm.isScriptCache() ? ocForm.loadScriptCache() : (ocForm.scriptArea.value || '');
-    //ocForm.scriptArea.value = rebuildWithSbatchHeader(baseTextFirst, newHeaderFirst);
-    ocForm.scriptArea.value = rebuildWithSbatchHeader2(baseTextFirst, newHeaderFirst);
+    ocForm.scriptArea.value = rebuildWithSbatchHeader(baseTextFirst, newHeaderFirst);
 
     // Overwrite of submit textarea (first run)
     ocForm.submitArea.value = ocForm.isSubmitCache() ? ocForm.loadSubmitCache() : Object.values(submitValues).join('\n');
@@ -308,6 +258,7 @@ ocForm.updateValues = function(fromId) {
   // Height adjustments
   ocForm.updateHeight(ocForm.scriptArea);
   ocForm.updateHeight(ocForm.submitArea);
+  console.groupEnd();
 };
 
 window.onload = ocForm.updateValues();

From b4ae07332b47698c305a4c09e36e89751773e862 Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Tue, 20 Jan 2026 13:22:13 -0600
Subject: [PATCH 14/22] remove console lines and comments

---
 views/form.erb | 21 ++-------------------
 1 file changed, 2 insertions(+), 19 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 67cdba5..8905f71 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -173,10 +173,8 @@ function splitText(text){
     return { shebang, header, body }
 }
 
-// Temporary function to test changes
+// Rebuild script area content by replacing only the content of the header
 function rebuildWithSbatchHeader(currentText, headerText) {
-  console.group("test function");
-  
   const { shebang: currentShebang, header: currentHeader, body: currentBody } = splitText(currentText);
   const { shebang: renderedShebang, header: renderedHeader, body: renderedBody } = splitText(headerText);
 
@@ -200,12 +198,8 @@ function rebuildWithSbatchHeader(currentText, headerText) {
     ...(hasTopSection && finalBody.length>0 ? [""] : []),
     ...finalBody
   ];
-  const finalText = combined.join("\n");
 
-  console.log("finalText", finalText)
-  console.groupEnd();
-
-  return finalText;
+  return combined.join("\n");
 }
 
 ocForm.isFirst = true;
@@ -224,7 +218,6 @@ ocForm.updateValues = function(fromId) {
     ocForm.updateSubmitContents(submitValues);
 
     // Overwrite of script textarea (first run)
-    //ocForm.scriptArea.value = ocForm.isScriptCache() ? ocForm.loadScriptCache() : Object.values(scriptValues).join('\n');
     const newHeaderFirst = Object.values(scriptValues).join('\n');
     const baseTextFirst = ocForm.isScriptCache() ? ocForm.loadScriptCache() : (ocForm.scriptArea.value || '');
     ocForm.scriptArea.value = rebuildWithSbatchHeader(baseTextFirst, newHeaderFirst);
@@ -238,23 +231,13 @@ ocForm.updateValues = function(fromId) {
     ocForm.updateSubmitContents(submitValues);
 
     // Overwrite of script textarea (subsequent runs)
-    //ocForm.scriptArea.value = Object.values(scriptValues).join('\n');
     const newHeaderNext = Object.values(scriptValues).join('\n');
-    //ocForm.scriptArea.value = rebuildWithSbatchHeader(ocForm.scriptArea.value || '', newHeaderNext);
     ocForm.scriptArea.value = rebuildWithSbatchHeader2(ocForm.scriptArea.value || '', newHeaderNext);
 
     // Overwrite of submit textarea (subsequent runs)
     ocForm.submitArea.value = Object.values(submitValues).join('\n')
   }
 
-  // Add a newline if it is not the last one
-  //if (!ocForm.scriptArea.value.endsWith('\n')){
-  //  ocForm.scriptArea.value += '\n';
-  //}
-  //if (!ocForm.submitArea.value.endsWith('\n')){
-  //  ocForm.submitArea.value += '\n';
-  //}
-
   // Height adjustments
   ocForm.updateHeight(ocForm.scriptArea);
   ocForm.updateHeight(ocForm.submitArea);

From 5e9e8a622594769a8ce792eeb5acb8916062dccf Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Mon, 26 Jan 2026 13:16:58 -0600
Subject: [PATCH 15/22] Messages to print in console for debugging

---
 views/form.erb | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/views/form.erb b/views/form.erb
index 8905f71..8373791 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -178,6 +178,15 @@ function rebuildWithSbatchHeader(currentText, headerText) {
   const { shebang: currentShebang, header: currentHeader, body: currentBody } = splitText(currentText);
   const { shebang: renderedShebang, header: renderedHeader, body: renderedBody } = splitText(headerText);
 
+  console.group("rebuildWithSbatchHeader");
+  console.log("currentShebang", currentShebang);
+  console.log("currentHeader", currentHeader);
+  console.log("currentBody", currentBody);
+  console.log("renderedShebang", renderedShebang);
+  console.log("renderedHeader", renderedHeader);
+  console.log("renderedBody", renderedBody);
+  console.groupEnd();
+
   const finalShebang = renderedShebang ? renderedShebang : currentShebang || '';
   const finalHeader = renderedHeader?.length>0 ? renderedHeader : currentHeader?.length>0 ? currentHeader : [];
 

From 24e35cee2023736c3a049d4ce59feabc9909288f Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Mon, 26 Jan 2026 14:04:45 -0600
Subject: [PATCH 16/22] Give priority to currentBody in rebuildWithSbatchHeader

---
 views/form.erb | 22 ++++++++--------------
 1 file changed, 8 insertions(+), 14 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 8373791..7b19b2f 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -178,15 +178,6 @@ function rebuildWithSbatchHeader(currentText, headerText) {
   const { shebang: currentShebang, header: currentHeader, body: currentBody } = splitText(currentText);
   const { shebang: renderedShebang, header: renderedHeader, body: renderedBody } = splitText(headerText);
 
-  console.group("rebuildWithSbatchHeader");
-  console.log("currentShebang", currentShebang);
-  console.log("currentHeader", currentHeader);
-  console.log("currentBody", currentBody);
-  console.log("renderedShebang", renderedShebang);
-  console.log("renderedHeader", renderedHeader);
-  console.log("renderedBody", renderedBody);
-  console.groupEnd();
-
   const finalShebang = renderedShebang ? renderedShebang : currentShebang || '';
   const finalHeader = renderedHeader?.length>0 ? renderedHeader : currentHeader?.length>0 ? currentHeader : [];
 
@@ -194,11 +185,14 @@ function rebuildWithSbatchHeader(currentText, headerText) {
   const filteredCurrentBody  = currentBody.filter(item => item.trim() !== "");
   let finalBody;
   if (filteredRenderedBody.length === 0 && filteredCurrentBody.length === 0) { finalBody = []; }
-  else if (filteredRenderedBody.length === 0) { finalBody = currentBody; }
-  else if (filteredCurrentBody.length === 0) { finalBody = renderedBody; }
-  else { finalBody = [...renderedBody, "", ...currentBody]; }
-  if (finalBody[0] === "") { finalBody.shift(); }
-  if (finalBody.at(-1) === "") { finalBody.pop(); }
+  else if (filteredCurrentBody.length>0) { finalBody = currentBody; } // Give priority to currentBody if not empty
+  else { finalBody = renderedBody; }
+  if (finalBody[0] === "") { finalBody.shift(); } // Remove first line if empty (it will be introduced if hasTopSection)
+  if (finalBody.at(-1) === "") { finalBody.pop(); } // Remove empty line at the end
+
+  console.group("rebuildWithSbatchHeader");
+  console.log("finalBody", finalBody);
+  console.groupEnd();
 
   const hasTopSection = (finalShebang?.trim()!=='') || (finalHeader.length>0);
   const combined = [

From e58327bc38888e880cc809ad3261be6428264c01 Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Mon, 26 Jan 2026 14:08:24 -0600
Subject: [PATCH 17/22] Fix error, function called the wrong way

---
 views/form.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/views/form.erb b/views/form.erb
index 7b19b2f..137d373 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -235,7 +235,7 @@ ocForm.updateValues = function(fromId) {
 
     // Overwrite of script textarea (subsequent runs)
     const newHeaderNext = Object.values(scriptValues).join('\n');
-    ocForm.scriptArea.value = rebuildWithSbatchHeader2(ocForm.scriptArea.value || '', newHeaderNext);
+    ocForm.scriptArea.value = rebuildWithSbatchHeader(ocForm.scriptArea.value || '', newHeaderNext);
 
     // Overwrite of submit textarea (subsequent runs)
     ocForm.submitArea.value = Object.values(submitValues).join('\n')

From f01c8cc9efaff89c9a583c17e4999fde613c6c7e Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Mon, 26 Jan 2026 14:19:18 -0600
Subject: [PATCH 18/22] remove mpirun test line from our rcc app

---
 rcc_apps/Slurm/form.yml.erb | 208 ++++++++++++++++++++++++++++++++++++
 views/form.erb              |   4 -
 2 files changed, 208 insertions(+), 4 deletions(-)
 create mode 100644 rcc_apps/Slurm/form.yml.erb

diff --git a/rcc_apps/Slurm/form.yml.erb b/rcc_apps/Slurm/form.yml.erb
new file mode 100644
index 0000000..89c9d38
--- /dev/null
+++ b/rcc_apps/Slurm/form.yml.erb
@@ -0,0 +1,208 @@
+<%
+require 'open3'
+
+class SlurmAccounts
+  def self.accounts
+    return @accounts if defined?(@accounts) && @accounts.is_a?(Array)
+
+    user = ENV['USER'] || ''
+    cmd = "/opt/slurm/bin/sacctmgr -nP show assoc user=#{user} format=account"
+
+    out, err, st = Open3.capture3(cmd)
+
+    if st.success? && out && !out.strip.empty?
+      accounts = out.to_s.split(/\s+/).reject(&:empty?).uniq
+    else
+      accounts = [""]
+    end
+
+    @accounts = Array(accounts)
+  end
+end
+
+accounts = SlurmAccounts.accounts
+accounts_size = accounts.size
+first_account = accounts[0]
+%>
+---
+form:
+  account:
+    label: "SLURM Account"
+    required: true
+<% if accounts_size == 1 && first_account == "" %>
+    widget: text
+<% else %>
+    widget: select
+    options:
+<% (0...accounts_size).each do |i| %>
+    - ["<%= accounts[i] %>", "<%= accounts[i] %>"]
+<% end %>
+<% end %>
+
+  partition:
+    widget: select
+    label: Partition
+    required: true
+    options:
+      - [ Normal, normal, 
+          hide-show_gpus_option, 
+          disable-cores2,
+          disable-gpus,
+          disable-gpus2,
+          disable-gpus_type ]
+      - [ High memory, bigmem, 
+          hide-show_mpi_option,
+          hide-nodes_tasks,
+          hide-show_gpus_option, 
+          disable-cores2,
+          disable-gpus,
+          disable-gpus2,
+          disable-gpus_type ]
+      - [ GPU, gpu,
+          hide-show_mpi_option,
+          hide-nodes_tasks,
+          hide-show_cores_option, 
+          disable-cores ]
+
+  show_cores_option:
+    widget: checkbox
+    options:
+      - [ "My job runs in parallel (multi-threaded)", "", show-cores ]
+
+  cores:
+    widget: number
+    label: "Number of threads (1 - 48)"
+    indent: 1
+    min: 1
+    max: 48
+    step: 1
+
+  show_gpus_option:
+    widget: checkbox
+    options:
+      - [ "My job runs in parallel (multi-threaded)", "", show-gpus_type, show-gpus, show-cores2 ]
+
+  gpus_type:
+    widget: select
+    label: "GPU type"
+    value: "First available"
+    options:
+      - [ "First available", "", disable-gpus2 ]
+      - [ "v100", "v100", show-gpus2, disable-gpus ]
+      - [ "a40", "a40", show-gpus2, disable-gpus ]
+      - [ "l40s", "l40s", show-gpus2, disable-gpus, set-label-gpus2: "Number of gpus (1 - 8)", set-max-gpus2: 8, seet-max-gpus: 4, set-label-cores2: "Threads per gpu (1 - 128)", set-max-cores2: 128 ]
+    help: Most jobs will NOT benefit from specifying a GPU type. Instead, it may potentially delay scheduling your job. Select 'First available' unless your program requires a specific type of GPU.
+
+  gpus:
+    widget: number
+    label: "Number of gpus (1 - 4)"
+    indent: 1
+    value: 1
+    min: 1
+    max: 4
+    step: 1
+
+  gpus2:
+    widget: number
+    label: "Number of gpus (1 - 4)"
+    indent: 1
+    value: 1
+    min: 1
+    max: 4
+    step: 1
+
+  cores2:
+    widget: number
+    label: "Threads per gpu (1 - 48)"
+    indent: 1
+    value: 1
+    min: 1
+    max: 48
+    step: 1
+
+  show_mpi_option:
+    widget: checkbox
+    options:
+      - [ "My job uses MPI", "", show-nodes_tasks ]
+
+  nodes_tasks:
+    widget: number
+    label: [ "Number of nodes (1 - 30)", "Number of tasks (1 - 48)" ]
+    size: 2
+    indent: 1
+    value: [ 1, 1 ]
+    min: [ 1, 1 ]
+    max: [ 30, 48 ]
+    step: [ 1, 1 ]
+
+  time:
+    widget: number
+    label: "Walltime hours (1 - 168)"
+    required: true
+    value: 2
+    min: 1
+    max: 168
+    step: 1
+
+  show_array_option:
+    widget: checkbox
+    options:
+      - [ "Show array options", "", show-array ]
+
+  array:
+    widget: number
+    label: [ "Array Job", [start index, last index] ]
+    size: 2
+    indent: 1
+    min: [0, 0]
+    help: Each job executed from an array job is assigned a task ID, which can be referenced in the shell script via the environment variable SLURM_ARRAY_TASK_ID.
+
+  show_mail_option:
+    widget: checkbox
+    options:
+      - [ "Show email options", "", show-mail_option, show-email ]
+    
+  mail_option:
+    widget: checkbox
+    label: "Mail option"
+    direction: horizontal
+    separator: ","
+    indent: 1
+    options:
+      - [ "Beginning of job execution", 'BEGIN',   enable-email ]
+      - [ "End of job execution",       'END',     enable-email ]
+      - [ "Fail of job",                'FAIL',    enable-email ]
+      - [ "All",                        'ALL',     enable-email ]
+      
+  email:
+    widget: email
+    label: Email
+    value: <%= ENV['USER'] %>@mcw.edu
+    indent: 2
+
+script: |
+  #!/bin/bash
+  #SBATCH --account=#{account}
+  #SBATCH --partition=#{partition}
+  #SBATCH --nodes=#{nodes_tasks_1}
+  #SBATCH --ntasks=#{nodes_tasks_2}
+  #SBATCH --cpus-per-task=#{cores}
+  #SBATCH --cpus-per-task=#{calc(gpus * cores2)}
+  #SBATCH --cpus-per-task=#{calc(gpus2 * cores2)}
+  #SBATCH --gres=gpu:#{gpus}
+  #SBATCH --gres=gpu:#{gpus_type}:#{gpus2}
+  #SBATCH --time=#{zeropadding(time,2)}:00:00
+  #SBATCH --mail-user=#{email}
+  #SBATCH --mail-type=#{mail_option}
+  #SBATCH --array=#{array_1}-#{array_2}
+
+check: |
+  index1_int = @array_1.to_i
+  index2_int = @array_2.to_i
+  msg_if_false = "Last index of array must be greater than start index."
+  oc_assert((index1_int==0 && index2_int==0) || index1_int<index2_int, msg_if_false)
+
+submit: |
+  #!/bin/bash
+
+  #{OC_SUBMIT_OPTIONS}=" -J "#{OC_JOB_NAME}
diff --git a/views/form.erb b/views/form.erb
index 137d373..e6706f9 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -190,10 +190,6 @@ function rebuildWithSbatchHeader(currentText, headerText) {
   if (finalBody[0] === "") { finalBody.shift(); } // Remove first line if empty (it will be introduced if hasTopSection)
   if (finalBody.at(-1) === "") { finalBody.pop(); } // Remove empty line at the end
 
-  console.group("rebuildWithSbatchHeader");
-  console.log("finalBody", finalBody);
-  console.groupEnd();
-
   const hasTopSection = (finalShebang?.trim()!=='') || (finalHeader.length>0);
   const combined = [
     ...(finalShebang ? [finalShebang] : []),

From 890a32464a0cbfc4c2814bac84cd16b2348cfa3b Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Mon, 26 Jan 2026 14:41:39 -0600
Subject: [PATCH 19/22] If body has an empty line, return empty body

---
 views/form.erb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/views/form.erb b/views/form.erb
index e6706f9..c68f4c7 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -91,6 +91,7 @@
     </div>
   </div>
 </form>
+
 <script>
 var ocForm = ocForm || {};
 ocForm.scriptArea = document.getElementById('<%= OC_SCRIPT_CONTENT %>');
@@ -170,6 +171,8 @@ function splitText(text){
       else if (body.at(-1)!="" || trimmed!="") { body.push(trimmed); }
     }
 
+    if (body.length === 1 && body[0] === "") return { shebang, header, body: [] };
+
     return { shebang, header, body }
 }
 

From e3f1e613756aa855789bfdd40ded9d3e8361870f Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Mon, 26 Jan 2026 15:08:19 -0600
Subject: [PATCH 20/22] allow other directives depending on the scheduler
 selected in conf.yml

---
 views/form.erb | 39 +++++++++++++++++++++++++++++++++++++--
 1 file changed, 37 insertions(+), 2 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index c68f4c7..8f9a1e8 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -97,7 +97,29 @@ var ocForm = ocForm || {};
 ocForm.scriptArea = document.getElementById('<%= OC_SCRIPT_CONTENT %>');
 ocForm.submitArea = document.getElementById('<%= SUBMIT_CONTENT %>');
 </script>
+
 <script src="form.js"></script>
+
+<%
+require "yaml"
+require "erb"
+require "pathname"
+
+app_root  = Pathname.new(__dir__).join("..").expand_path
+conf_path = app_root.join("conf.yml.erb")
+
+conf_hash =
+  if conf_path.exist?
+    rendered = ERB.new(conf_path.read).result(binding)
+    YAML.safe_load(rendered) || {}
+  else
+    {}
+  end
+
+# If scheduler is missing, this becomes "slurm"
+scheduler = conf_hash.fetch("scheduler", "slurm")
+%>
+
 <script>
 // Executes functions that should run once.
 ocForm.onceExec = function() {
@@ -156,7 +178,7 @@ document.addEventListener('keydown', function(event) {
   }
 });
 
-// Split text into shebang, header (SBATCH lines) and body
+// Split text into shebang, header (scheduler directive lines lines) and body
 function splitText(text){
     text = (text ?? '').toString();
     const lines = text.split('\n');
@@ -164,10 +186,23 @@ function splitText(text){
     const header = [];
     const body = [];
 
+    // Choose a directive for the header depending on the scheduler selected in conf.yml.erb
+    const scheduler = "<%= scheduler.to_s %>".trim().toLowerCase();
+    let directive;
+    if (scheduler === "slurm") { directive = "#SBATCH"; }
+    else if (scheduler === "pbs" || scheduler === "pbspro" || scheduler === "torque") { directive = "#PBS"; }
+    else if (scheduler === "grid_engine" || scheduler === "sge") { directive = "#$"; }
+    else if (scheduler === "lsf") { directive = "#BSUB"; }
+    else { directive = "#SBATCH"; }
+
+    console.group("splitText")
+    console.log("directive", directive)
+    console.groupEnd()
+
     for (const line of lines) {
       const trimmed = line.trim();
       if (!shebang && trimmed.startsWith("#!")) { shebang = trimmed; }
-      else if (trimmed.startsWith("#SBATCH")) { header.push(trimmed); }
+      else if (trimmed.startsWith(directive)) { header.push(trimmed); }
       else if (body.at(-1)!="" || trimmed!="") { body.push(trimmed); }
     }
 

From 6112236d405c7f77758734073c7ae0f891f1b588 Mon Sep 17 00:00:00 2001
From: monicagiraldochica
 <165931199+monicagiraldochica@users.noreply.github.com>
Date: Mon, 26 Jan 2026 15:09:53 -0600
Subject: [PATCH 21/22] Remove console printing

---
 views/form.erb | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/views/form.erb b/views/form.erb
index 8f9a1e8..5b2751f 100644
--- a/views/form.erb
+++ b/views/form.erb
@@ -195,10 +195,6 @@ function splitText(text){
     else if (scheduler === "lsf") { directive = "#BSUB"; }
     else { directive = "#SBATCH"; }
 
-    console.group("splitText")
-    console.log("directive", directive)
-    console.groupEnd()
-
     for (const line of lines) {
       const trimmed = line.trim();
       if (!shebang && trimmed.startsWith("#!")) { shebang = trimmed; }

From c441293b4d20271f64d8426ae3d4a5afa19ca1db Mon Sep 17 00:00:00 2001
From: Monica Keith <monicagiraldochica@gmail.com>
Date: Tue, 27 Jan 2026 13:45:43 -0600
Subject: [PATCH 22/22] remove MCW RCC files

---
 .vscode/settings.json       |  12 ---
 rcc_apps/Slurm/form.yml.erb | 208 ------------------------------------
 2 files changed, 220 deletions(-)
 delete mode 100644 .vscode/settings.json
 delete mode 100644 rcc_apps/Slurm/form.yml.erb

diff --git a/.vscode/settings.json b/.vscode/settings.json
deleted file mode 100644
index 161f38d..0000000
--- a/.vscode/settings.json
+++ /dev/null
@@ -1,12 +0,0 @@
-{
-    "cSpell.words": [
-        "accesskey",
-        "Idxs",
-        "oninput",
-        "onsubmit",
-        "sbatch",
-        "Sbatch",
-        "SBATCH",
-        "tabindex"
-    ]
-}
\ No newline at end of file
diff --git a/rcc_apps/Slurm/form.yml.erb b/rcc_apps/Slurm/form.yml.erb
deleted file mode 100644
index 89c9d38..0000000
--- a/rcc_apps/Slurm/form.yml.erb
+++ /dev/null
@@ -1,208 +0,0 @@
-<%
-require 'open3'
-
-class SlurmAccounts
-  def self.accounts
-    return @accounts if defined?(@accounts) && @accounts.is_a?(Array)
-
-    user = ENV['USER'] || ''
-    cmd = "/opt/slurm/bin/sacctmgr -nP show assoc user=#{user} format=account"
-
-    out, err, st = Open3.capture3(cmd)
-
-    if st.success? && out && !out.strip.empty?
-      accounts = out.to_s.split(/\s+/).reject(&:empty?).uniq
-    else
-      accounts = [""]
-    end
-
-    @accounts = Array(accounts)
-  end
-end
-
-accounts = SlurmAccounts.accounts
-accounts_size = accounts.size
-first_account = accounts[0]
-%>
----
-form:
-  account:
-    label: "SLURM Account"
-    required: true
-<% if accounts_size == 1 && first_account == "" %>
-    widget: text
-<% else %>
-    widget: select
-    options:
-<% (0...accounts_size).each do |i| %>
-    - ["<%= accounts[i] %>", "<%= accounts[i] %>"]
-<% end %>
-<% end %>
-
-  partition:
-    widget: select
-    label: Partition
-    required: true
-    options:
-      - [ Normal, normal, 
-          hide-show_gpus_option, 
-          disable-cores2,
-          disable-gpus,
-          disable-gpus2,
-          disable-gpus_type ]
-      - [ High memory, bigmem, 
-          hide-show_mpi_option,
-          hide-nodes_tasks,
-          hide-show_gpus_option, 
-          disable-cores2,
-          disable-gpus,
-          disable-gpus2,
-          disable-gpus_type ]
-      - [ GPU, gpu,
-          hide-show_mpi_option,
-          hide-nodes_tasks,
-          hide-show_cores_option, 
-          disable-cores ]
-
-  show_cores_option:
-    widget: checkbox
-    options:
-      - [ "My job runs in parallel (multi-threaded)", "", show-cores ]
-
-  cores:
-    widget: number
-    label: "Number of threads (1 - 48)"
-    indent: 1
-    min: 1
-    max: 48
-    step: 1
-
-  show_gpus_option:
-    widget: checkbox
-    options:
-      - [ "My job runs in parallel (multi-threaded)", "", show-gpus_type, show-gpus, show-cores2 ]
-
-  gpus_type:
-    widget: select
-    label: "GPU type"
-    value: "First available"
-    options:
-      - [ "First available", "", disable-gpus2 ]
-      - [ "v100", "v100", show-gpus2, disable-gpus ]
-      - [ "a40", "a40", show-gpus2, disable-gpus ]
-      - [ "l40s", "l40s", show-gpus2, disable-gpus, set-label-gpus2: "Number of gpus (1 - 8)", set-max-gpus2: 8, seet-max-gpus: 4, set-label-cores2: "Threads per gpu (1 - 128)", set-max-cores2: 128 ]
-    help: Most jobs will NOT benefit from specifying a GPU type. Instead, it may potentially delay scheduling your job. Select 'First available' unless your program requires a specific type of GPU.
-
-  gpus:
-    widget: number
-    label: "Number of gpus (1 - 4)"
-    indent: 1
-    value: 1
-    min: 1
-    max: 4
-    step: 1
-
-  gpus2:
-    widget: number
-    label: "Number of gpus (1 - 4)"
-    indent: 1
-    value: 1
-    min: 1
-    max: 4
-    step: 1
-
-  cores2:
-    widget: number
-    label: "Threads per gpu (1 - 48)"
-    indent: 1
-    value: 1
-    min: 1
-    max: 48
-    step: 1
-
-  show_mpi_option:
-    widget: checkbox
-    options:
-      - [ "My job uses MPI", "", show-nodes_tasks ]
-
-  nodes_tasks:
-    widget: number
-    label: [ "Number of nodes (1 - 30)", "Number of tasks (1 - 48)" ]
-    size: 2
-    indent: 1
-    value: [ 1, 1 ]
-    min: [ 1, 1 ]
-    max: [ 30, 48 ]
-    step: [ 1, 1 ]
-
-  time:
-    widget: number
-    label: "Walltime hours (1 - 168)"
-    required: true
-    value: 2
-    min: 1
-    max: 168
-    step: 1
-
-  show_array_option:
-    widget: checkbox
-    options:
-      - [ "Show array options", "", show-array ]
-
-  array:
-    widget: number
-    label: [ "Array Job", [start index, last index] ]
-    size: 2
-    indent: 1
-    min: [0, 0]
-    help: Each job executed from an array job is assigned a task ID, which can be referenced in the shell script via the environment variable SLURM_ARRAY_TASK_ID.
-
-  show_mail_option:
-    widget: checkbox
-    options:
-      - [ "Show email options", "", show-mail_option, show-email ]
-    
-  mail_option:
-    widget: checkbox
-    label: "Mail option"
-    direction: horizontal
-    separator: ","
-    indent: 1
-    options:
-      - [ "Beginning of job execution", 'BEGIN',   enable-email ]
-      - [ "End of job execution",       'END',     enable-email ]
-      - [ "Fail of job",                'FAIL',    enable-email ]
-      - [ "All",                        'ALL',     enable-email ]
-      
-  email:
-    widget: email
-    label: Email
-    value: <%= ENV['USER'] %>@mcw.edu
-    indent: 2
-
-script: |
-  #!/bin/bash
-  #SBATCH --account=#{account}
-  #SBATCH --partition=#{partition}
-  #SBATCH --nodes=#{nodes_tasks_1}
-  #SBATCH --ntasks=#{nodes_tasks_2}
-  #SBATCH --cpus-per-task=#{cores}
-  #SBATCH --cpus-per-task=#{calc(gpus * cores2)}
-  #SBATCH --cpus-per-task=#{calc(gpus2 * cores2)}
-  #SBATCH --gres=gpu:#{gpus}
-  #SBATCH --gres=gpu:#{gpus_type}:#{gpus2}
-  #SBATCH --time=#{zeropadding(time,2)}:00:00
-  #SBATCH --mail-user=#{email}
-  #SBATCH --mail-type=#{mail_option}
-  #SBATCH --array=#{array_1}-#{array_2}
-
-check: |
-  index1_int = @array_1.to_i
-  index2_int = @array_2.to_i
-  msg_if_false = "Last index of array must be greater than start index."
-  oc_assert((index1_int==0 && index2_int==0) || index1_int<index2_int, msg_if_false)
-
-submit: |
-  #!/bin/bash
-
-  #{OC_SUBMIT_OPTIONS}=" -J "#{OC_JOB_NAME}