Modernize scan workflow and web deployment

README.md

@@ -228,24 +228,52 @@ which matches how the packaged app currently handles simulation input/output.
 
 ###### Deploying on a web server ######
 
-The browser version requires a server-side setup in addition to the static
-HTML/JavaScript files.
+The repository includes the browser assets, CGI runner, and a deployment
+script for an Apache-style server. With the default settings, run:
 
-In particular:
+```bash
+sudo ./scripts/deploy-web.sh
+```
 
-* the browser build uses `TrimSPweb.js` rather than the Electron-specific
-  `TrimSPelec.js`
-* the simulation backend must be available on the server
-* a web-exposed helper/CGI layer is required to create input files, run the
-  backend, and return the generated output
+The script builds the static Fortran engine and installs:
 
-Notes:
+```text
+/var/www/html/TRIMSP-NL/             browser application
+/var/www/cgi-bin/singleTrimSP.cgi   CGI runner
+/usr/local/bin/trimspNL             TRIM.SP-NL engine
+```
 
-* this repository does not currently include the CGI/backend helper used by
-  the online deployment
-* a plain static web server is therefore not sufficient for running web
-  simulations from this checkout
-* static hosting can still be used to test page loading only
+Deployment paths and ownership can be changed through environment variables:
+
+| Variable | Default | Purpose |
+| --- | --- | --- |
+| `TRIMSP_WEB_TARGET` | `/var/www/html/TRIMSP-NL` | Browser asset directory |
+| `TRIMSP_CGI_TARGET` | `/var/www/cgi-bin/singleTrimSP.cgi` | Installed CGI path |
+| `TRIMSP_BIN_TARGET` | `/usr/local/bin/trimspNL` | Installed engine path |
+| `TRIMSP_WEB_OWNER` | `apache` | Web file owner |
+| `TRIMSP_WEB_GROUP` | `apache` | Web file group |
+| `TRIMSP_BUILD_STATIC` | `1` | Build the static engine before deployment |
+| `TRIMSP_BINARY_SOURCE` | `fortran/trimspNL-static` | Binary used when installing |
+
+For example, to deploy without rebuilding and use an existing binary:
+
+```bash
+sudo TRIMSP_BUILD_STATIC=0 \
+  TRIMSP_BINARY_SOURCE=/path/to/trimspNL \
+  ./scripts/deploy-web.sh
+```
+
+The web server must execute the CGI through `/cgi-bin/singleTrimSP.cgi` and
+serve simulation files written below filesystem `/tmp` through URL `/tmp/`.
+Review that mapping carefully so it exposes only the intended simulation
+artifacts. On SELinux systems, inspect denied operations with:
+
+```bash
+ausearch -m avc -ts recent
+```
+
+The Apache account needs permission to execute the CGI and engine and to create
+the per-run directories in `/tmp`.
 
 ### Contact ###
 

TrimSP.html

@@ -111,16 +111,27 @@
 	  </div>
 	</div>
 	<div id="Scans" class="tabcontent">
-	  <input type="checkbox" name="scanSeq" id="scanSeq" onChange="adjust_scans();">   Enable scan on
-	  <select name="scanType" id="scanType" onchange="adjust_scans();">
-	    <option value="scanLoop">Loop</option>
-	    <option value="scanVals">Set of values</option>
-	  </select>
-	  <div id="ScansControls" style="visibility: hidden;">
-	    <table style="width: 100%;">
-	      <tr>
-		<td colspan="1">Scan:
-		  <select name="comboScan" id="comboScan" onchange="">
+	  <section class="settings-panel scan-panel" aria-labelledby="scanPanelTitle">
+	    <div class="scan-heading">
+	      <div>
+		<span class="section-eyebrow">Execution plan</span>
+		<h2 id="scanPanelTitle">Parameter scan</h2>
+	      </div>
+	      <label class="scan-enable" for="scanSeq">
+		<input type="checkbox" name="scanSeq" id="scanSeq" onchange="adjust_scans();">
+		<span>Enable scan</span>
+	      </label>
+	    </div>
+	    <div id="ScansControls" hidden>
+	      <div class="scan-controls-grid">
+		<label class="settings-field" for="scanType"><span>Sequence</span>
+		  <select name="scanType" id="scanType" onchange="adjust_scans();">
+		    <option value="scanLoop">Range</option>
+		    <option value="scanVals">Set of values</option>
+		  </select>
+		</label>
+		<label class="settings-field" for="comboScan"><span>Parameter</span>
+		  <select name="comboScan" id="comboScan" onchange="updateScanSummary();">
 		    <option value="EScan">Energy [eV]</option>
 		    <option value="SigEScan">Energy sigma [eV]</option>
 		    <option value="AngleScan">Angle [deg]</option>
@@ -128,33 +139,23 @@
 		    <option value="NProjScan">Number of projectiles</option>
 		    <option value="dScan">Thickness of layer # 1</option>
 		  </select>
-		</td>
-		<td colspan="1">
-		  Threads:
-		  <input name="scanThreads" id="scanThreads" type="number" min="1" step="1" value="" onchange="adjust_scans();">
-		</td>
-	      </tr>
-	    </table>
-	  </div>
-	  <div id="ScansLine" style="visibility: hidden;">
-	    <br>Set of values: <input name="scanList" id="scanList" type="text" value="1000">
-	    Corresponding depth increment: <input name="scanListdz" id="scanListdz" type="text" value="">
-	  </div>
-	  <table id="ScansTable" style="width: 100%;visibility: hidden;">
-	    <tr>
-	      <td>
-		<!input type="radio" name="ScanType" value="Loop" checked onChange="">
-		<!input type="radio" name="ScanType" value="ScanList" onChange="">
-		From: <input name="scanFrom" id="scanFrom" type="text" value="1000">
-	      </td>
-	      <td>
-		Step: <input name="scanStep" id="scanStep" type="text" value="2000">
-	      </td>
-	      <td>
-		To: <input name="scanTo" id="scanTo" type="text" value="14000">
-	      </td>
-	    </tr>
-	  </table>
+		</label>
+		<label class="settings-field" for="scanThreads"><span>Workers</span>
+		  <input name="scanThreads" id="scanThreads" type="number" min="1" step="1" value="" oninput="adjust_scans();">
+		</label>
+	      </div>
+	      <div id="ScansTable" class="scan-values-panel scan-range-grid">
+		<label class="settings-field" for="scanFrom"><span>From</span><input name="scanFrom" id="scanFrom" type="text" value="1000" oninput="updateScanSummary();"></label>
+		<label class="settings-field" for="scanStep"><span>Step</span><input name="scanStep" id="scanStep" type="text" value="2000" oninput="updateScanSummary();"></label>
+		<label class="settings-field" for="scanTo"><span>To</span><input name="scanTo" id="scanTo" type="text" value="14000" oninput="updateScanSummary();"></label>
+	      </div>
+	      <div id="ScansLine" class="scan-values-panel scan-list-grid" hidden>
+		<label class="settings-field" for="scanList"><span>Values, separated by commas</span><input name="scanList" id="scanList" type="text" value="1000" oninput="updateScanSummary();"></label>
+		<label class="settings-field" for="scanListdz"><span>Matching depth increments (optional)</span><input name="scanListdz" id="scanListdz" type="text" value="" oninput="updateScanSummary();"></label>
+	      </div>
+	    </div>
+	    <div id="scanSummary" class="scan-summary" role="status" aria-live="polite">Single simulation using the Layers settings.</div>
+	  </section>
 	</div>
 	<div id="Plots" class="tabcontent">
 	  <table style="width: 100%;">

TrimSPlib.js

@@ -3351,11 +3351,12 @@ function adjust_table()
 
 function adjust_scans()
 {
-    // Deal with scans checkbox and type
     var scanSeq = document.getElementById("scanSeq").checked;
-    var sender = document.getElementById("scanSeq");
     var scanType = document.getElementById("scanType").value;
     var scanThreads = document.getElementById("scanThreads");
+    var scanControls = document.getElementById("ScansControls");
+    var scanRange = document.getElementById("ScansTable");
+    var scanList = document.getElementById("ScansLine");
 
     // Default to half the available local worker slots, rounded down, while
     // keeping at least one process. Web mode keeps the default at 1 because
@@ -3366,6 +3367,10 @@ function adjust_scans()
 	    availableThreads = Math.max(1, getParallelJobCount());
 	}
 	scanThreads.max = availableThreads;
+	scanThreads.disabled = amIWeb();
+	scanThreads.title = amIWeb()
+	    ? 'The web backend currently runs scan points sequentially.'
+	    : `This computer provides up to ${availableThreads} worker slots.`;
 
 	if (scanThreads.value === "" || Number(scanThreads.value) < 1) {
 	    scanThreads.value = Math.max(1, Math.floor(availableThreads / 2));
@@ -3374,23 +3379,85 @@ function adjust_scans()
 	}
     }
 
-    // consider only if scans checkbox is checked
-    if (scanSeq) {
-	ShowHide(1,'ScansControls');
-	// Which type of scan
-	if (scanType == "scanLoop") {
-	    ShowHide(1,'ScansTable');
-	    ShowHide(0,'ScansLine');
+    scanControls.hidden = !scanSeq;
+    if (!scanSeq) {
+	scanRange.hidden = true;
+	scanList.hidden = true;
+    } else if (scanType === "scanLoop") {
+	scanRange.hidden = false;
+	scanList.hidden = true;
+    } else {
+	scanRange.hidden = true;
+	scanList.hidden = false;
+    }
+
+    updateScanSummary();
+}
+
+function updateScanSummary()
+{
+    var summary = document.getElementById("scanSummary");
+    if (!summary) { return; }
+
+    if (!document.getElementById("scanSeq").checked) {
+	summary.dataset.level = "idle";
+	summary.textContent = "Single simulation using the Layers settings.";
+	return;
+    }
+
+    var scanType = document.getElementById("scanType").value;
+    var parameterSelect = document.getElementById("comboScan");
+    var parameter = parameterSelect.options[parameterSelect.selectedIndex].text;
+    var workers = Number(document.getElementById("scanThreads").value) || 1;
+    var pointCount = 0;
+    var detail = "";
+    var warning = "";
+
+    if (scanType === "scanLoop") {
+	var from = Number(document.getElementById("scanFrom").value);
+	var step = Number(document.getElementById("scanStep").value);
+	var to = Number(document.getElementById("scanTo").value);
+	if (!Number.isFinite(from) || !Number.isFinite(step) || !Number.isFinite(to)) {
+	    warning = "Enter numeric From, Step, and To values.";
+	} else if (step <= 0) {
+	    warning = "Step must be greater than zero.";
+	} else if (to < from) {
+	    warning = "To must be greater than or equal to From.";
 	} else {
-	    ShowHide(1,'ScansLine');
-	    ShowHide(0,'ScansTable');
+	    pointCount = Math.floor((to - from) / step) + 1;
+	    detail = `${from} to ${to}, step ${step}`;
 	}
     } else {
-	// Hide both
-	    ShowHide(0,'ScansControls');
-	    ShowHide(0,'ScansTable');
-	    ShowHide(0,'ScansLine');
+	var values = document.getElementById("scanList").value
+	    .split(",")
+	    .map(value => value.trim())
+	    .filter(value => value !== "");
+	var depthValues = document.getElementById("scanListdz").value
+	    .split(",")
+	    .map(value => value.trim())
+	    .filter(value => value !== "");
+	if (values.length === 0) {
+	    warning = "Enter at least one scan value.";
+	} else if (values.some(value => !Number.isFinite(Number(value)))) {
+	    warning = "Every scan value must be numeric.";
+	} else if (depthValues.length > 0 && depthValues.length !== values.length) {
+	    warning = "Depth increments must match the number of scan values.";
+	} else {
+	    pointCount = values.length;
+	    detail = values.join(", ");
+	}
     }
+
+    if (warning) {
+	summary.dataset.level = "warning";
+	summary.textContent = warning;
+	return;
+    }
+
+    summary.dataset.level = "ready";
+    var pointLabel = pointCount === 1 ? "point" : "points";
+    var workerLabel = workers === 1 ? "worker" : "workers";
+    summary.textContent = `${parameter} | ${pointCount} ${pointLabel} | ${workers} ${workerLabel} | ${detail}`;
 }
 
 function ProjSmartDefaults()
@@ -3419,17 +3486,6 @@ function ProjNumberLimit()
 }
 
 
-function ShowHide(onoff,item) {
-// this function can switch item to visible/hidden onoff=1/0
-    if(onoff){
-//       document.getElementById(item).style.display = 'block';
-       document.getElementById(item).style.visibility = "visible";
-    } else {
-//       document.getElementById(item).style.display = 'none';
-       document.getElementById(item).style.visibility = "hidden";
-    }
-}
-
 function prep_cfg(toggle) {
     // This function collects various values and returns
     // toggle=1  : returns object with all values

ZGUI.css

@@ -339,23 +339,90 @@ input[type="button"]:hover {
     background: #f5f8f5;
 }
 
-#ScansControls,
-#ScansLine,
-#ScansTable {
-    margin-top: 12px;
+.scan-panel {
+    margin: 0 auto;
+    max-width: 900px;
+    padding: 12px 14px;
 }
 
-#ScansControls table,
-#ScansTable {
+.scan-heading {
+    align-items: center;
+    display: flex;
+    justify-content: space-between;
+    margin-bottom: 12px;
+}
+
+.scan-heading h2 {
+    color: var(--trim-deep);
+    font-family: Georgia, "Times New Roman", serif;
+    font-size: 1.08rem;
+    margin: 0;
+}
+
+.scan-enable {
+    align-items: center;
+    background: var(--trim-panel-soft);
+    border: 1px solid var(--trim-border);
+    border-radius: 999px;
+    cursor: pointer;
+    display: flex;
+    font-size: 0.8rem;
+    font-weight: 700;
+    gap: 7px;
+    padding: 6px 10px;
+}
+
+.scan-enable input {
+    accent-color: var(--trim-accent);
+    height: 16px;
+    margin: 0;
+    width: 16px;
+}
+
+.scan-controls-grid {
+    display: grid;
+    gap: 9px;
+    grid-template-columns: minmax(160px, 0.8fr) minmax(240px, 1.4fr) minmax(100px, 0.5fr);
+}
+
+.scan-values-panel {
     background: var(--trim-panel-soft);
     border: 1px solid var(--trim-border);
     border-radius: 8px;
-    padding: 8px;
+    display: grid;
+    gap: 9px;
+    margin-top: 10px;
+    padding: 10px;
 }
 
-#ScansControls td,
-#ScansTable td {
-    padding: 6px;
+.scan-range-grid {
+    grid-template-columns: repeat(3, minmax(0, 1fr));
+}
+
+.scan-list-grid {
+    grid-template-columns: minmax(260px, 1.5fr) minmax(220px, 1fr);
+}
+
+.scan-summary {
+    background: #eef4f4;
+    border-left: 3px solid var(--trim-focus);
+    border-radius: 5px;
+    color: #31515a;
+    font-size: 0.8rem;
+    margin-top: 11px;
+    min-height: 31px;
+    padding: 7px 10px;
+}
+
+.scan-summary[data-level="idle"] {
+    border-left-color: #91a3a7;
+    color: var(--trim-muted);
+}
+
+.scan-summary[data-level="warning"] {
+    background: #fff1c9;
+    border-left-color: #c79824;
+    color: #674c0a;
 }
 
 #Plots > table td {
@@ -566,7 +633,10 @@ input[type="button"]:hover {
 
     .output-settings,
     .layers-workspace,
-    .projectile-grid {
+    .projectile-grid,
+    .scan-controls-grid,
+    .scan-range-grid,
+    .scan-list-grid {
 	grid-template-columns: 1fr;
     }
 

scripts/deploy-web.sh

@@ -0,0 +1,85 @@
+#!/usr/bin/env bash
+# Copyright (C) 2026 Zaher Salman
+# SPDX-License-Identifier: GPL-2.0-only
+
+set -euo pipefail
+
+project_root="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+web_target="${TRIMSP_WEB_TARGET:-/var/www/html/TRIMSP-NL}"
+cgi_target="${TRIMSP_CGI_TARGET:-/var/www/cgi-bin/singleTrimSP.cgi}"
+trimsp_target="${TRIMSP_BIN_TARGET:-/usr/local/bin/trimspNL}"
+web_owner="${TRIMSP_WEB_OWNER:-apache}"
+web_group="${TRIMSP_WEB_GROUP:-apache}"
+build_static="${TRIMSP_BUILD_STATIC:-1}"
+binary_source="${TRIMSP_BINARY_SOURCE:-$project_root/fortran/trimspNL-static}"
+plotly_source="$project_root/node_modules/plotly.js-dist/plotly.js"
+
+if [[ "$build_static" == "1" ]]; then
+    make -C "$project_root/fortran" trimspNL-static
+elif [[ "$build_static" != "0" ]]; then
+    printf 'TRIMSP_BUILD_STATIC must be 0 or 1, not %s\n' "$build_static" >&2
+    exit 2
+fi
+
+if [[ ! -f "$binary_source" ]]; then
+    printf 'TRIM.SP-NL binary not found: %s\n' "$binary_source" >&2
+    printf 'Build it first or set TRIMSP_BINARY_SOURCE.\n' >&2
+    exit 1
+fi
+
+if [[ ! -f "$plotly_source" ]]; then
+    printf 'Plotly browser bundle not found: %s\n' "$plotly_source" >&2
+    printf 'Run npm install before deploying.\n' >&2
+    exit 1
+fi
+
+perl -c "$project_root/singleTrimSP.cgi" >/dev/null
+
+# Install only files used by the browser application. Electron-specific code,
+# package metadata, tests, and Fortran sources stay outside the document root.
+install -d -m 0755 "$web_target" "$(dirname "$cgi_target")" "$(dirname "$trimsp_target")"
+install -m 0644 \
+    "$project_root/TrimSP.html" \
+    "$project_root/TrimSPlib.js" \
+    "$project_root/TrimSPweb.js" \
+    "$project_root/myplots.js" \
+    "$project_root/ZGUI.css" \
+    "$project_root/plotly.css" \
+    "$project_root/icon.png" \
+    "$web_target/"
+install -m 0644 "$plotly_source" "$web_target/plotly.js"
+ln -sfn TrimSP.html "$web_target/index.html"
+
+install -m 0755 "$binary_source" "$trimsp_target"
+
+# Keep the repository CGI generic while embedding the selected installed
+# binary path in the deployed copy.
+cgi_stage="$(mktemp)"
+trap 'rm -f "$cgi_stage"' EXIT
+escaped_trimsp_target="${trimsp_target//\\/\\\\}"
+escaped_trimsp_target="${escaped_trimsp_target//&/\\&}"
+escaped_trimsp_target="${escaped_trimsp_target//|/\\|}"
+sed "s|^\\\$trimbin=.*|\$trimbin=\"timeout 300 $escaped_trimsp_target\";|" \
+    "$project_root/singleTrimSP.cgi" > "$cgi_stage"
+install -m 0755 "$cgi_stage" "$cgi_target"
+
+if getent passwd "$web_owner" >/dev/null 2>&1 && getent group "$web_group" >/dev/null 2>&1; then
+    chown -R "$web_owner:$web_group" "$web_target"
+    chown "$web_owner:$web_group" "$cgi_target"
+else
+    printf 'Warning: owner/group %s:%s does not exist; ownership was not changed.\n' \
+        "$web_owner" "$web_group" >&2
+fi
+
+if command -v restorecon >/dev/null 2>&1; then
+    restorecon -RF "$web_target" "$cgi_target" "$trimsp_target" || true
+fi
+
+printf 'Installed TRIMSP-NL web assets in %s\n' "$web_target"
+printf 'Installed TRIMSP-NL CGI runner at %s\n' "$cgi_target"
+printf 'Installed TRIM.SP-NL engine at %s\n' "$trimsp_target"
+printf '\nThe web server must provide:\n'
+printf '  /cgi-bin/singleTrimSP.cgi -> %s\n' "$cgi_target"
+printf '  /tmp/ -> /tmp/ (simulation results and archives)\n'
+printf 'For SELinux deployments, verify CGI execution and write access with:\n'
+printf '  ausearch -m avc -ts recent\n'

singleTrimSP.cgi

@@ -0,0 +1,82 @@
+#!/usr/bin/perl 
+#
+# Copyright Zaher Salman 2023-.
+# zaher.salman@psi.ch
+
+######## Relevant subdirectories and urls ########
+# May need modification on different servers
+$trimbin="timeout 300 /usr/local/bin/trimspNL";
+$workroot="/tmp";
+
+# Nothing need to be changed from here on
+#######################################################################
+######## Main body of code ########
+use CGI;
+
+my $in = new CGI;
+# Collect parameters and their values from CGI
+my ($name,$value);
+$content = "";
+my $filename = "";
+my $rngType = "pcg32";
+my $lcount = 0;
+foreach $name ($in->param) {
+    $value=$in->param($name);
+    if ($name eq "fn") {
+	# This is the file name
+	$filename = $value;
+	@prefix = split(/\//,$filename);
+	$randName = $prefix[2];
+	$FILENAME = $prefix[3];
+    } elsif ($name eq "rngType") {
+	# RNG backend passed as the optional second trimspNL argument.
+	if ($value =~ /^(ranlux|pcg32|xoshiro|xoshiro256)$/) {
+	    $rngType = $value;
+	}
+    } elsif ( index($name, "line") == 0) {
+	# This is a line start counting
+	#if ($lcount <=14) {
+	    # Limit number of lines (15) to avoid abuse
+	    $content = $content.$value."\n";
+	#}
+	$lcount++;
+    }
+}
+$workPath = $workroot."/".$randName;
+if (-d $workPath) {
+# Directory exists, do nothing
+} else {
+    $cmd="mkdir ".$workPath;
+    system($cmd);
+}
+$filename = $workPath."/".$FILENAME;
+$fname = $filename;
+$fname =~ s/\.inp$//;
+$runBase = $FILENAME;
+$runBase =~ s/\.inp$//;
+open (OUTF,q{>}, $filename);
+print OUTF ($content);
+close(OUTF);
+
+print ("Content-type: text/ascii \n\n");
+if  (index($filename,"_Seq_Results.dat") != -1) {
+    # This is the final call of a scan
+    $cmd = "cd $workPath; rm -f edist;"; 
+    $cmd = $cmd."tar -cvzf ../$randName.tgz *; cd ..; rm -rf $randName;";
+} elsif (index($filename,"TrimSP.cfg") != -1) {
+    # Save config file only
+    $cmd = "cd $workPath;";
+} else {
+    # This is a call to simulate one step in a scan
+    $cmd = "cd $workPath; $trimbin $runBase $rngType >> /tmp/debug;";
+}
+system($cmd);
+#print "Written file $filename\n";
+#print $content;
+print "command $cmd\n";
+foreach $name ($in->param) {
+    $value=$in->param($name);
+    print $name,"=",$value,"\n";
+}
+    
+exit(0);