From 81cc612e695faee60e9ea4458ed004a643472bf5 Mon Sep 17 00:00:00 2001
From: jebus <lorsbach@envipath.com>
Date: Fri, 6 Mar 2026 03:15:44 +1300
Subject: [PATCH] [Feature] Populate Batch Predict Table by CSV (#339)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: https://git.envipath.com/enviPath/enviPy/pulls/339
---
 epdb/views.py                        |   2 +-
 templates/batch_predict_pathway.html | 179 ++++++++++++++++++++++++++-
 2 files changed, 174 insertions(+), 7 deletions(-)

diff --git a/epdb/views.py b/epdb/views.py
index 56884492..0cf559a2 100644
--- a/epdb/views.py
+++ b/epdb/views.py
@@ -2967,7 +2967,7 @@ def jobs(request):
                     raise BadRequest(f"Couldn't standardize SMILES {parts[0]}!")
 
                 # name is optional
-                name = parts[1] if len(parts) > 1 else None
+                name = ",".join(parts[1:]) if len(parts) > 1 else None
                 pred_data.append([smiles, name])
 
             max_tps = 50
diff --git a/templates/batch_predict_pathway.html b/templates/batch_predict_pathway.html
index b9e5412c..ed9f351c 100644
--- a/templates/batch_predict_pathway.html
+++ b/templates/batch_predict_pathway.html
@@ -9,6 +9,39 @@
       <input type="hidden" name="job-name" value="batch-predict" />
 
       <fieldset class="flex flex-col gap-4 md:flex-3/4">
+        <!-- CSV Upload Section -->
+        <div class="mb-6 rounded-lg border-2 border-dashed border-base-300 p-6">
+          <div class="flex flex-col gap-4">
+            <div
+              class="flex flex-col gap-3 sm:flex-row sm:items-center sm:justify-between"
+            >
+              <div class="flex-1">
+                <h3 class="text-base font-medium text-base-content mb-1">
+                  Load from CSV
+                </h3>
+                <p class="text-sm text-base-content/70">
+                  Upload a CSV file with SMILES and name columns, or insert
+                  manually in the table below
+                </p>
+              </div>
+              <div class="flex-shrink-0">
+                <input
+                  type="file"
+                  id="csv-file"
+                  accept=".csv,.txt"
+                  class="file-input file-input-bordered file-input-sm w-full sm:w-auto"
+                />
+              </div>
+            </div>
+            <div
+              class="text-xs text-base-content/50 border-t border-base-300 pt-3"
+            >
+              <strong>Format:</strong> First column = SMILES, Second column =
+              Name (headers optional) • Maximum 30 rows
+            </div>
+          </div>
+        </div>
+
         <table class="table table-zebra w-full">
           <thead>
             <tr>
@@ -113,10 +146,16 @@
   <script>
     const tableBody = document.getElementById("smiles-table-body");
     const addRowBtn = document.getElementById("add-row-btn");
+    const csvFileInput = document.getElementById("csv-file");
     const form = document.getElementById("smiles-form");
     const hiddenField = document.getElementById("substrates");
 
-    addRowBtn.addEventListener("click", () => {
+    // Function to create a new table row
+    function createTableRow(
+      smilesValue = "",
+      nameValue = "",
+      placeholder = true,
+    ) {
       const row = document.createElement("tr");
 
       const tdSmiles = document.createElement("td");
@@ -125,19 +164,147 @@
       const smilesInput = document.createElement("input");
       smilesInput.type = "text";
       smilesInput.className = "input input-bordered w-full smiles-input";
-      smilesInput.placeholder = "SMILES";
+      smilesInput.placeholder = placeholder ? "SMILES" : "";
+      smilesInput.value = smilesValue;
 
       const nameInput = document.createElement("input");
       nameInput.type = "text";
       nameInput.className = "input input-bordered w-full name-input";
-      nameInput.placeholder = "Name";
+      nameInput.placeholder = placeholder ? "Name" : "";
+      nameInput.value = nameValue;
 
-      tdSmiles.appendChild(smilesInput);
-      tdName.appendChild(nameInput);
+      const smilesLabel = document.createElement("label");
+      smilesLabel.appendChild(smilesInput);
+      tdSmiles.appendChild(smilesLabel);
+
+      const nameLabel = document.createElement("label");
+      nameLabel.appendChild(nameInput);
+      tdName.appendChild(nameLabel);
 
       row.appendChild(tdSmiles);
       row.appendChild(tdName);
 
+      return row;
+    }
+
+    // Function to clear the table
+    function clearTable() {
+      tableBody.innerHTML = "";
+    }
+
+    // Function to populate table from CSV data
+    function populateTableFromCSV(csvData) {
+      const lines = csvData.trim().split("\n");
+      const maxRows = 30;
+
+      // Clear existing table
+      clearTable();
+
+      // Skip header row if it looks like headers
+      const startIndex =
+        lines.length > 0 &&
+        (lines[0].toLowerCase().includes("smiles") ||
+          lines[0].toLowerCase().includes("name"))
+          ? 1
+          : 0;
+
+      let rowCount = 0;
+      for (let i = startIndex; i < lines.length && rowCount < maxRows; i++) {
+        const line = lines[i].trim();
+        if (!line) continue;
+
+        // Parse CSV line - split by comma, first part is SMILES, rest is name
+        const firstCommaIndex = line.indexOf(",");
+        let smiles = "";
+        let name = "";
+
+        if (firstCommaIndex === -1) {
+          // No comma found, treat entire line as SMILES
+          smiles = line.trim().replace(/^"(.*)"$/, "$1");
+        } else {
+          // Split at first comma only
+          smiles = line
+            .substring(0, firstCommaIndex)
+            .trim()
+            .replace(/^"(.*)"$/, "$1");
+          name = line
+            .substring(firstCommaIndex + 1)
+            .trim()
+            .replace(/^"(.*)"$/, "$1");
+        }
+
+        // Skip empty rows
+        if (!smiles && !name) continue;
+
+        const row = createTableRow(smiles, name, false);
+        tableBody.appendChild(row);
+        rowCount++;
+      }
+
+      // Add at least one empty row if no data was loaded
+      if (rowCount === 0) {
+        const row = createTableRow();
+        tableBody.appendChild(row);
+      }
+
+      // Show success message
+      if (rowCount > 0) {
+        const message =
+          rowCount >= maxRows
+            ? `Loaded ${rowCount} rows (maximum reached)`
+            : `Loaded ${rowCount} rows from CSV`;
+
+        // Create temporary success notification
+        const notification = document.createElement("div");
+        notification.className = "alert alert-success mb-4";
+        notification.innerHTML = `
+      <svg xmlns="http://www.w3.org/2000/svg" class="stroke-current shrink-0 h-6 w-6" fill="none" viewBox="0 0 24 24">
+        <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 12l2 2 4-4m6 2a9 9 0 11-18 0 9 9 0 0118 0z" />
+      </svg>
+      <span>${message}</span>
+    `;
+
+        // Insert notification before the table
+        const tableContainer = document.querySelector("table").parentNode;
+        tableContainer.insertBefore(
+          notification,
+          document.querySelector("table"),
+        );
+
+        // Remove notification after 3 seconds
+        setTimeout(() => {
+          if (notification.parentNode) {
+            notification.parentNode.removeChild(notification);
+          }
+        }, 3000);
+      }
+    }
+    // Handle CSV file selection
+    csvFileInput.addEventListener("change", function (event) {
+      const file = event.target.files[0];
+      if (!file) return;
+
+      // Check file type
+      if (!file.name.match(/\.(csv|txt)$/i)) {
+        alert("Please select a CSV or TXT file.");
+        return;
+      }
+
+      const reader = new FileReader();
+      reader.onload = function (e) {
+        try {
+          populateTableFromCSV(e.target.result);
+        } catch (error) {
+          console.error("Error parsing CSV:", error);
+          alert("Error parsing CSV file. Please check the file format.");
+        }
+      };
+      reader.readAsText(file);
+    });
+
+    // Handle add row button
+    addRowBtn.addEventListener("click", () => {
+      const row = createTableRow();
       tableBody.appendChild(row);
     });
 
@@ -154,7 +321,7 @@
         const smiles = smilesInputs[i].value.trim();
         const name = nameInputs[i]?.value.trim() ?? "";
 
-        // Skip emtpy rows
+        // Skip empty rows
         if (!smiles && !name) {
           continue;
         }