add a few more anon checks

atlas/templates/atlas/new_uploads.html

@@ -22,7 +22,7 @@
         </details>
         <details>
             <summary>Settings</summary>
-            <input type="checkbox" id="check-annonymisation-ocr" checked><label for="check-annonymisation-ocr">Check for annonymisation (OCR)</label>
+            <input type="checkbox" id="check-annonymisation-ocr"><label for="check-annonymisation-ocr">Check for annonymisation (OCR)</label>
             <input type="checkbox" id="show-thumbnails"><label for="Show thumbnails">Show thumbnails</label>
             <input type="checkbox" id="show-viewer"><label for="Show Viewer">Show viewer</label>
         </details>
@@ -47,6 +47,15 @@
         </div>
     </details>
 
+    <div class="alert alert-warning hide anon-alert" role="alert">
+        <p>The system has detected files that do not appear to be annonymised. These have been highlighted below.</p>
+
+        <p>If you believe this is a false positive please contact ross.kruger@nhs.net with details about the file that has been flagged.</p>
+
+        <details><summary>Override annonymisation check</summary>
+            <p>By clicking the button below you can override the annonymisation check and upload the files anyway. Only do this if you are sure this is a false positive.</p>
+            <button id="override-anon" _="on click remove @disabled from #uploadButton then alert('Upload enabled')">Override annonymisation check</button>
+    </div>
 
     <h4>Selected files:</h4>
     <div id="single-dicom-viewer" class="dicom-viewer" data-images="" data-annotations=''></div>
@@ -116,15 +125,12 @@
         }
 
         function uploadFiles(files_to_upload, current_chunk, total_chunks){
-            console.log("uploading", files_to_upload)
-
   // Create a FormData object to store the form data
             const formData = new FormData();
   // Append each selected file to the FormData object
             for (let i = 0; i < files_to_upload.length; i++) {
                 formData.append("files", files_to_upload[i]);
             }
-            console.log("formdata", formData)
             const xhr = new XMLHttpRequest();
             xhr.open("POST", "{% url 'api-1:upload_dicom' %}", true);
             xhr.setRequestHeader("X-CSRFToken", "{{ csrf_token }}");
@@ -134,8 +140,6 @@
                     window.upload_count += 1;
                     if (xhr.status === 200) {
                     // Handle successful response from the server
-                        console.log('Files uploaded successfully!');
-                        console.log(xhr.response);
                         window.upload_results["uploaded"].push(...JSON.parse(xhr.response)["uploaded"]);
                         window.upload_results["duplicates"].push(...JSON.parse(xhr.response)["duplicates"]);
                         window.upload_results["failed"].push(...JSON.parse(xhr.response)["failed"]);
@@ -180,14 +184,12 @@
             xhr.send(formData);
         }
 
-        function checkAnnonymisation(byteArray) {
+        function checkAnnonymisation(byteArray, file) {
         // We need to setup a try/catch block because parseDicom will throw an exception
         // if you attempt to parse a non dicom part 10 file (or one that is corrupted)
             try {
-                console.log("bytearray", byteArray)
             // parse byteArray into a DataSet object using the parseDicom library
                 var dataSet = dicomParser.parseDicom(byteArray);
-                console.log("ds", dataSet)
 
             // dataSet contains the parsed elements.  Each element is available via a property
             // in the dataSet.elements object.  The property name is based on the elements group
@@ -200,24 +202,25 @@
                 var study_description = dataSet.string('x00081030');
                 var accession_number = dataSet.string('x00080050').toLowerCase();
                 var patient_id = dataSet.string('x00100020').toLowerCase();
-                console.log("STUDY", study_description);
-                console.log("acc", accession_number);
-                console.log("pid", patient_id);
-
 
                 not_anon = false;
 
                 site_codes = ["ref", "rk9", "ra9", "rh8", "rbz", "rba"]
 
+                errors = []
                 for (let i = 0; i < site_codes.length; i++) {
-                    if (
+                    if ( accession_number.startsWith(site_codes[i]))
-                        accession_number.startsWith(site_codes[i]) ||
-                        patient_id.startsWith(site_codes[i])
-                    )
                     {
                         not_anon = true;
+                        errors.push(`Accession number starts with ${site_codes[i]} (${accession_number})`);
+                    }
+                    if ( patient_id.startsWith(site_codes[i]))
+                    {
+                        not_anon = true;
+                        errors.push(`Patient ID starts with ${site_codes[i]} (${patient_id})`);
                     }
                 }
+                console.log(errors)
 
                 if (not_anon) {
                     toastr.warning(`File does not appear to be annonymised<br/>Accession: ${accession_number} <br/>Patient ID: ${patient_id}<br/>`, 'Anonymisation warning', {
@@ -237,7 +240,16 @@
                         "showMethod": "fadeIn",
                         "hideMethod": "fadeOut",
                     });
-                    $("uploadButton").prop("disabled", true);
+                    $("#uploadButton").prop("disabled", true);
+                    $(".anon-alert").show();
+
+                    setTimeout(
+                    function(errors) {
+                        console.log(errors)
+                        // We delay this a few seconds otherwise it does not work
+                    $(`.dicom-file[data-path='${file.webkitRelativePath}']`).addClass("image-ident-warning").append($(`<div>${errors.join("<br/>")}</div>`));
+                    }, 2000, errors
+                    )
                 }
 
             // TODO: fix
@@ -269,7 +281,8 @@
                 return false;
             }
         }
-        async function loadDicomViewerTest(callback) {
+        async function loadDicomViewerUploads(callback) {
+            $("#uploadButton").attr("disabled", false);
             $("#single-dicom-viewer").hide();
             console.log("load")
             $("#single-dicom-viewer").empty()
@@ -285,7 +298,6 @@
 
             const readFile = (file, el) => {
                 reader(file).then(reader => {
-                    console.log("hello", file, el, image)
                     //if ($("#id_examination").find(":selected")[0].dataset.select2Id == "2") {
                     //    var byteArray = new Uint8Array(reader.result);
                     //    console.log("etrxact", reader)
@@ -296,7 +308,6 @@
                     image.title = file.name;
                     image.src = reader.result;
                     image.className = "temp-thumb";
-                    console.log("read", el);
                     $(el).append(image);
                     //images.push(reader.result);
                     loadViewer(images);
@@ -315,8 +326,7 @@
             const readDicomFile = (file) => {
                 return dicomReader(file).then(reader => {
                     var byteArray = new Uint8Array(reader.result);
-                    console.log("etrxact", reader)
+                    return checkAnnonymisation(byteArray, file);
-                    return checkAnnonymisation(byteArray);
                 });
             }
 
@@ -341,12 +351,12 @@
                     let item = document.createElement("li");
                     item.className = "dicom-file";
                     item.textContent = file.webkitRelativePath;
+                    item.dataset.path = file.webkitRelativePath;
                     output.appendChild(item);
                         //await readFile(file, item);
 
 
                     let url = URL.createObjectURL(file)
-                    console.log(url)
                     imageId = `wadouri:${url}`;
                     if ($("#show-viewer").is(":checked")) {
                         images.push(imageId);
@@ -384,8 +394,6 @@
                 }
             }
 
-            console.log(images)
-
 
             const event = new CustomEvent('loadDicomViewerUrls', {
                 "detail": {"images": images, "annontations": undefined}
@@ -401,7 +409,6 @@
 
         }
         function ocr(url, input) {
-            console.log("OCR", input)
             Tesseract.recognize(
                 url,
                 'eng',
@@ -414,7 +421,6 @@
                 l = text.toLowerCase();
                 uploading_el = $(`img[data-input-id='${input.id}'], div[data-input-id='${input.id}']`)
                 uploading_el.removeClass("image-ident-loading");
-                console.log("found text", l);
                 if (l.includes("accession") || l.includes("number") || l.search(
                     /(ref|rk9|rh8|ra9|rbz)\d+/g) > -1) {
                         console.log("Match found ", input);
@@ -457,7 +463,7 @@
                     //    output.appendChild(item);
                     //}
 
-                    loadDicomViewerTest();
+                    loadDicomViewerUploads();
                 },
                 false,
             );
@@ -469,4 +475,10 @@
         });
 
     </script>
+    <script type="text/hyperscript">
+
+        init
+         add @disabled to #uploadButton
+        end
+    </script>
 {% endblock %}