From a627dbcb4987a08a065d5ff50fb5a125b4b697d5 Mon Sep 17 00:00:00 2001
From: Mark Williams <mark.williams@diamond.ac.uk>
Date: Wed, 8 Apr 2026 13:20:54 +0100
Subject: [PATCH 1/3] LIMS-2015: Update d3-*, csv-file-validator and plotly.js
 libraries

---
 api/src/Page/Download.php                     |    1 +
 client/package-lock.json                      | 2373 ++++++-----------
 client/package.json                           |   10 +-
 .../modules/samples/components/PuckView.vue   |   20 +-
 .../modules/shipment/components/puck-view.vue |   27 +-
 .../xpdf/samples/views/vue-simplesample.vue   |   78 +-
 6 files changed, 908 insertions(+), 1601 deletions(-)

diff --git a/api/src/Page/Download.php b/api/src/Page/Download.php
index 5839f8c46..5ea525cca 100644
--- a/api/src/Page/Download.php
+++ b/api/src/Page/Download.php
@@ -155,6 +155,7 @@ function _auto_processing_plots()
                     // If we are looking for a specific plot (by attachment id) then OK...
                     if ($this->has_arg('aid')) {
                         $r['PLOTLY'] = true;
+                        error_log('LIMS-2148 - Plotly used for autoprocprogramattachmentid ' . $this->arg('aid'));
                     } else {
                         // ..if not, we should remove this from the list of returned plots
                         // Autoprocessing results use the same bespoke format for charts
diff --git a/client/package-lock.json b/client/package-lock.json
index c9ddd8a19..56cc12095 100644
--- a/client/package-lock.json
+++ b/client/package-lock.json
@@ -18,10 +18,10 @@
         "backgrid-paginator": "0.3.9",
         "backgrid-select-all": "0.3.5",
         "ci": "^2.2.0",
-        "csv-file-validator": "^1.7.4",
-        "d3-scale": "^3.2.3",
-        "d3-scale-chromatic": "^2.0.0",
-        "d3-selection": "^2.0.0",
+        "csv-file-validator": "^2.2.0",
+        "d3-scale": "^4.0.2",
+        "d3-scale-chromatic": "^3.1.0",
+        "d3-selection": "^3.0.0",
         "flot-axislabels": "^1.0.0",
         "flot-pie": "^1.0.0",
         "font-awesome": "^4.2.0",
@@ -34,7 +34,7 @@
         "jquery.flot.tooltip": "^0.9.0",
         "lodash-es": "^4.17.21",
         "markdown": "^0.5.0",
-        "plotly.js": "^1.52.2",
+        "plotly.js": "^2.35.3",
         "portal-vue": "2.1.7",
         "promise": "^8.0.3",
         "tailwindcss": "^1.9.5",
@@ -2701,7 +2701,6 @@
       "version": "0.3.3",
       "resolved": "https://registry.npmjs.org/@jridgewell/gen-mapping/-/gen-mapping-0.3.3.tgz",
       "integrity": "sha512-HLhSWOLRi875zjjMG/r+Nv0oCW8umGb0BgEhyX3dDX3egwZtB8PqLnjz3yedt8R5StBrzcg4aBpnh8UA9D1BoQ==",
-      "dev": true,
       "dependencies": {
         "@jridgewell/set-array": "^1.0.1",
         "@jridgewell/sourcemap-codec": "^1.4.10",
@@ -2715,7 +2714,6 @@
       "version": "3.1.0",
       "resolved": "https://registry.npmjs.org/@jridgewell/resolve-uri/-/resolve-uri-3.1.0.tgz",
       "integrity": "sha512-F2msla3tad+Mfht5cJq7LSXcdudKTWCVYUgw6pLFOOHSTtZlj6SWNYAp+AhuqLmWdBO2X5hPrLcu8cVP8fy28w==",
-      "dev": true,
       "engines": {
         "node": ">=6.0.0"
       }
@@ -2724,7 +2722,6 @@
       "version": "1.1.2",
       "resolved": "https://registry.npmjs.org/@jridgewell/set-array/-/set-array-1.1.2.tgz",
       "integrity": "sha512-xnkseuNADM0gt2bs+BvhO0p78Mk762YnZdsuzFV018NoG1Sj1SCQvpSqa7XUaTam5vAGasABV9qXASMKnFMwMw==",
-      "dev": true,
       "engines": {
         "node": ">=6.0.0"
       }
@@ -2733,7 +2730,6 @@
       "version": "0.3.3",
       "resolved": "https://registry.npmjs.org/@jridgewell/source-map/-/source-map-0.3.3.tgz",
       "integrity": "sha512-b+fsZXeLYi9fEULmfBrhxn4IrPlINf8fiNarzTof004v3lFdntdwa9PF7vFJqm3mg7s+ScJMxXaE3Acp1irZcg==",
-      "dev": true,
       "dependencies": {
         "@jridgewell/gen-mapping": "^0.3.0",
         "@jridgewell/trace-mapping": "^0.3.9"
@@ -2742,14 +2738,12 @@
     "node_modules/@jridgewell/sourcemap-codec": {
       "version": "1.4.15",
       "resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.15.tgz",
-      "integrity": "sha512-eF2rxCRulEKXHTRiDrDy6erMYWqNw4LPdQ8UQA4huuxaQsVeRPFl2oM8oDGxMFhJUWZf9McpLtJasDDZb/Bpeg==",
-      "dev": true
+      "integrity": "sha512-eF2rxCRulEKXHTRiDrDy6erMYWqNw4LPdQ8UQA4huuxaQsVeRPFl2oM8oDGxMFhJUWZf9McpLtJasDDZb/Bpeg=="
     },
     "node_modules/@jridgewell/trace-mapping": {
       "version": "0.3.18",
       "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.18.tgz",
       "integrity": "sha512-w+niJYzMHdd7USdiH2U6869nqhD2nbfZXND5Yp93qIbEmnDNk7PD48o+YchRVpzMU7M6jVCbenTR7PA1FLQ9pA==",
-      "dev": true,
       "dependencies": {
         "@jridgewell/resolve-uri": "3.1.0",
         "@jridgewell/sourcemap-codec": "1.4.14"
@@ -2758,13 +2752,13 @@
     "node_modules/@jridgewell/trace-mapping/node_modules/@jridgewell/sourcemap-codec": {
       "version": "1.4.14",
       "resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.14.tgz",
-      "integrity": "sha512-XPSJHWmi394fuUuzDnGz1wiKqWfo1yXecHQMRf2l6hztTO+nPru658AyDngaBe7isIxEkRsPR3FZh+s7iVa4Uw==",
-      "dev": true
+      "integrity": "sha512-XPSJHWmi394fuUuzDnGz1wiKqWfo1yXecHQMRf2l6hztTO+nPru658AyDngaBe7isIxEkRsPR3FZh+s7iVa4Uw=="
     },
     "node_modules/@mapbox/geojson-rewind": {
       "version": "0.5.2",
       "resolved": "https://registry.npmjs.org/@mapbox/geojson-rewind/-/geojson-rewind-0.5.2.tgz",
       "integrity": "sha512-tJaT+RbYGJYStt7wI3cq4Nl4SXxG8W7JDG5DMJu97V25RnbNg3QtQtf+KD+VLjNpWKYsRvXDNmNrBgEETr1ifA==",
+      "license": "ISC",
       "dependencies": {
         "get-stream": "^6.0.1",
         "minimist": "^1.2.6"
@@ -2776,7 +2770,8 @@
     "node_modules/@mapbox/geojson-types": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/@mapbox/geojson-types/-/geojson-types-1.0.2.tgz",
-      "integrity": "sha512-e9EBqHHv3EORHrSfbR9DqecPNn+AmuAoQxV6aL8Xu30bJMJR1o8PZLZzpk1Wq7/NfCbuhmakHTPYRhoqLsXRnw=="
+      "integrity": "sha512-e9EBqHHv3EORHrSfbR9DqecPNn+AmuAoQxV6aL8Xu30bJMJR1o8PZLZzpk1Wq7/NfCbuhmakHTPYRhoqLsXRnw==",
+      "license": "ISC"
     },
     "node_modules/@mapbox/jsonlint-lines-primitives": {
       "version": "2.0.2",
@@ -2790,6 +2785,7 @@
       "version": "1.5.0",
       "resolved": "https://registry.npmjs.org/@mapbox/mapbox-gl-supported/-/mapbox-gl-supported-1.5.0.tgz",
       "integrity": "sha512-/PT1P6DNf7vjEEiPkVIRJkvibbqWtqnyGaBz3nfRdcxclNSnSdaLU5tfAgcD7I8Yt5i+L19s406YLl1koLnLbg==",
+      "license": "BSD-3-Clause",
       "peerDependencies": {
         "mapbox-gl": ">=0.32.1 <2.0.0"
       }
@@ -2797,22 +2793,26 @@
     "node_modules/@mapbox/point-geometry": {
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/@mapbox/point-geometry/-/point-geometry-0.1.0.tgz",
-      "integrity": "sha512-6j56HdLTwWGO0fJPlrZtdU/B13q8Uwmo18Ck2GnGgN9PCFyKTZ3UbXeEdRFh18i9XQ92eH2VdtpJHpBD3aripQ=="
+      "integrity": "sha512-6j56HdLTwWGO0fJPlrZtdU/B13q8Uwmo18Ck2GnGgN9PCFyKTZ3UbXeEdRFh18i9XQ92eH2VdtpJHpBD3aripQ==",
+      "license": "ISC"
     },
     "node_modules/@mapbox/tiny-sdf": {
       "version": "1.2.5",
       "resolved": "https://registry.npmjs.org/@mapbox/tiny-sdf/-/tiny-sdf-1.2.5.tgz",
-      "integrity": "sha512-cD8A/zJlm6fdJOk6DqPUV8mcpyJkRz2x2R+/fYcWDYG3oWbG7/L7Yl/WqQ1VZCjnL9OTIMAn6c+BC5Eru4sQEw=="
+      "integrity": "sha512-cD8A/zJlm6fdJOk6DqPUV8mcpyJkRz2x2R+/fYcWDYG3oWbG7/L7Yl/WqQ1VZCjnL9OTIMAn6c+BC5Eru4sQEw==",
+      "license": "BSD-2-Clause"
     },
     "node_modules/@mapbox/unitbezier": {
       "version": "0.0.0",
       "resolved": "https://registry.npmjs.org/@mapbox/unitbezier/-/unitbezier-0.0.0.tgz",
-      "integrity": "sha512-HPnRdYO0WjFjRTSwO3frz1wKaU649OBFPX3Zo/2WZvuRi6zMiRGui8SnPQiQABgqCf8YikDe5t3HViTVw1WUzA=="
+      "integrity": "sha512-HPnRdYO0WjFjRTSwO3frz1wKaU649OBFPX3Zo/2WZvuRi6zMiRGui8SnPQiQABgqCf8YikDe5t3HViTVw1WUzA==",
+      "license": "BSD-2-Clause"
     },
     "node_modules/@mapbox/vector-tile": {
       "version": "1.3.1",
       "resolved": "https://registry.npmjs.org/@mapbox/vector-tile/-/vector-tile-1.3.1.tgz",
       "integrity": "sha512-MCEddb8u44/xfQ3oD+Srl/tNcQoqTw3goGk2oLsrFxOTc3dUp+kAnby3PvAeeBYSMSjSPD1nd1AJA6W49WnoUw==",
+      "license": "BSD-3-Clause",
       "dependencies": {
         "@mapbox/point-geometry": "~0.1.0"
       }
@@ -2821,10 +2821,43 @@
       "version": "3.1.0",
       "resolved": "https://registry.npmjs.org/@mapbox/whoots-js/-/whoots-js-3.1.0.tgz",
       "integrity": "sha512-Es6WcD0nO5l+2BOQS4uLfNPYQaNDfbot3X1XUoloz+x0mPDS3eeORZJl06HXjwBG1fOGwCRnzK88LMdxKRrd6Q==",
+      "license": "ISC",
       "engines": {
         "node": ">=6.0.0"
       }
     },
+    "node_modules/@maplibre/maplibre-gl-style-spec": {
+      "version": "20.4.0",
+      "resolved": "https://registry.npmjs.org/@maplibre/maplibre-gl-style-spec/-/maplibre-gl-style-spec-20.4.0.tgz",
+      "integrity": "sha512-AzBy3095fTFPjDjmWpR2w6HVRAZJ6hQZUCwk5Plz6EyfnfuQW1odeW5i2Ai47Y6TBA2hQnC+azscjBSALpaWgw==",
+      "license": "ISC",
+      "dependencies": {
+        "@mapbox/jsonlint-lines-primitives": "~2.0.2",
+        "@mapbox/unitbezier": "^0.0.1",
+        "json-stringify-pretty-compact": "^4.0.0",
+        "minimist": "^1.2.8",
+        "quickselect": "^2.0.0",
+        "rw": "^1.3.3",
+        "tinyqueue": "^3.0.0"
+      },
+      "bin": {
+        "gl-style-format": "dist/gl-style-format.mjs",
+        "gl-style-migrate": "dist/gl-style-migrate.mjs",
+        "gl-style-validate": "dist/gl-style-validate.mjs"
+      }
+    },
+    "node_modules/@maplibre/maplibre-gl-style-spec/node_modules/@mapbox/unitbezier": {
+      "version": "0.0.1",
+      "resolved": "https://registry.npmjs.org/@mapbox/unitbezier/-/unitbezier-0.0.1.tgz",
+      "integrity": "sha512-nMkuDXFv60aBr9soUG5q+GvZYL+2KZHVvsqFCzqnkGEf46U2fvmytHaEVc1/YZbiLn8X+eR3QzX1+dwDO1lxlw==",
+      "license": "BSD-2-Clause"
+    },
+    "node_modules/@maplibre/maplibre-gl-style-spec/node_modules/tinyqueue": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/tinyqueue/-/tinyqueue-3.0.0.tgz",
+      "integrity": "sha512-gRa9gwYU3ECmQYv3lslts5hxuIa90veaEcxDYuu3QGOIAEM2mOZkVHp48ANJuu1CURtRdHKUBY5Lm1tHV+sD4g==",
+      "license": "ISC"
+    },
     "node_modules/@nodelib/fs.scandir": {
       "version": "2.1.5",
       "resolved": "https://registry.npmjs.org/@nodelib/fs.scandir/-/fs.scandir-2.1.5.tgz",
@@ -2917,6 +2950,12 @@
         "node": ">=10"
       }
     },
+    "node_modules/@plotly/d3": {
+      "version": "3.8.2",
+      "resolved": "https://registry.npmjs.org/@plotly/d3/-/d3-3.8.2.tgz",
+      "integrity": "sha512-wvsNmh1GYjyJfyEBPKJLTMzgf2c2bEbSIL50lmqVUi+o1NHaLPi1Lb4v7VxXXJn043BhNyrxUrWI85Q+zmjOVA==",
+      "license": "BSD-3-Clause"
+    },
     "node_modules/@plotly/d3-sankey": {
       "version": "0.7.2",
       "resolved": "https://registry.npmjs.org/@plotly/d3-sankey/-/d3-sankey-0.7.2.tgz",
@@ -2948,6 +2987,39 @@
       "resolved": "https://registry.npmjs.org/d3-array/-/d3-array-1.2.4.tgz",
       "integrity": "sha512-KHW6M86R+FUPYGb3R5XiYjXPq7VzwxZ22buHhAEVG5ztoEcZZMLov530mmccaqA1GghZArjQV46fuc8kUqhhHw=="
     },
+    "node_modules/@plotly/mapbox-gl": {
+      "version": "1.13.4",
+      "resolved": "https://registry.npmjs.org/@plotly/mapbox-gl/-/mapbox-gl-1.13.4.tgz",
+      "integrity": "sha512-sR3/Pe5LqT/fhYgp4rT4aSFf1rTsxMbGiH6Hojc7PH36ny5Bn17iVFUjpzycafETURuFbLZUfjODO8LvSI+5zQ==",
+      "license": "SEE LICENSE IN LICENSE.txt",
+      "dependencies": {
+        "@mapbox/geojson-rewind": "^0.5.2",
+        "@mapbox/geojson-types": "^1.0.2",
+        "@mapbox/jsonlint-lines-primitives": "^2.0.2",
+        "@mapbox/mapbox-gl-supported": "^1.5.0",
+        "@mapbox/point-geometry": "^0.1.0",
+        "@mapbox/tiny-sdf": "^1.1.1",
+        "@mapbox/unitbezier": "^0.0.0",
+        "@mapbox/vector-tile": "^1.3.1",
+        "@mapbox/whoots-js": "^3.1.0",
+        "csscolorparser": "~1.0.3",
+        "earcut": "^2.2.2",
+        "geojson-vt": "^3.2.1",
+        "gl-matrix": "^3.2.1",
+        "grid-index": "^1.1.0",
+        "murmurhash-js": "^1.0.0",
+        "pbf": "^3.2.1",
+        "potpack": "^1.0.1",
+        "quickselect": "^2.0.0",
+        "rw": "^1.3.3",
+        "supercluster": "^7.1.0",
+        "tinyqueue": "^2.0.3",
+        "vt-pbf": "^3.1.1"
+      },
+      "engines": {
+        "node": ">=6.4.0"
+      }
+    },
     "node_modules/@plotly/point-cluster": {
       "version": "3.1.9",
       "resolved": "https://registry.npmjs.org/@plotly/point-cluster/-/point-cluster-3.1.9.tgz",
@@ -3017,55 +3089,72 @@
       }
     },
     "node_modules/@turf/area": {
-      "version": "6.5.0",
-      "resolved": "https://registry.npmjs.org/@turf/area/-/area-6.5.0.tgz",
-      "integrity": "sha512-xCZdiuojokLbQ+29qR6qoMD89hv+JAgWjLrwSEWL+3JV8IXKeNFl6XkEJz9HGkVpnXvQKJoRz4/liT+8ZZ5Jyg==",
+      "version": "7.3.4",
+      "resolved": "https://registry.npmjs.org/@turf/area/-/area-7.3.4.tgz",
+      "integrity": "sha512-UEQQFw2XwHpozSBAMEtZI3jDsAad4NnHL/poF7/S6zeDCjEBCkt3MYd6DSGH/cvgcOozxH/ky3/rIVSMZdx4vA==",
+      "license": "MIT",
       "dependencies": {
-        "@turf/helpers": "^6.5.0",
-        "@turf/meta": "^6.5.0"
+        "@turf/helpers": "7.3.4",
+        "@turf/meta": "7.3.4",
+        "@types/geojson": "^7946.0.10",
+        "tslib": "^2.8.1"
       },
       "funding": {
         "url": "https://opencollective.com/turf"
       }
     },
     "node_modules/@turf/bbox": {
-      "version": "6.5.0",
-      "resolved": "https://registry.npmjs.org/@turf/bbox/-/bbox-6.5.0.tgz",
-      "integrity": "sha512-RBbLaao5hXTYyyg577iuMtDB8ehxMlUqHEJiMs8jT1GHkFhr6sYre3lmLsPeYEi/ZKj5TP5tt7fkzNdJ4GIVyw==",
+      "version": "7.3.4",
+      "resolved": "https://registry.npmjs.org/@turf/bbox/-/bbox-7.3.4.tgz",
+      "integrity": "sha512-D5ErVWtfQbEPh11yzI69uxqrcJmbPU/9Y59f1uTapgwAwQHQztDWgsYpnL3ns8r1GmPWLP8sGJLVTIk2TZSiYA==",
+      "license": "MIT",
       "dependencies": {
-        "@turf/helpers": "^6.5.0",
-        "@turf/meta": "^6.5.0"
+        "@turf/helpers": "7.3.4",
+        "@turf/meta": "7.3.4",
+        "@types/geojson": "^7946.0.10",
+        "tslib": "^2.8.1"
       },
       "funding": {
         "url": "https://opencollective.com/turf"
       }
     },
     "node_modules/@turf/centroid": {
-      "version": "6.5.0",
-      "resolved": "https://registry.npmjs.org/@turf/centroid/-/centroid-6.5.0.tgz",
-      "integrity": "sha512-MwE1oq5E3isewPprEClbfU5pXljIK/GUOMbn22UM3IFPDJX0KeoyLNwghszkdmFp/qMGL/M13MMWvU+GNLXP/A==",
+      "version": "7.3.4",
+      "resolved": "https://registry.npmjs.org/@turf/centroid/-/centroid-7.3.4.tgz",
+      "integrity": "sha512-6c3kyTSKBrmiPMe75UkHw6MgedroZ6eR5usEvdlDhXgA3MudFPXIZkMFmMd1h9XeJ9xFfkmq+HPCdF0cOzvztA==",
+      "license": "MIT",
       "dependencies": {
-        "@turf/helpers": "^6.5.0",
-        "@turf/meta": "^6.5.0"
+        "@turf/helpers": "7.3.4",
+        "@turf/meta": "7.3.4",
+        "@types/geojson": "^7946.0.10",
+        "tslib": "^2.8.1"
       },
       "funding": {
         "url": "https://opencollective.com/turf"
       }
     },
     "node_modules/@turf/helpers": {
-      "version": "6.5.0",
-      "resolved": "https://registry.npmjs.org/@turf/helpers/-/helpers-6.5.0.tgz",
-      "integrity": "sha512-VbI1dV5bLFzohYYdgqwikdMVpe7pJ9X3E+dlr425wa2/sMJqYDhTO++ec38/pcPvPE6oD9WEEeU3Xu3gza+VPw==",
+      "version": "7.3.4",
+      "resolved": "https://registry.npmjs.org/@turf/helpers/-/helpers-7.3.4.tgz",
+      "integrity": "sha512-U/S5qyqgx3WTvg4twaH0WxF3EixoTCfDsmk98g1E3/5e2YKp7JKYZdz0vivsS5/UZLJeZDEElOSFH4pUgp+l7g==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/geojson": "^7946.0.10",
+        "tslib": "^2.8.1"
+      },
       "funding": {
         "url": "https://opencollective.com/turf"
       }
     },
     "node_modules/@turf/meta": {
-      "version": "6.5.0",
-      "resolved": "https://registry.npmjs.org/@turf/meta/-/meta-6.5.0.tgz",
-      "integrity": "sha512-RrArvtsV0vdsCBegoBtOalgdSOfkBrTJ07VkpiCnq/491W67hnMWmDu7e6Ztw0C3WldRYTXkg3SumfdzZxLBHA==",
+      "version": "7.3.4",
+      "resolved": "https://registry.npmjs.org/@turf/meta/-/meta-7.3.4.tgz",
+      "integrity": "sha512-tlmw9/Hs1p2n0uoHVm1w3ugw1I6L8jv9YZrcdQa4SH5FX5UY0ATrKeIvfA55FlL//PGuYppJp+eyg/0eb4goqw==",
+      "license": "MIT",
       "dependencies": {
-        "@turf/helpers": "^6.5.0"
+        "@turf/helpers": "7.3.4",
+        "@types/geojson": "^7946.0.10",
+        "tslib": "^2.8.1"
       },
       "funding": {
         "url": "https://opencollective.com/turf"
@@ -3120,7 +3209,6 @@
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@@ -15961,7 +15410,6 @@
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@@ -15970,7 +15418,6 @@
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@@ -15984,7 +15431,6 @@
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@@ -15993,7 +15439,6 @@
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@@ -16008,7 +15453,6 @@
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-      "dev": true,
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         "acorn": "bin/acorn"
       },
@@ -16019,14 +15463,12 @@
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-      "dev": true
+      "integrity": "sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ=="
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     "node_modules/terser/node_modules/source-map": {
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-      "dev": true,
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@@ -16035,7 +15477,6 @@
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-      "dev": true,
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@@ -16056,14 +15497,6 @@
         "node": ">=8"
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-      "resolved": "https://registry.npmjs.org/text-cache/-/text-cache-4.2.2.tgz",
-      "integrity": "sha512-zky+UDYiX0a/aPw/YTBD+EzKMlCTu1chFuCMZeAkgoRiceySdROu1V2kJXhCbtEdBhiOviYnAdGiSYl58HW0ZQ==",
-      "dependencies": {
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-      }
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       "resolved": "https://registry.npmjs.org/text-table/-/text-table-0.2.0.tgz",
@@ -16119,7 +15552,8 @@
     "node_modules/tinyqueue": {
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-      "integrity": "sha512-ppJZNDuKGgxzkHihX8v9v9G5f+18gzaTfrukGrq6ueg0lmH4nqVnA2IPG0AEH3jKEk2GRJCUhDoqpoiw3PHLBA=="
+      "integrity": "sha512-ppJZNDuKGgxzkHihX8v9v9G5f+18gzaTfrukGrq6ueg0lmH4nqVnA2IPG0AEH3jKEk2GRJCUhDoqpoiw3PHLBA==",
+      "license": "ISC"
     },
     "node_modules/tmpl": {
       "version": "1.0.5",
@@ -16146,6 +15580,7 @@
       "version": "1.0.1",
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+      "license": "MIT",
       "dependencies": {
         "parse-unit": "^1.0.1"
       }
@@ -16220,24 +15655,6 @@
         "node": ">=12"
       }
     },
-    "node_modules/triangulate-hypercube": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/triangulate-hypercube/-/triangulate-hypercube-1.0.1.tgz",
-      "integrity": "sha512-SAIacSBfUNfgeCna8q2i+1taOtFJkYuOqpduaJ1KUeOJpqc0lLKMYzPnZb4CA6KCOiD8Pd4YbuVq41wa9dvWyw==",
-      "dependencies": {
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-        "permutation-parity": "^1.0.0",
-        "permutation-rank": "^1.0.0"
-      }
-    },
-    "node_modules/triangulate-polyline": {
-      "version": "1.0.3",
-      "resolved": "https://registry.npmjs.org/triangulate-polyline/-/triangulate-polyline-1.0.3.tgz",
-      "integrity": "sha512-crJcVFtVPFYQ8r9iIhe9JqkauDvNWDSZLot8ly3DniSCO+zyUfKbtfD3fEoBaA5uMrQU/zBi11NBuVQeSToToQ==",
-      "dependencies": {
-        "cdt2d": "^1.0.0"
-      }
-    },
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       "resolved": "https://registry.npmjs.org/tsconfig/-/tsconfig-7.0.0.tgz",
@@ -16269,35 +15686,16 @@
       }
     },
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-      "version": "2.5.3",
-      "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.5.3.tgz",
-      "integrity": "sha512-mSxlJJwl3BMEQCUNnxXBU9jP4JBktcEGhURcPR6VQVlnP0FdDEsIaz0C35dXNGLyRfrATNofF0F5p2KPxQgB+w==",
-      "dev": true
-    },
-    "node_modules/turntable-camera-controller": {
-      "version": "3.0.1",
-      "resolved": "https://registry.npmjs.org/turntable-camera-controller/-/turntable-camera-controller-3.0.1.tgz",
-      "integrity": "sha512-UOGu9W/Mx053pAaczi0BEPqvWJOqSgtpdigWG9C8dX8rQVdyl2hWmpdJW3m15QrGxJtJHIhhDTHVtTZzPkd/FA==",
-      "dependencies": {
-        "filtered-vector": "^1.2.1",
-        "gl-mat4": "^1.0.2",
-        "gl-vec3": "^1.0.2"
-      }
-    },
-    "node_modules/two-product": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/two-product/-/two-product-1.0.2.tgz",
-      "integrity": "sha512-vOyrqmeYvzjToVM08iU52OFocWT6eB/I5LUWYnxeAPGXAhAxXYU/Yr/R2uY5/5n4bvJQL9AQulIuxpIsMoT8XQ=="
-    },
-    "node_modules/two-sum": {
-      "version": "1.0.0",
-      "resolved": "https://registry.npmjs.org/two-sum/-/two-sum-1.0.0.tgz",
-      "integrity": "sha512-phP48e8AawgsNUjEY2WvoIWqdie8PoiDZGxTDv70LDr01uX5wLEQbOgSP7Z/B6+SW5oLtbe8qaYX2fKJs3CGTw=="
+      "version": "2.8.1",
+      "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.8.1.tgz",
+      "integrity": "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w==",
+      "license": "0BSD"
     },
     "node_modules/type": {
-      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/type/-/type-1.2.0.tgz",
-      "integrity": "sha512-+5nt5AAniqsCnu2cEQQdpzCAh33kVx8n0VoFidKpB1dVVLAN/F+bgVOqOJqOnEnrhp222clB5p3vUlD+1QAnfg=="
+      "version": "2.7.3",
+      "resolved": "https://registry.npmjs.org/type/-/type-2.7.3.tgz",
+      "integrity": "sha512-8j+1QmAbPvLZow5Qpi6NCaN8FB60p/6x8/vfNqOk/hC+HuvFZhL4+WfekuhQLiqFZXOgQdrs3B+XxEmCc6b3FQ==",
+      "license": "ISC"
     },
     "node_modules/type-check": {
       "version": "0.4.0",
@@ -16342,6 +15740,7 @@
       "version": "1.2.0",
       "resolved": "https://registry.npmjs.org/typedarray-pool/-/typedarray-pool-1.2.0.tgz",
       "integrity": "sha512-YTSQbzX43yvtpfRtIDAYygoYtgT+Rpjuxy9iOpczrjpXLgGoyG7aS5USJXV2d3nn8uHTeb9rXDvzS27zUg5KYQ==",
+      "license": "MIT",
       "dependencies": {
         "bit-twiddle": "^1.0.0",
         "dup": "^1.0.0"
@@ -16438,16 +15837,6 @@
         "node": ">=4"
       }
     },
-    "node_modules/union-find": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/union-find/-/union-find-1.0.2.tgz",
-      "integrity": "sha512-wFA9bMD/40k7ZcpKVXfu6X1qD3ri5ryO8HUsuA1RnxPCQl66Mu6DgkxyR+XNnd+osD0aLENixcJVFj+uf+O4gw=="
-    },
-    "node_modules/uniq": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/uniq/-/uniq-1.0.1.tgz",
-      "integrity": "sha512-Gw+zz50YNKPDKXs+9d+aKAjVwpjNwqzvNpLigIruT4HA9lMZNdMqs9x07kKHB/L9WRzqp4+DlTU5s4wG2esdoA=="
-    },
     "node_modules/unique-filename": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/unique-filename/-/unique-filename-1.1.1.tgz",
@@ -16477,7 +15866,8 @@
     "node_modules/unquote": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/unquote/-/unquote-1.1.1.tgz",
-      "integrity": "sha512-vRCqFv6UhXpWxZPyGDh/F3ZpNv8/qo7w6iufLpQg9aKnQ71qM4B5KiI7Mia9COcjEhrO9LueHpMYjYzsWH3OIg=="
+      "integrity": "sha512-vRCqFv6UhXpWxZPyGDh/F3ZpNv8/qo7w6iufLpQg9aKnQ71qM4B5KiI7Mia9COcjEhrO9LueHpMYjYzsWH3OIg==",
+      "license": "MIT"
     },
     "node_modules/update-browserslist-db": {
       "version": "1.0.11",
@@ -16523,7 +15913,6 @@
       "version": "4.4.1",
       "resolved": "https://registry.npmjs.org/uri-js/-/uri-js-4.4.1.tgz",
       "integrity": "sha512-7rKUyy33Q1yc98pQ1DAmLtwX109F7TIfWlW1Ydo8Wl1ii1SeHieeh0HHfPeL2fMXK6z0s8ecKs9frCuLJvndBg==",
-      "dev": true,
       "dependencies": {
         "punycode": "^2.1.0"
       }
@@ -16609,20 +15998,6 @@
         "node": ">=10.12.0"
       }
     },
-    "node_modules/vectorize-text": {
-      "version": "3.2.2",
-      "resolved": "https://registry.npmjs.org/vectorize-text/-/vectorize-text-3.2.2.tgz",
-      "integrity": "sha512-34NVOCpMMQVXujU4vb/c6u98h6djI0jGdtC202H4Huvzn48B6ARsR7cmGh1xsAc0pHNQiUKGK/aHF05VtGv+eA==",
-      "dependencies": {
-        "cdt2d": "^1.0.0",
-        "clean-pslg": "^1.1.0",
-        "ndarray": "^1.0.11",
-        "planar-graph-to-polyline": "^1.0.6",
-        "simplify-planar-graph": "^2.0.1",
-        "surface-nets": "^1.0.0",
-        "triangulate-polyline": "^1.0.0"
-      }
-    },
     "node_modules/vee-validate": {
       "version": "2.2.15",
       "resolved": "https://registry.npmjs.org/vee-validate/-/vee-validate-2.2.15.tgz",
@@ -16632,6 +16007,7 @@
       "version": "3.1.3",
       "resolved": "https://registry.npmjs.org/vt-pbf/-/vt-pbf-3.1.3.tgz",
       "integrity": "sha512-2LzDFzt0mZKZ9IpVF2r69G9bXaP2Q2sArJCmcCgvfTdCCZzSyz4aCLoQyUilu37Ll56tCblIZrXFIjNUpGIlmA==",
+      "license": "MIT",
       "dependencies": {
         "@mapbox/point-geometry": "0.1.0",
         "@mapbox/vector-tile": "^1.3.1",
@@ -16918,7 +16294,6 @@
       "version": "2.4.0",
       "resolved": "https://registry.npmjs.org/watchpack/-/watchpack-2.4.0.tgz",
       "integrity": "sha512-Lcvm7MGST/4fup+ifyKi2hjyIAwcdI4HRgtvTpIUxBRhB+RFtUh8XtDOxUfctVCnhVi+QQj49i91OyvzkJl6cg==",
-      "dev": true,
       "dependencies": {
         "glob-to-regexp": "^0.4.1",
         "graceful-fs": "^4.1.2"
@@ -16930,12 +16305,8 @@
     "node_modules/weak-map": {
       "version": "1.0.8",
       "resolved": "https://registry.npmjs.org/weak-map/-/weak-map-1.0.8.tgz",
-      "integrity": "sha512-lNR9aAefbGPpHO7AEnY0hCFjz1eTkWCXYvkTRrTHs9qv8zJp+SkVYpzfLIFXQQiG3tVvbNFQgVg2bQS8YGgxyw=="
-    },
-    "node_modules/weakmap-shim": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/weakmap-shim/-/weakmap-shim-1.1.1.tgz",
-      "integrity": "sha512-/wNyG+1FpiHhnfQo+TuA/XAUpvOOkKVl0A4qpT+oGcj5SlZCLmM+M1Py/3Sj8sy+YrEauCVITOxCsZKo6sPbQg=="
+      "integrity": "sha512-lNR9aAefbGPpHO7AEnY0hCFjz1eTkWCXYvkTRrTHs9qv8zJp+SkVYpzfLIFXQQiG3tVvbNFQgVg2bQS8YGgxyw==",
+      "license": "Apache-2.0"
     },
     "node_modules/webgl-context": {
       "version": "2.2.0",
@@ -16958,7 +16329,6 @@
       "version": "5.88.0",
       "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.88.0.tgz",
       "integrity": "sha512-O3jDhG5e44qIBSi/P6KpcCcH7HD+nYIHVBhdWFxcLOcIGN8zGo5nqF3BjyNCxIh4p1vFdNnreZv2h2KkoAw3lw==",
-      "dev": true,
       "dependencies": {
         "@types/eslint-scope": "^3.7.3",
         "@types/estree": "^1.0.0",
@@ -17238,7 +16608,6 @@
       "version": "8.9.0",
       "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.9.0.tgz",
       "integrity": "sha512-jaVNAFBHNLXspO543WnNNPZFRtavh3skAkITqD0/2aeMkKZTN+254PyhwxFYrk3vQ1xfY+2wbesJMs/JC8/PwQ==",
-      "dev": true,
       "bin": {
         "acorn": "bin/acorn"
       },
@@ -17250,7 +16619,6 @@
       "version": "1.9.0",
       "resolved": "https://registry.npmjs.org/acorn-import-assertions/-/acorn-import-assertions-1.9.0.tgz",
       "integrity": "sha512-cmMwop9x+8KFhxvKrKfPYmN6/pKTYYHBqLa0DfvVZcKMJWNyWLnaqND7dx/qn66R7ewM1UX5XMaDVP5wlVTaVA==",
-      "dev": true,
       "peerDependencies": {
         "acorn": "^8"
       }
@@ -17259,7 +16627,6 @@
       "version": "3.2.3",
       "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.3.tgz",
       "integrity": "sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w==",
-      "dev": true,
       "engines": {
         "node": ">=10.13.0"
       }
@@ -17550,14 +16917,6 @@
       "funding": {
         "url": "https://github.com/sponsors/sindresorhus"
       }
-    },
-    "node_modules/zero-crossings": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/zero-crossings/-/zero-crossings-1.0.1.tgz",
-      "integrity": "sha512-iNIldMZaDtAyIJMJ8NnGVHeejH//y4eVmpXriM+q/B/BPNz+2E7oAgSnw9MXqCd3RbQ8W+hor7T2jEyRoc/s2A==",
-      "dependencies": {
-        "cwise-compiler": "^1.0.0"
-      }
     }
   }
 }
diff --git a/client/package.json b/client/package.json
index 47d7e72e6..598fa2315 100644
--- a/client/package.json
+++ b/client/package.json
@@ -66,10 +66,10 @@
     "backgrid-paginator": "0.3.9",
     "backgrid-select-all": "0.3.5",
     "ci": "^2.2.0",
-    "csv-file-validator": "^1.7.4",
-    "d3-scale": "^3.2.3",
-    "d3-scale-chromatic": "^2.0.0",
-    "d3-selection": "^2.0.0",
+    "csv-file-validator": "^2.2.0",
+    "d3-scale": "^4.0.2",
+    "d3-scale-chromatic": "^3.1.0",
+    "d3-selection": "^3.0.0",
     "flot-axislabels": "^1.0.0",
     "flot-pie": "^1.0.0",
     "font-awesome": "^4.2.0",
@@ -82,7 +82,7 @@
     "jquery.flot.tooltip": "^0.9.0",
     "lodash-es": "^4.17.21",
     "markdown": "^0.5.0",
-    "plotly.js": "^1.52.2",
+    "plotly.js": "^2.35.3",
     "portal-vue": "2.1.7",
     "promise": "^8.0.3",
     "tailwindcss": "^1.9.5",
diff --git a/client/src/js/modules/samples/components/PuckView.vue b/client/src/js/modules/samples/components/PuckView.vue
index 6aad77088..5b743dce2 100644
--- a/client/src/js/modules/samples/components/PuckView.vue
+++ b/client/src/js/modules/samples/components/PuckView.vue
@@ -128,9 +128,6 @@ export default {
         this.graphic = svg.append('g')
         this.labels = svg.append('g')
 
-        // The 'this' keyword gets bound to the d3 selection in 'on' method
-        let self = this
-
         // Draw circles for each sample location
         this.graphic.selectAll('.sample-cell')
           .data(this.preparedData)
@@ -144,19 +141,18 @@ export default {
             .style('stroke', '#666')
             .style('stroke-width', 4)
             .style("pointer-events","visible") // Required to capture mouse events on non-fill shapes
-            .on("click", function() {
-              let cellData = d3Select(this).data()[0]
-              self.onCellClicked(cellData)
+            .on("click", (event, d) => {
+              this.onCellClicked(d)
             })
             // Highlight is achieved by shrinking the cell radius
-            .on("mouseover", function() {
-              d3Select(this)
-                .attr('r', self.cell.highlightRadius)
+            .on("mouseover", (event) => {
+              d3Select(event.currentTarget)
+                .attr('r', this.cell.highlightRadius)
                 .style('stroke-width', 2)
             })
-            .on("mouseleave", function() {
-              d3Select(this)
-                .attr('r', self.cell.radius)
+            .on("mouseleave", (event) => {
+              d3Select(event.currentTarget)
+                .attr('r', this.cell.radius)
                 .style('stroke-width', 4)
             })
       },
diff --git a/client/src/js/modules/shipment/components/puck-view.vue b/client/src/js/modules/shipment/components/puck-view.vue
index b6e0cc85a..dca7cd701 100644
--- a/client/src/js/modules/shipment/components/puck-view.vue
+++ b/client/src/js/modules/shipment/components/puck-view.vue
@@ -196,8 +196,6 @@ export default {
       // Chart area
       this.graphic = svg.append('g')
       this.labels = svg.append('g')
-      // The 'this' keyword gets bound to the d3 selection in 'on' method
-      let self = this
       // Draw circles for each sample location
       this.graphic.selectAll('.sample-cell')
           .data(this.preparedData)
@@ -211,32 +209,25 @@ export default {
           .style('stroke', '#666')
           .style('stroke-width', 4)
           .style("pointer-events","visible") // Required to capture mouse events on non-fill shapes
-          .on("click", function() {
-            let cellData = d3Select(this).data()[0]
-            self.onCellClicked(cellData)
+          .on("click", (event, d) => {
+            this.onCellClicked(d)
           })
           // Highlight is achieved by shrinking the cell radius
-          .on("mouseover", function() {
-            d3Select(this)
-                .attr('r', self.cell.highlightRadius)
+          .on("mouseover", (event) => {
+            d3Select(event.currentTarget)
+                .attr('r', this.cell.highlightRadius)
                 .style('stroke-width', 2)
           })
-          .on("mouseleave", function() {
-            d3Select(this)
-                .attr('r', self.cell.radius)
+          .on("mouseleave", (event) => {
+            d3Select(event.currentTarget)
+                .attr('r', this.cell.radius)
                 .style('stroke-width', 4)
           })
     },
     // This method has some knowledge of the sample data
     // Used to inform the parent that a cell has been clicked
     onCellClicked: function(sampleData) {
-      if (sampleData && sampleData.BLSAMPLEID) {
-        // Convert to an actual index not string
-        this.$emit('cell-clicked', { location: + sampleData.LOCATION, type: 'puck' })
-      } else {
-        // All samples should have a location
-        this.$emit('cell-clicked', { location: + sampleData.LOCATION, type: 'puck' })
-      }
+      this.$emit('cell-clicked', { location: +sampleData.LOCATION, type: 'puck' })
     },
     updateSelected: function() {
       this.graphic.selectAll('.sample-cell')
diff --git a/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue b/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
index a1eeead75..f96e05a2a 100644
--- a/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
+++ b/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
@@ -34,7 +34,7 @@
               v-for="csvError in csvErrors"
               style="color:red; font-size:medium"
             >
-              {{ csvError }}
+              {{ csvError.message }}
             </li>
           </ul>
           <ul>
@@ -279,6 +279,7 @@
     const headerError = (headerName) => {
         return `Please add a column header for ${headerName}`
     }
+    let acronymTracker = []
 
     const csvConfig = {
         headers: [
@@ -287,6 +288,10 @@
                 inputName: 'acronym',
                 required: true,
                 requiredError,
+                unique: true,
+                uniqueError: function(headerName, rowNumber) {
+                    return `${headerName} is not unique in row ${rowNumber}`;
+                },
                 headerError
             },
             {
@@ -385,8 +390,6 @@
                 csvData: [],
                 csvErrors: [],
                 commaInComments: false,
-                duplicateAcronym: false,
-                duplicateAcronymRows: [],
                 proteinid: null,
                 externalid: null,
                 sampleGroupCollection: null,
@@ -700,8 +703,6 @@
             setCSVFile: function(event){
                 this.csvData = []
                 this.csvErrors = []
-                this.duplicateAcronym = false
-                this.duplicateAcronymRows = []
 
                 if(event.target.files.length === 0){
                     this.fileValid = false
@@ -712,38 +713,35 @@
                 this.csvFile = event.target.files[0]
                 var self = this
                 var ready = false
+                const fileInput = event && event.target
 
                 // callback function to make sure we have finished trimming white space from uploaded file
                 // before passing it through the CSVFileValidator
                 var check = function(){
                     if(ready === true){
+                        acronymTracker = []
                         CSVFileValidator(self.csvFile, csvConfig)
                         .then(csvData => {
                             self.csvData = csvData.data
-                            self.csvErrors = csvData.inValidMessages
+                            self.csvErrors = csvData.inValidData
 
                             if(self.commaInComments)
-                                self.csvErrors.push("Column count is greater than expected, you likely have a comma in a comment. Please remove any additional commas")
+                                self.csvErrors.push({ message: "Column count is greater than expected, you likely have a comma in a comment. Please remove any additional commas" })
 
                             if(self.csvData.length < 1 && self.csvErrors.length === 0){
-                                self.csvErrors.push("Only headers have been submitted, please add some sample information")
+                                self.csvErrors.push({ message: "Only headers have been submitted, please add some sample information" })
                             }
 
-                            if(self.duplicateAcronym)
-                                self.csvErrors = self.csvErrors.concat(self.duplicateAcronymRows)
-
-                            if(self.csvErrors.length === 0)
-                                self.fileValid = true
-                            else {
-                                self.fileValid = false
-                                event.target.value = ''
+                            self.fileValid = self.csvErrors.length === 0
+                            if (!self.fileValid && fileInput) {
+                                fileInput.value = ''
                             }
 
                             console.log(csvData.data)
-                            console.log(csvData.inValidMessages)
+                            console.log(csvData.inValidData)
                         })
                     } else {
-                        setTimeout(check, 1000)
+                        setTimeout(check, 100)
                     }
                 }
                 check()
@@ -758,58 +756,20 @@
                     self.commaInComments = false;
                     var newLineSplit = e.target.result.split("\n")
                     newLineSplit.forEach(function(row){
-                        var cells = row.split(',')
-                        if(cells.length > 5){
-                            self.commaInComments = true
-                            ready = true
-                        }
+                        if(row.split(',').length > 5) self.commaInComments = true
                     })
 
-                    // Display duplicate acronyms and the row they are on (only in file duplicates, not against database)
-                    // Hopefully this issue gets implemented then we can remove all this. https://github.com/shystruk/csv-file-validator/issues/20
-                    var acronyms = []
-                    var acronymIndex = 5
-
-                    for(var i=0; i<newLineSplit.length; i++){
-                        var cells = newLineSplit[i].split(',')
-
-                        for(var j=0; j<cells.length; j++){
-                            // if first row check which column is the Acronym
-                            if(i === 0){
-                                if(cells[j] === 'Acronym'){
-                                    acronymIndex = j
-                                    break
-                                }
-                            }
-                            // ignore any non acronym columns
-                            if(j !== acronymIndex) break
-
-                            for(let k=0; k < acronyms.length; k++){
-                                if(acronyms[k] === cells[j]){
-                                    var currentRow = i
-                                    self.duplicateAcronym = true
-                                    self.duplicateAcronymRows.push(cells[j] + ' is a duplicate acronym on row ' + ++currentRow)
-                                    break
-                                }
-                            }
-
-                            acronyms[i] = cells[acronymIndex]
-                        }
-                    }
-
                     // Remove all leading and trailing white space
                     // Also clean up trailing commas on each row to ensure new line works as expected
                     var trimmed = ''
                     newLineSplit.forEach(function(row){
                         var cells = row.split(',')
                         cells.forEach(function(cell, index){
-                            i = index + 1
                             trimmed += cell.trim()
-                            if(cells.length !== i){
+                            if(cells.length !== index + 1){
                                 trimmed += ','
                             } else {
-                                if(trimmed.endsWith(','))
-                                    trimmed = trimmed.substring(0, trimmed.length-1)
+                                if(trimmed.endsWith(',')) trimmed = trimmed.slice(0, -1)
                                 trimmed += "\n"
                             }
                         })

From 9001f3a99e5d8608a8170c55c057c5d4e8bc9e02 Mon Sep 17 00:00:00 2001
From: Mark Williams <mark.williams@diamond.ac.uk>
Date: Wed, 8 Apr 2026 17:27:31 +0100
Subject: [PATCH 2/3] LIMS-2015: Remove debug code

---
 .../js/modules/types/xpdf/samples/views/vue-simplesample.vue    | 2 --
 1 file changed, 2 deletions(-)

diff --git a/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue b/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
index f96e05a2a..375aaf672 100644
--- a/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
+++ b/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
@@ -279,7 +279,6 @@
     const headerError = (headerName) => {
         return `Please add a column header for ${headerName}`
     }
-    let acronymTracker = []
 
     const csvConfig = {
         headers: [
@@ -719,7 +718,6 @@
                 // before passing it through the CSVFileValidator
                 var check = function(){
                     if(ready === true){
-                        acronymTracker = []
                         CSVFileValidator(self.csvFile, csvConfig)
                         .then(csvData => {
                             self.csvData = csvData.data

From ae3f66bf84ee599cec8b12df7ed49ad79ce10932 Mon Sep 17 00:00:00 2001
From: Mark Williams <mark.williams@diamond.ac.uk>
Date: Mon, 18 May 2026 12:38:13 +0100
Subject: [PATCH 3/3] LIMS-2015: Fix merge conflicts

---
 client/package-lock.json                            | 13 +------------
 client/package.json                                 | 13 +------------
 .../types/xpdf/samples/views/vue-simplesample.vue   | 13 -------------
 3 files changed, 2 insertions(+), 37 deletions(-)

diff --git a/client/package-lock.json b/client/package-lock.json
index 3c6baf1f3..654c52ee4 100644
--- a/client/package-lock.json
+++ b/client/package-lock.json
@@ -18,17 +18,10 @@
         "backgrid-paginator": "0.3.9",
         "backgrid-select-all": "0.3.5",
         "ci": "^2.2.0",
-<<<<<<< improvement/LIMS-2015/update-js-libraries
         "csv-file-validator": "^2.2.0",
         "d3-scale": "^4.0.2",
         "d3-scale-chromatic": "^3.1.0",
         "d3-selection": "^3.0.0",
-=======
-        "csv-file-validator": "^1.10.2",
-        "d3-scale": "^3.2.3",
-        "d3-scale-chromatic": "^2.0.0",
-        "d3-selection": "^2.0.0",
->>>>>>> master
         "flot-axislabels": "^1.0.0",
         "flot-pie": "^1.0.0",
         "font-awesome": "^4.2.0",
@@ -41,12 +34,8 @@
         "jquery.flot.tooltip": "^0.9.0",
         "lodash-es": "^4.17.21",
         "markdown": "^0.5.0",
-<<<<<<< improvement/LIMS-2015/update-js-libraries
-        "plotly.js": "^2.35.3",
-=======
         "papaparse": "^5.4.1",
-        "plotly.js": "^1.52.2",
->>>>>>> master
+        "plotly.js": "^2.35.3",
         "portal-vue": "2.1.7",
         "promise": "^8.0.3",
         "tailwindcss": "^1.9.5",
diff --git a/client/package.json b/client/package.json
index 5d220cadb..b130f2440 100644
--- a/client/package.json
+++ b/client/package.json
@@ -66,17 +66,10 @@
     "backgrid-paginator": "0.3.9",
     "backgrid-select-all": "0.3.5",
     "ci": "^2.2.0",
-<<<<<<< improvement/LIMS-2015/update-js-libraries
     "csv-file-validator": "^2.2.0",
     "d3-scale": "^4.0.2",
     "d3-scale-chromatic": "^3.1.0",
     "d3-selection": "^3.0.0",
-=======
-    "csv-file-validator": "^1.10.2",
-    "d3-scale": "^3.2.3",
-    "d3-scale-chromatic": "^2.0.0",
-    "d3-selection": "^2.0.0",
->>>>>>> master
     "flot-axislabels": "^1.0.0",
     "flot-pie": "^1.0.0",
     "font-awesome": "^4.2.0",
@@ -89,12 +82,8 @@
     "jquery.flot.tooltip": "^0.9.0",
     "lodash-es": "^4.17.21",
     "markdown": "^0.5.0",
-<<<<<<< improvement/LIMS-2015/update-js-libraries
-    "plotly.js": "^2.35.3",
-=======
     "papaparse": "^5.4.1",
-    "plotly.js": "^1.52.2",
->>>>>>> master
+    "plotly.js": "^2.35.3",
     "portal-vue": "2.1.7",
     "promise": "^8.0.3",
     "tailwindcss": "^1.9.5",
diff --git a/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue b/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
index 051930ed3..375aaf672 100644
--- a/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
+++ b/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
@@ -288,13 +288,8 @@
                 required: true,
                 requiredError,
                 unique: true,
-<<<<<<< improvement/LIMS-2015/update-js-libraries
                 uniqueError: function(headerName, rowNumber) {
                     return `${headerName} is not unique in row ${rowNumber}`;
-=======
-                uniqueError: function(headerName, rowNumber){
-                    return `${headerName} is not unique in row ${rowNumber}`
->>>>>>> master
                 },
                 headerError
             },
@@ -735,17 +730,9 @@
                                 self.csvErrors.push({ message: "Only headers have been submitted, please add some sample information" })
                             }
 
-<<<<<<< improvement/LIMS-2015/update-js-libraries
                             self.fileValid = self.csvErrors.length === 0
                             if (!self.fileValid && fileInput) {
                                 fileInput.value = ''
-=======
-                            if(self.csvErrors.length === 0)
-                                self.fileValid = true
-                            else {
-                                self.fileValid = false
-                                event.target.value = ''
->>>>>>> master
                             }
 
                             console.log(csvData.data)