From e6df08d71dba983b301d663d36ad915df43b51c2 Mon Sep 17 00:00:00 2001
From: Andy Boughton <abought@gmail.com>
Date: Wed, 15 Dec 2021 16:29:43 -0500
Subject: [PATCH 1/3] Downgrade tabulator to v4, due to some "fascinating"
 build issues involving tabulator.css in a webpack 5 environment

Also fix minor display quirks with plot height
---
 package-lock.json                 | 743 +-----------------------------
 package.json                      |   4 +-
 src/components/ExportData.vue     |   2 +-
 src/components/TabulatorTable.vue |  11 +-
 src/util/lz-helpers.js            |   3 +-
 vue.config.js                     |  18 -
 6 files changed, 14 insertions(+), 767 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index dd90fd8..02bbb4b 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "localzoom",
-  "version": "0.9.3",
+  "version": "0.9.4",
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   "requires": true,
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@@ -1846,12 +1846,6 @@
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-      "dev": true,
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-      "dev": true,
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@@ -6238,18 +6151,6 @@
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@@ -6451,17 +6284,6 @@
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     },
-    "stdout-stream": {
-      "version": "1.4.1",
-      "resolved": "https://registry.npmjs.org/stdout-stream/-/stdout-stream-1.4.1.tgz",
-      "integrity": "sha512-j4emi03KXqJWcIeF8eIXkjMFN1Cmb8gUlDYGeBALLPo5qdyTfA9bOtl8m33lRoC+vFMkP3gl0WsDr6+gzxbbTA==",
-      "dev": true,
-      "requires": {
-        "readable-stream": "^2.0.1"
-      }
-    },
     "stealthy-require": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/stealthy-require/-/stealthy-require-1.1.1.tgz",
@@ -12527,15 +11840,6 @@
       "integrity": "sha512-BrpvfNAE3dcvq7ll3xVumzjKjZQ5tI1sEUIKr3Uoks0XUl45St3FlatVqef9prk4jRDzhW6WZg+3bk93y6pLjA==",
       "dev": true
     },
-    "strip-indent": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/strip-indent/-/strip-indent-1.0.1.tgz",
-      "integrity": "sha1-DHlipq3vp7vUrDZkYKY4VSrhoKI=",
-      "dev": true,
-      "requires": {
-        "get-stdin": "^4.0.1"
-      }
-    },
     "strip-json-comments": {
       "version": "2.0.1",
       "resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-2.0.1.tgz",
@@ -12952,9 +12256,9 @@
       }
     },
     "tabulator-tables": {
-      "version": "5.0.7",
-      "resolved": "https://registry.npmjs.org/tabulator-tables/-/tabulator-tables-5.0.7.tgz",
-      "integrity": "sha512-aMSgLba3uGJJ287pku/T5BazGGkWnnlCYDjDVMvLkeiUNBD2enMBYuskauQFM9Rq0dhiXklg1JhvvmgzvxB8eg=="
+      "version": "4.9.3",
+      "resolved": "https://registry.npmjs.org/tabulator-tables/-/tabulator-tables-4.9.3.tgz",
+      "integrity": "sha512-iwwQqAEGGxlgrBpcmJJvMJrfjGLcCXOB3AOb/DGkXqBy1YKoYA36hIl7qXGp6Jo8dSkzFAlDT6pKLZgyhs9OnQ=="
     },
     "tapable": {
       "version": "0.1.10",
@@ -12962,17 +12266,6 @@
       "integrity": "sha1-KcNXB8K3DlDQdIK10gLo7URtr9Q=",
       "dev": true
     },
-    "tar": {
-      "version": "2.2.2",
-      "resolved": "https://registry.npmjs.org/tar/-/tar-2.2.2.tgz",
-      "integrity": "sha512-FCEhQ/4rE1zYv9rYXJw/msRqsnmlje5jHP6huWeBZ704jUTy02c5AZyWujpMR1ax6mVw9NyJMfuK2CMDWVIfgA==",
-      "dev": true,
-      "requires": {
-        "block-stream": "*",
-        "fstream": "^1.0.12",
-        "inherits": "2"
-      }
-    },
     "terser": {
       "version": "4.8.0",
       "resolved": "https://registry.npmjs.org/terser/-/terser-4.8.0.tgz",
@@ -13378,21 +12671,6 @@
         }
       }
     },
-    "trim-newlines": {
-      "version": "1.0.0",
-      "resolved": "https://registry.npmjs.org/trim-newlines/-/trim-newlines-1.0.0.tgz",
-      "integrity": "sha1-WIeWa7WCpFA6QetST301ARgVphM=",
-      "dev": true
-    },
-    "true-case-path": {
-      "version": "1.0.3",
-      "resolved": "https://registry.npmjs.org/true-case-path/-/true-case-path-1.0.3.tgz",
-      "integrity": "sha512-m6s2OdQe5wgpFMC+pAJ+q9djG82O2jcHPOI6RNg1yy9rCYR+WD6Nbpl32fDpfC56nirdRy+opFa/Vk7HYhqaew==",
-      "dev": true,
-      "requires": {
-        "glob": "^7.1.2"
-      }
-    },
     "tryer": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/tryer/-/tryer-1.0.1.tgz",
@@ -14665,15 +13943,6 @@
       "integrity": "sha1-2e8H3Od7mQK4o6j6SzHD4/fm6Ho=",
       "dev": true
     },
-    "wide-align": {
-      "version": "1.1.5",
-      "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.5.tgz",
-      "integrity": "sha512-eDMORYaPNZ4sQIuuYPDHdQvf4gyCF9rEEV/yPxGfwPkRodwEgiMUUXTx/dex+Me0wxx53S+NgUHaP7y3MGlDmg==",
-      "dev": true,
-      "requires": {
-        "string-width": "^1.0.2 || 2 || 3 || 4"
-      }
-    },
     "word-wrap": {
       "version": "1.2.3",
       "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.3.tgz",
diff --git a/package.json b/package.json
index c3dd083..61fb27e 100644
--- a/package.json
+++ b/package.json
@@ -22,7 +22,7 @@
     "bootstrap-vue": "^2.21.2",
     "locuszoom": "git+https://github.com/statgen/locuszoom.git#33316cd",
     "lodash": "^4.17.11",
-    "tabulator-tables": "^5.0.7",
+    "tabulator-tables": "^4.9.3",
     "vue": "^2.6.14",
     "vue-bootstrap-typeahead": "^0.2.6"
   },
@@ -36,8 +36,6 @@
     "@vue/test-utils": "^1.2.2",
     "autoprefixer": "^9.8.8",
     "chai": "^4.3.4",
-    "node-sass": "^4.9.0",
-    "sass-loader": "^7.0.1",
     "source-map-loader": "^0.2.4",
     "vue-template-compiler": "^2.6.14"
   }
diff --git a/src/components/ExportData.vue b/src/components/ExportData.vue
index 4e4e5c0..0024521 100644
--- a/src/components/ExportData.vue
+++ b/src/components/ExportData.vue
@@ -150,7 +150,7 @@ export default {
           :columns="table_config"
           :initial-sort="[{column: 'assoc:log_pvalue', dir: 'desc'}]"
           :table_data="table_data"
-          height="300px"
+          height="500px"
           placeholder="No data available for selected study in the specified region"
           @connected="table = $event" />
       </div>
diff --git a/src/components/TabulatorTable.vue b/src/components/TabulatorTable.vue
index eaaf90d..2b68ee8 100644
--- a/src/components/TabulatorTable.vue
+++ b/src/components/TabulatorTable.vue
@@ -1,6 +1,6 @@
 <script>
-import {TabulatorFull as Tabulator} from 'tabulator-tables';
-import 'tabulator-tables/dist/css/tabulator_bootstrap4.css';
+import Tabulator from 'tabulator-tables';
+import 'tabulator-tables/dist/css/bootstrap/tabulator_bootstrap4.css';
 
 export default {
     name: 'TabulatorTable',
@@ -33,15 +33,12 @@ export default {
         this.tabulator = null;
     },
     mounted() {
-        const { table_data, columns, initialSort, layout, layoutColumnsOnNewData, height, placeholder } = this;
+        const { table_data: data, columns, initialSort, layout, layoutColumnsOnNewData, height, placeholder } = this;
         this.tabulator = new Tabulator(
             this.$refs.table,
-            { data: [], columns, initialSort, layout, layoutColumnsOnNewData, height, placeholder },
+            { data, columns, initialSort, layout, layoutColumnsOnNewData, height, placeholder },
         );
 
-        this.tabulator.on('tableBuilt', () => {
-            this.tabulator.setData(table_data);
-        });
         // Expose a reference to the raw table object, for advanced usages such as click events
         this.$emit('connected', this.tabulator);
     },
diff --git a/src/util/lz-helpers.js b/src/util/lz-helpers.js
index a3b1c07..3bd7e83 100644
--- a/src/util/lz-helpers.js
+++ b/src/util/lz-helpers.js
@@ -79,6 +79,7 @@ LocusZoom.Layouts.add('data_layer', 'localzoom_assoc', localzoom_assoc_layer);
 const localzoom_assoc_panel = function () {
     // LocalZoom renders an association track with several annotations that are not combined anywhere else; we define a custom track
     const base = LocusZoom.Layouts.get('panel', 'association', {
+        min_height: 300,
         height: 300,
         data_layers: [
             LocusZoom.Layouts.get('data_layer', 'significance'),
@@ -253,7 +254,7 @@ function createGwasStudyLayout(
             namespace,
             title: {
                 text: `GWAS Catalog hits for ${display_name}`,
-                style: { 'font-size': '14px' },
+                style: { 'font-size': '150%' },
                 x: 50,
             },
         }),
diff --git a/vue.config.js b/vue.config.js
index d14426d..fc9bd88 100644
--- a/vue.config.js
+++ b/vue.config.js
@@ -1,5 +1,3 @@
-const path = require('path');
-
 const autoprefixer = require('autoprefixer');
 
 module.exports = {
@@ -15,22 +13,6 @@ module.exports = {
             .use('source-map-loader')
             .loader('source-map-loader')
             .end();
-
-        // Tabulator v5 uses babel syntax that, by default, vue cli doesn't know how to transpile. Add support in.
-        //  TODO: This should be removable in the future as newer vue cli releases stabilize.
-        config.module
-            .rule('supportChaining')
-            .test(/\.js$/)
-            .include
-            .add(path.resolve('node_modules/tabulator-tables'))
-            .end()
-            .use('babel-loader')
-            .loader('babel-loader')
-            .tap((options) => ({
-                ...options,
-                plugins : ['@babel/plugin-proposal-optional-chaining'],
-            }))
-            .end();
     },
     configureWebpack: {
         // Ensure that (decent) source maps are used, even in development

From f0bdeb9ab0a4b73d65110a8af4f740cce39ce3cf Mon Sep 17 00:00:00 2001
From: Andy Boughton <abought@gmail.com>
Date: Mon, 28 Feb 2022 13:29:21 -0500
Subject: [PATCH 2/3] Use Lzjs v0.14.0-beta.4

---
 package-lock.json | 89 +++++++++++++++++++++++++++--------------------
 package.json      |  2 +-
 2 files changed, 53 insertions(+), 38 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 02bbb4b..d5c6113 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -6053,9 +6053,9 @@
       }
     },
     "follow-redirects": {
-      "version": "1.13.2",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.13.2.tgz",
-      "integrity": "sha512-6mPTgLxYm3r6Bkkg0vNM0HTjfGrOEtsfbhagQvbxDEsEkpNhw582upBaoRZylzen6krEmxXJgt9Ju6HiI4O7BA==",
+      "version": "1.14.9",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.9.tgz",
+      "integrity": "sha512-MQDfihBQYMcyy5dhRDJUHcw7lb2Pv/TuE6xP1vyraLukNDHKbDxDNaOE3NbCAdKQApno+GPRyo1YAp89yCjK4w==",
       "dev": true
     },
     "for-in": {
@@ -7710,14 +7710,29 @@
       }
     },
     "locuszoom": {
-      "version": "git+https://github.com/statgen/locuszoom.git#33316cde4b0270aa7b8c027a68b8f65b1bd843f5",
-      "from": "git+https://github.com/statgen/locuszoom.git#33316cd",
+      "version": "git+https://github.com/statgen/locuszoom.git#674d25cc7fb338ff6c2b378e538e6de2b0ec5a8a",
+      "from": "git+https://github.com/statgen/locuszoom.git#674d25c",
       "requires": {
+        "@hapi/topo": "^5.1.0",
         "d3": "^5.16.0",
         "gwas-credible-sets": "^0.1.0",
         "just-clone": "^3.2.1",
-        "tabix-reader": "^1.0.1",
-        "undercomplicate": "^0.1.1"
+        "tabix-reader": "^1.0.1"
+      },
+      "dependencies": {
+        "@hapi/hoek": {
+          "version": "9.2.1",
+          "resolved": "https://registry.npmjs.org/@hapi/hoek/-/hoek-9.2.1.tgz",
+          "integrity": "sha512-gfta+H8aziZsm8pZa0vj04KO6biEiisppNgA1kbJvFrrWu9Vm7eaUEy76DIxsuTaWvti5fkJVhllWc6ZTE+Mdw=="
+        },
+        "@hapi/topo": {
+          "version": "5.1.0",
+          "resolved": "https://registry.npmjs.org/@hapi/topo/-/topo-5.1.0.tgz",
+          "integrity": "sha512-foQZKJig7Ob0BMAYBfcJk8d77QtOe7Wo4ox7ff1lQYoNNAb6jwcY1ncdoy2e9wQZzvNy7ODZCYJkK8kzmcAnAg==",
+          "requires": {
+            "@hapi/hoek": "^9.0.0"
+          }
+        }
       }
     },
     "lodash": {
@@ -8540,9 +8555,33 @@
       }
     },
     "node-fetch": {
-      "version": "2.6.1",
-      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.1.tgz",
-      "integrity": "sha512-V4aYg89jEoVRxRb2fJdAg8FHvI7cEyYdVAh94HH0UIK8oJxUfkjlDQN9RbMx+bEjP7+ggMiFRprSti032Oipxw=="
+      "version": "2.6.7",
+      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz",
+      "integrity": "sha512-ZjMPFEfVx5j+y2yF35Kzx5sF7kDzxuDj6ziH4FFbOp87zKDZNx8yExJIb05OGF4Nlt9IHFIMBkRl41VdvcNdbQ==",
+      "requires": {
+        "whatwg-url": "^5.0.0"
+      },
+      "dependencies": {
+        "tr46": {
+          "version": "0.0.3",
+          "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz",
+          "integrity": "sha1-gYT9NH2snNwYWZLzpmIuFLnZq2o="
+        },
+        "webidl-conversions": {
+          "version": "3.0.1",
+          "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz",
+          "integrity": "sha1-JFNCdeKnvGvnvIZhHMFq4KVlSHE="
+        },
+        "whatwg-url": {
+          "version": "5.0.0",
+          "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
+          "integrity": "sha1-lmRU6HZUYuN2RNNib2dCzotwll0=",
+          "requires": {
+            "tr46": "~0.0.3",
+            "webidl-conversions": "^3.0.0"
+          }
+        }
+      }
     },
     "node-forge": {
       "version": "0.10.0",
@@ -12786,30 +12825,6 @@
         }
       }
     },
-    "undercomplicate": {
-      "version": "0.1.1",
-      "resolved": "https://registry.npmjs.org/undercomplicate/-/undercomplicate-0.1.1.tgz",
-      "integrity": "sha512-F/rOQ2x3YgH5YcEU+xUKxbv1GGF1znTrBi7MRvqtcDgwubNQ/HGLZbgZh2mHpX0z9AM0T2Pg3zqPwKWYK+VJhQ==",
-      "requires": {
-        "@hapi/topo": "^5.1.0",
-        "just-clone": "^3.2.1"
-      },
-      "dependencies": {
-        "@hapi/hoek": {
-          "version": "9.2.1",
-          "resolved": "https://registry.npmjs.org/@hapi/hoek/-/hoek-9.2.1.tgz",
-          "integrity": "sha512-gfta+H8aziZsm8pZa0vj04KO6biEiisppNgA1kbJvFrrWu9Vm7eaUEy76DIxsuTaWvti5fkJVhllWc6ZTE+Mdw=="
-        },
-        "@hapi/topo": {
-          "version": "5.1.0",
-          "resolved": "https://registry.npmjs.org/@hapi/topo/-/topo-5.1.0.tgz",
-          "integrity": "sha512-foQZKJig7Ob0BMAYBfcJk8d77QtOe7Wo4ox7ff1lQYoNNAb6jwcY1ncdoy2e9wQZzvNy7ODZCYJkK8kzmcAnAg==",
-          "requires": {
-            "@hapi/hoek": "^9.0.0"
-          }
-        }
-      }
-    },
     "unicode-canonical-property-names-ecmascript": {
       "version": "1.0.4",
       "resolved": "https://registry.npmjs.org/unicode-canonical-property-names-ecmascript/-/unicode-canonical-property-names-ecmascript-1.0.4.tgz",
@@ -13052,9 +13067,9 @@
       }
     },
     "url-parse": {
-      "version": "1.5.3",
-      "resolved": "https://registry.npmjs.org/url-parse/-/url-parse-1.5.3.tgz",
-      "integrity": "sha512-IIORyIQD9rvj0A4CLWsHkBBJuNqWpFQe224b6j9t/ABmquIS0qDU2pY6kl6AuOrL5OkCXHMCFNe1jBcuAggjvQ==",
+      "version": "1.5.10",
+      "resolved": "https://registry.npmjs.org/url-parse/-/url-parse-1.5.10.tgz",
+      "integrity": "sha512-WypcfiRhfeUP9vvF0j6rw0J3hrWrw6iZv3+22h6iRMJ/8z1Tj6XfLP4DsUix5MhMPnXpiHDoKyoZ/bdCkwBCiQ==",
       "dev": true,
       "requires": {
         "querystringify": "^2.1.1",
diff --git a/package.json b/package.json
index 61fb27e..f7d2107 100644
--- a/package.json
+++ b/package.json
@@ -20,7 +20,7 @@
     "@sentry/browser": "^4.5.2",
     "bootstrap": "^4.4.1",
     "bootstrap-vue": "^2.21.2",
-    "locuszoom": "git+https://github.com/statgen/locuszoom.git#33316cd",
+    "locuszoom": "git+https://github.com/statgen/locuszoom.git#674d25c",
     "lodash": "^4.17.11",
     "tabulator-tables": "^4.9.3",
     "vue": "^2.6.14",

From 4fd566c2b4e1d7f72cbcdf27b4108b69e0fb745b Mon Sep 17 00:00:00 2001
From: Andy Boughton <abought@gmail.com>
Date: Mon, 28 Feb 2022 14:01:30 -0500
Subject: [PATCH 3/3] Release 0.9.5

---
 package-lock.json | 5 ++---
 package.json      | 2 +-
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index d5c6113..9117a91 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "localzoom",
-  "version": "0.9.4",
+  "version": "0.9.5",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
@@ -14067,8 +14067,7 @@
       "dependencies": {
         "ansi-regex": {
           "version": "5.0.0",
-          "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.0.tgz",
-          "integrity": "sha512-bY6fj56OUQ0hU1KjFNDQuJFezqKdrAyFdIevADiqrWHwSlbmBNMHp5ak2f40Pm8JTFyM2mqxkG6ngkHO11f/lg==",
+          "resolved": "",
           "dev": true
         },
         "ansi-styles": {
diff --git a/package.json b/package.json
index f7d2107..d28b5ae 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "localzoom",
-  "version": "0.9.4",
+  "version": "0.9.5",
   "license": "MIT",
   "engines": {
     "node": ">=10.13.0"