From 7f2ef8a8a3d8784daf083f2b26c933e64c8a6d8f Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Thu, 19 Dec 2019 13:05:28 -0500 Subject: [PATCH 1/6] Avoid implicit `event` argument --- assets/js/pages/gwas_upload.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/js/pages/gwas_upload.js b/assets/js/pages/gwas_upload.js index 10474f3..e17c0d1 100644 --- a/assets/js/pages/gwas_upload.js +++ b/assets/js/pages/gwas_upload.js @@ -185,7 +185,7 @@ fileField.addEventListener('click', function(e) { e.target.value = null; }); -fileField.addEventListener('change', function (e) { +fileField.addEventListener('change', function (event) { // Custom validators for uploaded file // Ref: https://developer.mozilla.org/en-US/docs/Web/Guide/HTML/HTML5/Constraint_validation#Limiting_the_size_of_a_file_before_its_upload fileField.setCustomValidity(''); From ec5b6fdcda4401d2ec642477fa7433a7fa59ea56 Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Thu, 19 Dec 2019 15:18:44 -0500 Subject: [PATCH 2/6] Fix nearest gene sort error ("match is not a function" when auto-detecting sort type) --- assets/js/pages/gwas_summary.js | 1 + 1 file changed, 1 insertion(+) diff --git a/assets/js/pages/gwas_summary.js b/assets/js/pages/gwas_summary.js index be407fe..176d77f 100644 --- a/assets/js/pages/gwas_summary.js +++ b/assets/js/pages/gwas_summary.js @@ -44,6 +44,7 @@ function createTopHitsTable(selector, data, region_url) { { title: 'Nearest gene(s)', field: 'nearest_genes', + sorter: 'string', formatter: cell => { const genes = cell.getValue() || []; // There will be studies that predate this feature, and won't have a value // Convert the list of ensg/symbol objects to a string- eventually we can add links to ext DB From 80e3881551384cef2383a6bc71eedcdca55d3e97 Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Thu, 16 Jan 2020 17:55:35 -0500 Subject: [PATCH 3/6] Incorporate bugfixes + features from newest localzoom --- assets/js/pages/gwas_region.js | 6 +- assets/js/pages/gwas_upload.js | 4 +- assets/js/util/lz-helpers.js | 2 +- assets/vue/gwas_region.vue | 8 +- assets/vue/gwas_upload.vue | 2 +- .../templates/gwas/gwas_region.html | 29 +- package.json | 4 +- yarn.lock | 1738 +++++++++-------- 8 files changed, 924 insertions(+), 869 deletions(-) diff --git a/assets/js/pages/gwas_region.js b/assets/js/pages/gwas_region.js index 7faeaaf..45366a0 100644 --- a/assets/js/pages/gwas_region.js +++ b/assets/js/pages/gwas_region.js @@ -2,9 +2,9 @@ import Vue from 'vue'; import App from '../../vue/gwas_region.vue'; import { paramsFromUrl } from 'locuszoom/dist/ext/lz-dynamic-urls.min'; -import { stateUrlMapping } from 'locuszoom-tabix/src/util/lz-helpers'; -import { getBasicSources, createStudyLayout, getBasicLayout } from 'locuszoom-tabix/src/util/lz-helpers'; +import { stateUrlMapping, getBasicSources, createStudyLayout, getBasicLayout } from 'localzoom/src/util/lz-helpers'; +import count_region_view from 'localzoom/src/util/metrics'; import { createStudyAssocSources } from '../util/lz-helpers'; function makePlot(template_vars) { @@ -38,4 +38,6 @@ function makePlot(template_vars) { })}).$mount('#app'); } +// On page load, generate a plot, and send Google Analytics metrics if applicable window.lz_widget = makePlot(window.template_args); +count_region_view(); diff --git a/assets/js/pages/gwas_upload.js b/assets/js/pages/gwas_upload.js index e17c0d1..4c9a667 100644 --- a/assets/js/pages/gwas_upload.js +++ b/assets/js/pages/gwas_upload.js @@ -9,8 +9,8 @@ import pako from 'pako'; import App from '../../vue/gwas_upload.vue'; -import { isHeader } from 'locuszoom-tabix/src/gwas/sniffers'; -import { makeParser } from 'locuszoom-tabix/src/gwas/parsers'; +import { isHeader } from 'localzoom/src/gwas/sniffers'; +import { makeParser } from 'localzoom/src/gwas/parsers'; const PREVIEW_BYTES = 5000; // enough for 50-100 lines const MAX_UPLOAD_SIZE = 1048576 * 1000; // 1000 MiB # FIXME: Currently upload limit is only implemented in the frontend diff --git a/assets/js/util/lz-helpers.js b/assets/js/util/lz-helpers.js index 9f917fb..12de44a 100644 --- a/assets/js/util/lz-helpers.js +++ b/assets/js/util/lz-helpers.js @@ -4,7 +4,7 @@ import LocusZoom from 'locuszoom'; -import { sourceName} from 'locuszoom-tabix/src/util/lz-helpers'; +import { sourceName} from 'localzoom/src/util/lz-helpers'; LocusZoom.KnownDataSources.extend('AssociationLZ', 'AssociationApi', { getURL(state, chain,fields) { diff --git a/assets/vue/gwas_region.vue b/assets/vue/gwas_region.vue index 6a55b53..86db97b 100644 --- a/assets/vue/gwas_region.vue +++ b/assets/vue/gwas_region.vue @@ -1,9 +1,9 @@ - {% endif %} - {% endblock %} diff --git a/package.json b/package.json index ffa7448..004fba6 100644 --- a/package.json +++ b/package.json @@ -31,8 +31,8 @@ "d3": "3.5.16", "d3-tip": "0.9.0", "gwas-credible-sets": "^0.1.0", - "locuszoom": "0.10.0", - "locuszoom-tabix": "https://github.com/statgen/localzoom#918fd75", + "localzoom": "https://github.com/statgen/localzoom#v0.5.2", + "locuszoom": "0.10.1", "pako": "^1.0.8", "underscore": "1.8.3", "vue": "^2.6.10", diff --git a/yarn.lock b/yarn.lock index a5c1667..75a46b3 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2,637 +2,707 @@ # yarn lockfile v1 -"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.5.5": - version "7.5.5" - resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.5.5.tgz#bc0782f6d69f7b7d49531219699b988f669a8f9d" - integrity sha512-27d4lZoomVyo51VegxI20xZPuSHusqbQag/ztrBC7wegWoQ1nLREPVSKSW8byhTlzTKyNE4ifaTA6lCp7JjpFw== +"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.8.3": + version "7.8.3" + resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.8.3.tgz#33e25903d7481181534e12ec0a25f16b6fcf419e" + integrity sha512-a9gxpmdXtZEInkCSHUJDLHZVBgb1QS0jhss4cPP93EW7s+uC5bikET2twEF3KV+7rDblJcmNvTR7VJejqd2C2g== dependencies: - 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version "1.1.1" - resolved "https://registry.yarnpkg.com/ansi-regex/-/ansi-regex-1.1.1.tgz#41c847194646375e6a1a5d10c3ca054ef9fc980d" - integrity sha1-QchHGUZGN15qGl0Qw8oFTvn8mA0= - ansi-regex@^2.0.0: version "2.1.1" resolved "https://registry.yarnpkg.com/ansi-regex/-/ansi-regex-2.1.1.tgz#c3b33ab5ee360d86e0e628f0468ae7ef27d654df" @@ -1066,7 +1131,7 @@ asynckit@^0.4.0: resolved "https://registry.yarnpkg.com/asynckit/-/asynckit-0.4.0.tgz#c79ed97f7f34cb8f2ba1bc9790bcc366474b4b79" integrity sha1-x57Zf380y48robyXkLzDZkdLS3k= -atob@^2.1.1: +atob@^2.1.2: version "2.1.2" resolved "https://registry.yarnpkg.com/atob/-/atob-2.1.2.tgz#6d9517eb9e030d2436666651e86bd9f6f13533c9" integrity sha512-Wm6ukoaOGJi/73p/cl2GvLjTI5JM1k/O14isD73YML8StrH/7/lRFgmg8nICZgD3bZZvjwCGxtMOD3wWNAu8cg== @@ -1077,9 +1142,9 @@ aws-sign2@~0.7.0: integrity sha1-tG6JCTSpWR8tL2+G1+ap8bP+dqg= aws4@^1.8.0: - version "1.8.0" - resolved "https://registry.yarnpkg.com/aws4/-/aws4-1.8.0.tgz#f0e003d9ca9e7f59c7a508945d7b2ef9a04a542f" - integrity sha512-ReZxvNHIOv88FlT7rxcXIIC0fPt4KZqZbOlivyWtXLt8ESx84zd3kMC6iK5jVeS2qt+g7ftS7ye4fi06X5rtRQ== + version "1.9.1" + resolved "https://registry.yarnpkg.com/aws4/-/aws4-1.9.1.tgz#7e33d8f7d449b3f673cd72deb9abdc552dbe528e" + integrity sha512-wMHVg2EOHaMRxbzgFJ9gtjOOCrI80OHLG14rxi28XwOW8ux6IiEbRCGGGqCtdAIg4FQCbW20k9RsT4y3gJlFug== babel-loader@^8.0.5: version "8.0.6" @@ -1138,6 +1203,13 @@ binary-extensions@^1.0.0: resolved "https://registry.yarnpkg.com/binary-extensions/-/binary-extensions-1.13.1.tgz#598afe54755b2868a5330d2aff9d4ebb53209b65" integrity sha512-Un7MIEDdUC5gNpcGDV97op1Ywk748MpHcFTHoYs6qnj1Z3j7I53VG3nwZhKzoBZmbdRNnb6WRdFlwl7tSDuZGw== +bindings@^1.5.0: + version "1.5.0" + resolved "https://registry.yarnpkg.com/bindings/-/bindings-1.5.0.tgz#10353c9e945334bc0511a6d90b38fbc7c9c504df" + integrity sha512-p2q/t/mhvuOj/UeLlV6566GD/guowlr0hHxClI0W9m7MWYkL1F0hLo+0Aexs9HSPCtR1SXQ0TD3MMKrXZajbiQ== + dependencies: + file-uri-to-path "1.0.0" + block-stream@*: version "0.0.9" resolved "https://registry.yarnpkg.com/block-stream/-/block-stream-0.0.9.tgz#13ebfe778a03205cfe03751481ebb4b3300c126a" @@ -1146,9 +1218,9 @@ block-stream@*: inherits "~2.0.0" bluebird@^3.1.1, bluebird@^3.5.5: - 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bootstrap ">=4.3.1 <5.0.0" - popper.js "^1.15.0" - portal-vue "^2.1.6" + bootstrap ">=4.4.1 <5.0.0" + popper.js "^1.16.0" + portal-vue "^2.1.7" vue-functional-data-merge "^3.1.0" -"bootstrap@>=4.3.1 <5.0.0", bootstrap@^4.1.3, bootstrap@^4.3.1: - version "4.3.1" - resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-4.3.1.tgz#280ca8f610504d99d7b6b4bfc4b68cec601704ac" - integrity sha512-rXqOmH1VilAt2DyPzluTi2blhk17bO7ef+zLLPlWvG494pDxcM234pJ8wTc/6R40UWizAIIMgxjvxZg5kmsbag== +"bootstrap@>=4.4.1 <5.0.0", bootstrap@^4.1.3, bootstrap@^4.3.1: + version "4.4.1" + resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-4.4.1.tgz#8582960eea0c5cd2bede84d8b0baf3789c3e8b01" + integrity sha512-tbx5cHubwE6e2ZG7nqM3g/FZ5PQEDMWmMGNrCUBVRPHXTJaH7CBDdsLeu3eCh3B1tzAxTnAbtmrzvWEvT2NNEA== brace-expansion@^1.1.7: version "1.1.11" @@ -1259,14 +1331,14 @@ browserify-zlib@^0.2.0: dependencies: pako "~1.0.5" -browserslist@^4.6.0, browserslist@^4.6.6: - version "4.7.0" - resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.7.0.tgz#9ee89225ffc07db03409f2fee524dc8227458a17" - integrity sha512-9rGNDtnj+HaahxiVV38Gn8n8Lr8REKsel68v1sPFfIGEK6uSXTY3h9acgiT1dZVtOOUtifo/Dn8daDQ5dUgVsA== +browserslist@^4.8.2, browserslist@^4.8.3: + version "4.8.3" + resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.8.3.tgz#65802fcd77177c878e015f0e3189f2c4f627ba44" + integrity sha512-iU43cMMknxG1ClEZ2MDKeonKE1CCrFVkQK2AqO2YWFmvIrx4JWrvQ4w4hQez6EpVI8rHTtqh/ruHHDHSOKxvUg== dependencies: - caniuse-lite "^1.0.30000989" - electron-to-chromium "^1.3.247" - node-releases "^1.1.29" + caniuse-lite "^1.0.30001017" + electron-to-chromium "^1.3.322" + node-releases "^1.1.44" buffer-from@^1.0.0: version "1.1.1" @@ -1279,9 +1351,9 @@ buffer-xor@^1.0.3: integrity sha1-JuYe0UIvtw3ULm42cp7VHYVf6Nk= buffer@^4.3.0: - version "4.9.1" - resolved "https://registry.yarnpkg.com/buffer/-/buffer-4.9.1.tgz#6d1bb601b07a4efced97094132093027c95bc298" - integrity sha1-bRu2AbB6TvztlwlBMgkwJ8lbwpg= + version "4.9.2" + resolved "https://registry.yarnpkg.com/buffer/-/buffer-4.9.2.tgz#230ead344002988644841ab0244af8c44bbe3ef8" + integrity sha512-xq+q3SRMOxGivLhBNaUdC64hDTQwejJ+H0T/NB1XMtTVEwNTrfFF3gAxiyW0Bu/xWEGhjVKgUcMhCrUy2+uCWg== dependencies: base64-js "^1.0.2" ieee754 "^1.1.4" @@ -1369,10 +1441,10 @@ camelcase@^5.0.0, camelcase@^5.2.0: resolved "https://registry.yarnpkg.com/camelcase/-/camelcase-5.3.1.tgz#e3c9b31569e106811df242f715725a1f4c494320" integrity sha512-L28STB170nwWS63UjtlEOE3dldQApaJXZkOI1uMFfzf3rRuPegHaHesyee+YxQ+W6SvRDQV6UrdOdRiR153wJg== -caniuse-lite@^1.0.30000989: - 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version "2.20.0" - resolved "https://registry.yarnpkg.com/commander/-/commander-2.20.0.tgz#d58bb2b5c1ee8f87b0d340027e9e94e222c5a422" - integrity sha512-7j2y+40w61zy6YC2iRNpUe/NwhNyoXrYpHMrSunaMG64nRnaf96zO/KMQR4OyN/UnE5KLyEBnKHd4aG3rskjpQ== + version "2.20.3" + resolved "https://registry.yarnpkg.com/commander/-/commander-2.20.3.tgz#fd485e84c03eb4881c20722ba48035e8531aeb33" + integrity sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ== commondir@^1.0.1: version "1.0.1" @@ -1569,16 +1641,14 @@ concat-stream@^1.5.0: typedarray "^0.0.6" consola@^2.10.1: - version "2.10.1" - resolved "https://registry.yarnpkg.com/consola/-/consola-2.10.1.tgz#4693edba714677c878d520e4c7e4f69306b4b927" - integrity sha512-4sxpH6SGFYLADfUip4vuY65f/gEogrzJoniVhNUYkJHtng0l8ZjnDCqxxrSVRHOHwKxsy8Vm5ONZh1wOR3/l/w== + version "2.11.3" + resolved "https://registry.yarnpkg.com/consola/-/consola-2.11.3.tgz#f7315836224c143ac5094b47fd4c816c2cd1560e" + integrity sha512-aoW0YIIAmeftGR8GSpw6CGQluNdkWMWh3yEFjH/hmynTYnMtibXszii3lxCXmk8YxJtI3FAK5aTiquA5VH68Gw== console-browserify@^1.1.0: - version "1.1.0" - resolved "https://registry.yarnpkg.com/console-browserify/-/console-browserify-1.1.0.tgz#f0241c45730a9fc6323b206dbf38edc741d0bb10" - integrity sha1-8CQcRXMKn8YyOyBtvzjtx0HQuxA= - dependencies: - date-now "^0.1.4" + version "1.2.0" + resolved "https://registry.yarnpkg.com/console-browserify/-/console-browserify-1.2.0.tgz#67063cef57ceb6cf4993a2ab3a55840ae8c49336" + integrity sha512-ZMkYO/LkF17QvCPqM0gxw8yUzigAOZOSWSHg91FH6orS7vcEj5dVZTidN2fQ14yBSdg97RqhSNwLUXInd52OTA== console-control-strings@^1.0.0, console-control-strings@~1.1.0: version "1.1.0" @@ -1597,10 +1667,10 @@ constants-browserify@^1.0.0: resolved "https://registry.yarnpkg.com/constants-browserify/-/constants-browserify-1.0.0.tgz#c20b96d8c617748aaf1c16021760cd27fcb8cb75" integrity sha1-wguW2MYXdIqvHBYCF2DNJ/y4y3U= -convert-source-map@^1.1.0: - version "1.6.0" - resolved "https://registry.yarnpkg.com/convert-source-map/-/convert-source-map-1.6.0.tgz#51b537a8c43e0f04dec1993bffcdd504e758ac20" - integrity sha512-eFu7XigvxdZ1ETfbgPBohgyQ/Z++C0eEhTor0qRwBw9unw+L0/6V8wkSuGgzdThkiS5lSpdptOQPD8Ak40a+7A== +convert-source-map@^1.7.0: + version "1.7.0" + resolved "https://registry.yarnpkg.com/convert-source-map/-/convert-source-map-1.7.0.tgz#17a2cb882d7f77d3490585e2ce6c524424a3a442" + integrity sha512-4FJkXzKXEDB1snCFZlLP4gpC3JILicCpGbzG9f9G7tGqGCzETQ2hWPrcinA9oU4wtf2biUaEH5065UnMeR33oA== dependencies: safe-buffer "~5.1.1" @@ -1621,13 +1691,13 @@ copy-descriptor@^0.1.0: resolved "https://registry.yarnpkg.com/copy-descriptor/-/copy-descriptor-0.1.1.tgz#676f6eb3c39997c2ee1ac3a924fd6124748f578d" integrity sha1-Z29us8OZl8LuGsOpJP1hJHSPV40= -core-js-compat@^3.1.1: - 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eslint-visitor-keys "^1.0.0" + eslint-visitor-keys "^1.1.0" -eslint-visitor-keys@^1.0.0: +eslint-visitor-keys@^1.0.0, eslint-visitor-keys@^1.1.0: version "1.1.0" resolved "https://registry.yarnpkg.com/eslint-visitor-keys/-/eslint-visitor-keys-1.1.0.tgz#e2a82cea84ff246ad6fb57f9bde5b46621459ec2" integrity sha512-8y9YjtM1JBJU/A9Kc+SbaOV4y29sSWckBwMHa+FGtVj5gN/sbnKDf6xJUl+8g7FAij9LVaP8C24DUiH/f/2Z9A== @@ -2105,9 +2174,9 @@ esutils@^2.0.2: integrity sha512-kVscqXk4OCp68SZ0dkgEKVi6/8ij300KBWTJq32P/dYeWTSwK41WyTxalN1eRmA5Z9UU/LX9D7FWSmV9SAYx6g== events@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/events/-/events-3.0.0.tgz#9a0a0dfaf62893d92b875b8f2698ca4114973e88" - integrity sha512-Dc381HFWJzEOhQ+d8pkNon++bk9h6cdAoAj4iE6Q4y6xgTzySWXlKn05/TVNpjnfRqi/X0EpJEJohPjNI3zpVA== + version "3.1.0" + resolved "https://registry.yarnpkg.com/events/-/events-3.1.0.tgz#84279af1b34cb75aa88bf5ff291f6d0bd9b31a59" + integrity sha512-Rv+u8MLHNOdMjTAFeT3nCjHn2aGlx435FP/sDHNaRhDEMwyI/aB22Kj2qIN8R0cw3z28psEQLYwxVKLsKrMgWg== evp_bytestokey@^1.0.0, evp_bytestokey@^1.0.3: version "1.0.3" @@ -2209,11 +2278,11 @@ fast-deep-equal@^2.0.1: integrity sha1-ewUhjd+WZ79/Nwv3/bLLFf3Qqkk= fast-json-stable-stringify@^2.0.0: - 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node-pre-gyp "^0.12.0" fstream@^1.0.0, fstream@^1.0.12: version "1.0.12" @@ -2417,6 +2491,11 @@ gaze@^1.0.0: dependencies: globule "^1.0.0" +gensync@^1.0.0-beta.1: + version "1.0.0-beta.1" + resolved "https://registry.yarnpkg.com/gensync/-/gensync-1.0.0-beta.1.tgz#58f4361ff987e5ff6e1e7a210827aa371eaac269" + integrity sha512-r8EC6NO1sngH/zdD9fiRDLdcgnbayXah+mLgManTaIZJqEC1MZstmnox8KpnI2/fxQwrp5OpCOYWLp4rBl4Jcg== + get-caller-file@^1.0.1: version "1.0.3" resolved "https://registry.yarnpkg.com/get-caller-file/-/get-caller-file-1.0.3.tgz#f978fa4c90d1dfe7ff2d6beda2a515e713bdcf4a" @@ -2465,9 +2544,9 @@ glob-parent@^3.1.0: path-dirname "^1.0.0" glob@^7.0.0, glob@^7.0.3, glob@^7.1.2, glob@^7.1.3, glob@^7.1.4, glob@~7.1.1: - version "7.1.4" - resolved "https://registry.yarnpkg.com/glob/-/glob-7.1.4.tgz#aa608a2f6c577ad357e1ae5a5c26d9a8d1969255" - integrity sha512-hkLPepehmnKk41pUGm3sYxoFs/umurYfYJCerbXEyFIWcAzvpipAgVkBqqT9RBKMGjnq6kMuyYwha6csxbiM1A== + version "7.1.6" + resolved "https://registry.yarnpkg.com/glob/-/glob-7.1.6.tgz#141f33b81a7c2492e125594307480c46679278a6" + integrity sha512-LwaxwyZ72Lk7vZINtNNrywX0ZuLyStrdDtabefZKAY5ZGJhVtgdznluResxNmPitE0SAO+O26sWTHeKSI2wMBA== dependencies: fs.realpath "^1.0.0" inflight "^1.0.4" @@ -2518,9 +2597,9 @@ globals@^11.1.0, globals@^11.7.0: integrity sha512-WOBp/EEGUiIsJSp7wcv/y6MO+lV9UoncWqxuFfm8eBwzWNgyfBd6Gz+IeKQ9jCmyhoH99g15M3T+QaVHFjizVA== globule@^1.0.0: - 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mime-db "1.40.0" + mime-db "1.43.0" mimic-fn@^1.0.0: version "1.2.0" @@ -3488,20 +3582,20 @@ minimist@^1.1.3, minimist@^1.2.0: resolved "https://registry.yarnpkg.com/minimist/-/minimist-1.2.0.tgz#a35008b20f41383eec1fb914f4cd5df79a264284" integrity sha1-o1AIsg9BOD7sH7kU9M1d95omQoQ= -minipass@^2.2.1, minipass@^2.3.5: - version "2.5.1" - resolved "https://registry.yarnpkg.com/minipass/-/minipass-2.5.1.tgz#cf435a9bf9408796ca3a3525a8b851464279c9b8" - integrity sha512-dmpSnLJtNQioZFI5HfQ55Ad0DzzsMAb+HfokwRTNXwEQjepbTkl5mtIlSVxGIkOkxlpX7wIn5ET/oAd9fZ/Y/Q== +minipass@^2.6.0, minipass@^2.8.6, minipass@^2.9.0: + version "2.9.0" + resolved "https://registry.yarnpkg.com/minipass/-/minipass-2.9.0.tgz#e713762e7d3e32fed803115cf93e04bca9fcc9a6" + integrity sha512-wxfUjg9WebH+CUDX/CdbRlh5SmfZiy/hpkxaRI16Y9W56Pa75sWgd/rvFilSgrauD9NyFymP/+JFV3KwzIsJeg== dependencies: safe-buffer "^5.1.2" yallist "^3.0.0" minizlib@^1.2.1: - version "1.2.1" - resolved "https://registry.yarnpkg.com/minizlib/-/minizlib-1.2.1.tgz#dd27ea6136243c7c880684e8672bb3a45fd9b614" - 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integrity sha512-pnzH6dnFEsR2aa2SJaKb1uSCl3QmIsJ8dEkj0Fky+2AwMMcC9doMqLOQIH6wVTEKaVfKVvLSk5qxPBEZT9mywg== + version "4.6.3" + resolved "https://registry.yarnpkg.com/terser/-/terser-4.6.3.tgz#e33aa42461ced5238d352d2df2a67f21921f8d87" + integrity sha512-Lw+ieAXmY69d09IIc/yqeBqXpEQIpDGZqT34ui1QWXIUpR2RjbqEkT8X7Lgex19hslSqcWM5iMN2kM11eMsESQ== dependencies: commander "^2.20.0" source-map "~0.6.1" @@ -5240,11 +5325,6 @@ trim-newlines@^1.0.0: resolved "https://registry.yarnpkg.com/trim-newlines/-/trim-newlines-1.0.0.tgz#5887966bb582a4503a41eb524f7d35011815a613" integrity sha1-WIeWa7WCpFA6QetST301ARgVphM= -trim-right@^1.0.1: - version "1.0.1" - resolved "https://registry.yarnpkg.com/trim-right/-/trim-right-1.0.1.tgz#cb2e1203067e0c8de1f614094b9fe45704ea6003" - integrity sha1-yy4SAwZ+DI3h9hQJS5/kVwTqYAM= - "true-case-path@^1.0.2": version "1.0.3" resolved "https://registry.yarnpkg.com/true-case-path/-/true-case-path-1.0.3.tgz#f813b5a8c86b40da59606722b144e3225799f47d" @@ -5440,9 +5520,9 @@ verror@1.10.0: extsprintf "^1.2.0" vm-browserify@^1.0.1: - 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version "15.7.1" - resolved "https://registry.yarnpkg.com/vue-loader/-/vue-loader-15.7.1.tgz#6ccacd4122aa80f69baaac08ff295a62e3aefcfd" - integrity sha512-fwIKtA23Pl/rqfYP5TSGK7gkEuLhoTvRYW+TU7ER3q9GpNLt/PjG5NLv3XHRDiTg7OPM1JcckBgds+VnAc+HbA== + version "15.8.3" + resolved "https://registry.yarnpkg.com/vue-loader/-/vue-loader-15.8.3.tgz#857cb9e30eb5fc25e66db48dce7e4f768602a23c" + integrity sha512-yFksTFbhp+lxlm92DrKdpVIWMpranXnTEuGSc0oW+Gk43M9LWaAmBTnfj5+FCdve715mTHvo78IdaXf5TbiTJg== dependencies: - "@vue/component-compiler-utils" "^3.0.0" + "@vue/component-compiler-utils" "^3.1.0" hash-sum "^1.0.2" loader-utils "^1.1.0" vue-hot-reload-api "^2.3.0" @@ -5489,9 +5569,9 @@ vue-style-loader@^4.1.0: loader-utils "^1.0.2" vue-template-compiler@^2.6.7: - version "2.6.10" - resolved "https://registry.yarnpkg.com/vue-template-compiler/-/vue-template-compiler-2.6.10.tgz#323b4f3495f04faa3503337a82f5d6507799c9cc" - integrity sha512-jVZkw4/I/HT5ZMvRnhv78okGusqe0+qH2A0Em0Cp8aq78+NK9TII263CDVz2QXZsIT+yyV/gZc/j/vlwa+Epyg== + version "2.6.11" + resolved "https://registry.yarnpkg.com/vue-template-compiler/-/vue-template-compiler-2.6.11.tgz#c04704ef8f498b153130018993e56309d4698080" + integrity sha512-KIq15bvQDrcCjpGjrAhx4mUlyyHfdmTaoNfeoATHLAiWB+MU3cx4lOzMwrnUh9cCxy0Lt1T11hAFY6TQgroUAA== dependencies: de-indent "^1.0.2" he "^1.1.0" @@ -5502,9 +5582,9 @@ vue-template-es2015-compiler@^1.9.0: integrity sha512-4gDntzrifFnCEvyoO8PqyJDmguXgVPxKiIxrBKjIowvL9l+N66196+72XVYR8BBf1Uv1Fgt3bGevJ+sEmxfZzw== vue@^2.0.0, vue@^2.5.17, vue@^2.6.10: - version "2.6.10" - resolved "https://registry.yarnpkg.com/vue/-/vue-2.6.10.tgz#a72b1a42a4d82a721ea438d1b6bf55e66195c637" - integrity sha512-ImThpeNU9HbdZL3utgMCq0oiMzAkt1mcgy3/E6zWC/G6AaQoeuFdsl9nDhTDU3X1R6FK7nsIUuRACVcjI+A2GQ== + version "2.6.11" + resolved "https://registry.yarnpkg.com/vue/-/vue-2.6.11.tgz#76594d877d4b12234406e84e35275c6d514125c5" + integrity sha512-VfPwgcGABbGAue9+sfrD4PuwFar7gPb1yl1UK1MwXoQPAw0BKSqWfoYCT/ThFrdEVWoI51dBuyCoiNU9bZDZxQ== vuejs-paginator@^2.0.2: version "2.0.2" @@ -5524,18 +5604,18 @@ watchpack@^1.6.0: neo-async "^2.5.0" webpack-bundle-tracker@^0.4.2-beta: - version "0.4.2-beta" - resolved "https://registry.yarnpkg.com/webpack-bundle-tracker/-/webpack-bundle-tracker-0.4.2-beta.tgz#263c3a3db8722aaab0083763154e5f025e47825d" - integrity sha512-CCyJbCQnRtjR1sk97u/H5DtJibrIcJ79MnntMyjOpc9HCmfIQYgt7ze7i/Z+DStBZ4NC4HxqGDsB///2Na1DTA== + version "0.4.3" + resolved "https://registry.yarnpkg.com/webpack-bundle-tracker/-/webpack-bundle-tracker-0.4.3.tgz#48a3e2226ddb9d24d704640ab4168c2d120f4526" + integrity sha512-Sl/+OsNhFAH3/c6XADupRu8jLvGojfXX0pZIIm3O5ZcJqkHHqlY4nLG+NVRcbDgM/jOeWimKDGQMVEa8FBeJ2g== dependencies: deep-extend "^0.6.0" mkdirp "^0.5.1" - strip-ansi "^2.0.1" + strip-ansi "^5.2.0" webpack-cli@^3.2.3: - version "3.3.8" - resolved "https://registry.yarnpkg.com/webpack-cli/-/webpack-cli-3.3.8.tgz#caeaebcc26f685db1736e5decd3f01aac30123ec" - integrity sha512-RANYSXwikSWINjHMd/mtesblNSpjpDLoYTBtP99n1RhXqVI/wxN40Auqy42I7y4xrbmRBoA5Zy5E0JSBD5XRhw== + version "3.3.10" + resolved "https://registry.yarnpkg.com/webpack-cli/-/webpack-cli-3.3.10.tgz#17b279267e9b4fb549023fae170da8e6e766da13" + integrity sha512-u1dgND9+MXaEt74sJR4PR7qkPxXUSQ0RXYq8x1L6Jg1MYVEmGPrH6Ah6C4arD4r0J1P5HKjRqpab36k0eIzPqg== dependencies: chalk "2.4.2" cross-spawn "6.0.5" @@ -5565,9 +5645,9 @@ webpack-sources@^1.4.0, webpack-sources@^1.4.1: source-map "~0.6.1" webpack@^4.29.5: - version "4.39.3" - resolved "https://registry.yarnpkg.com/webpack/-/webpack-4.39.3.tgz#a02179d1032156b713b6ec2da7e0df9d037def50" - integrity sha512-BXSI9M211JyCVc3JxHWDpze85CvjC842EvpRsVTc/d15YJGlox7GIDd38kJgWrb3ZluyvIjgenbLDMBQPDcxYQ== + version "4.41.5" + resolved "https://registry.yarnpkg.com/webpack/-/webpack-4.41.5.tgz#3210f1886bce5310e62bb97204d18c263341b77c" + integrity sha512-wp0Co4vpyumnp3KlkmpM5LWuzvZYayDwM2n17EHFr4qxBBbRokC7DJawPJC7TfSFZ9HZ6GsdH40EBj4UV0nmpw== dependencies: "@webassemblyjs/ast" "1.8.5" "@webassemblyjs/helper-module-context" "1.8.5" @@ -5589,7 +5669,7 @@ webpack@^4.29.5: node-libs-browser "^2.2.1" schema-utils "^1.0.0" tapable "^1.1.3" - terser-webpack-plugin "^1.4.1" + terser-webpack-plugin "^1.4.3" watchpack "^1.6.0" webpack-sources "^1.4.1" @@ -5617,10 +5697,10 @@ wide-align@^1.1.0: dependencies: string-width "^1.0.2 || 2" -wordwrap@~1.0.0: - version "1.0.0" - resolved "https://registry.yarnpkg.com/wordwrap/-/wordwrap-1.0.0.tgz#27584810891456a4171c8d0226441ade90cbcaeb" - integrity sha1-J1hIEIkUVqQXHI0CJkQa3pDLyus= +word-wrap@~1.2.3: + version "1.2.3" + resolved "https://registry.yarnpkg.com/word-wrap/-/word-wrap-1.2.3.tgz#610636f6b1f703891bd34771ccb17fb93b47079c" + integrity sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ== worker-farm@^1.7.0: version "1.7.0" @@ -5679,9 +5759,9 @@ yallist@^2.1.2: integrity sha1-HBH5IY8HYImkfdUS+TxmmaaoHVI= yallist@^3.0.0, yallist@^3.0.2, yallist@^3.0.3: - version "3.0.3" - resolved "https://registry.yarnpkg.com/yallist/-/yallist-3.0.3.tgz#b4b049e314be545e3ce802236d6cd22cd91c3de9" - integrity sha512-S+Zk8DEWE6oKpV+vI3qWkaK+jSbIK86pCwe2IF/xwIpQ8jEuxpw9NyaGjmp9+BoJv5FV2piqCDcoCtStppiq2A== + version "3.1.1" + resolved "https://registry.yarnpkg.com/yallist/-/yallist-3.1.1.tgz#dbb7daf9bfd8bac9ab45ebf602b8cbad0d5d08fd" + integrity sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g== yargs-parser@^13.1.0: version "13.1.1" From 68d80a759a569d56f907c103d97b2612cf0e567b Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Thu, 13 Feb 2020 16:25:00 -0500 Subject: [PATCH 4/6] Fix clipping of gene labels on manhattan plot (backport Pheweb features) --- assets/js/util/pheweb_plots.js | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/assets/js/util/pheweb_plots.js b/assets/js/util/pheweb_plots.js index 5743bfd..08a03c7 100644 --- a/assets/js/util/pheweb_plots.js +++ b/assets/js/util/pheweb_plots.js @@ -20,6 +20,10 @@ function fmt(format) { function create_gwas_plot(variant_bins, unbinned_variants, {url_prefix = null, tooltip_template = null} = {}) { // FIXME: Replace global variables with options object + // Order from weakest to strongest pvalue, so that the strongest variant will be on top (z-order) and easily hoverable + // In the DOM, later siblings are displayed over top of (and occluding) earlier siblings. + unbinned_variants = _.sortBy(unbinned_variants, function(d) { return d.neg_log_pvalue; }); + const get_chrom_offsets = _.memoize(function() { const chrom_padding = 2e7; const chrom_extents = {}; @@ -120,7 +124,7 @@ function create_gwas_plot(variant_bins, unbinned_variants, {url_prefix = null, t const plot_margin = { 'left': 70, 'right': 30, - 'top': 10, + 'top': 20, 'bottom': 50, }; const plot_width = svg_width - plot_margin.left - plot_margin.right; From 40e2eb1dab10c977ad6786af2846b40b7cddcdb3 Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Thu, 13 Feb 2020 16:43:21 -0500 Subject: [PATCH 5/6] Update LocalZoom and zorp dependencies: - Constraints table - Click to label point - Zorp with faster closure-based parser --- assets/js/pages/gwas_region.js | 2 +- package.json | 4 +- requirements/base.txt | 2 +- yarn.lock | 151 +++------------------------------ 4 files changed, 18 insertions(+), 141 deletions(-) diff --git a/assets/js/pages/gwas_region.js b/assets/js/pages/gwas_region.js index 45366a0..18b3bb6 100644 --- a/assets/js/pages/gwas_region.js +++ b/assets/js/pages/gwas_region.js @@ -38,6 +38,6 @@ function makePlot(template_vars) { })}).$mount('#app'); } -// On page load, generate a plot, and send Google Analytics metrics if applicable +// On page load, generate a plot, and send Google Analytics metrics for first plot rendered window.lz_widget = makePlot(window.template_args); count_region_view(); diff --git a/package.json b/package.json index 004fba6..5340349 100644 --- a/package.json +++ b/package.json @@ -31,8 +31,8 @@ "d3": "3.5.16", "d3-tip": "0.9.0", "gwas-credible-sets": "^0.1.0", - "localzoom": "https://github.com/statgen/localzoom#v0.5.2", - "locuszoom": "0.10.1", + "localzoom": "https://github.com/statgen/localzoom#v0.5.3", + "locuszoom": "https://github.com/statgen/locuszoom#42f7c64127893f5f1b00ddf9b81acf369179dc36", "pako": "^1.0.8", "underscore": "1.8.3", "vue": "^2.6.10", diff --git a/requirements/base.txt b/requirements/base.txt index bd1443b..50969ab 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -35,5 +35,5 @@ pyyaml # Required for OpenAPI rendering boltons~=19.1 scipy~=1.2 python-magic==0.4.15 -zorp==0.1.1 +git+git://github.com/abought/zorp.git@893d383 genelocator==1.1.1 diff --git a/yarn.lock b/yarn.lock index 75a46b3..6a2717c 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1852,13 +1852,6 @@ debug@^2.2.0, debug@^2.3.3: dependencies: ms "2.0.0" -debug@^3.2.6: - version "3.2.6" - resolved "https://registry.yarnpkg.com/debug/-/debug-3.2.6.tgz#e83d17de16d8a7efb7717edbe5fb10135eee629b" - integrity sha512-mel+jf7nrtEl5Pn1Qx46zARXKDpBbvzezse7p7LqINmdoIk8PYP5SySaxEmYv6TZ0JyEKA1hsCId6DIhgITtWQ== - dependencies: - ms "^2.1.1" - debug@^4.0.1, debug@^4.1.0: version "4.1.1" resolved "https://registry.yarnpkg.com/debug/-/debug-4.1.1.tgz#3b72260255109c6b589cee050f1d516139664791" @@ -1945,11 +1938,6 @@ detect-file@^1.0.0: resolved "https://registry.yarnpkg.com/detect-file/-/detect-file-1.0.0.tgz#f0d66d03672a825cb1b73bdb3fe62310c8e552b7" integrity sha1-8NZtA2cqglyxtzvbP+YjEMjlUrc= -detect-libc@^1.0.2: - version "1.0.3" - resolved "https://registry.yarnpkg.com/detect-libc/-/detect-libc-1.0.3.tgz#fa137c4bd698edf55cd5cd02ac559f91a4c4ba9b" - integrity sha1-+hN8S9aY7fVc1c0CrFWfkaTEups= - diffie-hellman@^5.0.0: version "5.0.3" resolved "https://registry.yarnpkg.com/diffie-hellman/-/diffie-hellman-5.0.3.tgz#40e8ee98f55a2149607146921c63e1ae5f3d2875" @@ -2420,13 +2408,6 @@ from2@^2.1.0, from2@^2.1.1: inherits "^2.0.1" readable-stream "^2.0.0" -fs-minipass@^1.2.5: - version "1.2.7" - resolved "https://registry.yarnpkg.com/fs-minipass/-/fs-minipass-1.2.7.tgz#ccff8570841e7fe4265693da88936c55aed7f7c7" - integrity sha512-GWSSJGFy4e9GUeCcbIkED+bgAoFyj7XF1mV8rma3QW4NIqX9Kyx79N/PF61H5udOV3aY1IaMLs6pGbH71nlCTA== - dependencies: - minipass "^2.6.0" - fs-write-stream-atomic@^1.0.8: version "1.0.10" resolved "https://registry.yarnpkg.com/fs-write-stream-atomic/-/fs-write-stream-atomic-1.0.10.tgz#b47df53493ef911df75731e70a9ded0189db40c9" @@ -2782,7 +2763,7 @@ https-browserify@^1.0.0: resolved "https://registry.yarnpkg.com/https-browserify/-/https-browserify-1.0.0.tgz#ec06c10e0a34c0f2faf199f7fd7fc78fffd03c73" integrity sha1-7AbBDgo0wPL68Zn3/X/Hj//QPHM= -iconv-lite@^0.4.24, iconv-lite@^0.4.4: +iconv-lite@^0.4.24: version "0.4.24" resolved "https://registry.yarnpkg.com/iconv-lite/-/iconv-lite-0.4.24.tgz#2022b4b25fbddc21d2f524974a474aafe733908b" integrity sha512-v3MXnZAcvnywkTUEZomIActle7RXXeedOR31wwl7VlyoXO4Qi9arvSenNQWne1TcRwhCL1HwLI21bEqdpj8/rA== @@ -2811,13 +2792,6 @@ iferr@^0.1.5: resolved "https://registry.yarnpkg.com/iferr/-/iferr-0.1.5.tgz#c60eed69e6d8fdb6b3104a1fcbca1c192dc5b501" integrity sha1-xg7taebY/bazEEofy8ocGS3FtQE= -ignore-walk@^3.0.1: - version "3.0.3" - resolved "https://registry.yarnpkg.com/ignore-walk/-/ignore-walk-3.0.3.tgz#017e2447184bfeade7c238e4aefdd1e8f95b1e37" - integrity sha512-m7o6xuOaT1aqheYHKf8W6J5pYH85ZI9w077erOzLje3JsB1gkafkAhHHY19dqjulgIZHFm32Cp5uNZgcQqdJKw== - dependencies: - minimatch "^3.0.4" - ignore@^4.0.6: version "4.0.6" resolved "https://registry.yarnpkg.com/ignore/-/ignore-4.0.6.tgz#750e3db5862087b4737ebac8207ffd1ef27b25fc" @@ -2889,7 +2863,7 @@ inherits@2.0.3: resolved "https://registry.yarnpkg.com/inherits/-/inherits-2.0.3.tgz#633c2c83e3da42a502f52466022480f4208261de" integrity sha1-Yzwsg+PaQqUC9SRmAiSA9CCCYd4= -ini@^1.3.4, ini@^1.3.5, ini@~1.3.0: +ini@^1.3.4, ini@^1.3.5: version "1.3.5" resolved "https://registry.yarnpkg.com/ini/-/ini-1.3.5.tgz#eee25f56db1c9ec6085e0c22778083f596abf927" integrity sha512-RZY5huIKCMRWDUqZlEi72f/lmXKMvuszcMBduliQ3nnWbx9X/ZBQO7DijMEYS9EhHBb2qacRUMtC7svLwe0lcw== @@ -3331,15 +3305,15 @@ loader-utils@1.2.3, loader-utils@^1.0.1, loader-utils@^1.0.2, loader-utils@^1.1. emojis-list "^2.0.0" json5 "^1.0.1" -"localzoom@https://github.com/statgen/localzoom#v0.5.2": - version "0.5.2" - resolved "https://github.com/statgen/localzoom#e21b0db09687ba2429f25222678a3de6586fc2dd" +"localzoom@https://github.com/statgen/localzoom#v0.5.3": + version "0.5.3" + resolved "https://github.com/statgen/localzoom#7426e4e4736c77a6152e692dd8a704390787cffe" dependencies: "@sentry/browser" "^4.5.2" bootstrap "^4.1.3" bootstrap-vue "^2.0.0-rc.11" gwas-credible-sets "^0.1.0" - locuszoom "0.10.1" + locuszoom "https://github.com/statgen/locuszoom#42f7c64127893f5f1b00ddf9b81acf369179dc36" lodash "^4.17.11" tabix-reader "https://github.com/abought/tabix-reader" tabulator-tables "^4.1.4" @@ -3354,10 +3328,9 @@ locate-path@^3.0.0: p-locate "^3.0.0" path-exists "^3.0.0" -locuszoom@0.10.1: - version "0.10.1" - resolved "https://registry.yarnpkg.com/locuszoom/-/locuszoom-0.10.1.tgz#dadd71dadbcb309de0aaa9209e11a1c1d7d5f0f9" - integrity sha512-ASMZ+1Y0dBgclZgSs1PFm1Sfbk/CWPv2WNPVosDtN7ejDxwVMiiCB/99ZtBUEDhsILu05epA0NRjvp4V8AWMHw== +"locuszoom@https://github.com/statgen/locuszoom#42f7c64127893f5f1b00ddf9b81acf369179dc36": + version "0.10.2" + resolved "https://github.com/statgen/locuszoom#42f7c64127893f5f1b00ddf9b81acf369179dc36" dependencies: d3 "3.5.17" promise-polyfill "^8.1.3" @@ -3582,21 +3555,6 @@ minimist@^1.1.3, minimist@^1.2.0: resolved "https://registry.yarnpkg.com/minimist/-/minimist-1.2.0.tgz#a35008b20f41383eec1fb914f4cd5df79a264284" integrity sha1-o1AIsg9BOD7sH7kU9M1d95omQoQ= -minipass@^2.6.0, minipass@^2.8.6, minipass@^2.9.0: - version "2.9.0" - resolved "https://registry.yarnpkg.com/minipass/-/minipass-2.9.0.tgz#e713762e7d3e32fed803115cf93e04bca9fcc9a6" - integrity sha512-wxfUjg9WebH+CUDX/CdbRlh5SmfZiy/hpkxaRI16Y9W56Pa75sWgd/rvFilSgrauD9NyFymP/+JFV3KwzIsJeg== - dependencies: - safe-buffer "^5.1.2" - yallist "^3.0.0" - -minizlib@^1.2.1: - version "1.3.3" - resolved "https://registry.yarnpkg.com/minizlib/-/minizlib-1.3.3.tgz#2290de96818a34c29551c8a8d301216bd65a861d" - integrity sha512-6ZYMOEnmVsdCeTJVE0W9ZD+pVnE8h9Hma/iOwwRDsdQoePpoX56/8B6z3P9VNwppJuBKNRuFDRNRqRWexT9G9Q== - dependencies: - minipass "^2.9.0" - mississippi@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/mississippi/-/mississippi-3.0.0.tgz#ea0a3291f97e0b5e8776b363d5f0a12d94c67022" @@ -3682,15 +3640,6 @@ natural-compare@^1.4.0: resolved "https://registry.yarnpkg.com/natural-compare/-/natural-compare-1.4.0.tgz#4abebfeed7541f2c27acfb29bdbbd15c8d5ba4f7" integrity sha1-Sr6/7tdUHywnrPspvbvRXI1bpPc= -needle@^2.2.1: - version "2.4.0" - resolved "https://registry.yarnpkg.com/needle/-/needle-2.4.0.tgz#6833e74975c444642590e15a750288c5f939b57c" - integrity sha512-4Hnwzr3mi5L97hMYeNl8wRW/Onhy4nUKR/lVemJ8gJedxxUyBLm9kkrDColJvoSfwi0jCNhD+xCdOtiGDQiRZg== - dependencies: - debug "^3.2.6" - iconv-lite "^0.4.4" - sax "^1.2.4" - neo-async@^2.5.0, neo-async@^2.6.1: version "2.6.1" resolved "https://registry.yarnpkg.com/neo-async/-/neo-async-2.6.1.tgz#ac27ada66167fa8849a6addd837f6b189ad2081c" @@ -3753,22 +3702,6 @@ node-libs-browser@^2.2.1: util "^0.11.0" vm-browserify "^1.0.1" -node-pre-gyp@*: - version "0.14.0" - resolved "https://registry.yarnpkg.com/node-pre-gyp/-/node-pre-gyp-0.14.0.tgz#9a0596533b877289bcad4e143982ca3d904ddc83" - integrity sha512-+CvDC7ZttU/sSt9rFjix/P05iS43qHCOOGzcr3Ry99bXG7VX953+vFyEuph/tfqoYu8dttBkE86JSKBO2OzcxA== - dependencies: - detect-libc "^1.0.2" - mkdirp "^0.5.1" - needle "^2.2.1" - nopt "^4.0.1" - npm-packlist "^1.1.6" - npmlog "^4.0.2" - rc "^1.2.7" - rimraf "^2.6.1" - semver "^5.3.0" - tar "^4.4.2" - node-releases@^1.1.44: version "1.1.45" resolved "https://registry.yarnpkg.com/node-releases/-/node-releases-1.1.45.tgz#4cf7e9175d71b1317f15ffd68ce63bce1d53e9f2" @@ -3806,14 +3739,6 @@ node-sass@^4.11.0: dependencies: abbrev "1" -nopt@^4.0.1: - version "4.0.1" - resolved "https://registry.yarnpkg.com/nopt/-/nopt-4.0.1.tgz#d0d4685afd5415193c8c7505602d0d17cd64474d" - integrity sha1-0NRoWv1UFRk8jHUFYC0NF81kR00= - dependencies: - abbrev "1" - osenv "^0.1.4" - normalize-package-data@^2.3.2, normalize-package-data@^2.3.4: version "2.5.0" resolved "https://registry.yarnpkg.com/normalize-package-data/-/normalize-package-data-2.5.0.tgz#e66db1838b200c1dfc233225d12cb36520e234a8" @@ -3845,26 +3770,6 @@ normalize-url@2.0.1: query-string "^5.0.1" sort-keys "^2.0.0" -npm-bundled@^1.0.1: - version "1.1.1" - resolved "https://registry.yarnpkg.com/npm-bundled/-/npm-bundled-1.1.1.tgz#1edd570865a94cdb1bc8220775e29466c9fb234b" - integrity sha512-gqkfgGePhTpAEgUsGEgcq1rqPXA+tv/aVBlgEzfXwA1yiUJF7xtEt3CtVwOjNYQOVknDk0F20w58Fnm3EtG0fA== - dependencies: - npm-normalize-package-bin "^1.0.1" - -npm-normalize-package-bin@^1.0.1: - version "1.0.1" - resolved "https://registry.yarnpkg.com/npm-normalize-package-bin/-/npm-normalize-package-bin-1.0.1.tgz#6e79a41f23fd235c0623218228da7d9c23b8f6e2" - integrity sha512-EPfafl6JL5/rU+ot6P3gRSCpPDW5VmIzX959Ob1+ySFUuuYHWHekXpwdUZcKP5C+DS4GEtdJluwBjnsNDl+fSA== - -npm-packlist@^1.1.6: - version "1.4.7" - resolved "https://registry.yarnpkg.com/npm-packlist/-/npm-packlist-1.4.7.tgz#9e954365a06b80b18111ea900945af4f88ed4848" - integrity sha512-vAj7dIkp5NhieaGZxBJB8fF4R0078rqsmhJcAfXZ6O7JJhjhPK96n5Ry1oZcfLXgfun0GWTZPOxaEyqv8GBykQ== - dependencies: - ignore-walk "^3.0.1" - npm-bundled "^1.0.1" - npm-run-path@^2.0.0: version "2.0.2" resolved "https://registry.yarnpkg.com/npm-run-path/-/npm-run-path-2.0.2.tgz#35a9232dfa35d7067b4cb2ddf2357b1871536c5f" @@ -3872,7 +3777,7 @@ npm-run-path@^2.0.0: dependencies: path-key "^2.0.0" -"npmlog@0 || 1 || 2 || 3 || 4", npmlog@^4.0.0, npmlog@^4.0.2: +"npmlog@0 || 1 || 2 || 3 || 4", npmlog@^4.0.0: version "4.1.2" resolved "https://registry.yarnpkg.com/npmlog/-/npmlog-4.1.2.tgz#08a7f2a8bf734604779a9efa4ad5cc717abb954b" integrity sha512-2uUqazuKlTaSI/dC8AzicUck7+IrEaOnN/e0jd3Xtt1KcGpwx30v50mL7oPyr/h9bL3E4aZccVwpwP+5W9Vjkg== @@ -3992,7 +3897,7 @@ os-tmpdir@^1.0.0, os-tmpdir@~1.0.2: resolved "https://registry.yarnpkg.com/os-tmpdir/-/os-tmpdir-1.0.2.tgz#bbe67406c79aa85c5cfec766fe5734555dfa1274" integrity sha1-u+Z0BseaqFxc/sdm/lc0VV36EnQ= -osenv@0, osenv@^0.1.4: +osenv@0: version "0.1.5" resolved "https://registry.yarnpkg.com/osenv/-/osenv-0.1.5.tgz#85cdfafaeb28e8677f416e287592b5f3f49ea410" integrity sha512-0CWcCECdMVc2Rw3U5w9ZjqX6ga6ubk1xDVKxtBQPK7wis/0F2r9T6k4ydGYhecl7YUBxBVxhL5oisPsNxAPe2g== @@ -4423,16 +4328,6 @@ randomfill@^1.0.3: randombytes "^2.0.5" safe-buffer "^5.1.0" -rc@^1.2.7: - version "1.2.8" - resolved "https://registry.yarnpkg.com/rc/-/rc-1.2.8.tgz#cd924bf5200a075b83c188cd6b9e211b7fc0d3ed" - integrity sha512-y3bGgqKj3QBdxLbLkomlohkvsA8gdAiUQlSBJnBhfn+BPxg4bc62d8TcBW15wavDfgexCgccckhcZvywyQYPOw== - dependencies: - deep-extend "^0.6.0" - ini "~1.3.0" - minimist "^1.2.0" - strip-json-comments "~2.0.1" - read-pkg-up@^1.0.1: version "1.0.1" resolved "https://registry.yarnpkg.com/read-pkg-up/-/read-pkg-up-1.0.1.tgz#9d63c13276c065918d57f002a57f40a1b643fb02" @@ -4747,11 +4642,6 @@ sass-loader@^7.1.0: pify "^4.0.1" semver "^6.3.0" -sax@^1.2.4: - version "1.2.4" - resolved "https://registry.yarnpkg.com/sax/-/sax-1.2.4.tgz#2816234e2378bddc4e5354fab5caa895df7100d9" - integrity sha512-NqVDv9TpANUjFm0N8uM5GxL36UgKi9/atZw+x7YFnQ8ckwFGKrl4xX4yWtrey3UJm5nP1kUbnYgLopqWNSRhWw== - schema-utils@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/schema-utils/-/schema-utils-1.0.0.tgz#0b79a93204d7b600d4b2850d1f66c2a34951c770" @@ -4769,7 +4659,7 @@ scss-tokenizer@^0.2.3: js-base64 "^2.1.8" source-map "^0.4.2" -"semver@2 || 3 || 4 || 5", semver@^5.3.0, semver@^5.4.1, semver@^5.5.0, semver@^5.5.1, semver@^5.6.0: +"semver@2 || 3 || 4 || 5", semver@^5.4.1, semver@^5.5.0, semver@^5.5.1, semver@^5.6.0: version "5.7.1" resolved "https://registry.yarnpkg.com/semver/-/semver-5.7.1.tgz#a954f931aeba508d307bbf069eff0c01c96116f7" integrity sha512-sauaDf/PZdVgrLTNYHRtpXa1iRiKcaebiKQ1BJdpQlWH2lCvexQdX55snPFyK7QzpudqbCI0qXFfOasHdyNDGQ== @@ -5143,7 +5033,7 @@ strip-indent@^1.0.1: dependencies: get-stdin "^4.0.1" -strip-json-comments@^2.0.1, strip-json-comments@~2.0.1: +strip-json-comments@^2.0.1: version "2.0.1" resolved "https://registry.yarnpkg.com/strip-json-comments/-/strip-json-comments-2.0.1.tgz#3c531942e908c2697c0ec344858c286c7ca0a60a" integrity sha1-PFMZQukIwml8DsNEhYwobHygpgo= @@ -5203,19 +5093,6 @@ tar@^2.0.0: fstream "^1.0.12" inherits "2" -tar@^4.4.2: - version "4.4.13" - resolved "https://registry.yarnpkg.com/tar/-/tar-4.4.13.tgz#43b364bc52888d555298637b10d60790254ab525" - integrity sha512-w2VwSrBoHa5BsSyH+KxEqeQBAllHhccyMFVHtGtdMpF4W7IRWfZjFiQceJPChOeTsSDVUpER2T8FA93pr0L+QA== - dependencies: - chownr "^1.1.1" - fs-minipass "^1.2.5" - minipass "^2.8.6" - minizlib "^1.2.1" - mkdirp "^0.5.0" - safe-buffer "^5.1.2" - yallist "^3.0.3" - terser-webpack-plugin@^1.4.3: version "1.4.3" resolved "https://registry.yarnpkg.com/terser-webpack-plugin/-/terser-webpack-plugin-1.4.3.tgz#5ecaf2dbdc5fb99745fd06791f46fc9ddb1c9a7c" @@ -5758,7 +5635,7 @@ yallist@^2.1.2: resolved "https://registry.yarnpkg.com/yallist/-/yallist-2.1.2.tgz#1c11f9218f076089a47dd512f93c6699a6a81d52" integrity sha1-HBH5IY8HYImkfdUS+TxmmaaoHVI= -yallist@^3.0.0, yallist@^3.0.2, yallist@^3.0.3: +yallist@^3.0.2: version "3.1.1" resolved "https://registry.yarnpkg.com/yallist/-/yallist-3.1.1.tgz#dbb7daf9bfd8bac9ab45ebf602b8cbad0d5d08fd" integrity sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g== From 03de8baf24768d7cd1b9327f591af6d90595fdb7 Mon Sep 17 00:00:00 2001 From: Andy Boughton Date: Fri, 14 Feb 2020 14:21:54 -0500 Subject: [PATCH 6/6] Add a low-risk migration for model metadata options --- .../gwas/migrations/0006_auto_20200214_1919.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 locuszoom_plotting_service/gwas/migrations/0006_auto_20200214_1919.py diff --git a/locuszoom_plotting_service/gwas/migrations/0006_auto_20200214_1919.py b/locuszoom_plotting_service/gwas/migrations/0006_auto_20200214_1919.py new file mode 100644 index 0000000..43aa3f5 --- /dev/null +++ b/locuszoom_plotting_service/gwas/migrations/0006_auto_20200214_1919.py @@ -0,0 +1,17 @@ +# Generated by Django 2.0.13 on 2020-02-14 19:19 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ('gwas', '0005_auto_20190929_0344'), + ] + + operations = [ + migrations.AlterModelOptions( + name='analysisinfo', + options={'verbose_name_plural': 'GWAS Analysis Metadata'}, + ), + ]