From 893ecd1ac74accb794b1428dfad1788ceac4dbb9 Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Fri, 16 Aug 2019 18:08:35 -0500 Subject: [PATCH 1/9] Update packages to fix security warnings --- index.html | 2 +- package-lock.json | 386 ++++++++++++++++++++++++---------------------- package.json | 15 +- 3 files changed, 212 insertions(+), 191 deletions(-) diff --git a/index.html b/index.html index c25428b..a1f2388 100644 --- a/index.html +++ b/index.html @@ -239,7 +239,7 @@

-

© 2018 Payton Lab - Powered by MyGene.info, EBI Expression Atlas, CTDbase, WormBase, and UniProtKB.

+

© 2019 Payton Lab - Powered by MyGene.info, EBI Expression Atlas, CTDbase, WormBase, and UniProtKB.

diff --git a/package-lock.json b/package-lock.json index 66faf82..bfe9bba 100644 --- a/package-lock.json +++ b/package-lock.json @@ -5,9 +5,9 @@ "requires": true, "dependencies": { "@types/node": { - "version": "8.10.17", - "resolved": "https://registry.npmjs.org/@types/node/-/node-8.10.17.tgz", - "integrity": "sha512-3N3FRd/rA1v5glXjb90YdYUa+sOB7WrkU2rAhKZnF4TKD86Cym9swtulGuH0p9nxo7fP5woRNa8b0oFTpCO1bg==", + "version": "8.10.51", + "resolved": "https://registry.npmjs.org/@types/node/-/node-8.10.51.tgz", + "integrity": "sha512-cArrlJp3Yv6IyFT/DYe+rlO8o3SIHraALbBW/+CcCYW/a9QucpLI+n2p4sRxAvl2O35TiecpX2heSZtJjvEO+Q==", "dev": true }, "ProtVista": { @@ -36,15 +36,15 @@ } }, "ajv": { - "version": "5.5.2", - "resolved": "https://registry.npmjs.org/ajv/-/ajv-5.5.2.tgz", - "integrity": "sha1-c7Xuyj+rZT49P5Qis0GtQiBdyWU=", + "version": "6.10.2", + "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.10.2.tgz", + "integrity": "sha512-TXtUUEYHuaTEbLZWIKUr5pmBuhDLy+8KYtPYdcV8qC+pOZL+NKqYwvWSRrVXHn+ZmRRAu8vJTAznH7Oag6RVRw==", "dev": true, "requires": { - "co": "4.6.0", - "fast-deep-equal": "1.1.0", + "fast-deep-equal": "2.0.1", "fast-json-stable-stringify": "2.0.0", - "json-schema-traverse": "0.3.1" + "json-schema-traverse": "0.4.1", + "uri-js": "4.2.2" } }, "anatomogram": { @@ -52,7 +52,7 @@ "resolved": "https://registry.npmjs.org/anatomogram/-/anatomogram-1.7.0.tgz", "integrity": "sha512-7+NlAaYpcNbecUKF/EWLYuk4TOSsAv1SySnMAYQCaryn9nTKqz3glLN5prSMm8w9HN5A99fswZikHssSQDjAiw==", "requires": { - "lodash": "4.17.10", + "lodash": "4.17.15", "prop-types": "15.6.2", "react": "16.4.1", "react-dom": "16.4.1", @@ -116,10 +116,13 @@ "integrity": "sha1-5QNHYR1+aQlDIIu9r+vLwvuGbUY=" }, "asn1": { - "version": "0.2.3", - "resolved": "https://registry.npmjs.org/asn1/-/asn1-0.2.3.tgz", - "integrity": "sha1-2sh4dxPJlmhJ/IGAd36+nB3fO4Y=", - "dev": true + "version": "0.2.4", + "resolved": "https://registry.npmjs.org/asn1/-/asn1-0.2.4.tgz", + "integrity": "sha512-jxwzQpLQjSmWXgwaCZE9Nz+glAG01yF1QnWgbhGwHI5A6FRIEY6IVqtHhIepHqI7/kyEyQEagBC5mBEFlIYvdg==", + "dev": true, + "requires": { + "safer-buffer": "2.1.2" + } }, "assert-plus": { "version": "1.0.0", @@ -140,9 +143,9 @@ "dev": true }, "aws4": { - 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"dev": true, - "optional": true + "dev": true }, "typedarray": { "version": "0.0.6", @@ -2155,6 +2164,15 @@ "resolved": "https://registry.npmjs.org/underscore/-/underscore-1.9.1.tgz", "integrity": "sha512-5/4etnCkd9c8gwgowi5/om/mYO5ajCaOgdzj/oW+0eQV9WxKBDZw5+ycmKmeaTXjInS/W0BzpGLo2xR2aBwZdg==" }, + "uri-js": { + "version": "4.2.2", + "resolved": "https://registry.npmjs.org/uri-js/-/uri-js-4.2.2.tgz", + "integrity": "sha512-KY9Frmirql91X2Qgjry0Wd4Y+YTdrdZheS8TFwvkbLWf/G5KNJDCh6pKL5OZctEW4+0Baa5idK2ZQuELRwPznQ==", + "dev": true, + "requires": { + "punycode": "2.1.1" + } + }, "urijs": { "version": "1.19.1", "resolved": "https://registry.npmjs.org/urijs/-/urijs-1.19.1.tgz", @@ -2166,18 +2184,18 @@ "integrity": "sha1-RQ1Nyfpw3nMnYvvS1KKJgUGaDM8=" }, "uuid": { - "version": "3.2.1", - "resolved": "https://registry.npmjs.org/uuid/-/uuid-3.2.1.tgz", - "integrity": "sha512-jZnMwlb9Iku/O3smGWvZhauCf6cvvpKi4BKRiliS3cxnI+Gz9j5MEpTz2UFuXiKPJocb7gnsLHwiS05ige5BEA==", + "version": "3.3.2", + "resolved": "https://registry.npmjs.org/uuid/-/uuid-3.3.2.tgz", + "integrity": "sha512-yXJmeNaw3DnnKAOKJE51sL/ZaYfWJRl1pK9dr19YFCu0ObS231AB1/LbqTKRAQ5kw8A90rA6fr4riOUpTZvQZA==", "dev": true }, "validate-npm-package-license": { - "version": "3.0.3", - "resolved": "https://registry.npmjs.org/validate-npm-package-license/-/validate-npm-package-license-3.0.3.tgz", - "integrity": "sha512-63ZOUnL4SIXj4L0NixR3L1lcjO38crAbgrTpl28t8jjrfuiOBL5Iygm+60qPs/KsZGzPNg6Smnc/oY16QTjF0g==", + "version": "3.0.4", + "resolved": "https://registry.npmjs.org/validate-npm-package-license/-/validate-npm-package-license-3.0.4.tgz", + "integrity": "sha512-DpKm2Ui/xN7/HQKCtpZxoRWBhZ9Z0kqtygG8XCgNQ8ZlDnxuQmWhj566j8fN4Cu3/JmbhsDo7fcAJq4s9h27Ew==", "dev": true, "requires": { - "spdx-correct": "3.0.0", + "spdx-correct": "3.1.0", "spdx-expression-parse": "3.0.0" } }, diff --git a/package.json b/package.json index fd6f2b7..65a09f7 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "Genotify", "productName": "Genotify", - "version": "1.2.1", + "version": "1.2.2", "author": "Jared Andrews", "license": "GPL-3.0", "repository": "https://github.com/j-andrews7/Genotify", @@ -13,16 +13,19 @@ "linpack": "electron-packager . --platform=linux --out ./release-builds --arch=x64 --overwrite --asar --icon=./assets/icons/png/1024x1024.png --appCopyright=\"Copyright © 2018 Payton Lab. All rights reserved.\"" }, "devDependencies": { - "electron": "~2.0.2" + "electron": "~2.0.8" }, "dependencies": { - "jquery": "3.3.1", - "bootstrap": "4.1.1", - "popper.js": "1.14.3", + "jquery": "3.4.0", + "bootstrap": "4.3.1", + "popper.js": "1.14.7", "load-json-file": "~4.0.0", "datatables.net": "1.10.16", "datatables.net-dt": "1.10.16", "expression-atlas-heatmap-highcharts": "4.4.1", - "ProtVista": "j-andrews7/ProtVista" + "ProtVista": "j-andrews7/ProtVista", + "extend": ">=3.0.2", + "lodash.mergewith": ">=4.6.2", + "lodash": ">=4.17.13" } } From d6efd88e2d0a2c617bbfc5414e2899e022200105 Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Fri, 16 Aug 2019 18:09:35 -0500 Subject: [PATCH 2/9] copyright updates --- package.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index 65a09f7..103ad31 100644 --- a/package.json +++ b/package.json @@ -8,9 +8,9 @@ "main": "main.js", "scripts": { "start": "electron .", - "winpack": "electron-packager . --platform=win32 --out ./release-builds --arch=x64 --overwrite --asar --icon=./assets/icons/windows/icon.ico --win32metadata.CompanyName=\"Genotify\" --win32metadata.ProductName=\"Genotify\" --win32metadata.FileDescription=\"Genotify\" --appCopyright=\"Copyright © 2018 Payton Lab. All rights reserved.\"", - "osxpack": "electron-packager . --platform=darwin --out ./release-builds --arch=x64 --overwrite --asar --icon=./assets/icons/mac/1024x1024.icns --appCopyright=\"Copyright © 2018 Payton Lab. All rights reserved.\"", - "linpack": "electron-packager . --platform=linux --out ./release-builds --arch=x64 --overwrite --asar --icon=./assets/icons/png/1024x1024.png --appCopyright=\"Copyright © 2018 Payton Lab. All rights reserved.\"" + "winpack": "electron-packager . --platform=win32 --out ./release-builds --arch=x64 --overwrite --asar --icon=./assets/icons/windows/icon.ico --win32metadata.CompanyName=\"Genotify\" --win32metadata.ProductName=\"Genotify\" --win32metadata.FileDescription=\"Genotify\" --appCopyright=\"Copyright © 2019 Payton Lab. All rights reserved.\"", + "osxpack": "electron-packager . --platform=darwin --out ./release-builds --arch=x64 --overwrite --asar --icon=./assets/icons/mac/1024x1024.icns --appCopyright=\"Copyright © 2019 Payton Lab. All rights reserved.\"", + "linpack": "electron-packager . --platform=linux --out ./release-builds --arch=x64 --overwrite --asar --icon=./assets/icons/png/1024x1024.png --appCopyright=\"Copyright © 2019 Payton Lab. All rights reserved.\"" }, "devDependencies": { "electron": "~2.0.8" From efcfc6b72d0e85cb2a080fa031fd23c433972cce Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Fri, 16 Aug 2019 18:44:50 -0500 Subject: [PATCH 3/9] Fix #40 & bump version. --- package-lock.json | 2 +- renderer.js | 29 ++++++++++++++++++++++++++++- 2 files changed, 29 insertions(+), 2 deletions(-) diff --git a/package-lock.json b/package-lock.json index bfe9bba..0cc4b7f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "Genotify", - "version": "1.2.1", + "version": "1.2.2", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/renderer.js b/renderer.js index 526ae55..b5af3e3 100644 --- a/renderer.js +++ b/renderer.js @@ -527,6 +527,12 @@ function renderProtein(data) { targ.innerHTML = 'No data available for this protein.'; return; }; + + //Snag only first Uniprot ID if multiple in array. + if (Array.isArray(data)) { + data = data[0] + }; + var instance = new ProtVista({ el: targ, uniprotacc: data @@ -893,7 +899,7 @@ function parseGeneData(data) { undefined) { uniprot = { db: 'http://www.uniprot.org/uniprot/', - ident: data.uniprot['Swiss-Prot'] + ident: checkArray(data.uniprot['Swiss-Prot']) }; uniprotSum = getUniprotSummary(data.uniprot['Swiss-Prot']); protein = data.uniprot['Swiss-Prot']; @@ -982,6 +988,22 @@ function parseGeneData(data) { }); }; +// Check if ID is an array. If so, return first element. +function checkArray(id) { + return new Promise(function(resolve, reject) { + if (!id) { + reject(); + } + + // Necessary for edge cases where multiple IDs are returned. + if (Array.isArray(id)) { + id = id[0]; + } + + resolve(id); + }); +} + // Fetch the function summary for given protein from UniprotKB. function getUniprotSummary(id) { return new Promise(function(resolve, reject) { @@ -989,6 +1011,11 @@ function getUniprotSummary(id) { reject(); } + // Necessary for edge cases where multiple IDs are returned. + if (Array.isArray(id)) { + id = id[0]; + } + var summary; fetch('https://www.uniprot.org/uniprot/' + id + '.xml').then( From 3d0de7083431deb5b700b1d3c6a02f5f232bdb7e Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Sat, 17 Aug 2019 00:11:02 -0500 Subject: [PATCH 4/9] Simplify uniprot multiple id check so unresolved promises don't occur. --- renderer.js | 31 +++++++++++-------------------- 1 file changed, 11 insertions(+), 20 deletions(-) diff --git a/renderer.js b/renderer.js index b5af3e3..f167fb3 100644 --- a/renderer.js +++ b/renderer.js @@ -897,10 +897,17 @@ function parseGeneData(data) { if (data.hasOwnProperty('uniprot') && data.uniprot['Swiss-Prot'] !== undefined) { - uniprot = { - db: 'http://www.uniprot.org/uniprot/', - ident: checkArray(data.uniprot['Swiss-Prot']) - }; + if (Array.isArray(data.uniprot['Swiss-Prot'])) { + uniprot = { + db: 'http://www.uniprot.org/uniprot/', + ident: data.uniprot['Swiss-Prot'][0] + }; + } else { + uniprot = { + db: 'http://www.uniprot.org/uniprot/', + ident: data.uniprot['Swiss-Prot'] + }; + } uniprotSum = getUniprotSummary(data.uniprot['Swiss-Prot']); protein = data.uniprot['Swiss-Prot']; } @@ -988,22 +995,6 @@ function parseGeneData(data) { }); }; -// Check if ID is an array. If so, return first element. -function checkArray(id) { - return new Promise(function(resolve, reject) { - if (!id) { - reject(); - } - - // Necessary for edge cases where multiple IDs are returned. - if (Array.isArray(id)) { - id = id[0]; - } - - resolve(id); - }); -} - // Fetch the function summary for given protein from UniprotKB. function getUniprotSummary(id) { return new Promise(function(resolve, reject) { From b3ae058566bb98c97e585f871712431aff8d60ae Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Sat, 17 Aug 2019 00:42:40 -0500 Subject: [PATCH 5/9] Fix #44 --- renderer.js | 24 ++++++++++++++++++++---- species.json | 3 ++- 2 files changed, 22 insertions(+), 5 deletions(-) diff --git a/renderer.js b/renderer.js index f167fb3..19397b2 100644 --- a/renderer.js +++ b/renderer.js @@ -395,11 +395,20 @@ function displayHits(hitsList) { for (i in hitsList.hits) { var hit = hitsList.hits[i]; var spec = 'NA'; + var symbol = 'NA'; + + // Check if species is in our list. if (speciesObj[hit.taxid] !== undefined) { spec = speciesObj[hit.taxid]; - } else {} + } + + // Check if symbol is part of the hit. + if (hit.symbol !== undefined) { + symbol = hit.symbol; + } + dataSet.push([ - hit.symbol, + symbol, hit._id, spec, hit._score.toFixed(2) @@ -744,6 +753,7 @@ function parseGeneData(data) { var gobp = null; var gomf = null; var gocc = null; + var symbol = null; if (data.hasOwnProperty('go')) { if (data.go.hasOwnProperty('BP')) { @@ -912,6 +922,12 @@ function parseGeneData(data) { protein = data.uniprot['Swiss-Prot']; } + if (data.hasOwnProperty('symbol') !== undefined) { + symbol = data.symbol; + } else { + symbol = "NA" + } + if (data.hasOwnProperty('WormBase') || data.hasOwnProperty( 'uniprot')) { Promise.all([wormbaseSum, uniprotSum]).then(function(values) { @@ -945,7 +961,7 @@ function parseGeneData(data) { 'gocc': gocc, 'uniprot-summary': uniprotSum, 'wormbase-summary': wormbaseSum, - 'gene-symbol': data.symbol, + 'gene-symbol': symbol, 'gene-name': data.name, 'gene-id': { db: 'https://www.ncbi.nlm.nih.gov/gene/', @@ -983,7 +999,7 @@ function parseGeneData(data) { 'gocc': gocc, 'uniprot-summary': uniprotSum, 'wormbase-summary': wormbaseSum, - 'gene-symbol': data.symbol, + 'gene-symbol': symbol, 'gene-name': data.name, 'gene-id': { db: 'https://www.ncbi.nlm.nih.gov/gene/', diff --git a/species.json b/species.json index 31e29d4..0ce461f 100644 --- a/species.json +++ b/species.json @@ -676595,5 +676595,6 @@ "190324":"Collodictyon", "190325":"Collodictyon triciliatum", "177250":"Diphylleia", -"190327":"Diphylleia rotans" +"190327":"Diphylleia rotans", +"81972":"Aegla longirostri" } From 3248203e59d6d5bcccf8bb144782b6edef263a92 Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Sat, 17 Aug 2019 00:59:23 -0500 Subject: [PATCH 6/9] Update to new version of electron with hope of fixing #45 --- package-lock.json | 268 +++++++++++++++++++--------------------------- package.json | 2 +- 2 files changed, 113 insertions(+), 157 deletions(-) diff --git a/package-lock.json b/package-lock.json index 0cc4b7f..02c2cd3 100644 --- a/package-lock.json +++ b/package-lock.json @@ -5,9 +5,9 @@ "requires": true, "dependencies": { "@types/node": { - "version": "8.10.51", - "resolved": "https://registry.npmjs.org/@types/node/-/node-8.10.51.tgz", - "integrity": "sha512-cArrlJp3Yv6IyFT/DYe+rlO8o3SIHraALbBW/+CcCYW/a9QucpLI+n2p4sRxAvl2O35TiecpX2heSZtJjvEO+Q==", + "version": "10.14.15", + "resolved": "https://registry.npmjs.org/@types/node/-/node-10.14.15.tgz", + "integrity": "sha512-CBR5avlLcu0YCILJiDIXeU2pTw7UK/NIxfC63m7d7CVamho1qDEzXKkOtEauQRPMy6MI8mLozth+JJkas7HY6g==", "dev": true }, "ProtVista": { @@ -164,12 +164,6 @@ } } }, - "balanced-match": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.0.tgz", - "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=", - "dev": true - }, "bcrypt-pbkdf": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/bcrypt-pbkdf/-/bcrypt-pbkdf-1.0.2.tgz", @@ -184,16 +178,6 @@ "resolved": "https://registry.npmjs.org/bootstrap/-/bootstrap-4.3.1.tgz", "integrity": "sha512-rXqOmH1VilAt2DyPzluTi2blhk17bO7ef+zLLPlWvG494pDxcM234pJ8wTc/6R40UWizAIIMgxjvxZg5kmsbag==" }, - "brace-expansion": { - "version": "1.1.11", - "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz", - "integrity": "sha512-iCuPHDFgrHX7H2vEI/5xpz07zSHB00TpugqhmYtVmMO6518mCuRMoOYFldEBl0g187ufozdaHgWKcYFb61qGiA==", - "dev": true, - "requires": { - "balanced-match": "1.0.0", - "concat-map": "0.0.1" - } - }, "buffer-from": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/buffer-from/-/buffer-from-1.1.1.tgz", @@ -301,12 +285,6 @@ "resolved": "https://registry.npmjs.org/component-indexof/-/component-indexof-0.0.3.tgz", "integrity": "sha1-EdCRMSI5648yyPJa6csAL/6NPCQ=" }, - "concat-map": { - "version": "0.0.1", - "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz", - "integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s=", - "dev": true - }, "concat-stream": { "version": "1.6.2", "resolved": "https://registry.npmjs.org/concat-stream/-/concat-stream-1.6.2.tgz", @@ -421,12 +399,12 @@ } }, "debug": { - "version": "2.6.9", - "resolved": "https://registry.npmjs.org/debug/-/debug-2.6.9.tgz", - "integrity": "sha512-bC7ElrdJaJnPbAP+1EotYvqZsb3ecl5wi6Bfi6BJTUcNowp6cvspg0jXznRTKDjm/E7AdgFBVeAPVMNcKGsHMA==", + "version": "3.2.6", + "resolved": "https://registry.npmjs.org/debug/-/debug-3.2.6.tgz", + "integrity": "sha512-mel+jf7nrtEl5Pn1Qx46zARXKDpBbvzezse7p7LqINmdoIk8PYP5SySaxEmYv6TZ0JyEKA1hsCId6DIhgITtWQ==", "dev": true, "requires": { - "ms": "2.0.0" + "ms": "2.1.2" } }, "decamelize": { @@ -511,31 +489,31 @@ } }, "electron": { - "version": "2.0.18", - "resolved": "https://registry.npmjs.org/electron/-/electron-2.0.18.tgz", - "integrity": "sha512-PQRHtFvLxHdJzMMIwTddUtkS+Te/fZIs+PHO+zPmTUTBE76V3Od3WRGzMQwiJHxN679licmCKhJpMyxZfDEVWQ==", + "version": "3.1.13", + "resolved": "https://registry.npmjs.org/electron/-/electron-3.1.13.tgz", + "integrity": "sha512-aRNywoUSO1Va/lpU4nz3K6GDyFqYtlOnHGLcERAAHfhB+IJrJ34cUJW4FVBpm43AwvUdAeuCkVKRLtOmrgx5CA==", "dev": true, "requires": { - "@types/node": "8.10.51", - "electron-download": "3.3.0", + "@types/node": "10.14.15", + "electron-download": "4.1.1", "extract-zip": "1.6.7" } }, "electron-download": { - "version": "3.3.0", - "resolved": "https://registry.npmjs.org/electron-download/-/electron-download-3.3.0.tgz", - "integrity": "sha1-LP1U1pZsAZxNSa1l++Zcyc3vaMg=", + "version": "4.1.1", + "resolved": "https://registry.npmjs.org/electron-download/-/electron-download-4.1.1.tgz", + "integrity": "sha512-FjEWG9Jb/ppK/2zToP+U5dds114fM1ZOJqMAR4aXXL5CvyPE9fiqBK/9YcwC9poIFQTEJk/EM/zyRwziziRZrg==", "dev": true, "requires": { - "debug": "2.6.9", - "fs-extra": "0.30.0", - "home-path": "1.0.6", + "debug": "3.2.6", + "env-paths": "1.0.0", + "fs-extra": "4.0.3", "minimist": "1.2.0", "nugget": "2.0.1", - "path-exists": "2.1.0", + "path-exists": "3.0.0", "rc": "1.2.8", "semver": "5.7.1", - "sumchecker": "1.3.1" + "sumchecker": "2.0.2" } }, "encoding": { @@ -551,6 +529,12 @@ "resolved": "https://registry.npmjs.org/entities/-/entities-1.1.1.tgz", "integrity": "sha1-blwtClYhtdra7O+AuQ7ftc13cvA=" }, + "env-paths": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/env-paths/-/env-paths-1.0.0.tgz", + "integrity": "sha1-QWgTO0K7BcOKNbGuQ5fIKYqzaeA=", + "dev": true + }, "error-ex": { "version": "1.3.1", "resolved": "https://registry.npmjs.org/error-ex/-/error-ex-1.3.1.tgz", @@ -559,12 +543,6 @@ "is-arrayish": "0.2.1" } }, - "es6-promise": { - "version": "4.2.8", - "resolved": "https://registry.npmjs.org/es6-promise/-/es6-promise-4.2.8.tgz", - "integrity": "sha512-HJDGx5daxeIvxdBxvG2cb9g4tEvwIk3i8+nhX0yGrYmZUzbkdg8QbDevheDB8gd0//uPj4c1EQua8Q+MViT0/w==", - "dev": true - }, "escape-string-regexp": { "version": "1.0.5", "resolved": "https://registry.npmjs.org/escape-string-regexp/-/escape-string-regexp-1.0.5.tgz", @@ -636,6 +614,23 @@ "debug": "2.6.9", "mkdirp": "0.5.1", "yauzl": "2.4.1" + }, + "dependencies": { + "debug": { + "version": "2.6.9", + "resolved": "https://registry.npmjs.org/debug/-/debug-2.6.9.tgz", + "integrity": "sha512-bC7ElrdJaJnPbAP+1EotYvqZsb3ecl5wi6Bfi6BJTUcNowp6cvspg0jXznRTKDjm/E7AdgFBVeAPVMNcKGsHMA==", + "dev": true, + "requires": { + "ms": "2.0.0" + } + }, + "ms": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/ms/-/ms-2.0.0.tgz", + "integrity": "sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=", + "dev": true + } } }, "extsprintf": { @@ -692,6 +687,17 @@ "requires": { "path-exists": "2.1.0", "pinkie-promise": "2.0.1" + }, + "dependencies": { + "path-exists": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-2.1.0.tgz", + "integrity": "sha1-D+tsZPD8UY2adU3V77YscCJ2H0s=", + "dev": true, + "requires": { + "pinkie-promise": "2.0.1" + } + } } }, "forever-agent": { @@ -712,24 +718,16 @@ } }, "fs-extra": { - 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"wrappy": { - "version": "1.0.2", - "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=", - "dev": true - }, "xtend": { "version": "2.1.2", "resolved": "https://registry.npmjs.org/xtend/-/xtend-2.1.2.tgz", diff --git a/package.json b/package.json index 103ad31..9717dd7 100644 --- a/package.json +++ b/package.json @@ -13,7 +13,7 @@ "linpack": "electron-packager . --platform=linux --out ./release-builds --arch=x64 --overwrite --asar --icon=./assets/icons/png/1024x1024.png --appCopyright=\"Copyright © 2019 Payton Lab. All rights reserved.\"" }, "devDependencies": { - "electron": "~2.0.8" + "electron": "~3.1.13" }, "dependencies": { "jquery": "3.4.0", From 3b87ead9f82f6100473a0a1c1c5eac23c2d20977 Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Sat, 17 Aug 2019 01:11:21 -0500 Subject: [PATCH 7/9] Mention potential gotcha during source install. --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index e3df8b1..dc95ba6 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,9 @@ This program aims to give you access to all of the resources you could ever want --- ## Installation -Just download the [release](https://github.com/j-andrews7/GenotifyDesktop/releases) for your OS, unpack, and run. To build from source with `node.js`, you can clone the repo and run `npm install` followed by `npm start`. +Just download the [release](https://github.com/j-andrews7/GenotifyDesktop/releases) for your OS, unpack, and run. To build from source with `node.js`, you can clone the repo and run `npm install` followed by `npm start`. + +If you run into `permissin denied` errors during the postinstall script, try adding the `--unsafe-perm=true --allow-root` arguments. ## Basic Usage Genotify is dead simple to use. Type a query into the search box and click the search button, hit enter, or use the hotkey `ctrl+q` (or `cmd+q`) to query from clipboard (even if Genotify isn't focused!). Search for and select species with the species filter, or filter hits in the hits table dynamically. Clicking on a different hit in the hits table will show the information for that hit. Expand the various sections to read what said gene does, explore expression data, see disease associations, or view links out to various data sources. Clicking on a text box will copy its contents to your clipboard for easy copying. From 486f84882e89c526a5da9edf752ee694dbd08a08 Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Sat, 17 Aug 2019 01:43:09 -0500 Subject: [PATCH 8/9] Update CHANGELOG.md --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 07a5e0a..5cf4afc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,13 @@ ## Change log +### _**v1.2.2**_ +**Release date: August 17th, 2019** + - Upgraded a bunch of dependency versions to fix most security issues [#43](https://github.com/j-andrews7/Genotify/issues/43). + - Upgraded to Electron 3.1.13, which fixed the menu bar being impossible to see on linux [#45](https://github.com/j-andrews7/Genotify/issues/45). + - Fixed a bug that caused the Hits datatable to throw mad errors when hits had no symbol provided [#44](https://github.com/j-andrews7/Genotify/issues/44). + - Fixed a long standing bug due to multiple Uniprot IDs being returned. This caused errors in retrieving the Uniprot Summary and ProtVista data [#40](https://github.com/j-andrews7/Genotify/issues/40). + - Fix issues building from source on linux [#42](https://github.com/j-andrews7/Genotify/issues/42) - thanks to @hmontenegro for reporting and help troubleshooting. + ### _**v1.2.1**_ **Release date: August 15th, 2018** - Added a link back to CTDbase in the disease associations table. From d8730eaeb13266db9cc3a5cdc2cda58f8639fa36 Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Sat, 17 Aug 2019 14:24:29 -0500 Subject: [PATCH 9/9] Update splash and use link. --- assets/splash/Splash.svg | 172 ++++++++++++++++++++++++++++++++++++++- main.js | 5 +- 2 files changed, 174 insertions(+), 3 deletions(-) diff --git a/assets/splash/Splash.svg b/assets/splash/Splash.svg index 83d45d0..16d23e2 100644 --- a/assets/splash/Splash.svg +++ b/assets/splash/Splash.svg @@ -1 +1,171 @@ -Artboard 1 \ No newline at end of file + + + + +Artboard 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/main.js b/main.js index 848bee7..987fd34 100644 --- a/main.js +++ b/main.js @@ -25,7 +25,8 @@ function createWindow() { height: 1200, minWidth: 450, icon: path.join(__dirname, 'assets/icons/png/64x64.png'), - show: false + show: false, + title: "Genotify" }); // Splash screen. @@ -147,7 +148,7 @@ function createMenu() { label: 'How to Use', click() { require('electron').shell.openExternal( - 'https://github.com/j-andrews7/GenotifyDesktop/') + 'https://github.com/j-andrews7/Genotify/') } }] }]