diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json
index f180ebb67..aa9065055 100644
--- a/jbrowse/package-lock.json
+++ b/jbrowse/package-lock.json
@@ -9,13 +9,13 @@
"version": "1.0.0",
"dependencies": {
"@gmod/vcf": "^5.0.10",
- "@jbrowse/core": "^2.6.2",
- "@jbrowse/plugin-linear-genome-view": "^2.6.2",
- "@jbrowse/plugin-svg": "^2.6.2",
- "@jbrowse/plugin-variants": "^2.6.2",
- "@jbrowse/react-linear-genome-view": "^2.6.2",
+ "@jbrowse/core": "^2.7.0",
+ "@jbrowse/plugin-linear-genome-view": "^2.7.0",
+ "@jbrowse/plugin-svg": "^2.7.0",
+ "@jbrowse/plugin-variants": "^2.7.0",
+ "@jbrowse/react-linear-genome-view": "^2.7.0",
"@labkey/api": "^1.25.0",
- "@labkey/components": "^2.381.1",
+ "@labkey/components": "^2.0.0",
"@mui/x-data-grid": "^6.0.1",
"assert": "^2.0.0",
"browserify-zlib": "^0.2.0",
@@ -37,8 +37,7 @@
"typescript": "^5.1.6",
"util": "^0.12.5",
"uuid": "^9.0.0",
- "vm-browserify": "^1.1.2",
- "xlsx": "https://cdn.sheetjs.com/xlsx-0.19.3/xlsx-0.19.3.tgz"
+ "vm-browserify": "^1.1.2"
},
"devDependencies": {
"@labkey/build": "6.15.0",
@@ -1811,23 +1810,23 @@
"dev": true
},
"node_modules/@babel/runtime": {
- "version": "7.22.6",
- "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.22.6.tgz",
- "integrity": "sha512-wDb5pWm4WDdF6LFUde3Jl8WzPA+3ZbxYqkC6xAXuD3irdEHN1k0NfTRrJD8ZD378SJ61miMLCqIOXYhd8x+AJQ==",
+ "version": "7.23.2",
+ "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.23.2.tgz",
+ "integrity": "sha512-mM8eg4yl5D6i3lu2QKPuPH4FArvJ8KhTofbE7jwMUv9KX5mBvwPAqnV3MlyBNqdp9RyRKP6Yck8TrfYrPvX3bg==",
"dependencies": {
- "regenerator-runtime": "^0.13.11"
+ "regenerator-runtime": "^0.14.0"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/runtime-corejs2": {
- "version": "7.22.6",
- "resolved": "https://registry.npmjs.org/@babel/runtime-corejs2/-/runtime-corejs2-7.22.6.tgz",
- "integrity": "sha512-GTJVRjzQIHUBwRzuWxPII87XoWxXzILBJrQh5gqIV6q6m231Y0BBA9NKta5FV5Lbl8z5gS3+m6YSoKJp0KQJ4g==",
+ "version": "7.23.2",
+ "resolved": "https://registry.npmjs.org/@babel/runtime-corejs2/-/runtime-corejs2-7.23.2.tgz",
+ "integrity": "sha512-lTwRWGcAUBANnxD0A4c5/wKQ0eLhgdAy9kdY2rzTmmliumBQ8u8awykMnaQAnZR3PC47jLRjGoj+hozZqy9Bww==",
"dependencies": {
"core-js": "^2.6.12",
- "regenerator-runtime": "^0.13.11"
+ "regenerator-runtime": "^0.14.0"
},
"engines": {
"node": ">=6.9.0"
@@ -1840,6 +1839,16 @@
"deprecated": "core-js@<3.23.3 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Some versions have web compatibility issues. Please, upgrade your dependencies to the actual version of core-js.",
"hasInstallScript": true
},
+ "node_modules/@babel/runtime-corejs2/node_modules/regenerator-runtime": {
+ "version": "0.14.0",
+ "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.14.0.tgz",
+ "integrity": "sha512-srw17NI0TUWHuGa5CFGGmhfNIeja30WMBfbslPNhf6JrqQlLN5gcrvig1oqPxiVaXb0oW0XRKtH6Nngs5lKCIA=="
+ },
+ "node_modules/@babel/runtime/node_modules/regenerator-runtime": {
+ "version": "0.14.0",
+ "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.14.0.tgz",
+ "integrity": "sha512-srw17NI0TUWHuGa5CFGGmhfNIeja30WMBfbslPNhf6JrqQlLN5gcrvig1oqPxiVaXb0oW0XRKtH6Nngs5lKCIA=="
+ },
"node_modules/@babel/template": {
"version": "7.22.15",
"resolved": "https://registry.npmjs.org/@babel/template/-/template-7.22.15.tgz",
@@ -2223,23 +2232,44 @@
"integrity": "sha512-EsBwpc7hBUJWAsNPBmJy4hxWx12v6bshQsldrVmjxJoc3isbxhOrF2IcCpaXxfvq03NwkI7sbsOLXbYuqF/8Ww=="
},
"node_modules/@flatten-js/interval-tree": {
- "version": "1.0.21",
- "resolved": "https://registry.npmjs.org/@flatten-js/interval-tree/-/interval-tree-1.0.21.tgz",
- "integrity": "sha512-TcxTNMkWBPqLicuFw9FViOZSVuug8MRRISUMDOCFzMI9FZ97BTjxiq8V168VifuEq9ERHhP2ltmGCovwS+KACw=="
+ "version": "1.1.1",
+ "resolved": "https://registry.npmjs.org/@flatten-js/interval-tree/-/interval-tree-1.1.1.tgz",
+ "integrity": "sha512-IsD8MPvzlbrUZnqychSEPM0dX6DXFG6ObFVbJs8asb5cwUOCek+Qi10W/mK7N9aqKkNpOSSzEIkrhHOiOXZlXw=="
},
"node_modules/@floating-ui/core": {
- "version": "1.3.1",
- "resolved": "https://registry.npmjs.org/@floating-ui/core/-/core-1.3.1.tgz",
- "integrity": "sha512-Bu+AMaXNjrpjh41znzHqaz3r2Nr8hHuHZT6V2LBKMhyMl0FgKA62PNYbqnfgmzOhoWZj70Zecisbo4H1rotP5g=="
+ "version": "1.5.0",
+ "resolved": "https://registry.npmjs.org/@floating-ui/core/-/core-1.5.0.tgz",
+ "integrity": "sha512-kK1h4m36DQ0UHGj5Ah4db7R0rHemTqqO0QLvUqi1/mUUp3LuAWbWxdxSIf/XsnH9VS6rRVPLJCncjRzUvyCLXg==",
+ "dependencies": {
+ "@floating-ui/utils": "^0.1.3"
+ }
},
"node_modules/@floating-ui/dom": {
- "version": "1.4.5",
- "resolved": "https://registry.npmjs.org/@floating-ui/dom/-/dom-1.4.5.tgz",
- "integrity": "sha512-96KnRWkRnuBSSFbj0sFGwwOUd8EkiecINVl0O9wiZlZ64EkpyAOG3Xc2vKKNJmru0Z7RqWNymA+6b8OZqjgyyw==",
+ "version": "1.5.3",
+ "resolved": "https://registry.npmjs.org/@floating-ui/dom/-/dom-1.5.3.tgz",
+ "integrity": "sha512-ClAbQnEqJAKCJOEbbLo5IUlZHkNszqhuxS4fHAVxRPXPya6Ysf2G8KypnYcOTpx6I8xcgF9bbHb6g/2KpbV8qA==",
+ "dependencies": {
+ "@floating-ui/core": "^1.4.2",
+ "@floating-ui/utils": "^0.1.3"
+ }
+ },
+ "node_modules/@floating-ui/react-dom": {
+ "version": "2.0.2",
+ "resolved": "https://registry.npmjs.org/@floating-ui/react-dom/-/react-dom-2.0.2.tgz",
+ "integrity": "sha512-5qhlDvjaLmAst/rKb3VdlCinwTF4EYMiVxuuc/HVUjs46W0zgtbMmAZ1UTsDrRTxRmUEzl92mOtWbeeXL26lSQ==",
"dependencies": {
- "@floating-ui/core": "^1.3.1"
+ "@floating-ui/dom": "^1.5.1"
+ },
+ "peerDependencies": {
+ "react": ">=16.8.0",
+ "react-dom": ">=16.8.0"
}
},
+ "node_modules/@floating-ui/utils": {
+ "version": "0.1.6",
+ "resolved": "https://registry.npmjs.org/@floating-ui/utils/-/utils-0.1.6.tgz",
+ "integrity": "sha512-OfX7E2oUDYxtBvsuS4e/jSn4Q9Qb6DzgeYtsAdkPZ47znpoNsMgZw0+tVijiv3uGNR6dgNlty6r9rzIzHjtd/A=="
+ },
"node_modules/@gmod/bam": {
"version": "2.0.0",
"resolved": "https://registry.npmjs.org/@gmod/bam/-/bam-2.0.0.tgz",
@@ -2262,9 +2292,9 @@
"integrity": "sha512-XsP+KhQif4bjX1kbuSiySJFNAehNxgLb6hPRGJ9QsUr8ajHkuXGdrHmFUTUUXhDwVX2R5bY4JNZEwbUiMhV+MA=="
},
"node_modules/@gmod/bbi": {
- "version": "4.0.1",
- "resolved": "https://registry.npmjs.org/@gmod/bbi/-/bbi-4.0.1.tgz",
- "integrity": "sha512-SNYhAiKsucrsyzj0p9nyfaOroaYE7eX61FVKCI3e/x6ken/vjFJFDNcDyRqWdA4RHzEygkQapGpJx1d3+rN76Q==",
+ "version": "4.0.2",
+ "resolved": "https://registry.npmjs.org/@gmod/bbi/-/bbi-4.0.2.tgz",
+ "integrity": "sha512-ZAPdrmghSOLoikqXM+zLxsYRjPoGXPTi2a9T5myN89RJ7O1HlcZ6IIb4VvVuWoaI/2OjX+XHB1wxVwED/jlLDQ==",
"dependencies": {
"abortable-promise-cache": "^1.4.1",
"binary-parser": "^2.1.0",
@@ -2357,9 +2387,9 @@
}
},
"node_modules/@gmod/indexedfasta": {
- "version": "2.0.4",
- "resolved": "https://registry.npmjs.org/@gmod/indexedfasta/-/indexedfasta-2.0.4.tgz",
- "integrity": "sha512-gOvFfA0czZrUO1le1jgO2BKIYxB2q14PHAjggLy8Va0UWaN3rszqWbKHSfaNFqycaeoZVFPEPpVDvlgtoo4x5A==",
+ "version": "2.1.0",
+ "resolved": "https://registry.npmjs.org/@gmod/indexedfasta/-/indexedfasta-2.1.0.tgz",
+ "integrity": "sha512-I7kzSwlK0kxy05K1jsvRPsDr7vV7i/7EI1GMDzCqszn8FtwTlgkdQOYAuhK4kM5SIZrCEG3yAg+TQJmcsv33ug==",
"dependencies": {
"@gmod/bgzf-filehandle": "^1.4.0",
"generic-filehandle": "^3.0.0"
@@ -2578,9 +2608,9 @@
}
},
"node_modules/@jbrowse/core": {
- "version": "2.6.2",
- "resolved": "https://registry.npmjs.org/@jbrowse/core/-/core-2.6.2.tgz",
- "integrity": "sha512-Z/b/7L6Z8vP1HRrluDSWD/kqzKFsHKSLWVrPw9sb3pYlATFDdGCeJiGhwtjTOaYwjGOQyFqvulH1DShvdRkBDg==",
+ "version": "2.7.0",
+ "resolved": "https://registry.npmjs.org/@jbrowse/core/-/core-2.7.0.tgz",
+ "integrity": "sha512-7Jh/p+sUOdSJAFuCfzawNG/Lg9UutzRTu4kJd/lZ1MBn5s1DufBk2W66rYYn8ZLwyFbUbeSQkbD0XFRd4c8vjw==",
"dependencies": {
"@babel/runtime": "^7.17.9",
"@gmod/bgzf-filehandle": "^1.4.3",
@@ -2590,8 +2620,8 @@
"canvas-sequencer": "^3.1.0",
"canvas2svg": "^1.0.16",
"clone": "^2.1.2",
- "clsx": "^1.0.4",
- "color": "^3.1.3",
+ "clsx": "^2.0.0",
+ "colord": "^2.9.3",
"copy-to-clipboard": "^3.3.1",
"deepmerge": "^4.2.2",
"detect-node": "^2.1.0",
@@ -2609,14 +2639,13 @@
"rbush": "^3.0.1",
"react-error-boundary": "^4.0.3",
"serialize-error": "^8.0.0",
- "shortid": "^2.2.13",
"svg-path-generator": "^1.1.0"
},
"peerDependencies": {
"@mui/material": "^5.0.0",
"@mui/x-data-grid": "^6.0.1",
"mobx": "^6.0.0",
- "mobx-react": "^7.0.0",
+ "mobx-react": "^9.0.0",
"mobx-state-tree": "^5.0.0",
"prop-types": "^15.0.0",
"react": ">=16.8.0",
@@ -2626,16 +2655,15 @@
}
},
"node_modules/@jbrowse/plugin-alignments": {
- "version": "2.6.2",
- "resolved": "https://registry.npmjs.org/@jbrowse/plugin-alignments/-/plugin-alignments-2.6.2.tgz",
- "integrity": "sha512-iRdatiDcDNls9Jt7uTiwkKzC7qcOgaYO/Vx61i9LKqgyNxu232WVvpfxfnw56gXLjr7nR6jKgz+hKQKKYMWi1w==",
+ "version": "2.7.0",
+ "resolved": "https://registry.npmjs.org/@jbrowse/plugin-alignments/-/plugin-alignments-2.7.0.tgz",
+ "integrity": "sha512-30zTgBXV4VjB1mnubaKp6Vo23yL0ReQAiEHg4a55I0mleJbk+oC1OdLGYt6ec5tzl11ad5n88U/E0yGW0Wpe0A==",
"dependencies": {
"@gmod/bam": "^2.0.0",
"@gmod/cram": "^1.7.1",
"@mui/icons-material": "^5.0.1",
"canvas2svg": "^1.0.16",
"clone": "^2.1.2",
- "color": "^3.1.2",
"copy-to-clipboard": "^3.3.1",
"fast-deep-equal": "^3.1.3",
"generic-filehandle": "^3.0.0"
@@ -2646,55 +2674,17 @@
"@jbrowse/plugin-wiggle": "^2.0.0",
"@mui/material": "^5.0.0",
"mobx": "^6.0.0",
- "mobx-react": "^7.0.0",
+ "mobx-react": "^9.0.0",
"mobx-state-tree": "^5.0.0",
"react": ">=16.8.0",
"rxjs": "^7.0.0",
"tss-react": "^4.0.0"
}
},
- "node_modules/@jbrowse/plugin-authentication": {
- "version": "2.6.2",
- "resolved": "https://registry.npmjs.org/@jbrowse/plugin-authentication/-/plugin-authentication-2.6.2.tgz",
- "integrity": "sha512-dIRo2BxzQ8wIhepLSixFiYjfwNTw9PG/0j5vnIkXIMtWqgUXOYXYaeZ/lU2uYL5KpfFaUSNQ/XchAQ2PuJnQbA==",
- "dependencies": {
- "crypto-js": "^3.0.0",
- "generic-filehandle": "^3.0.0"
- },
- "peerDependencies": {
- "@jbrowse/core": "^2.0.0",
- "@mui/material": "^5.0.0",
- "mobx": "^6.0.0",
- "mobx-react": "^7.0.0",
- "mobx-state-tree": "^5.0.0",
- "react": ">=16.8.0",
- "react-dom": ">=16.8.0",
- "rxjs": "^7.0.0"
- }
- },
- "node_modules/@jbrowse/plugin-bed": {
- "version": "2.6.2",
- "resolved": "https://registry.npmjs.org/@jbrowse/plugin-bed/-/plugin-bed-2.6.2.tgz",
- "integrity": "sha512-EQPgAJwWIvKEuYiSd2YBG9pmi5C6lQUmY5AR37DTvw7wU10UnP7hK6wuaM9EgMa/aJs0IHckVShgVR0csax/ig==",
- "dependencies": {
- "@flatten-js/interval-tree": "^1.0.15",
- "@gmod/bbi": "^4.0.0",
- "@gmod/bed": "^2.1.2",
- "@gmod/bgzf-filehandle": "^1.4.3",
- "@gmod/tabix": "^1.5.6"
- },
- "peerDependencies": {
- "@jbrowse/core": "^2.0.0",
- "mobx": "^6.0.0",
- "mobx-react": "^7.0.0",
- "mobx-state-tree": "^5.0.0",
- "rxjs": "^7.0.0"
- }
- },
"node_modules/@jbrowse/plugin-circular-view": {
- "version": "2.6.2",
- "resolved": "https://registry.npmjs.org/@jbrowse/plugin-circular-view/-/plugin-circular-view-2.6.2.tgz",
- "integrity": "sha512-27nc1ZCfiAGqi1xzeXUY4HvC2xiAf6VRwK1uIL14DQcAzu7tb2a1hqTkXpOLNpw2I7gTTYGdVeDV0uT2E+CZXA==",
+ "version": "2.7.0",
+ "resolved": "https://registry.npmjs.org/@jbrowse/plugin-circular-view/-/plugin-circular-view-2.7.0.tgz",
+ "integrity": "sha512-nJ3dAOvwQP3KRNqAsN69dwdShE/q+dRos8mfkW5awtDZ9R+KH0G6BgWM2s8tNU2i6ner9lB5XFcwijZjNvLu2w==",
"dependencies": {
"@mui/icons-material": "^5.0.1",
"@types/file-saver": "^2.0.0",
@@ -2705,7 +2695,7 @@
"@jbrowse/core": "^2.0.0",
"@mui/material": "^5.0.0",
"mobx": "^6.0.0",
- "mobx-react": "^7.0.0",
+ "mobx-react": "^9.0.0",
"mobx-state-tree": "^5.0.0",
"react": ">=16.8.0",
"react-dom": ">=16.8.0",
@@ -2713,9 +2703,9 @@
}
},
"node_modules/@jbrowse/plugin-config": {
- "version": "2.6.2",
- "resolved": "https://registry.npmjs.org/@jbrowse/plugin-config/-/plugin-config-2.6.2.tgz",
- "integrity": "sha512-An156jYmJV2M9WrlB3uTq9dr6N7+y2Ja4dAOJESDpHL5tSr7aVxrahmYQKFzRiaikFjH/GM0fPf9xdIFeM8HNQ==",
+ "version": "2.7.0",
+ "resolved": "https://registry.npmjs.org/@jbrowse/plugin-config/-/plugin-config-2.7.0.tgz",
+ "integrity": "sha512-XuX8HUoECcJhx81Utfmb5Bg263kosauDn5d20iOkpBqWD72bY7IZMzh0rPHyWdfg56Le/9hx/GMOk6jDDfozrw==",
"dependencies": {
"@mui/icons-material": "^5.0.1",
"pluralize": "^8.0.0"
@@ -2724,7 +2714,7 @@
"@jbrowse/core": "^2.0.0",
"@mui/material": "^5.0.0",
"mobx": "^6.0.0",
- "mobx-react": "^7.0.0",
+ "mobx-react": "^9.0.0",
"mobx-state-tree": "^5.0.0",
"react": ">=16.8.0",
"react-dom": ">=16.8.0",
@@ -2733,14 +2723,14 @@
}
},
"node_modules/@jbrowse/plugin-data-management": {
- "version": "2.6.2",
- "resolved": "https://registry.npmjs.org/@jbrowse/plugin-data-management/-/plugin-data-management-2.6.2.tgz",
- "integrity": "sha512-tyT++xR3R84+z0OCR5TAMujrvPuFBR+KultiDfyzEvfbXq2JYF/hdFQpffmht+QYG5z/FEt21yICqa8JmcSWEg==",
+ "version": "2.7.0",
+ "resolved": "https://registry.npmjs.org/@jbrowse/plugin-data-management/-/plugin-data-management-2.7.0.tgz",
+ "integrity": "sha512-iMPd3Dwv5gQqgpzg3w2tDxpyZ5nGuBEbK4t589umtG9uQ1OKM6Ew2Rxh3PjbAInCB/s3aidEQTUb52BeZAgnYw==",
"dependencies": {
"@gmod/ucsc-hub": "^0.1.6",
"@mui/icons-material": "^5.0.1",
"@mui/x-data-grid": "^6.0.1",
- "clsx": "^1.1.0",
+ "clsx": "^2.0.0",
"react-virtualized-auto-sizer": "^1.0.2",
"react-vtree": "^3.0.0-beta.1",
"react-window": "^1.8.6"
@@ -2748,80 +2738,70 @@
"peerDependencies": {
"@jbrowse/core": "^2.0.0",
"@jbrowse/plugin-config": "^2.0.0",
+ "@jbrowse/product-core": "^2.0.0",
"@mui/material": "^5.0.0",
"mobx": "^6.0.0",
- "mobx-react": "^7.0.0",
+ "mobx-react": "^9.0.0",
"mobx-state-tree": "^5.0.0",
"react": ">=16.8.0",
"tss-react": "^4.0.0"
}
},
- "node_modules/@jbrowse/plugin-gccontent": {
- "version": "2.6.2",
- "resolved": "https://registry.npmjs.org/@jbrowse/plugin-gccontent/-/plugin-gccontent-2.6.2.tgz",
- "integrity": "sha512-iNqO9ZdjDuPxBfjVyNGH5c4J13fxbwCV1TwaYzJWn1gNFQIs6bmnNu5jzHbS1xuCzzj+Nys4EbQcuEFRcA/0ag==",
+ "node_modules/@jbrowse/plugin-data-management/node_modules/memoize-one": {
+ "version": "5.2.1",
+ "resolved": "https://registry.npmjs.org/memoize-one/-/memoize-one-5.2.1.tgz",
+ "integrity": "sha512-zYiwtZUcYyXKo/np96AGZAckk+FWWsUdJ3cHGGmld7+AhvcWmQyGCYUh1hc4Q/pkOhb65dQR/pqCyK0cOaHz4Q=="
+ },
+ "node_modules/@jbrowse/plugin-data-management/node_modules/react-virtualized-auto-sizer": {
+ "version": "1.0.20",
+ "resolved": "https://registry.npmjs.org/react-virtualized-auto-sizer/-/react-virtualized-auto-sizer-1.0.20.tgz",
+ "integrity": "sha512-OdIyHwj4S4wyhbKHOKM1wLSj/UDXm839Z3Cvfg2a9j+He6yDa6i5p0qQvEiCnyQlGO/HyfSnigQwuxvYalaAXA==",
"peerDependencies": {
- "@jbrowse/core": "^2.0.0",
- "@jbrowse/plugin-linear-genome-view": "^2.0.0",
- "@jbrowse/plugin-sequence": "^2.0.0",
- "@jbrowse/plugin-wiggle": "^2.0.0",
- "@mui/material": "^5.0.0",
- "mobx": "^6.0.0",
- "mobx-react": "^7.0.0",
- "mobx-state-tree": "^5.0.0",
- "react": ">=16.8.0",
- "rxjs": "^7.0.0"
+ "react": "^15.3.0 || ^16.0.0-alpha || ^17.0.0 || ^18.0.0-rc",
+ "react-dom": "^15.3.0 || ^16.0.0-alpha || ^17.0.0 || ^18.0.0-rc"
}
},
- "node_modules/@jbrowse/plugin-gff3": {
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"dependencies": {
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@@ -12100,17 +12248,17 @@
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+ "version": "29.7.0",
+ "resolved": "https://registry.npmjs.org/jest-validate/-/jest-validate-29.7.0.tgz",
+ "integrity": "sha512-ZB7wHqaRGVw/9hST/OuFUReG7M8vKeq0/J2egIGLdvjHCmYqGARhzXmtgi+gVeZ5uXFF219aOc3Ls2yLg27tkw==",
"dev": true,
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@@ -12199,18 +12347,18 @@
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+ "version": "29.7.0",
+ "resolved": "https://registry.npmjs.org/jest-watcher/-/jest-watcher-29.7.0.tgz",
+ "integrity": "sha512-49Fg7WXkU3Vl2h6LbLtMQ/HyB6rXSIX7SqvBLQmssRBGN9I0PNvPmAmCWSOY6SOvrjhI/F7/bGAv9RtnsPA03g==",
"dev": true,
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- "@jest/types": "^29.6.1",
+ "@jest/test-result": "^29.7.0",
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"chalk": "^4.0.0",
"emittery": "^0.13.1",
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@@ -12288,13 +12436,13 @@
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+ "version": "29.7.0",
+ "resolved": "https://registry.npmjs.org/jest-worker/-/jest-worker-29.7.0.tgz",
+ "integrity": "sha512-eIz2msL/EzL9UFTFFx7jBTkeZfku0yUAyZZZmJ93H2TYEiroIx2PQjEXcwYtYl8zXCxb+PAmA2hLIt/6ZEkPHw==",
"dev": true,
"dependencies": {
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- "jest-util": "^29.6.1",
+ "jest-util": "^29.7.0",
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@@ -12335,9 +12483,9 @@
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+ "version": "3.7.1",
+ "resolved": "https://registry.npmjs.org/jquery/-/jquery-3.7.1.tgz",
+ "integrity": "sha512-m4avr8yL8kmFN8psrbFFFmB/If14iN5o9nw/NgnnM+kybDJpRsAynV2BsfpTYrTRysYUdADVD7CkUUizgkpLfg=="
},
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@@ -12391,68 +12539,13 @@
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- "dev": true,
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- "node_modules/jsdom/node_modules/webidl-conversions": {
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- "dev": true,
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+ "node": ">=14"
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+ "canvas": "^2.5.0"
},
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- "bufferutil": {
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- },
- "utf-8-validate": {
+ "canvas": {
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}
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@@ -12474,9 +12567,10 @@
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},
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+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-1.0.0.tgz",
+ "integrity": "sha512-NM8/P9n3XjXhIZn1lLhkFaACTOURQXjWhV4BA/RnOv8xvgqtqpAX9IO4mRQxSx1Rlo4tqzeqb0sOlruaOy3dug==",
+ "dev": true
},
"node_modules/json-stable-stringify": {
"version": "1.0.2",
@@ -12537,9 +12631,9 @@
}
},
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+ "version": "3.7.0",
+ "resolved": "https://registry.npmjs.org/jspdf-autotable/-/jspdf-autotable-3.7.0.tgz",
+ "integrity": "sha512-K6R5U4W4E2RoINRMUvcAKmTwGMyN5DE634G35dcXyGuqzhjY4AgOBDss5+M91HEznvZ28k7rk0gAo8WfeDIXLw==",
"peerDependencies": {
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}
@@ -12753,6 +12847,54 @@
"lz-string": "bin/bin.js"
}
},
+ "node_modules/make-dir": {
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/make-dir/-/make-dir-4.0.0.tgz",
+ "integrity": "sha512-hXdUTZYIVOt1Ex//jAQi+wTZZpUpwBj/0QsOzqegb3rGMMeJiSEu5xLHnYfBrRV4RH2+OCSOO95Is/7x1WJ4bw==",
+ "dev": true,
+ "dependencies": {
+ "semver": "^7.5.3"
+ },
+ "engines": {
+ "node": ">=10"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/sindresorhus"
+ }
+ },
+ "node_modules/make-dir/node_modules/lru-cache": {
+ "version": "6.0.0",
+ "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-6.0.0.tgz",
+ "integrity": "sha512-Jo6dJ04CmSjuznwJSS3pUeWmd/H0ffTlkXXgwZi+eq1UCmqQwCh+eLsYOYCwY991i2Fah4h1BEMCx4qThGbsiA==",
+ "dev": true,
+ "dependencies": {
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+ },
+ "engines": {
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+ }
+ },
+ "node_modules/make-dir/node_modules/semver": {
+ "version": "7.5.4",
+ "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.4.tgz",
+ "integrity": "sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA==",
+ "dev": true,
+ "dependencies": {
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+ },
+ "bin": {
+ "semver": "bin/semver.js"
+ },
+ "engines": {
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+ "node_modules/make-dir/node_modules/yallist": {
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+ "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
+ "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==",
+ "dev": true
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"resolved": "https://registry.npmjs.org/make-error/-/make-error-1.3.6.tgz",
@@ -12829,9 +12971,9 @@
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- "version": "4.8.8",
- "resolved": "https://registry.npmjs.org/tss-react/-/tss-react-4.8.8.tgz",
- "integrity": "sha512-V57AU6J42LLhYhRGSxDVi9VLUaoQtV6y2Kb1e0uqabe3w61G9R8gkUiX4DHZUReboRY9rwExPWz0LVZIgqQ98Q==",
+ "version": "4.9.2",
+ "resolved": "https://registry.npmjs.org/tss-react/-/tss-react-4.9.2.tgz",
+ "integrity": "sha512-0qOuDpar3q3N59Jsl50oDd+Zu3wfXv2rdf4VlPzvuekH6mkAgUVobZV3j69NPH0nm3Vv5xDRACjVUqVWmaNW0g==",
"dependencies": {
"@emotion/cache": "*",
"@emotion/serialize": "*",
@@ -17285,11 +17488,15 @@
"peerDependencies": {
"@emotion/react": "^11.4.1",
"@emotion/server": "^11.4.0",
+ "@mui/material": "^5.0.0",
"react": "^16.8.0 || ^17.0.2 || ^18.0.0"
},
"peerDependenciesMeta": {
"@emotion/server": {
"optional": true
+ },
+ "@mui/material": {
+ "optional": true
}
}
},
@@ -17539,12 +17746,12 @@
}
},
"node_modules/url": {
- "version": "0.11.1",
- "resolved": "https://registry.npmjs.org/url/-/url-0.11.1.tgz",
- "integrity": "sha512-rWS3H04/+mzzJkv0eZ7vEDGiQbgquI1fGfOad6zKvgYQi1SzMmhl7c/DdRGxhaWrVH6z0qWITo8rpnxK/RfEhA==",
+ "version": "0.11.3",
+ "resolved": "https://registry.npmjs.org/url/-/url-0.11.3.tgz",
+ "integrity": "sha512-6hxOLGfZASQK/cijlZnZJTq8OXAkt/3YGfQX45vvMYXpZoo8NdWZcY73K108Jf759lS1Bv/8wXnHDTSz17dSRw==",
"dependencies": {
"punycode": "^1.4.1",
- "qs": "^6.11.0"
+ "qs": "^6.11.2"
}
},
"node_modules/url-parse": {
@@ -17583,6 +17790,14 @@
"react": "^16.8.0 || ^17.0.0 || ^18.0.0"
}
},
+ "node_modules/use-sync-external-store": {
+ "version": "1.2.0",
+ "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.2.0.tgz",
+ "integrity": "sha512-eEgnFxGQ1Ife9bzYs6VLi8/4X6CObHMw9Qr9tPY43iKwsPw8xE8+EFsf/2cFZ5S3esXgpWgtSCtLNS41F+sKPA==",
+ "peerDependencies": {
+ "react": "^16.8.0 || ^17.0.0 || ^18.0.0"
+ }
+ },
"node_modules/util": {
"version": "0.12.5",
"resolved": "https://registry.npmjs.org/util/-/util-0.12.5.tgz",
@@ -17625,27 +17840,37 @@
}
},
"node_modules/uuid": {
- "version": "9.0.0",
- "resolved": "https://registry.npmjs.org/uuid/-/uuid-9.0.0.tgz",
- "integrity": "sha512-MXcSTerfPa4uqyzStbRoTgt5XIe3x5+42+q1sDuy3R5MDk66URdLMOZe5aPX/SQd+kuYAh0FdP/pO28IkQyTeg==",
+ "version": "9.0.1",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-9.0.1.tgz",
+ "integrity": "sha512-b+1eJOlsR9K8HJpow9Ok3fiWOWSIcIzXodvv0rQjVoOVNpWMpxf1wZNpt4y9h10odCNrqnYp1OBzRktckBe3sA==",
+ "funding": [
+ "https://github.com/sponsors/broofa",
+ "https://github.com/sponsors/ctavan"
+ ],
"bin": {
"uuid": "dist/bin/uuid"
}
},
"node_modules/v8-to-istanbul": {
- "version": "9.1.0",
- "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-9.1.0.tgz",
- "integrity": "sha512-6z3GW9x8G1gd+JIIgQQQxXuiJtCXeAjp6RaPEPLv62mH3iPHPxV6W3robxtCzNErRo6ZwTmzWhsbNvjyEBKzKA==",
+ "version": "9.1.3",
+ "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-9.1.3.tgz",
+ "integrity": "sha512-9lDD+EVI2fjFsMWXc6dy5JJzBsVTcQ2fVkfBvncZ6xJWG9wtBhOldG+mHkSL0+V1K/xgZz0JDO5UT5hFwHUghg==",
"dev": true,
"dependencies": {
"@jridgewell/trace-mapping": "^0.3.12",
"@types/istanbul-lib-coverage": "^2.0.1",
- "convert-source-map": "^1.6.0"
+ "convert-source-map": "^2.0.0"
},
"engines": {
"node": ">=10.12.0"
}
},
+ "node_modules/v8-to-istanbul/node_modules/convert-source-map": {
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/convert-source-map/-/convert-source-map-2.0.0.tgz",
+ "integrity": "sha512-Kvp459HrV2FEJ1CAsi1Ku+MY3kasH19TFykTz2xWmMeq6bk2NU3XXvfJ+Q61m0xktWwt+1HSYf3JZsTms3aRJg==",
+ "dev": true
+ },
"node_modules/value-equal": {
"version": "0.4.0",
"resolved": "https://registry.npmjs.org/value-equal/-/value-equal-0.4.0.tgz",
@@ -17734,14 +17959,19 @@
}
},
"node_modules/webidl-conversions": {
- "version": "3.0.1",
- "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz",
- "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ=="
+ "version": "7.0.0",
+ "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-7.0.0.tgz",
+ "integrity": "sha512-VwddBukDzu71offAQR975unBIGqfKZpM+8ZX6ySk8nYhVoo5CYaZyzt3YBvYtRtO+aoGlqxPg/B87NGVZ/fu6g==",
+ "dev": true,
+ "engines": {
+ "node": ">=12"
+ }
},
"node_modules/webpack": {
- "version": "5.88.2",
- "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.88.2.tgz",
- "integrity": "sha512-JmcgNZ1iKj+aiR0OvTYtWQqJwq37Pf683dY9bVORwVbUrDhLhdn/PlO2sHsFHPkj7sHNQF3JwaAkp49V+Sq1tQ==",
+ "version": "5.89.0",
+ "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.89.0.tgz",
+ "integrity": "sha512-qyfIC10pOr70V+jkmud8tMfajraGCZMBWJtrmuBymQKCrLTRejBI8STDp1MCyZu/QTdZSeacCQYpYNQVOzX5kw==",
+ "peer": true,
"dependencies": {
"@types/eslint-scope": "^3.7.3",
"@types/estree": "^1.0.0",
@@ -17824,13 +18054,25 @@
"node": ">= 10"
}
},
- "node_modules/webpack-bundle-analyzer/node_modules/is-plain-object": {
- "version": "5.0.0",
- "resolved": "https://registry.npmjs.org/is-plain-object/-/is-plain-object-5.0.0.tgz",
- "integrity": "sha512-VRSzKkbMm5jMDoKLbltAkFQ5Qr7VDiTFGXxYFXXowVj387GeGNOCsOH6Msy00SGZ3Fp84b1Naa1psqgcCIEP5Q==",
+ "node_modules/webpack-bundle-analyzer/node_modules/ws": {
+ "version": "7.5.9",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.9.tgz",
+ "integrity": "sha512-F+P9Jil7UiSKSkppIiD94dN07AwvFixvLIj1Og1Rl9GGMuNipJnV9JzjD6XuqmAeiswGvUmNLjr5cFuXwNS77Q==",
"dev": true,
"engines": {
- "node": ">=0.10.0"
+ "node": ">=8.3.0"
+ },
+ "peerDependencies": {
+ "bufferutil": "^4.0.1",
+ "utf-8-validate": "^5.0.2"
+ },
+ "peerDependenciesMeta": {
+ "bufferutil": {
+ "optional": true
+ },
+ "utf-8-validate": {
+ "optional": true
+ }
}
},
"node_modules/webpack-cli": {
@@ -17969,27 +18211,6 @@
}
}
},
- "node_modules/webpack-dev-server/node_modules/ws": {
- "version": "8.14.2",
- "resolved": "https://registry.npmjs.org/ws/-/ws-8.14.2.tgz",
- "integrity": "sha512-wEBG1ftX4jcglPxgFCMJmZ2PLtSbJ2Peg6TmpJFTbe9GZYOQCDPdMYu/Tm0/bGZkw8paZnJY45J4K2PZrLYq8g==",
- "dev": true,
- "engines": {
- "node": ">=10.0.0"
- },
- "peerDependencies": {
- "bufferutil": "^4.0.1",
- "utf-8-validate": ">=5.0.2"
- },
- "peerDependenciesMeta": {
- "bufferutil": {
- "optional": true
- },
- "utf-8-validate": {
- "optional": true
- }
- }
- },
"node_modules/webpack-merge": {
"version": "5.10.0",
"resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.10.0.tgz",
@@ -18012,10 +18233,42 @@
"node": ">=10.13.0"
}
},
+ "node_modules/webpack/node_modules/ajv": {
+ "version": "6.12.6",
+ "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.6.tgz",
+ "integrity": "sha512-j3fVLgvTo527anyYyJOGTYJbG+vnnQYvE0m5mmkc1TK+nxAppkCLMIL0aZ4dblVCNoGShhm+kzE4ZUykBoMg4g==",
+ "peer": true,
+ "dependencies": {
+ "fast-deep-equal": "^3.1.1",
+ "fast-json-stable-stringify": "^2.0.0",
+ "json-schema-traverse": "^0.4.1",
+ "uri-js": "^4.2.2"
+ },
+ "funding": {
+ "type": "github",
+ "url": "https://github.com/sponsors/epoberezkin"
+ }
+ },
+ "node_modules/webpack/node_modules/ajv-keywords": {
+ "version": "3.5.2",
+ "resolved": "https://registry.npmjs.org/ajv-keywords/-/ajv-keywords-3.5.2.tgz",
+ "integrity": "sha512-5p6WTN0DdTGVQk6VjcEju19IgaHudalcfabD7yhDGeA6bcQnmL+CpveLJq/3hvfwd1aof6L386Ougkx6RfyMIQ==",
+ "peer": true,
+ "peerDependencies": {
+ "ajv": "^6.9.1"
+ }
+ },
+ "node_modules/webpack/node_modules/json-schema-traverse": {
+ "version": "0.4.1",
+ "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-0.4.1.tgz",
+ "integrity": "sha512-xbbCH5dCYU5T8LcEhhuh7HJ88HXuW3qsI3Y0zOZFKfZEHcpWiHU/Jxzk629Brsab/mMiHQti9wMP+845RPe3Vg==",
+ "peer": true
+ },
"node_modules/webpack/node_modules/schema-utils": {
"version": "3.3.0",
"resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.3.0.tgz",
"integrity": "sha512-pN/yOAvcC+5rQ5nERGuwrjLlYvLTbCibnZ1I7B1LaiAz9BRBlE9GMgE/eqV30P7aJQUf7Ddimy/RsbYO/GrVGg==",
+ "peer": true,
"dependencies": {
"@types/json-schema": "^7.0.8",
"ajv": "^6.12.5",
@@ -18086,12 +18339,16 @@
}
},
"node_modules/whatwg-url": {
- "version": "5.0.0",
- "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
- "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==",
+ "version": "11.0.0",
+ "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-11.0.0.tgz",
+ "integrity": "sha512-RKT8HExMpoYx4igMiVMY83lN6UeITKJlBQ+vR/8ZJ8OCdSiN3RwCq+9gH0+Xzj0+5IrM6i4j/6LuvzbZIQgEcQ==",
+ "dev": true,
"dependencies": {
- "tr46": "~0.0.3",
- "webidl-conversions": "^3.0.0"
+ "tr46": "^3.0.0",
+ "webidl-conversions": "^7.0.0"
+ },
+ "engines": {
+ "node": ">=12"
}
},
"node_modules/which": {
@@ -18278,16 +18535,16 @@
}
},
"node_modules/ws": {
- "version": "7.5.9",
- "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.9.tgz",
- "integrity": "sha512-F+P9Jil7UiSKSkppIiD94dN07AwvFixvLIj1Og1Rl9GGMuNipJnV9JzjD6XuqmAeiswGvUmNLjr5cFuXwNS77Q==",
+ "version": "8.14.2",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.14.2.tgz",
+ "integrity": "sha512-wEBG1ftX4jcglPxgFCMJmZ2PLtSbJ2Peg6TmpJFTbe9GZYOQCDPdMYu/Tm0/bGZkw8paZnJY45J4K2PZrLYq8g==",
"dev": true,
"engines": {
- "node": ">=8.3.0"
+ "node": ">=10.0.0"
},
"peerDependencies": {
"bufferutil": "^4.0.1",
- "utf-8-validate": "^5.0.2"
+ "utf-8-validate": ">=5.0.2"
},
"peerDependenciesMeta": {
"bufferutil": {
@@ -18298,18 +18555,6 @@
}
}
},
- "node_modules/xlsx": {
- "version": "0.19.3",
- "resolved": "https://cdn.sheetjs.com/xlsx-0.19.3/xlsx-0.19.3.tgz",
- "integrity": "sha512-8IfgFctB7fkvqkTGF2MnrDrC6vzE28Wcc1aSbdDQ+4/WFtzfS73YuapbuaPZwGqpR2e0EeDMIrFOJubQVLWFNA==",
- "license": "Apache-2.0",
- "bin": {
- "xlsx": "bin/xlsx.njs"
- },
- "engines": {
- "node": ">=0.8"
- }
- },
"node_modules/xml-name-validator": {
"version": "4.0.0",
"resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-4.0.0.tgz",
diff --git a/jbrowse/package.json b/jbrowse/package.json
index cfda8a548..bef13d669 100644
--- a/jbrowse/package.json
+++ b/jbrowse/package.json
@@ -16,13 +16,13 @@
},
"dependencies": {
"@gmod/vcf": "^5.0.10",
- "@jbrowse/core": "^2.6.2",
- "@jbrowse/plugin-linear-genome-view": "^2.6.2",
- "@jbrowse/plugin-svg": "^2.6.2",
- "@jbrowse/plugin-variants": "^2.6.2",
- "@jbrowse/react-linear-genome-view": "^2.6.2",
+ "@jbrowse/core": "^2.7.0",
+ "@jbrowse/plugin-linear-genome-view": "^2.7.0",
+ "@jbrowse/plugin-svg": "^2.7.0",
+ "@jbrowse/plugin-variants": "^2.7.0",
+ "@jbrowse/react-linear-genome-view": "^2.7.0",
"@labkey/api": "^1.25.0",
- "@labkey/components": "^2.381.1",
+ "@labkey/components": "^2.0.0",
"@mui/x-data-grid": "^6.0.1",
"assert": "^2.0.0",
"browserify-zlib": "^0.2.0",
@@ -44,8 +44,7 @@
"typescript": "^5.1.6",
"util": "^0.12.5",
"uuid": "^9.0.0",
- "vm-browserify": "^1.1.2",
- "xlsx": "https://cdn.sheetjs.com/xlsx-0.19.3/xlsx-0.19.3.tgz"
+ "vm-browserify": "^1.1.2"
},
"devDependencies": {
"@labkey/build": "6.15.0",
diff --git a/jbrowse/src/client/JBrowse/Browser/Browser.spec.tsx b/jbrowse/src/client/JBrowse/Browser/Browser.spec.tsx
index 4b6a7b87b..eb45a97d5 100644
--- a/jbrowse/src/client/JBrowse/Browser/Browser.spec.tsx
+++ b/jbrowse/src/client/JBrowse/Browser/Browser.spec.tsx
@@ -86,7 +86,10 @@ jest.mock('@labkey/api', () => {
},
ActionURL: {
buildURL: jest.fn()
- }
+ },
+ getServerContext: jest.fn(() => {
+ return {devMode: true}
+ })
}
})
const mockedRequest = mocked(Ajax)
@@ -110,7 +113,7 @@ describe('JBrowse 2 Browser', () => {
return {} as XMLHttpRequest;
});
const wrapper = mount();
- expect(wrapper.find('.MuiPaper-root')).toHaveLength(2)
+ expect(wrapper.find('.MuiPaper-root')).toHaveLength(4)
});
});
diff --git a/jbrowse/src/client/JBrowse/utils.ts b/jbrowse/src/client/JBrowse/utils.ts
index 630abe642..0502b0bc7 100644
--- a/jbrowse/src/client/JBrowse/utils.ts
+++ b/jbrowse/src/client/JBrowse/utils.ts
@@ -566,6 +566,7 @@ export async function fetchFieldTypeInfo(sessionId: string, trackId: string, suc
successCallback(fields, groups, promotedFilters)
},
failure: function(res){
+ console.error(res)
failureCallback("There was an error while fetching field types: " + res.status + "\n Status Body: " + res.statusText + "\n Session ID:" + sessionId)
},
params: {sessionId: sessionId, trackId: trackId},
diff --git a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
index 9b78379c7..da351e587 100644
--- a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
+++ b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
@@ -1018,6 +1018,9 @@ private void prepareLuceneIndex(Logger log) throws PipelineJobException
args.add("-O");
args.add(indexDir.getPath());
+ args.add("--validation-stringency");
+ args.add("LENIENT");
+
List infoFieldsForFullTextSearch = getInfoFieldsToIndex();
for (String field : infoFieldsForFullTextSearch)
{