diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json
index 044b5e267..a272bd98a 100644
--- a/jbrowse/package-lock.json
+++ b/jbrowse/package-lock.json
@@ -8,44 +8,45 @@
"name": "jbrowse-lk",
"version": "1.0.0",
"dependencies": {
- "@gmod/vcf": "^5.0.10",
- "@jbrowse/core": "^2.15.0",
- "@jbrowse/plugin-linear-genome-view": "^2.15.0",
- "@jbrowse/plugin-svg": "^2.15.0",
- "@jbrowse/plugin-variants": "^2.15.0",
- "@jbrowse/react-linear-genome-view": "^2.15.0",
- "@labkey/api": "^1.35.0",
- "@labkey/components": "^5.0.0",
- "@mui/x-data-grid": "^7.0.0",
- "@yao-pkg/pkg": "^5.12.0",
- "assert": "^2.0.0",
+ "@gmod/vcf": "^6.0.9",
+ "@jbrowse/core": "^3.2.0",
+ "@jbrowse/plugin-linear-genome-view": "^3.2.0",
+ "@jbrowse/plugin-svg": "^3.2.0",
+ "@jbrowse/plugin-variants": "^3.2.0",
+ "@jbrowse/product-core": "^3.2.0",
+ "@jbrowse/react-linear-genome-view2": "^3.2.0",
+ "@labkey/api": "^1.39.0",
+ "@labkey/components": "^6.32.2",
+ "@mui/x-data-grid": "^7.28.1",
+ "@yao-pkg/pkg": "^6.3.2",
+ "assert": "^2.1.0",
"browserify-zlib": "^0.2.0",
"buffer": "^6.0.3",
"child_process": "^1.0.2",
"fs": "^0.0.1-security",
- "jquery": "^3.7.0",
- "jspdf": "^2.5.1",
- "jspdf-autotable": "^3.5.31",
- "node-polyfill-webpack-plugin": "2.0.1",
+ "jquery": "^3.7.1",
+ "jspdf": "^3.0.0",
+ "jspdf-autotable": "^5.0.2",
+ "node-polyfill-webpack-plugin": "4.1.0",
"path-browserify": "^1.0.1",
- "react": "^18.0.0",
+ "react": "^18.3.0",
"react-data-grid": "7.0.0-beta.46",
- "react-dom": "^18.0.0",
- "react-google-charts": "^4.0.1",
- "react-select": "^5.8.0",
- "regenerator-runtime": "^0.13.11",
+ "react-dom": "^18.3.0",
+ "react-google-charts": "^5.2.1",
+ "react-select": "^5.10.1",
+ "regenerator-runtime": "^0.14.1",
"stream-browserify": "^3.0.0",
"util": "^0.12.5",
- "uuid": "^9.0.0",
+ "uuid": "^11.1.0",
"vm-browserify": "^1.1.2"
},
"devDependencies": {
- "@labkey/build": "^8.3.0",
- "@types/jexl": "^2.3.1",
- "@types/jquery": "^3.0.0",
+ "@labkey/build": "^8.4.0",
+ "@types/jexl": "^2.3.4",
+ "@types/jquery": "^3.5.32",
"@types/node": "^20.14.11",
- "@types/react": "^18.0.0",
- "@types/react-dom": "^18.0.0",
+ "@types/react": "^18.3.0",
+ "@types/react-dom": "^18.3.0",
"rimraf": "^6.0.1",
"typescript": "^5.1.6"
}
@@ -385,24 +386,24 @@
}
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"node_modules/@babel/helpers": {
- "version": "7.26.7",
- "resolved": "https://registry.npmjs.org/@babel/helpers/-/helpers-7.26.7.tgz",
- "integrity": "sha512-8NHiL98vsi0mbPQmYAGWwfcFaOy4j2HY49fXJCfuDcdE7fMIsH9a7GdaeXpIBsbT7307WU8KCMp5pUVDNL4f9A==",
+ "version": "7.27.0",
+ "resolved": "https://registry.npmjs.org/@babel/helpers/-/helpers-7.27.0.tgz",
+ "integrity": "sha512-U5eyP/CTFPuNE3qk+WZMxFkp/4zUzdceQlfzf7DdGdhp+Fezd7HD+i8Y24ZuTMKX3wQBld449jijbGq6OdGNQg==",
"dev": true,
"dependencies": {
- "@babel/template": "^7.25.9",
- "@babel/types": "^7.26.7"
+ "@babel/template": "^7.27.0",
+ "@babel/types": "^7.27.0"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/parser": {
- "version": "7.26.8",
- "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.26.8.tgz",
- "integrity": "sha512-TZIQ25pkSoaKEYYaHbbxkfL36GNsQ6iFiBbeuzAkLnXayKR1yP1zFe+NxuZWWsUyvt8icPU9CCq0sgWGXR1GEw==",
+ "version": "7.27.0",
+ "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.27.0.tgz",
+ "integrity": "sha512-iaepho73/2Pz7w2eMS0Q5f83+0RKI7i4xmiYeBmDzfRVbQtTOG7Ts0S4HzJVsTMGI9keU8rNfuZr8DKfSt7Yyg==",
"dependencies": {
- "@babel/types": "^7.26.8"
+ "@babel/types": "^7.27.0"
},
"bin": {
"parser": "bin/babel-parser.js"
@@ -1586,9 +1587,9 @@
}
},
"node_modules/@babel/runtime": {
- "version": "7.25.6",
- "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.25.6.tgz",
- "integrity": "sha512-VBj9MYyDb9tuLq7yzqjgzt6Q+IBQLrGZfdjOekyEirZPHxXWoTSGUTMrpsfi58Up73d13NfYLv8HT9vmznjzhQ==",
+ "version": "7.27.0",
+ "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.27.0.tgz",
+ "integrity": "sha512-VtPOkrdPHZsKc/clNqyi9WUA8TINkZ4cGk63UUE3u4pmB2k+ZMQRDuIOagv8UVd6j7k0T3+RRIb7beKTebNbcw==",
"dependencies": {
"regenerator-runtime": "^0.14.0"
},
@@ -1596,19 +1597,14 @@
"node": ">=6.9.0"
}
},
- "node_modules/@babel/runtime/node_modules/regenerator-runtime": {
- "version": "0.14.1",
- "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.14.1.tgz",
- "integrity": "sha512-dYnhHh0nJoMfnkZs6GmmhFknAGRrLznOu5nc9ML+EJxGvrx6H7teuevqVqCuPcPK//3eDrrjQhehXVx9cnkGdw=="
- },
"node_modules/@babel/template": {
- "version": "7.26.8",
- "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.26.8.tgz",
- "integrity": "sha512-iNKaX3ZebKIsCvJ+0jd6embf+Aulaa3vNBqZ41kM7iTWjx5qzWKXGHiJUW3+nTpQ18SG11hdF8OAzKrpXkb96Q==",
+ "version": "7.27.0",
+ "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.27.0.tgz",
+ "integrity": "sha512-2ncevenBqXI6qRMukPlXwHKHchC7RyMuu4xv5JBXRfOGVcTy1mXCD12qrp7Jsoxll1EV3+9sE4GugBVRjT2jFA==",
"dependencies": {
"@babel/code-frame": "^7.26.2",
- "@babel/parser": "^7.26.8",
- "@babel/types": "^7.26.8"
+ "@babel/parser": "^7.27.0",
+ "@babel/types": "^7.27.0"
},
"engines": {
"node": ">=6.9.0"
@@ -1632,9 +1628,9 @@
}
},
"node_modules/@babel/types": {
- "version": "7.26.8",
- "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.26.8.tgz",
- "integrity": "sha512-eUuWapzEGWFEpHFxgEaBG8e3n6S8L3MSu0oda755rOfabWPnh0Our1AozNFVUxGFIhbKgd1ksprsoDGMinTOTA==",
+ "version": "7.27.0",
+ "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.27.0.tgz",
+ "integrity": "sha512-H45s8fVLYjbhFH62dIJ3WtmJ6RSPt/3DRO0ZcT2SUiYiQyz3BLVb9ADEnLl91m74aQPS3AzzeajZHYOalWe3bg==",
"dependencies": {
"@babel/helper-string-parser": "^7.25.9",
"@babel/helper-validator-identifier": "^7.25.9"
@@ -2020,9 +2016,9 @@
}
},
"node_modules/@floating-ui/react-dom": {
- "version": "2.1.1",
- "resolved": "https://registry.npmjs.org/@floating-ui/react-dom/-/react-dom-2.1.1.tgz",
- "integrity": "sha512-4h84MJt3CHrtG18mGsXuLCHMrug49d7DFkU0RMIyshRveBeyV2hmV/pDaF2Uxtu8kgq5r46llp5E5FQiR0K2Yg==",
+ "version": "2.1.2",
+ "resolved": "https://registry.npmjs.org/@floating-ui/react-dom/-/react-dom-2.1.2.tgz",
+ "integrity": "sha512-06okr5cgPzMNBy+Ycse2A6udMi4bqwW/zgBF/rwjcNqWkyr82Mcg8b0vjX8OJpZFy/FKjJmw6wV7t44kK6kW7A==",
"dependencies": {
"@floating-ui/dom": "^1.0.0"
},
@@ -2032,9 +2028,9 @@
}
},
"node_modules/@floating-ui/utils": {
- "version": "0.2.7",
- "resolved": "https://registry.npmjs.org/@floating-ui/utils/-/utils-0.2.7.tgz",
- "integrity": "sha512-X8R8Oj771YRl/w+c1HqAC1szL8zWQRwFvgDwT129k9ACdBoud/+/rX9V0qiMl6LWUdP9voC2nDVZYPMQQsb6eA=="
+ "version": "0.2.9",
+ "resolved": "https://registry.npmjs.org/@floating-ui/utils/-/utils-0.2.9.tgz",
+ "integrity": "sha512-MDWhGtE+eHw5JW7lq4qhc5yRLS11ERl1c7Z6Xd0a58DozHES6EnNNwUWbMiG4J9Cgj053Bhk8zvlhFYKVhULwg=="
},
"node_modules/@gmod/abortable-promise-cache": {
"version": "2.0.1",
@@ -2042,42 +2038,32 @@
"integrity": "sha512-6PQTJv+uxAb8XE/oL2Uh4EmFJpn65YOTSqGn8HLNXrWRlW1Clp1Oze6biHeRCMonLwEx4oH4bPeyjdcMnNP8pw=="
},
"node_modules/@gmod/bam": {
- "version": "2.0.4",
- "resolved": "https://registry.npmjs.org/@gmod/bam/-/bam-2.0.4.tgz",
- "integrity": "sha512-lV/eM/ITwVPovyn4d8iDWyRP/zIuzHUylV5y5LJm0ZBm9nQfFwE25KpHKzoZ7a/0197Dxl+jJEjKzSlDN8YNZA==",
+ "version": "5.0.7",
+ "resolved": "https://registry.npmjs.org/@gmod/bam/-/bam-5.0.7.tgz",
+ "integrity": "sha512-d1WR54/198O28YbVZK0Ui0mmtHmFHS76s3/4KhqngZmibEdZJtlWPaVBMOkasukqc4ysSl1Z7en8qujqnJtXVg==",
"dependencies": {
"@gmod/abortable-promise-cache": "^2.0.0",
- "@gmod/bgzf-filehandle": "^1.4.4",
+ "@gmod/bgzf-filehandle": "^2.0.1",
"crc": "^4.3.2",
- "generic-filehandle": "^3.0.0",
- "long": "^4.0.0",
+ "generic-filehandle2": "^1.0.0",
"quick-lru": "^4.0.0"
},
"engines": {
"node": ">=6"
}
},
- "node_modules/@gmod/bbi": {
- "version": "5.0.2",
- "resolved": "https://registry.npmjs.org/@gmod/bbi/-/bbi-5.0.2.tgz",
- "integrity": "sha512-sqBwF7hTQI1wHgzc50y2jgEjSVYta3oSZeKUffNhR002fBpeU5c//7EoY0f1X8JrK97rTYTkZCGcGn2pd5lhOQ==",
+ "node_modules/@gmod/bam/node_modules/@gmod/bgzf-filehandle": {
+ "version": "2.0.4",
+ "resolved": "https://registry.npmjs.org/@gmod/bgzf-filehandle/-/bgzf-filehandle-2.0.4.tgz",
+ "integrity": "sha512-MV1V3X2uF0vqN93dkEhL8TUiJMTHyaJQFuLZttKAl8vH5utN2gKJf/3PTW8f7r5X+GgyftuTcfIpHHD5+3mJiQ==",
"dependencies": {
- "@gmod/abortable-promise-cache": "^2.0.0",
- "buffer": "^6.0.3",
- "generic-filehandle": "^3.0.0",
- "pako": "^2.0.0",
- "quick-lru": "^4.0.0",
- "rxjs": "^7.8.0"
+ "generic-filehandle2": "^1.0.0",
+ "pako": "^1.0.11"
},
"engines": {
"node": ">=6"
}
},
- "node_modules/@gmod/bbi/node_modules/pako": {
- "version": "2.1.0",
- "resolved": "https://registry.npmjs.org/pako/-/pako-2.1.0.tgz",
- "integrity": "sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug=="
- },
"node_modules/@gmod/bed": {
"version": "2.1.3",
"resolved": "https://registry.npmjs.org/@gmod/bed/-/bed-2.1.3.tgz",
@@ -2086,29 +2072,13 @@
"node": ">=6"
}
},
- "node_modules/@gmod/bgzf-filehandle": {
- "version": "1.4.7",
- "resolved": "https://registry.npmjs.org/@gmod/bgzf-filehandle/-/bgzf-filehandle-1.4.7.tgz",
- "integrity": "sha512-f/oXwWwsBe4nYN82mQ+Sz++/zH6EOyBCRqxFdv04SBkreQvilf3cql6F8ZAMMBq1f/abzBc0U0zJIMF9CLM7QQ==",
- "dependencies": {
- "es6-promisify": "^7.0.0",
- "generic-filehandle": "^3.0.0",
- "long": "^4.0.0",
- "pako": "^1.0.11"
- },
- "engines": {
- "node": ">=6"
- }
- },
"node_modules/@gmod/cram": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/@gmod/cram/-/cram-3.0.5.tgz",
- "integrity": "sha512-bHBc9bFNfG7rC+EEawhR9eaE0HBn/503T4DYbYCPjX+va/soxaD7+Ai9CT5/fk7uiM0oARXL+3YCwn54IShpxg==",
+ "version": "4.0.10",
+ "resolved": "https://registry.npmjs.org/@gmod/cram/-/cram-4.0.10.tgz",
+ "integrity": "sha512-kYN24I7AT61cBUIl/jdZxt3MATi1wa0w+DIkteNGGA70F7pkhlHHtHm6lOBIq8mOQCWNlhXu+ia7HI+ck8LKzg==",
"dependencies": {
- "@jkbonfield/htscodecs": "^0.5.1",
- "bzip2": "^0.1.1",
"crc": "^4.3.2",
- "long": "^4.0.0",
+ "generic-filehandle2": "^1.0.0",
"md5": "^2.2.1",
"pako": "^1.0.4",
"quick-lru": "^4.0.1",
@@ -2118,41 +2088,42 @@
"node": ">=6"
}
},
- "node_modules/@gmod/gff": {
- "version": "1.3.0",
- "resolved": "https://registry.npmjs.org/@gmod/gff/-/gff-1.3.0.tgz",
- "integrity": "sha512-OjEnQLR6iIcrau603blFfUkmnWGDVfOu/LQoJNa7TsvKnjWlHYPlvqb5h2IV7wI+zElDY648mQ9zrElt2uR80A==",
- "dependencies": {
- "stream-browserify": "^3.0.0"
- },
- "bin": {
- "gff-to-json": "dist/gff-to-json.js"
- }
- },
"node_modules/@gmod/http-range-fetcher": {
- "version": "3.0.4",
- "resolved": "https://registry.npmjs.org/@gmod/http-range-fetcher/-/http-range-fetcher-3.0.4.tgz",
- "integrity": "sha512-j/WtsUgxf4dRmWJ2WTBdZ4svMe0hMIETmfrqusXxxieyPCI4+tgtST1Fvo5MOCSrpaVH5BGsnoo/Mcs/Dsp/nQ==",
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/@gmod/http-range-fetcher/-/http-range-fetcher-4.0.0.tgz",
+ "integrity": "sha512-vT/2ZPV1TukaN5huvFmXgMi5SLKA8tTWIMAvkSbZyzicmpdGS0Bz7PwPEJtX6AhzP3Pv+ucu3fn2b4WF7DCYAw==",
"dependencies": {
"quick-lru": "^4.0.0"
}
},
"node_modules/@gmod/indexedfasta": {
- "version": "2.1.1",
- "resolved": "https://registry.npmjs.org/@gmod/indexedfasta/-/indexedfasta-2.1.1.tgz",
- "integrity": "sha512-JM0n0EMHwOlur4ojUZ0FgloHtbFO1qJG2PZGg8NrRHUeBtTqfLebGg+38kJibotWwtKjH6AB8NK2HrdJMAMTLg==",
+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/@gmod/indexedfasta/-/indexedfasta-3.0.1.tgz",
+ "integrity": "sha512-i/YwSvF6kxbUL8lp+uL0UFpCynJu/9fZfWSGTVf7ANuQLtDcdTsfKt3wMEx61Lh45LCrjDeAoV1kN1ehFHVWww==",
"dependencies": {
- "@gmod/bgzf-filehandle": "^1.4.0",
- "generic-filehandle": "^3.0.0"
+ "@gmod/bgzf-filehandle": "^2.0.0",
+ "generic-filehandle2": "^1.0.0"
},
"engines": {
"node": ">=12"
}
},
+ "node_modules/@gmod/indexedfasta/node_modules/@gmod/bgzf-filehandle": {
+ "version": "2.0.4",
+ "resolved": "https://registry.npmjs.org/@gmod/bgzf-filehandle/-/bgzf-filehandle-2.0.4.tgz",
+ "integrity": "sha512-MV1V3X2uF0vqN93dkEhL8TUiJMTHyaJQFuLZttKAl8vH5utN2gKJf/3PTW8f7r5X+GgyftuTcfIpHHD5+3mJiQ==",
+ "dependencies": {
+ "generic-filehandle2": "^1.0.0",
+ "pako": "^1.0.11"
+ },
+ "engines": {
+ "node": ">=6"
+ }
+ },
"node_modules/@gmod/nclist": {
- "version": "1.0.3",
- "resolved": "https://registry.npmjs.org/@gmod/nclist/-/nclist-1.0.3.tgz",
- "integrity": "sha512-qA1QKjC9HuLWd/XfyuBQ6ZN7T5edeW2xQkwWYiWWzd9TnnthHxPnLw4Bxw+SSj6sb9t93oPH546Z5HiMDinZEw==",
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/@gmod/nclist/-/nclist-2.0.0.tgz",
+ "integrity": "sha512-F/yyNDgfw4OZj1yJEu1ejWd3za5KbSZV5g9U6YFG9hw4HHLemTyK2e4Yle1Km7dLdWU3iPskTjBm0iuDxyTDQA==",
"dependencies": {
"@gmod/abortable-promise-cache": "^2.0.0",
"@jridgewell/resolve-uri": "^3.1.2",
@@ -2163,48 +2134,59 @@
}
},
"node_modules/@gmod/tabix": {
- "version": "1.5.15",
- "resolved": "https://registry.npmjs.org/@gmod/tabix/-/tabix-1.5.15.tgz",
- "integrity": "sha512-R9lF8Iq5csM9GG2jAlHbBdvhBVr1KDkBVxHz10GdGp3dv88z0Z3RtAmCnvmj9WtH010yIdKmWxGwKmxYFZxFXQ==",
+ "version": "2.0.5",
+ "resolved": "https://registry.npmjs.org/@gmod/tabix/-/tabix-2.0.5.tgz",
+ "integrity": "sha512-E9skkvg5bLYnX3XbQwLejqTufQiWm7aMbJLrttouPIAb430++uWZyMR3Qta9GmKCiSQ0LOTjokVWJDe0b9qdOw==",
"dependencies": {
"@gmod/abortable-promise-cache": "^2.0.0",
- "@gmod/bgzf-filehandle": "^1.3.3",
- "generic-filehandle": "^3.0.0",
- "long": "^4.0.0",
+ "@gmod/bgzf-filehandle": "^2.0.1",
+ "generic-filehandle2": "^1.0.0",
"quick-lru": "^4.0.0"
},
"engines": {
"node": ">=6"
}
},
+ "node_modules/@gmod/tabix/node_modules/@gmod/bgzf-filehandle": {
+ "version": "2.0.4",
+ "resolved": "https://registry.npmjs.org/@gmod/bgzf-filehandle/-/bgzf-filehandle-2.0.4.tgz",
+ "integrity": "sha512-MV1V3X2uF0vqN93dkEhL8TUiJMTHyaJQFuLZttKAl8vH5utN2gKJf/3PTW8f7r5X+GgyftuTcfIpHHD5+3mJiQ==",
+ "dependencies": {
+ "generic-filehandle2": "^1.0.0",
+ "pako": "^1.0.11"
+ },
+ "engines": {
+ "node": ">=6"
+ }
+ },
"node_modules/@gmod/trix": {
- "version": "2.0.6",
- "resolved": "https://registry.npmjs.org/@gmod/trix/-/trix-2.0.6.tgz",
- "integrity": "sha512-J12/c8kRHw8mxoVpHTeG6B7w9aGOmFdOGRxhljjaUmcMiFB7CFinPtApsoOSO/e6TYI40E5zd5n3+Q2ZC89Qww==",
+ "version": "3.0.2",
+ "resolved": "https://registry.npmjs.org/@gmod/trix/-/trix-3.0.2.tgz",
+ "integrity": "sha512-bVAWWT+dWhKmL+Pjl2P7cKeqeLzl3Ip504nFgK5NwDgsDziQjutl1lU4cEgPf+KN1r1HoR1PT5DbDnb5AEPH8A==",
"engines": {
"node": ">=10"
}
},
"node_modules/@gmod/twobit": {
- "version": "2.0.1",
- "resolved": "https://registry.npmjs.org/@gmod/twobit/-/twobit-2.0.1.tgz",
- "integrity": "sha512-uHiWjslhsE1AkX39ndbrADSceP9xOBb3BmJ2QCcu8Tw1ej0YnsaQv+hWbwVJ2K+EO439jocgtVfkmohGB78ZUA==",
+ "version": "4.0.1",
+ "resolved": "https://registry.npmjs.org/@gmod/twobit/-/twobit-4.0.1.tgz",
+ "integrity": "sha512-aMmRhKERoLidFG3yyncd50RtfMlYgBu3eI5dNrqDaMvX63gVOyFs89Phc0YbFgVI76TP9gXqAmRAyyBI4i7/OA==",
"dependencies": {
- "generic-filehandle": "^3.0.0"
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+ "funding": {
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@@ -3274,10 +3537,10 @@
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@@ -3288,42 +3551,13 @@
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},
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+ "react": "^17.0.0 || ^18.0.0 || ^19.0.0"
}
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+ "dev": true,
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"dev": true,
- "license": "MIT",
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}
@@ -3846,6 +4059,12 @@
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- "license": "ISC",
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+ "resolved": "https://registry.npmjs.org/semver/-/semver-7.7.1.tgz",
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"bin": {
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- "license": "MIT",
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"engines": {
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- "license": "MIT",
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}
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"dependencies": {
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@@ -4312,16 +4476,10 @@
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- "license": "MIT",
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"license": "(MIT OR Apache-2.0)",
@@ -4631,9 +4783,15 @@
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},
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@@ -4733,11 +4892,21 @@
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- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/browserify-aes/-/browserify-aes-1.2.0.tgz",
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@@ -4749,7 +4918,8 @@
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"node_modules/browserify-cipher": {
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@@ -4758,7 +4928,8 @@
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@@ -4767,16 +4938,22 @@
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},
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+ "resolved": "https://registry.npmjs.org/console-browserify/-/console-browserify-1.2.0.tgz",
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},
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"version": "1.0.0",
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"version": "0.5.4",
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"version": "4.0.4",
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}
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+ "resolved": "https://registry.npmjs.org/bn.js/-/bn.js-4.12.1.tgz",
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"version": "1.2.0",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/create-hash/-/create-hash-1.2.0.tgz",
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- "license": "MIT",
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"create-hash": "^1.1.0",
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+ "node": ">= 0.10"
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+ "funding": {
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}
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"node_modules/crypto-js": {
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@@ -5944,7 +6140,8 @@
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- "license": "MIT",
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+ "resolved": "https://registry.npmjs.org/bn.js/-/bn.js-4.12.1.tgz",
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},
"node_modules/domain-browser": {
- "version": "4.23.0",
- "license": "Artistic-2.0",
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+ "resolved": "https://registry.npmjs.org/domain-browser/-/domain-browser-4.22.0.tgz",
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+ "version": "3.2.4",
+ "resolved": "https://registry.npmjs.org/dompurify/-/dompurify-3.2.4.tgz",
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+ }
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"node_modules/domutils": {
"version": "2.8.0",
@@ -6083,9 +6275,16 @@
"dev": true,
"license": "MIT"
},
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+ "resolved": "https://registry.npmjs.org/duplexer2/-/duplexer2-0.1.4.tgz",
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+ "dependencies": {
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"node_modules/eastasianwidth": {
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- "dev": true,
"license": "MIT"
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@@ -6113,8 +6312,9 @@
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"node_modules/elliptic/node_modules/bn.js": {
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+ "version": "4.12.1",
+ "resolved": "https://registry.npmjs.org/bn.js/-/bn.js-4.12.1.tgz",
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"dev": true,
@@ -6316,7 +6502,8 @@
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"node_modules/evp_bytestokey": {
"version": "1.0.3",
- "license": "MIT",
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"safe-buffer": "^5.1.1"
@@ -6394,6 +6581,7 @@
},
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"license": "MIT",
"dependencies": {
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@@ -6408,6 +6596,7 @@
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+ "dev": true,
"license": "ISC",
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@@ -6435,6 +6624,7 @@
},
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+ "dev": true,
"license": "ISC",
"dependencies": {
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@@ -6452,8 +6642,9 @@
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"version": "2.0.5",
@@ -6461,6 +6652,7 @@
},
"node_modules/fill-range": {
"version": "7.1.1",
+ "dev": true,
"license": "MIT",
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@@ -6469,13 +6661,6 @@
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@@ -6587,7 +6772,6 @@
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@@ -6602,7 +6786,6 @@
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@@ -6818,16 +7001,16 @@
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},
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- "license": "MIT",
+ "version": "11.3.0",
+ "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-11.3.0.tgz",
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"jsonfile": "^6.0.1",
"universalify": "^2.0.0"
},
"engines": {
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+ "node": ">=14.14"
}
},
"node_modules/fs-monkey": {
@@ -6849,20 +7032,14 @@
"url": "https://github.com/sponsors/ljharb"
}
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- "version": "3.2.0",
- "license": "MIT",
- "dependencies": {
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+ "node_modules/generic-filehandle2": {
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+ "resolved": "https://registry.npmjs.org/generic-filehandle2/-/generic-filehandle2-1.0.0.tgz",
+ "integrity": "sha512-jXfyNk1zhsR0Xf2sLm4vgeYSP1q1XbeSVG0TRSnOCKLb2CojPNJyy57nKi6QWmt83yGSHZGay8qIn7YWyl2V5w==",
"engines": {
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}
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"resolved": "https://registry.npmjs.org/gensync/-/gensync-1.0.0-beta.2.tgz",
@@ -6874,7 +7051,8 @@
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"version": "2.0.5",
- "license": "ISC",
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"engines": {
"node": "6.* || 8.* || >= 10.*"
}
@@ -6907,6 +7085,11 @@
"node": ">=6.0"
}
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+ "resolved": "https://registry.npmjs.org/gff-nostream/-/gff-nostream-1.3.4.tgz",
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+ },
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@@ -6973,24 +7156,6 @@
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"license": "MIT",
@@ -7076,19 +7241,21 @@
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"dependencies": {
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"inherits": "^2.0.4",
@@ -10702,7 +11056,8 @@
},
"node_modules/stream-http/node_modules/readable-stream": {
"version": "3.6.2",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-3.6.2.tgz",
+ "integrity": "sha512-9u/sniCrY3D5WdsERHzHE4G2YCXqoG5FTHUiCC4SIbr6XcLZBY05ya9EKjYek9O5xOAwjGq+1JdGBAS7Q9ScoA==",
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"string_decoder": "^1.1.1",
@@ -10741,7 +11096,6 @@
"node_modules/string-width-cjs": {
"name": "string-width",
"version": "4.2.3",
- "dev": true,
"license": "MIT",
"dependencies": {
"emoji-regex": "^8.0.0",
@@ -10765,7 +11119,6 @@
"node_modules/strip-ansi-cjs": {
"name": "strip-ansi",
"version": "6.0.1",
- "dev": true,
"license": "MIT",
"dependencies": {
"ansi-regex": "^5.0.1"
@@ -10825,11 +11178,6 @@
"url": "https://github.com/sponsors/ljharb"
}
},
- "node_modules/svg-path-generator": {
- "version": "1.1.0",
- "resolved": "https://registry.npmjs.org/svg-path-generator/-/svg-path-generator-1.1.0.tgz",
- "integrity": "sha512-eapn3syFa828HJRI3Wv+ceq7K/TUo/wA31w5oyerA3CNz02YkLM8aSjXA851+0qhc1ibihiJHxy54eacm2/euQ=="
- },
"node_modules/svg-pathdata": {
"version": "6.0.3",
"license": "MIT",
@@ -10850,9 +11198,26 @@
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}
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+ "node_modules/tar": {
+ "version": "7.4.3",
+ "resolved": "https://registry.npmjs.org/tar/-/tar-7.4.3.tgz",
+ "integrity": "sha512-5S7Va8hKfV7W5U6g3aYxXmlPoZVAwUMy9AOKyF2fVuZa2UD3qZjg578OrLRt8PcNN1PleVaL/5/yYATNL0ICUw==",
+ "dependencies": {
+ "@isaacs/fs-minipass": "^4.0.0",
+ "chownr": "^3.0.0",
+ "minipass": "^7.1.2",
+ "minizlib": "^3.0.1",
+ "mkdirp": "^3.0.1",
+ "yallist": "^5.0.0"
+ },
+ "engines": {
+ "node": ">=18"
+ }
+ },
"node_modules/tar-fs": {
- "version": "2.1.1",
- "license": "MIT",
+ "version": "2.1.2",
+ "resolved": "https://registry.npmjs.org/tar-fs/-/tar-fs-2.1.2.tgz",
+ "integrity": "sha512-EsaAXwxmx8UB7FRKqeozqEPop69DXcmYwTQwXvyAPF352HJsPdkVhvTaDPYqfNgruveJIJy3TA2l+2zj8LJIJA==",
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"chownr": "^1.1.1",
"mkdirp-classic": "^0.5.2",
@@ -10886,6 +11251,22 @@
"node": ">= 6"
}
},
+ "node_modules/tar/node_modules/chownr": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/chownr/-/chownr-3.0.0.tgz",
+ "integrity": "sha512-+IxzY9BZOQd/XuYPRmrvEVjF/nqj5kgT4kEq7VofrDoM1MxoRjEWkrCC3EtLi59TVawxTAn+orJwFQcrqEN1+g==",
+ "engines": {
+ "node": ">=18"
+ }
+ },
+ "node_modules/tar/node_modules/yallist": {
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/yallist/-/yallist-5.0.0.tgz",
+ "integrity": "sha512-YgvUTfwqyc7UXVMrB+SImsVYSmTS8X/tSrtdNZMImM+n7+QTriRXyXim0mBrTXNeqzVF0KWGgHPeiyViFFrNDw==",
+ "engines": {
+ "node": ">=18"
+ }
+ },
"node_modules/terser": {
"version": "5.31.3",
"license": "BSD-2-Clause",
@@ -11045,7 +11426,8 @@
},
"node_modules/timers-browserify": {
"version": "2.0.12",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/timers-browserify/-/timers-browserify-2.0.12.tgz",
+ "integrity": "sha512-9phl76Cqm6FhSX9Xe1ZUAMLtm1BLkKj2Qd5ApyWkXzsMRaA7dgr81kf4wJmQf/hAvg8EEyJxDo3du/0KlhPiKQ==",
"dependencies": {
"setimmediate": "^1.0.4"
},
@@ -11062,15 +11444,48 @@
"version": "1.6.0",
"license": "MIT"
},
- "node_modules/to-fast-properties": {
- "version": "2.0.0",
- "license": "MIT",
+ "node_modules/tinyglobby": {
+ "version": "0.2.12",
+ "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.12.tgz",
+ "integrity": "sha512-qkf4trmKSIiMTs/E63cxH+ojC2unam7rJ0WrauAzpT3ECNTxGRMlaXxVbfxMUC/w0LaYk6jQ4y/nGR9uBO3tww==",
+ "dependencies": {
+ "fdir": "^6.4.3",
+ "picomatch": "^4.0.2"
+ },
"engines": {
- "node": ">=4"
+ "node": ">=12.0.0"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/SuperchupuDev"
+ }
+ },
+ "node_modules/tinyglobby/node_modules/fdir": {
+ "version": "6.4.3",
+ "resolved": "https://registry.npmjs.org/fdir/-/fdir-6.4.3.tgz",
+ "integrity": "sha512-PMXmW2y1hDDfTSRc9gaXIuCCRpuoz3Kaz8cUelp3smouvfT632ozg2vrT6lJsHKKOF59YLbOGfAWGUcKEfRMQw==",
+ "peerDependencies": {
+ "picomatch": "^3 || ^4"
+ },
+ "peerDependenciesMeta": {
+ "picomatch": {
+ "optional": true
+ }
+ }
+ },
+ "node_modules/tinyglobby/node_modules/picomatch": {
+ "version": "4.0.2",
+ "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.2.tgz",
+ "integrity": "sha512-M7BAV6Rlcy5u+m6oPhAPFgJTzAioX/6B0DxyvDlo9l8+T3nLKbrczg2WLUyzd45L8RqfUMyGPzekbMvX2Ldkwg==",
+ "engines": {
+ "node": ">=12"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/jonschlinkert"
}
},
"node_modules/to-regex-range": {
"version": "5.0.1",
+ "dev": true,
"license": "MIT",
"dependencies": {
"is-number": "^7.0.0"
@@ -11101,6 +11516,11 @@
"node": ">=6"
}
},
+ "node_modules/tr46": {
+ "version": "0.0.3",
+ "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz",
+ "integrity": "sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw=="
+ },
"node_modules/tree-dump": {
"version": "1.0.2",
"dev": true,
@@ -11146,7 +11566,8 @@
},
"node_modules/tty-browserify": {
"version": "0.0.1",
- "license": "MIT"
+ "resolved": "https://registry.npmjs.org/tty-browserify/-/tty-browserify-0.0.1.tgz",
+ "integrity": "sha512-C3TaO7K81YvjCgQH9Q1S3R3P3BtN3RIM8n+OvX4il1K1zgE8ZhI0op7kClgkxtutIE8hQrcrHBXvIheqKUUCxw=="
},
"node_modules/tunnel-agent": {
"version": "0.6.0",
@@ -11159,13 +11580,11 @@
}
},
"node_modules/type-fest": {
- "version": "0.21.3",
- "dev": true,
- "license": "(MIT OR CC0-1.0)",
- "optional": true,
- "peer": true,
+ "version": "4.38.0",
+ "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-4.38.0.tgz",
+ "integrity": "sha512-2dBz5D5ycHIoliLYLi0Q2V7KRaDlH0uWIvmk7TYlAg5slqwiPv1ezJdZm1QEM0xgk29oYWMCbIG7E6gHpvChlg==",
"engines": {
- "node": ">=10"
+ "node": ">=16"
},
"funding": {
"url": "https://github.com/sponsors/sindresorhus"
@@ -11272,6 +11691,18 @@
"node": ">= 0.8"
}
},
+ "node_modules/unzipper": {
+ "version": "0.12.3",
+ "resolved": "https://registry.npmjs.org/unzipper/-/unzipper-0.12.3.tgz",
+ "integrity": "sha512-PZ8hTS+AqcGxsaQntl3IRBw65QrBI6lxzqDEL7IAo/XCEqRTKGfOX56Vea5TH9SZczRVxuzk1re04z/YjuYCJA==",
+ "dependencies": {
+ "bluebird": "~3.7.2",
+ "duplexer2": "~0.1.4",
+ "fs-extra": "^11.2.0",
+ "graceful-fs": "^4.2.2",
+ "node-int64": "^0.4.0"
+ }
+ },
"node_modules/update-browserslist-db": {
"version": "1.1.2",
"resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.1.2.tgz",
@@ -11310,7 +11741,8 @@
},
"node_modules/url": {
"version": "0.11.4",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/url/-/url-0.11.4.tgz",
+ "integrity": "sha512-oCwdVC7mTuWiPyjLUz/COz5TLk6wgp0RCsN+wHZ2Ekneac9w8uuV0njcbbie2ME+Vs+d6duwmYuR3HgQXs1fOg==",
"dependencies": {
"punycode": "^1.4.1",
"qs": "^6.12.3"
@@ -11321,14 +11753,15 @@
},
"node_modules/url/node_modules/punycode": {
"version": "1.4.1",
- "license": "MIT"
+ "resolved": "https://registry.npmjs.org/punycode/-/punycode-1.4.1.tgz",
+ "integrity": "sha512-jmYNElW7yvO7TV33CjSmvSiE2yco3bV2czu/OzDKdMNVZQWfxCblURLhf+47syQRBntjfLdd/H0egrzIG+oaFQ=="
},
"node_modules/use-isomorphic-layout-effect": {
- "version": "1.1.2",
- "resolved": "https://registry.npmjs.org/use-isomorphic-layout-effect/-/use-isomorphic-layout-effect-1.1.2.tgz",
- "integrity": "sha512-49L8yCO3iGT/ZF9QttjwLF/ZD9Iwto5LnH5LmEdk/6cFmXddqi2ulF0edxTwjj+7mqvpVVGQWvbXZdn32wRSHA==",
+ "version": "1.2.0",
+ "resolved": "https://registry.npmjs.org/use-isomorphic-layout-effect/-/use-isomorphic-layout-effect-1.2.0.tgz",
+ "integrity": "sha512-q6ayo8DWoPZT0VdG4u3D3uxcgONP3Mevx2i2b0434cwWBoL+aelL1DzkXI6w3PhTZzUeR2kaVlZn70iCiseP6w==",
"peerDependencies": {
- "react": "^16.8.0 || ^17.0.0 || ^18.0.0"
+ "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0"
},
"peerDependenciesMeta": {
"@types/react": {
@@ -11390,14 +11823,15 @@
}
},
"node_modules/uuid": {
- "version": "9.0.1",
+ "version": "11.1.0",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-11.1.0.tgz",
+ "integrity": "sha512-0/A9rDy9P7cJ+8w1c9WD9V//9Wj15Ce2MPz8Ri6032usz+NfePxx5AcN3bN+r6ZL6jEo066/yNYB3tn4pQEx+A==",
"funding": [
"https://github.com/sponsors/broofa",
"https://github.com/sponsors/ctavan"
],
- "license": "MIT",
"bin": {
- "uuid": "dist/bin/uuid"
+ "uuid": "dist/esm/bin/uuid"
}
},
"node_modules/vary": {
@@ -11413,36 +11847,6 @@
"resolved": "https://registry.npmjs.org/velocity-animate/-/velocity-animate-1.5.2.tgz",
"integrity": "sha512-m6EXlCAMetKztO1ppBhGU1/1MR3IiEevO6ESq6rcrSQ3Q77xYSW13jkfXW88o4xMrkXJhy/U7j4wFR/twMB0Eg=="
},
- "node_modules/vis-data": {
- "version": "7.1.9",
- "resolved": "https://registry.npmjs.org/vis-data/-/vis-data-7.1.9.tgz",
- "integrity": "sha512-COQsxlVrmcRIbZMMTYwD+C2bxYCFDNQ2EHESklPiInbD/Pk3JZ6qNL84Bp9wWjYjAzXfSlsNaFtRk+hO9yBPWA==",
- "funding": {
- "type": "opencollective",
- "url": "https://opencollective.com/visjs"
- },
- "peerDependencies": {
- "uuid": "^3.4.0 || ^7.0.0 || ^8.0.0 || ^9.0.0",
- "vis-util": "^5.0.1"
- }
- },
- "node_modules/vis-network": {
- "version": "9.1.9",
- "resolved": "https://registry.npmjs.org/vis-network/-/vis-network-9.1.9.tgz",
- "integrity": "sha512-Ft+hLBVyiLstVYSb69Q1OIQeh3FeUxHJn0WdFcq+BFPqs+Vq1ibMi2sb//cxgq1CP7PH4yOXnHxEH/B2VzpZYA==",
- "funding": {
- "type": "opencollective",
- "url": "https://opencollective.com/visjs"
- },
- "peerDependencies": {
- "@egjs/hammerjs": "^2.0.0",
- "component-emitter": "^1.3.0",
- "keycharm": "^0.2.0 || ^0.3.0 || ^0.4.0",
- "uuid": "^3.4.0 || ^7.0.0 || ^8.0.0 || ^9.0.0",
- "vis-data": "^6.3.0 || ^7.0.0",
- "vis-util": "^5.0.1"
- }
- },
"node_modules/vis-util": {
"version": "5.0.7",
"resolved": "https://registry.npmjs.org/vis-util/-/vis-util-5.0.7.tgz",
@@ -11483,6 +11887,11 @@
"minimalistic-assert": "^1.0.0"
}
},
+ "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=="
+ },
"node_modules/webpack": {
"version": "5.96.1",
"resolved": "https://registry.npmjs.org/webpack/-/webpack-5.96.1.tgz",
@@ -11818,9 +12227,17 @@
"node": ">=0.8.0"
}
},
+ "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==",
+ "dependencies": {
+ "tr46": "~0.0.3",
+ "webidl-conversions": "^3.0.0"
+ }
+ },
"node_modules/which": {
"version": "2.0.2",
- "dev": true,
"license": "ISC",
"dependencies": {
"isexe": "^2.0.0"
@@ -11856,7 +12273,8 @@
},
"node_modules/wrap-ansi": {
"version": "7.0.0",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
+ "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==",
"dependencies": {
"ansi-styles": "^4.0.0",
"string-width": "^4.1.0",
@@ -11872,7 +12290,6 @@
"node_modules/wrap-ansi-cjs": {
"name": "wrap-ansi",
"version": "7.0.0",
- "dev": true,
"license": "MIT",
"dependencies": {
"ansi-styles": "^4.0.0",
@@ -11912,7 +12329,8 @@
},
"node_modules/xtend": {
"version": "4.0.2",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz",
+ "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==",
"engines": {
"node": ">=0.4"
}
@@ -11927,7 +12345,8 @@
},
"node_modules/y18n": {
"version": "5.0.8",
- "license": "ISC",
+ "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz",
+ "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==",
"engines": {
"node": ">=10"
}
@@ -11947,7 +12366,8 @@
},
"node_modules/yargs": {
"version": "16.2.0",
- "license": "MIT",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz",
+ "integrity": "sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw==",
"dependencies": {
"cliui": "^7.0.2",
"escalade": "^3.1.1",
@@ -11961,9 +12381,10 @@
"node": ">=10"
}
},
- "node_modules/yargs/node_modules/yargs-parser": {
+ "node_modules/yargs-parser": {
"version": "20.2.9",
- "license": "ISC",
+ "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz",
+ "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==",
"engines": {
"node": ">=10"
}
diff --git a/jbrowse/package.json b/jbrowse/package.json
index 4fba61e57..3807eef04 100644
--- a/jbrowse/package.json
+++ b/jbrowse/package.json
@@ -14,44 +14,45 @@
"jb-pkg": "npm run prepareCli && npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli"
},
"dependencies": {
- "@gmod/vcf": "^5.0.10",
- "@jbrowse/core": "^2.15.0",
- "@jbrowse/plugin-linear-genome-view": "^2.15.0",
- "@jbrowse/plugin-svg": "^2.15.0",
- "@jbrowse/plugin-variants": "^2.15.0",
- "@jbrowse/react-linear-genome-view": "^2.15.0",
- "@labkey/api": "^1.35.0",
- "@labkey/components": "^5.0.0",
- "@mui/x-data-grid": "^7.0.0",
- "@yao-pkg/pkg": "^5.12.0",
- "assert": "^2.0.0",
+ "@gmod/vcf": "^6.0.9",
+ "@jbrowse/core": "^3.2.0",
+ "@jbrowse/product-core": "^3.2.0",
+ "@jbrowse/plugin-linear-genome-view": "^3.2.0",
+ "@jbrowse/plugin-svg": "^3.2.0",
+ "@jbrowse/plugin-variants": "^3.2.0",
+ "@jbrowse/react-linear-genome-view2": "^3.2.0",
+ "@labkey/api": "^1.39.0",
+ "@labkey/components": "^6.32.2",
+ "@mui/x-data-grid": "^7.28.1",
+ "@yao-pkg/pkg": "^6.3.2",
+ "assert": "^2.1.0",
"browserify-zlib": "^0.2.0",
"buffer": "^6.0.3",
"child_process": "^1.0.2",
"fs": "^0.0.1-security",
- "jquery": "^3.7.0",
- "jspdf": "^2.5.1",
- "jspdf-autotable": "^3.5.31",
- "node-polyfill-webpack-plugin": "2.0.1",
+ "jquery": "^3.7.1",
+ "jspdf": "^3.0.0",
+ "jspdf-autotable": "^5.0.2",
+ "node-polyfill-webpack-plugin": "4.1.0",
"path-browserify": "^1.0.1",
- "react": "^18.0.0",
+ "react": "^18.3.0",
"react-data-grid": "7.0.0-beta.46",
- "react-dom": "^18.0.0",
- "react-google-charts": "^4.0.1",
- "react-select": "^5.8.0",
- "regenerator-runtime": "^0.13.11",
+ "react-dom": "^18.3.0",
+ "react-google-charts": "^5.2.1",
+ "react-select": "^5.10.1",
+ "regenerator-runtime": "^0.14.1",
"stream-browserify": "^3.0.0",
"util": "^0.12.5",
- "uuid": "^9.0.0",
+ "uuid": "^11.1.0",
"vm-browserify": "^1.1.2"
},
"devDependencies": {
- "@labkey/build": "^8.3.0",
- "@types/jexl": "^2.3.1",
- "@types/jquery": "^3.0.0",
+ "@labkey/build": "^8.4.0",
+ "@types/jexl": "^2.3.4",
+ "@types/jquery": "^3.5.32",
"@types/node": "^20.14.11",
- "@types/react": "^18.0.0",
- "@types/react-dom": "^18.0.0",
+ "@types/react": "^18.3.0",
+ "@types/react-dom": "^18.3.0",
"rimraf": "^6.0.1",
"typescript": "^5.1.6"
}
diff --git a/jbrowse/src/client/JBrowse/Browser/Browser.tsx b/jbrowse/src/client/JBrowse/Browser/Browser.tsx
index 58ca9f155..8eff240e9 100644
--- a/jbrowse/src/client/JBrowse/Browser/Browser.tsx
+++ b/jbrowse/src/client/JBrowse/Browser/Browser.tsx
@@ -1,6 +1,6 @@
import React, { useEffect, useState } from 'react';
-import { JBrowseLinearGenomeView, ViewModel } from '@jbrowse/react-linear-genome-view';
+import { JBrowseLinearGenomeView, ViewModel } from '@jbrowse/react-linear-genome-view2'
import { createTheme } from '@mui/material/styles';
import LogSession from './plugins/LogSession/index';
import ExtendedVariantPlugin from './plugins/ExtendedVariantPlugin/index';
diff --git a/jbrowse/src/client/JBrowse/Browser/app.tsx b/jbrowse/src/client/JBrowse/Browser/app.tsx
index d749df1ea..8b000d9d1 100644
--- a/jbrowse/src/client/JBrowse/Browser/app.tsx
+++ b/jbrowse/src/client/JBrowse/Browser/app.tsx
@@ -1,9 +1,7 @@
-import React from 'react';
-import ReactDOM from 'react-dom';
-
import View from './Browser';
+import { createRoot } from 'react-dom/client';
+import React from 'react';
-// Need to wait for container element to be available in labkey wrapper before render
window.addEventListener('DOMContentLoaded', (event) => {
- ReactDOM.render(, document.getElementById('app'))
+ createRoot(document.getElementById('app')).render()
});
diff --git a/jbrowse/src/client/JBrowse/Browser/dev.tsx b/jbrowse/src/client/JBrowse/Browser/dev.tsx
index c622a6c88..0b64adbe2 100644
--- a/jbrowse/src/client/JBrowse/Browser/dev.tsx
+++ b/jbrowse/src/client/JBrowse/Browser/dev.tsx
@@ -1,10 +1,7 @@
-import React from 'react';
-import ReactDOM from 'react-dom';
-
import View from './Browser';
+import { createRoot } from 'react-dom/client';
+import React from 'react';
-const render = () => {
- ReactDOM.render(, document.getElementById('app'));
-};
-
-render();
\ No newline at end of file
+window.addEventListener('DOMContentLoaded', (event) => {
+ createRoot(document.getElementById('app')).render()
+}, true);
diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVariantAdapter.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVariantAdapter.ts
index 9d3729df7..d7973773b 100644
--- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVariantAdapter.ts
+++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVariantAdapter.ts
@@ -27,7 +27,7 @@ export default class extends VcfTabixAdapter {
observer.next(v)
})
observer.complete()
- }, opts.signal)
+ }, opts.stopToken)
}
private async getFeaturesAsArray(query: NoAssemblyRegion, opts: BaseOptions = {}) {
diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts
index 8c4988e63..0af562dab 100644
--- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts
+++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts
@@ -1,32 +1,14 @@
import { VcfFeature } from '@jbrowse/plugin-variants'
-import VcfParser from '@gmod/vcf'
+import VcfParser, { Variant } from '@gmod/vcf';
export default class ExtendedVcfFeature extends VcfFeature {
- private readonly vcfParser: VcfParser
-
- constructor(args: { variant: any; parser: VcfParser; id: string }) {
+ constructor(args: { variant: Variant; parser: VcfParser; id: string }) {
args.variant = ExtendedVcfFeature.extractImpact(args.variant)
- //args.variant = ExtendedVcfFeature.calculateVariableSamples(args.variant)
super(args)
-
- this.vcfParser = args.parser
- }
-
- public getInfoFieldMeta(propKey: string): VcfParser {
- const map = this.vcfParser.getMetadata("INFO")
-
- return map ? map[propKey] : null
}
- static extractImpact(variant: {
- REF: string
- POS: number
- ALT: string[]
- CHROM: string
- INFO: any
- ID: string[]
- }) {
+ static extractImpact(variant: Variant) {
// Only append if not present:
if (variant.INFO["IMPACT"]) {
return(variant);
diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/VcfTabixAdapter.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/VcfTabixAdapter.ts
index 31d3d9e84..fca6a3e64 100644
--- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/VcfTabixAdapter.ts
+++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/VcfTabixAdapter.ts
@@ -1,46 +1,57 @@
+import { TabixIndexedFile } from '@gmod/tabix'
+import VcfParser from '@gmod/vcf'
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
import {
- BaseFeatureDataAdapter,
- BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
+ fetchAndMaybeUnzipText,
+ updateStatus,
+} from '@jbrowse/core/util'
import { openLocation } from '@jbrowse/core/util/io'
import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature } from '@jbrowse/core/util'
-import { TabixIndexedFile } from '@gmod/tabix'
-import VcfParser from '@gmod/vcf'
+
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
+import type { Feature } from '@jbrowse/core/util'
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types'
import { VcfFeature } from '@jbrowse/plugin-variants';
+function shorten2(name: string, max = 70) {
+ return name.length > max ? `${name.slice(0, max)}...` : name
+}
+
export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
private configured?: Promise<{
vcf: TabixIndexedFile
parser: VcfParser
}>
- private async configurePre() {
- const pm = this.pluginManager
+ private async configurePre(_opts?: BaseOptions) {
const vcfGzLocation = this.getConf('vcfGzLocation')
const location = this.getConf(['index', 'location'])
const indexType = this.getConf(['index', 'indexType'])
- const filehandle = openLocation(vcfGzLocation, pm)
+ const filehandle = openLocation(vcfGzLocation, this.pluginManager)
const isCSI = indexType === 'CSI'
const vcf = new TabixIndexedFile({
filehandle,
- csiFilehandle: isCSI ? openLocation(location, pm) : undefined,
- tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined,
- chunkCacheSize: 50 * 2 ** 20
+ csiFilehandle: isCSI
+ ? openLocation(location, this.pluginManager)
+ : undefined,
+ tbiFilehandle: !isCSI
+ ? openLocation(location, this.pluginManager)
+ : undefined,
+ chunkCacheSize: 50 * 2 ** 20,
})
- const header = await vcf.getHeader()
return {
vcf,
- parser: new VcfParser({ header }),
+ parser: new VcfParser({
+ header: await vcf.getHeader(),
+ }),
}
}
- protected async configure() {
+ protected async configurePre2() {
if (!this.configured) {
- this.configured = this.configurePre().catch(e => {
+ this.configured = this.configurePre().catch((e: unknown) => {
this.configured = undefined
throw e
})
@@ -48,39 +59,100 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
return this.configured
}
+ async configure(opts?: BaseOptions) {
+ const { statusCallback = () => {} } = opts || {}
+ return updateStatus('Downloading index', statusCallback, () =>
+ this.configurePre2(),
+ )
+ }
public async getRefNames(opts: BaseOptions = {}) {
- const { vcf } = await this.configure()
+ const { vcf } = await this.configure(opts)
return vcf.getReferenceSequenceNames(opts)
}
- async getHeader() {
- const { vcf } = await this.configure()
+ async getHeader(opts?: BaseOptions) {
+ const { vcf } = await this.configure(opts)
return vcf.getHeader()
}
- async getMetadata() {
- const { parser } = await this.configure()
+ async getMetadata(opts?: BaseOptions) {
+ const { parser } = await this.configure(opts)
return parser.getMetadata()
}
public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
return ObservableCreate(async observer => {
const { refName, start, end } = query
- const { vcf, parser } = await this.configure()
- await vcf.getLines(refName, start, end, {
- lineCallback: (line, fileOffset) => {
- observer.next(
- new VcfFeature({
- variant: parser.parseLine(line),
- parser,
- id: `${this.id}-vcf-${fileOffset}`,
- }),
- )
- },
- ...opts,
- })
+ const { statusCallback = () => {} } = opts
+ const { vcf, parser } = await this.configure(opts)
+
+ await updateStatus('Downloading variants', statusCallback, () =>
+ vcf.getLines(refName, start, end, {
+ lineCallback: (line, fileOffset) => {
+ observer.next(
+ new VcfFeature({
+ variant: parser.parseLine(line),
+ parser,
+ id: `${this.id}-vcf-${fileOffset}`,
+ }),
+ )
+ },
+ ...opts,
+ }),
+ )
observer.complete()
- }, opts.signal)
+ }, opts.stopToken)
+ }
+
+ async getSources() {
+ const conf = this.getConf('samplesTsvLocation')
+ if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
+ const { parser } = await this.configure()
+ return parser.samples.map(name => ({
+ name,
+ }))
+ } else {
+ const txt = await fetchAndMaybeUnzipText(
+ openLocation(conf, this.pluginManager),
+ )
+ const lines = txt.split(/\n|\r\n|\r/)
+ const header = lines[0]!.split('\t')
+ const { parser } = await this.configure()
+ const metadataLines = lines
+ .slice(1)
+ .filter(f => !!f)
+ .map(line => {
+ const [name, ...rest] = line.split('\t')
+ return {
+ ...Object.fromEntries(
+ // force col 0 to be called name
+ rest.map((c, idx) => [header[idx + 1]!, c] as const),
+ ),
+ name: name!,
+ }
+ })
+ const vcfSampleSet = new Set(parser.samples)
+ const metadataSet = new Set(metadataLines.map(r => r.name))
+ const metadataNotInVcfSamples = [...metadataSet].filter(
+ f => !vcfSampleSet.has(f),
+ )
+ const vcfSamplesNotInMetadata = [...vcfSampleSet].filter(
+ f => !metadataSet.has(f),
+ )
+ if (metadataNotInVcfSamples.length) {
+ console.warn(
+ `There are ${metadataNotInVcfSamples.length} samples in metadata file (${metadataLines.length} lines) not in VCF (${parser.samples.length} samples):`,
+ shorten2(metadataNotInVcfSamples.join(',')),
+ )
+ }
+ if (vcfSamplesNotInMetadata.length) {
+ console.warn(
+ `There are ${vcfSamplesNotInMetadata.length} samples in VCF file (${parser.samples.length} samples) not in metadata file (${metadataLines.length} lines):`,
+ shorten2(vcfSamplesNotInMetadata.map(m => m).join(',')),
+ )
+ }
+ return metadataLines.filter(f => vcfSampleSet.has(f.name))
+ }
}
public freeResources(/* { region } */): void {}
diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/ExtendedVariantRendering.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/ExtendedVariantRendering.tsx
index 650e833bb..22fa99691 100644
--- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/ExtendedVariantRendering.tsx
+++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/ExtendedVariantRendering.tsx
@@ -1,10 +1,10 @@
-import jexl from 'jexl';
import { SvgFeatureRendererReactComponent } from '@jbrowse/plugin-svg';
import { observer } from 'mobx-react';
import React from 'react';
import { deserializeFilters } from '../../InfoFilterWidget/filterUtil';
import Diamond from './Diamond';
import { passesInfoFilters, passesSampleFilters } from '../../../../../utils';
+import { VcfFeature } from '@jbrowse/plugin-variants';
export function ExtendedVariantRendering(props) {
const { features, rendererConfig } = props
@@ -17,11 +17,11 @@ export function ExtendedVariantRendering(props) {
const sampleFilters = activeSamples.value ? activeSamples.value.split(',') : null
- function diamondValidator(feature) {
+ function diamondValidator(feature: VcfFeature) {
return feature.get('type') === "SNV";
}
- function isFeatureDisplayed(feature) {
+ function isFeatureDisplayed(feature: VcfFeature) {
return passesInfoFilters(feature, expandedFilters) && passesSampleFilters(feature, sampleFilters)
}
diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
index 3c3ddced5..1fe878691 100644
--- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
+++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
@@ -407,7 +407,7 @@ export default jbrowse => {
feat["INFO"] = null
return (
-
+
{message}
('jbrowseSearchWebpart', (target: string, sessionId: string) => {
- ReactDOM.render(
-
- , document.getElementById(target));
-});
+ createRoot(document.getElementById(target)).render()
+});
\ No newline at end of file
diff --git a/jbrowse/src/client/JBrowse/Search/webpart/dev.tsx b/jbrowse/src/client/JBrowse/Search/webpart/dev.tsx
index 5ce2a10cb..830b70c6b 100644
--- a/jbrowse/src/client/JBrowse/Search/webpart/dev.tsx
+++ b/jbrowse/src/client/JBrowse/Search/webpart/dev.tsx
@@ -1,11 +1,9 @@
import React from 'react';
-import ReactDOM from 'react-dom';
+import { createRoot } from 'react-dom/client';
import { App } from '@labkey/api';
import StandaloneSearch from '../StandaloneSearch';
-const render = (target: string, sessionId: string) => {
- ReactDOM.render(, document.getElementById(target));
-};
-
-App.registerApp('jbrowseSearchWebpart', render, true /* hot */);
\ No newline at end of file
+App.registerApp('jbrowseSearchWebpart', (target: string, sessionId: string) => {
+ createRoot(document.getElementById(target)).render()
+}, true);
\ No newline at end of file
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/VariantTable.tsx b/jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx
similarity index 96%
rename from jbrowse/src/client/JBrowse/VariantSearch/VariantTable.tsx
rename to jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx
index 75dd70709..a0332e66f 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/VariantTable.tsx
+++ b/jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx
@@ -11,12 +11,11 @@ import ExtendedVariantPlugin from '../Browser/plugins/ExtendedVariantPlugin/inde
import VariantTableWidget from './components/VariantTableWidget';
import { fetchSession } from '../utils';
import { ErrorBoundary } from './components/ErrorBoundary';
-import LoadingIndicator from './components/LoadingIndicator';
import deepmerge from '@mui/utils/deepmerge';
const nativePlugins = [ExtendedVariantPlugin, LogSession]
-function VariantTable() {
+function VariantSearch() {
const queryParam = new URLSearchParams(window.location.search);
const sessionId = queryParam.get('session') || queryParam.get('database') || queryParam.get('sessionId')
const locString = queryParam.get('location') || queryParam.get('loc')
@@ -97,4 +96,4 @@ function VariantTable() {
)
}
-export default observer(VariantTable)
+export default observer(VariantSearch)
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/app.tsx b/jbrowse/src/client/JBrowse/VariantSearch/app.tsx
index 79bedd318..9565db3a1 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/app.tsx
+++ b/jbrowse/src/client/JBrowse/VariantSearch/app.tsx
@@ -1,9 +1,8 @@
import React from 'react';
-import ReactDOM from 'react-dom';
-import VariantTable from './VariantTable';
+import VariantSearch from './VariantSearch';
+import { createRoot } from 'react-dom/client';
-// Need to wait for container element to be available in labkey wrapper before render
window.addEventListener('DOMContentLoaded', (event) => {
- ReactDOM.render(, document.getElementById('app'))
+ createRoot(document.getElementById('app')).render()
});
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx b/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx
index daaefc0e5..162a0308a 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx
+++ b/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx
@@ -1,10 +1,8 @@
import React from 'react';
-import ReactDOM from 'react-dom';
-import VariantTable from './VariantTable';
+import VariantSearch from './VariantSearch';
+import { createRoot } from 'react-dom/client';
-const render = () => {
- ReactDOM.render(, document.getElementById('app'));
-};
-
-render();
\ No newline at end of file
+window.addEventListener('DOMContentLoaded', (event) => {
+ createRoot(document.getElementById('app')).render()
+}, true);
diff --git a/jbrowse/src/client/JBrowse/VariantTable/app.tsx b/jbrowse/src/client/JBrowse/VariantTable/app.tsx
index 79bedd318..7ffd104e6 100644
--- a/jbrowse/src/client/JBrowse/VariantTable/app.tsx
+++ b/jbrowse/src/client/JBrowse/VariantTable/app.tsx
@@ -1,9 +1,8 @@
import React from 'react';
-import ReactDOM from 'react-dom';
import VariantTable from './VariantTable';
+import { createRoot } from 'react-dom/client';
-// Need to wait for container element to be available in labkey wrapper before render
window.addEventListener('DOMContentLoaded', (event) => {
- ReactDOM.render(, document.getElementById('app'))
+ createRoot(document.getElementById('app')).render()
});
diff --git a/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx
index 0a7757eaf..a7b58ebc4 100644
--- a/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx
+++ b/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx
@@ -101,10 +101,11 @@ const VariantTableWidget = observer(props => {
// Maintain a cached list of all non-WT samples at this position:
filteredFeatures.forEach(variant => {
- if (!variant.get('INFO')['variableSamples'] && variant.get('SAMPLES')) {
+ if (!variant.get('INFO')['variableSamples']) {
variant.get('INFO')['variableSamples'] = []
- Object.keys(variant.get('SAMPLES')).forEach(function(sampleId) {
- const gt = variant.get('SAMPLES')[sampleId]["GT"] ? variant.get('SAMPLES')[sampleId]["GT"][0] : null
+ const genotypes = variant.get('GENOTYPES')()
+ Object.keys(genotypes).forEach(function(sampleId) {
+ const gt = genotypes[sampleId] ? genotypes[sampleId] : null
if (isVariant(gt)) {
variant.get('INFO')['variableSamples'].push(sampleId)
}
diff --git a/jbrowse/src/client/JBrowse/VariantTable/dev.tsx b/jbrowse/src/client/JBrowse/VariantTable/dev.tsx
index daaefc0e5..3e874750c 100644
--- a/jbrowse/src/client/JBrowse/VariantTable/dev.tsx
+++ b/jbrowse/src/client/JBrowse/VariantTable/dev.tsx
@@ -1,10 +1,8 @@
import React from 'react';
-import ReactDOM from 'react-dom';
import VariantTable from './VariantTable';
+import { createRoot } from 'react-dom/client';
-const render = () => {
- ReactDOM.render(, document.getElementById('app'));
-};
-
-render();
\ No newline at end of file
+window.addEventListener('DOMContentLoaded', (event) => {
+ createRoot(document.getElementById('app')).render()
+}, true);
diff --git a/jbrowse/src/client/JBrowse/jbrowse.css b/jbrowse/src/client/JBrowse/jbrowse.css
index 276f91c79..26614061a 100644
--- a/jbrowse/src/client/JBrowse/jbrowse.css
+++ b/jbrowse/src/client/JBrowse/jbrowse.css
@@ -1,13 +1,18 @@
/* This corrects a border that placed a small vertical line to the top-left of the search field */
fieldset.MuiOutlinedInput-notchedOutline > legend {
- border-style: none;
+ border-style: none;
}
html {
- font-size: 16px !important;
+ font-size: 16px !important;
}
/* Increase font size for tooltips: */
div[class^="makeStyles-tooltip-"] {
- font-size: 12px;
+ font-size: 12px;
+}
+
+.MuiDialog-paperScrollPaper {
+ max-height: 95vh;
+ overflow-y: scroll;
}
\ No newline at end of file
diff --git a/jbrowse/src/client/JBrowse/utils.ts b/jbrowse/src/client/JBrowse/utils.ts
index e69b0b3e7..1602ff088 100644
--- a/jbrowse/src/client/JBrowse/utils.ts
+++ b/jbrowse/src/client/JBrowse/utils.ts
@@ -1,10 +1,9 @@
import { isEmptyObject } from 'jquery';
import jexl from 'jexl';
-import { createViewState, loadPlugins } from '@jbrowse/react-linear-genome-view';
+import { createViewState, loadPlugins } from '@jbrowse/react-linear-genome-view2';
import { ActionURL, Ajax } from '@labkey/api';
import {
getGridNumericOperators,
- GridCellParams,
GridColDef,
GridColType,
GridComparatorFn,
@@ -12,6 +11,7 @@ import {
GridFilterOperator
} from '@mui/x-data-grid';
import { ParsedLocString, parseLocString } from '@jbrowse/core/util';
+import { VcfFeature } from '@jbrowse/plugin-variants';
export function arrayMax(array) {
return Array.isArray(array) ? Math.max(...array) : array
@@ -43,21 +43,15 @@ export function passesInfoFilters(feature, filters) {
return true
}
-export function passesSampleFilters(feature, sampleIDs){
+export function passesSampleFilters(variant : VcfFeature, sampleIDs){
if (!sampleIDs || sampleIDs.length === 0) {
return true
}
- const featureVariant = feature.variant ?? feature.data
- const samples = featureVariant.SAMPLES || featureVariant.samples
- if (!samples || isEmptyObject(samples)) {
- return false
- }
-
// Preferentially use pre-computed values:
- if (featureVariant.INFO._variableSamples) {
+ if (variant.get('INFO')['_variableSamples']) {
for (const sampleId of sampleIDs) {
- if (featureVariant.INFO._variableSamples.indexOf(sampleId) > -1) {
+ if (variant.get('INFO')._variableSamples.indexOf(sampleId) > -1) {
return true
}
}
@@ -65,9 +59,14 @@ export function passesSampleFilters(feature, sampleIDs){
return false
}
+ const genotypes = variant.get('GENOTYPES')()
+ if (!genotypes || isEmptyObject(genotypes)) {
+ return false
+ }
+
for (const sampleId of sampleIDs) {
- if (samples[sampleId]) {
- const gt = samples[sampleId]["GT"][0]
+ if (genotypes[sampleId]) {
+ const gt = genotypes[sampleId]
// If any sample in the whitelist is non-WT, show this site. Otherwise filter.
if (isVariant(gt)) {
diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
index f6ef69be3..2199ccc99 100644
--- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
+++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
@@ -303,6 +303,7 @@ private void testLoadingConfigFilters(){
// Wait for variants to load:
getDriver().findElements(getVariantWithinTrack("mgap_hg38", "SNV T -> G"));
+ getDriver().findElements(getVariantWithinTrack("mgap_hg38", "SNV A -> T"));
Assert.assertEquals("Incorrect number of variants", 7, getTotalVariantFeatures());
@@ -495,10 +496,10 @@ private void testGenotypeFrequencies()
assertElementPresent(Locator.tagWithText("td", "3041"));
assertElementPresent(Locator.tagWithText("span", "Genotype Frequency (2329)"));
assertElementPresent(Locator.tagWithText("a", "Click here to view sample-level genotypes"));
- while(isTextPresent("Loading")){
+ while (isTextPresent("Loading")){
sleep(10);
}
- assertElementPresent(Locator.tagWithAttributeContaining("div","id","reactgooglegraph"));
+ waitForElement(Locator.tagWithAttributeContaining("div","id","reactgooglegraph"));
}
@Override
diff --git a/singlecell/resources/chunks/MergeSeurat.R b/singlecell/resources/chunks/MergeSeurat.R
index 134005614..56fb0291d 100644
--- a/singlecell/resources/chunks/MergeSeurat.R
+++ b/singlecell/resources/chunks/MergeSeurat.R
@@ -53,6 +53,11 @@ mergeBatchInMemory <- function(datasetIdToFilePath, saveFile) {
return(saveFile)
}
+if (is.null(maxAllowableInputFileSizeMb)) {
+ logger::log_info('maxAllowableInputFileSizeMb not provided, defaulting to 200')
+ maxAllowableInputFileSizeMb <- 200
+}
+
mergeBatch <- function(seuratObjects, outerBatchIdx, maxBatchSize = 20, maxInputFileSizeMb = maxAllowableInputFileSizeMb) {
logger::log_info(paste0('Beginning outer batch: ', outerBatchIdx, ' with total files: ', length(seuratObjects)))
diff --git a/singlecell/resources/chunks/RunEscape.R b/singlecell/resources/chunks/RunEscape.R
index 582d0589f..af9c44251 100644
--- a/singlecell/resources/chunks/RunEscape.R
+++ b/singlecell/resources/chunks/RunEscape.R
@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
printName(datasetId)
seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
- seuratObj <- CellMembrane::RunEscape(seuratObj, outputAssayName = outputAssayName, doPlot = TRUE, performDimRedux = performDimRedux)
+ seuratObj <- CellMembrane::RunEscape(seuratObj, outputAssayBaseName = outputAssayBaseName, doPlot = TRUE, performDimRedux = performDimRedux)
saveData(seuratObj, datasetId)
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java
index 84e299ca7..639f4f094 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java
@@ -21,9 +21,9 @@ public static class Provider extends AbstractPipelineStepProvider