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OVE is now under @TeselaGen namespace (#4489)
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* switch to new ove and bio-parsers package

* update bio-parsers and ove
now they provide a license
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@MarcelBolten
MarcelBolten committed Jul 28, 2023
1 parent e80df9e commit b63f358
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Showing 4 changed files with 68 additions and 61 deletions.
8 changes: 3 additions & 5 deletions package.json
View file
Expand Up @@ -9,15 +9,15 @@
"3dmol": "^2.0.2",
"@deltablot/chemdoodle-web-mini": "^9.2.1",
"@deltablot/malle": "^2.3.0",
"@deltablot/open-vector-editor-umd": "^18.0.0",
"@deltablot/tg-oss-ove-umd": "^0.3.2",
"@fancyapps/fancybox": "3.5.*",
"@fullcalendar/bootstrap": "^6.1.5",
"@fullcalendar/core": "^6.1.5",
"@fullcalendar/daygrid": "^6.1.5",
"@fullcalendar/interaction": "^6.1.5",
"@fullcalendar/list": "^6.1.5",
"@fullcalendar/timegrid": "^6.1.5",
"bio-parsers": "^9.0.1",
"@teselagen/bio-parsers": "^0.3.2",
"bootstrap": "^4.5.0",
"bootstrap-markdown-fa5": "2.10.*",
"bootstrap-select": "^1.13.18",
Expand All @@ -43,8 +43,6 @@
"tinymce": "^5.10.0",
"ts-loader": "^9.1.1",
"typescript": "^5.1.6",
"ve-range-utils": "^2.6.3",
"ve-sequence-utils": "^5.1.6",
"webpack": "^5.9.0",
"webpack-cli": "^5.0.0"
},
Expand Down Expand Up @@ -95,7 +93,7 @@
"full": "yarn phpcs && yarn jslint && yarn csslint && yarn psalm && yarn phpstan && yarn test unit",
"jslint": "eslint --ext .ts src/ts",
"jslint-ci": "eslint --ext .ts --quiet src/ts",
"ove": "mkdir -p web/assets/ove/ && cp node_modules/@deltablot/open-vector-editor-umd/* web/assets/ove/ && rm -f web/assets/ove/open-vector-editor.js*",
"ove": "mkdir -p web/assets/ove/ && bash -c 'cp node_modules/@deltablot/tg-oss-ove-umd/{index.umd.js,style.css} web/assets/ove/'",
"phan": "phan --allow-polyfill-parser -k src/tools/phan-config.php",
"phpcs": "./vendor/bin/php-cs-fixer fix --config=.php-cs-fixer.dist.php -v",
"phpcs-dry": "./vendor/bin/php-cs-fixer fix --config=.php-cs-fixer.dist.php -v --dry-run --stop-on-violation",
Expand Down
4 changes: 2 additions & 2 deletions src/templates/head.html
View file
Expand Up @@ -23,8 +23,8 @@

<title>{{ App.pageTitle }} - eLabFTW</title>
<!-- load open vector editor -->
<link rel='stylesheet' type='text/css' href='assets/ove/main.css?v={{ v }}'>
<script defer src='assets/ove/open-vector-editor.min.js?v={{ v }}'></script>
<link rel='stylesheet' type='text/css' href='assets/ove/style.css?v={{ v }}'>
<script defer src='assets/ove/index.umd.js?v={{ v }}'></script>

<!-- see builder.js to see what gets inside these files -->
<!-- CSS -->
Expand Down
3 changes: 2 additions & 1 deletion src/ts/ove.ts
View file
Expand Up @@ -12,7 +12,7 @@ declare global {
}
}

import { anyToJson } from 'bio-parsers/umd/bio-parsers';
import { anyToJson } from '@teselagen/bio-parsers';
import { notif, reloadElement } from './misc';
import { Action, Model } from './interfaces';
import { Api } from './Apiv2.class';
Expand Down Expand Up @@ -152,6 +152,7 @@ export function displayPlasmidViewer(about: DOMStringMap): void {
onSave: function(opts = {} as any): void { // , sequenceDataToSave, editorState, onSuccessCallback could be used as parameter
savePlasmidMapAsImage(opts);
},
allowMultipleFeatureDirections: true,
PropertiesProps: {
// the list of tabs shown in the Properties panel
propertiesList: [
Expand Down
114 changes: 61 additions & 53 deletions yarn.lock
View file
Expand Up @@ -75,10 +75,10 @@
resolved "https://registry.yarnpkg.com/@deltablot/malle/-/malle-2.5.0.tgz#e2c1e042a6de49431bbd9b94bedd5cf9da4726d2"
integrity sha512-Bur6mrxLd+tUJrKRP3n+vqSnrgk6ZQWA2GicsRrrdrFWjZPAWT1WpP8n1Dw47bb8CdOQo/adNVJcsdKL35PcsQ==

"@deltablot/open-vector-editor-umd@^18.0.0":
version "18.3.2"
resolved "https://registry.yarnpkg.com/@deltablot/open-vector-editor-umd/-/open-vector-editor-umd-18.3.2.tgz#cf6b603866ca8bac6e8a3ce9c65adcc03669918b"
integrity sha512-uSbUaAvih1LDudSOTYQnXOauH0YkXQRHMWZ9diLGfy6ikZ/Re6Xp+/f16qTyv9VyngcJlVdrijsTNOy2HKh5mA==
"@deltablot/tg-oss-ove-umd@^0.3.2":
version "0.3.2"
resolved "https://registry.yarnpkg.com/@deltablot/tg-oss-ove-umd/-/tg-oss-ove-umd-0.3.2.tgz#d5f4e9b3b438584e933b3b5dfb52f43f5b37b773"
integrity sha512-U/mxDJ4rMrPSp/Y0RiedKQC+BR/5UZO6lHknDLhwOEo3PGvGet8YtFnwhDAWeEkgjEa6RRHlwmscX+VLH4baAg==

"@discoveryjs/json-ext@0.5.7", "@discoveryjs/json-ext@^0.5.0":
version "0.5.7"
Expand Down Expand Up @@ -287,6 +287,41 @@
resolved "https://registry.yarnpkg.com/@sphinxxxx/color-conversion/-/color-conversion-2.2.2.tgz#03ecc29279e3c0c832f6185a5bfa3497858ac8ca"
integrity sha512-XExJS3cLqgrmNBIP3bBw6+1oQ1ksGjFh0+oClDKFYpCCqx/hlqwWO5KO/S63fzUo67SxI9dMrF0y5T/Ey7h8Zw==

"@teselagen/bio-parsers@^0.3.2":
version "0.3.2"
resolved "https://registry.yarnpkg.com/@teselagen/bio-parsers/-/bio-parsers-0.3.2.tgz#739b55db1042e5e56481687f3b701c2fb1756910"
integrity sha512-oVsx3W9KA2B/09BbCxQaDw1GDQn2snw31jw+8wzK3PkolOPnTqy2Y2e9Q8yKBBsbdwXd0VVV1eKv3twg/gSGlQ==
dependencies:
"@gmod/gff" "^1.2.1"
"@teselagen/range-utils" "0.3.2"
"@teselagen/sequence-utils" "0.3.2"
buffer "^6.0.3"
bufferpack "^0.0.6"
color "^4.2.3"
fast-xml-parser "^4.2.5"
fflate "^0.8.0"
lodash "^4.17.21"
string_decoder "^1.3.0"
validate.io-nonnegative-integer-array "^1.0.1"

"@teselagen/range-utils@0.3.2":
version "0.3.2"
resolved "https://registry.yarnpkg.com/@teselagen/range-utils/-/range-utils-0.3.2.tgz#5cb5c34aa84b22d687eb42d5d00e1b1531c0d206"
integrity sha512-ZXQIjrfeZuTkla7JH1if2HcqOiLEAGoLG3DuCsbu0gR4wR01zr5681WkFPIAdpZ7k0+rjH58+JFltN04e8Ym7Q==
dependencies:
lodash "^4.17.21"

"@teselagen/sequence-utils@0.3.2":
version "0.3.2"
resolved "https://registry.yarnpkg.com/@teselagen/sequence-utils/-/sequence-utils-0.3.2.tgz#729ee073c5054bbd1ad0bde55eb2b5d8c814bf98"
integrity sha512-8q3AG1MSN2N1lR60Hk4Kt+ISVVfRsSEKPMrT8SPjzOP01Gc7AG3otQ4eEhcZdEHDXFpX6wMDwrFpIjNGqanQ+Q==
dependencies:
"@teselagen/range-utils" "0.3.2"
bson-objectid "^2.0.4"
escape-string-regexp "^5.0.0"
jsondiffpatch "0.4.1"
string-splice "^1.3.0"

"@trysound/sax@0.2.0":
version "0.2.0"
resolved "https://registry.yarnpkg.com/@trysound/sax/-/sax-0.2.0.tgz#cccaab758af56761eb7bf37af6f03f326dd798ad"
Expand Down Expand Up @@ -785,21 +820,6 @@ binary-extensions@^2.0.0:
resolved "https://registry.yarnpkg.com/binary-extensions/-/binary-extensions-2.2.0.tgz#75f502eeaf9ffde42fc98829645be4ea76bd9e2d"
integrity sha512-jDctJ/IVQbZoJykoeHbhXpOlNBqGNcwXJKJog42E5HDPUwQTSdjCHdihjj0DlnheQ7blbT6dHOafNAiS8ooQKA==

bio-parsers@^9.0.1:
version "9.3.6"
resolved "https://registry.yarnpkg.com/bio-parsers/-/bio-parsers-9.3.6.tgz#a0476ec23780981b0cec37a4f3ad76cce36c1a5d"
integrity sha512-/zJIMSsJgjrg/hbefbNWrrMTElhfbq/NkHkuoLjbBrkRI0cvnr6Vz4Ljf5P6Bgk9u4MOTDwN/qd3GnqOkdYsIA==
dependencies:
"@gmod/gff" "^1.2.1"
buffer "^6.0.3"
bufferpack "^0.0.6"
color "^4.2.3"
fast-xml-parser "^4.0.9"
fflate "^0.7.4"
lodash "^4.17.21"
string_decoder "^1.3.0"
validate.io-nonnegative-integer-array "^1.0.1"

boolbase@^1.0.0:
version "1.0.0"
resolved "https://registry.yarnpkg.com/boolbase/-/boolbase-1.0.0.tgz#68dff5fbe60c51eb37725ea9e3ed310dcc1e776e"
Expand Down Expand Up @@ -845,10 +865,10 @@ browserslist@^4.0.0, browserslist@^4.14.5, browserslist@^4.21.4:
node-releases "^2.0.12"
update-browserslist-db "^1.0.11"

bson-objectid@^1.1.1:
version "1.3.1"
resolved "https://registry.yarnpkg.com/bson-objectid/-/bson-objectid-1.3.1.tgz#11e4ce4c3419161fd388113781bb62c1dfbce34b"
integrity sha512-eQBNQXsisEAXlwiSy8zRNZdW2xDBJaEVkTPbodYR9hGxxtE548Qq7ilYOd8WAQ86xF7NRUdiWSQ1pa/TkKiE2A==
bson-objectid@^2.0.4:
version "2.0.4"
resolved "https://registry.yarnpkg.com/bson-objectid/-/bson-objectid-2.0.4.tgz#339211572ef97dc98f2d68eaee7b99b7be59a089"
integrity sha512-vgnKAUzcDoa+AeyYwXCoHyF2q6u/8H46dxu5JN+4/TZeq/Dlinn0K6GvxsCLb3LHUJl0m/TLiEK31kUwtgocMQ==

buffer-from@^1.0.0:
version "1.1.2"
Expand Down Expand Up @@ -1320,6 +1340,11 @@ escape-string-regexp@^4.0.0:
resolved "https://registry.yarnpkg.com/escape-string-regexp/-/escape-string-regexp-4.0.0.tgz#14ba83a5d373e3d311e5afca29cf5bfad965bf34"
integrity sha512-TtpcNJ3XAzx3Gq8sWRzJaVajRs0uVxA2YAkdb1jm2YkPz4G6egUFAyA3n5vtEIZefPk5Wa4UXbKuS5fKkJWdgA==

escape-string-regexp@^5.0.0:
version "5.0.0"
resolved "https://registry.yarnpkg.com/escape-string-regexp/-/escape-string-regexp-5.0.0.tgz#4683126b500b61762f2dbebace1806e8be31b1c8"
integrity sha512-/veY75JbMK4j1yjvuUxuVsiS/hr/4iHs9FTT6cgTexxdE0Ly/glccBAkloH/DofkjRbZU3bnoj38mOmhkZ0lHw==

eslint-scope@5.1.1, eslint-scope@^5.1.1:
version "5.1.1"
resolved "https://registry.yarnpkg.com/eslint-scope/-/eslint-scope-5.1.1.tgz#e786e59a66cb92b3f6c1fb0d508aab174848f48c"
Expand Down Expand Up @@ -1465,10 +1490,10 @@ fast-levenshtein@^2.0.6:
resolved "https://registry.yarnpkg.com/fast-levenshtein/-/fast-levenshtein-2.0.6.tgz#3d8a5c66883a16a30ca8643e851f19baa7797917"
integrity sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw==

fast-xml-parser@^4.0.9:
version "4.2.5"
resolved "https://registry.yarnpkg.com/fast-xml-parser/-/fast-xml-parser-4.2.5.tgz#a6747a09296a6cb34f2ae634019bf1738f3b421f"
integrity sha512-B9/wizE4WngqQftFPmdaMYlXoJlJOYxGQOanC77fq9k8+Z0v5dDSVh+3glErdIROP//s/jgb7ZuxKfB8nVyo0g==
fast-xml-parser@^4.2.5:
version "4.2.6"
resolved "https://registry.yarnpkg.com/fast-xml-parser/-/fast-xml-parser-4.2.6.tgz#30ad37b014c16e31eec0e01fbf90a85cedb4eacf"
integrity sha512-Xo1qV++h/Y3Ng8dphjahnYe+rGHaaNdsYOBWL9Y9GCPKpNKilJtilvWkLcI9f9X2DoKTLsZsGYAls5+JL5jfLA==
dependencies:
strnum "^1.0.5"

Expand All @@ -1484,10 +1509,10 @@ fastq@^1.6.0:
dependencies:
reusify "^1.0.4"

fflate@^0.7.4:
version "0.7.4"
resolved "https://registry.yarnpkg.com/fflate/-/fflate-0.7.4.tgz#61587e5d958fdabb5a9368a302c25363f4f69f50"
integrity sha512-5u2V/CDW15QM1XbbgS+0DfPxVB+jUKhWEKuuFuHncbk3tEEqzmoXL+2KyOFuKGqOnmdIy0/davWF1CkuwtibCw==
fflate@^0.8.0:
version "0.8.0"
resolved "https://registry.yarnpkg.com/fflate/-/fflate-0.8.0.tgz#f93ad1dcbe695a25ae378cf2386624969a7cda32"
integrity sha512-FAdS4qMuFjsJj6XHbBaZeXOgaypXp8iw/Tpyuq/w3XA41jjLHT8NPA+n7czH/DDhdncq0nAyDZmPeWXh2qmdIg==

file-entry-cache@^6.0.1:
version "6.0.1"
Expand Down Expand Up @@ -1923,10 +1948,10 @@ json-stable-stringify-without-jsonify@^1.0.1:
resolved "https://registry.yarnpkg.com/json-stable-stringify-without-jsonify/-/json-stable-stringify-without-jsonify-1.0.1.tgz#9db7b59496ad3f3cfef30a75142d2d930ad72651"
integrity sha512-Bdboy+l7tA3OGW6FjyFHWkP5LuByj1Tk33Ljyq0axyzdk9//JSi2u3fP1QSmd1KNwq6VOKYGlAu87CisVir6Pw==

jsondiffpatch@^0.3.11:
version "0.3.11"
resolved "https://registry.yarnpkg.com/jsondiffpatch/-/jsondiffpatch-0.3.11.tgz#43f9443a0d081b5f79d413fe20f302079e493201"
integrity sha512-Xi3Iygdt/BGhml6bdUFhgDki1TgOsp3hG3iiH3KtzP+CahtGcdPfKRLlnZbSw+3b1umZkhmKrqXUgUcKenyhtA==
jsondiffpatch@0.4.1:
version "0.4.1"
resolved "https://registry.yarnpkg.com/jsondiffpatch/-/jsondiffpatch-0.4.1.tgz#9fb085036767f03534ebd46dcd841df6070c5773"
integrity sha512-t0etAxTUk1w5MYdNOkZBZ8rvYYN5iL+2dHCCx/DpkFm/bW28M6y5nUS83D4XdZiHy35Fpaw6LBb+F88fHZnVCw==
dependencies:
chalk "^2.3.0"
diff-match-patch "^1.0.0"
Expand Down Expand Up @@ -2018,7 +2043,7 @@ lodash.uniq@^4.5.0:
resolved "https://registry.yarnpkg.com/lodash.uniq/-/lodash.uniq-4.5.0.tgz#d0225373aeb652adc1bc82e4945339a842754773"
integrity sha512-xfBaXQd9ryd9dlSDvnvI0lvxfLJlYAZzXomUYzLKtUeOQvOP5piqAWuGtrhWeqaXK9hhoM/iyJc5AV+XfsX3HQ==

lodash@^4.17.20, lodash@^4.17.21, lodash@^4.17.4:
lodash@^4.17.20, lodash@^4.17.21:
version "4.17.21"
resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.21.tgz#679591c564c3bffaae8454cf0b3df370c3d6911c"
integrity sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg==
Expand Down Expand Up @@ -3321,23 +3346,6 @@ vanilla-picker@^2.12.1:
dependencies:
"@sphinxxxx/color-conversion" "^2.2.2"

ve-range-utils@^2.6.3:
version "2.6.6"
resolved "https://registry.yarnpkg.com/ve-range-utils/-/ve-range-utils-2.6.6.tgz#e562cac42b24b57217d9de74177549c150ddc62a"
integrity sha512-uN3E1xuvBnVOjgLjOAcTXcxeOje1owuBExH0vrwkV226UGEQ2elp0t6xzOVDr0XPEMQo4t2qdbBWTQvdcuxGdQ==
dependencies:
lodash "^4.17.4"

ve-sequence-utils@^5.1.6:
version "5.2.16"
resolved "https://registry.yarnpkg.com/ve-sequence-utils/-/ve-sequence-utils-5.2.16.tgz#04ca10991c188fc870d251f38d555a2bfe50e879"
integrity sha512-Iav6W6EfVKrXHlkqroZpEf90y1Xitsv/Mt6fHb00a9ECgkInFZq2boKnEuQRbrlzd3jtcqppYzJmOPeb9FS8Zw==
dependencies:
bson-objectid "^1.1.1"
escape-string-regexp "^1.0.5"
jsondiffpatch "^0.3.11"
string-splice "^1.3.0"

watchpack@^2.4.0:
version "2.4.0"
resolved "https://registry.yarnpkg.com/watchpack/-/watchpack-2.4.0.tgz#fa33032374962c78113f93c7f2fb4c54c9862a5d"
Expand Down

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