diff --git a/package-lock.json b/package-lock.json index 5119ae50e..37ffca5c8 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "p3-web", - "version": "3.31.1", + "version": "3.35.5", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "p3-web", - "version": "3.31.1", + "version": "3.35.5", "hasInstallScript": true, "dependencies": { "body-parser": "^1.19.0", @@ -21,7 +21,7 @@ "cytoscape-panzoom": "^2.5.2", "dagre": "^0.8.2", "debug": "^2.6.9", - "ejs": "^2.5.7", + "ejs": "^3.1.10", "express": "^4.16.3", "express-formidable": "^1.0.0", "feedparser": "^1.1.4", @@ -1580,8 +1580,7 @@ "node_modules/balanced-match": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.2.tgz", - "integrity": "sha512-3oSeUO0TMV67hN1AmbXsK4yaqU7tjiHlbxRDZOpH0KW9+CeX4bRAaX0Anxt0tx2MrpRpWwQaPwIlISEJhYU5Pw==", - "dev": true + "integrity": 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"resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz", + "integrity": "sha512-EykJT/Q1KjTWctppgIAgfSO0tKVuZUjhgMr17kqTumMl6Afv3EISleU7qZUzoXDFTAHTDC4NOoG/ZxU3EvlMPQ==", + "engines": { + "node": ">=8" + } + }, + "node_modules/jake/node_modules/minimatch": { + "version": "3.1.2", + "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.2.tgz", + "integrity": "sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw==", + "dependencies": { + "brace-expansion": "^1.1.7" + }, + "engines": { + "node": "*" + } + }, + "node_modules/jake/node_modules/supports-color": { + "version": "7.2.0", + "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz", + "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==", + "dependencies": { + "has-flag": "^4.0.0" + }, + "engines": { + "node": ">=8" + } + }, "node_modules/jbrowse": { "resolved": 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"integrity": "sha512-w1cEuf3S+DrLCQL7ET6kz+gmlJdbq9J7yXCSjK/OZCPA+qEN1WyF4ZAf0YYJa4/shHJra2t/d/r8SV4Ji+x+8Q==", + "requires": { + "minimatch": "^5.0.1" + }, + "dependencies": { + "brace-expansion": { + "version": "2.0.1", + "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.1.tgz", + "integrity": "sha512-XnAIvQ8eM+kC6aULx6wuQiwVsnzsi9d3WxzV3FpWTGA19F621kwdbsAcFKXgKUHZWsy+mY6iL1sHTxWEFCytDA==", + "requires": { + "balanced-match": "^1.0.0" + } + }, + "minimatch": { + "version": "5.1.6", + "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-5.1.6.tgz", + "integrity": "sha512-lKwV/1brpG6mBUFHtb7NUmtABCb2WZZmm2wNiOA5hAb8VdCS4B3dtMWyvcoViccwAW/COERjXLt0zP1zXUN26g==", + "requires": { + "brace-expansion": "^2.0.1" + } + } + } + }, "filename-regex": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/filename-regex/-/filename-regex-2.0.1.tgz", @@ -15862,6 +16014,75 @@ "textextensions": "~1.0.0" } }, + "jake": { + "version": "10.8.7", + "resolved": "https://registry.npmjs.org/jake/-/jake-10.8.7.tgz", + "integrity": "sha512-ZDi3aP+fG/LchyBzUM804VjddnwfSfsdeYkwt8NcbKRvo4rFkjhs456iLFn3k2ZUWvNe4i48WACDbza8fhq2+w==", + "requires": { + "async": "^3.2.3", + "chalk": "^4.0.2", + "filelist": "^1.0.4", + "minimatch": "^3.1.2" + }, + "dependencies": { + "ansi-styles": { + "version": "4.3.0", + "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz", + "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==", + "requires": { + "color-convert": "^2.0.1" + } + }, + "async": { + "version": "3.2.5", + "resolved": "https://registry.npmjs.org/async/-/async-3.2.5.tgz", + "integrity": "sha512-baNZyqaaLhyLVKm/DlvdW051MSgO6b8eVfIezl9E5PqWxFgzLm/wQntEW4zOytVburDEr0JlALEpdOFwvErLsg==" + }, + "chalk": { + "version": "4.1.2", + "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.2.tgz", + "integrity": 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"express": "^4.16.3", "express-formidable": "^1.0.0", "feedparser": "^1.1.4", diff --git a/public/js/msa/package-lock.json b/public/js/msa/package-lock.json index a22368a14..25dfd55df 100644 --- a/public/js/msa/package-lock.json +++ b/public/js/msa/package-lock.json @@ -7646,10 +7646,16 @@ "optional": true }, "node_modules/nanoid": { - "version": "3.3.4", - "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.4.tgz", - "integrity": "sha512-MqBkQh/OHTS2egovRtLk45wEyNXwF+cokD+1YPf9u5VfJiRdAiRwB2froX5Co9Rh20xs4siNPm8naNotSD6RBw==", + "version": "3.3.7", + "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.7.tgz", + "integrity": "sha512-eSRppjcPIatRIMC1U6UngP8XFcz8MQWGQdt1MTBQ7NaAmvXDfvNxbvWV3x2y6CdEUciCSsDHDQZbhYaB8QEo2g==", "dev": true, + "funding": [ + { + "type": "github", + "url": "https://github.com/sponsors/ai" + } + ], "bin": { "nanoid": "bin/nanoid.cjs" }, @@ -8410,9 +8416,9 @@ } }, "node_modules/postcss": { - "version": "8.4.17", - "resolved": 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"sha512-R0XvVJ9WusLiqTCEiGCmICCMplcCkIwwR11mOSD9CR5u+IXYdiseeEuXCVAjS54zqwkLcPNnmU4OeJ6tUrWhDw==", + "version": "1.2.0", + "resolved": "https://registry.npmjs.org/source-map-js/-/source-map-js-1.2.0.tgz", + "integrity": "sha512-itJW8lvSA0TXEphiRoawsCksnlf8SyvmFzIhltqAHluXd88pkCd+cXJVHTDwdCr0IzwptSm035IHQktUu1QUMg==", "dev": true }, "source-map-resolve": { diff --git a/public/js/p3/widget/app/FastqUtil.js b/public/js/p3/widget/app/FastqUtil.js index 8875f0684..93e51e4a4 100644 --- a/public/js/p3/widget/app/FastqUtil.js +++ b/public/js/p3/widget/app/FastqUtil.js @@ -107,15 +107,11 @@ define([ var filter = { id: 'paired_filter', condition: 'paired_filter', label: 'Paired_Filter', icon: this.getConditionIcon() }; - var scrub = { - id: 'scrub_human', condition: 'scrub_human', label: 'Scrub_Human', icon: this.getConditionIcon() - }; // temporary until contrasts table added this.updateConditionStore(trim, false); this.updateConditionStore(filter, false); this.updateConditionStore(fastqc, false); this.updateConditionStore(align, false); - this.updateConditionStore(scrub, false); this.action_select.labelFunc = this.showConditionLabels; // this.block_condition.show(); // this.read1.set('value',"/" + window.App.user.id +"/home/");