diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 53f2ec315d..f73a02cd78 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -4,8 +4,79 @@ The Narrative Interface allows users to craft KBase Narratives using a combinati This is built on the Jupyter Notebook v6.5.7 and IPython 8.28.x (more notes will follow). +## Version 5.5.0 +- UIP-52 - fix integration tests +- PTV-1913 - force backup authentication cookie to reset on load +- URO-362 - add text for DOI requests +- URO-366 - users should be able to paste usernames into the share search field +- URO-352 - add support for DTS manifest.json importer files for bulk import +- adjust the readonly / writeable display toggle icon + +- Python dependencies updated to the following versions: + - coverage: 7.10.1 + - pytest: 8.4.1 + - pytest-cov: 6.2.1 + - pytest-recording: 0.13.4 + - ruff: 0.12.7 + - beautifulsoup4: 4.13.4 + - certifi: 2025.7.14 + - cryptography: 45.0.5 + - jsonschema: 4.25.0 + - markdown: 3.8.2 + - pillow: 11.3.0 + - plotly: 6.2.0 + - pycurl: 7.45.6 + - pygments: 2.19.2 + - pyopenssl: 25.1.0 + - rsa: 4.9.1 + - setuptools: 80.9.0 + - sympy: 1.14.0 + - ipywidgets: 8.1.7 + - jinja2: 3.1.6 + - pandas: 2.3.1 + - pymongo: 4.13.2 + - requests: 2.32.4 + - statsmodels: 0.14.5 + - tornado: 6.5.1 + +- Javascript dependencies updated to the following versions: + - dompurify: 3.2.6 + - follow-redirects: 1.15.11 + - plotly.js-dist-min: 3.1.0 + - @babel/traverse: 7.28.0 + - @eslint/eslintrc: 3.3.1 + - @eslint/js: 9.33.0 + - @wdio/browserstack-service: 9.19.1 + - @wdio/cli: 9.19.1 + - @wdio/local-runner: 9.19.1 + - @wdio/mocha-framework: 9.19.1 + - @wdio/spec-reporter: 9.19.1 + - autoprefixer: 10.4.21 + - axios: 1.11.0 + - chromedriver: 139.0.0 + - commander: 14.0.0 + - cssnano: 7.1.0 + - eslint: 9.33.0 + - eslint-config-prettier: 10.1.8 + - glob: 11.0.3 + - globals: 16.3.0 + - jquery-migrate: 3.5.2 + - lint-staged: 16.1.5 + - postcss: 8.5.6 + - postcss-cli: 11.0.1 + - prettier: 3.6.2 + - puppeteer: 24.16.1 + - sass: 1.90.0 + - selenium-standalone: 10.0.2 + - selenium-webdriver: 4.35.0 + - stylelint: 16.23.1 + - stylelint-config-recommended: 17.0.0 + - stylelint-config-standard: 39.0.0 + - terser: 5.43.1 + + ## Version 5.4.3 -URO-363 - add note to the sharing panel to contact KBase about DOIs +- URO-363 - add note to the sharing panel to contact KBase about DOIs - Python `requirements-general.txt` and `requirements.txt` merged into a single file so that all runtime deps are installed in one place. diff --git a/kbase-extension/kbase_templates/narrative_header.html b/kbase-extension/kbase_templates/narrative_header.html index 7c66e1f39c..9362487ca8 100644 --- a/kbase-extension/kbase_templates/narrative_header.html +++ b/kbase-extension/kbase_templates/narrative_header.html @@ -27,7 +27,7 @@
Created by: - +
diff --git a/kbase-extension/static/kbase/config/staging_upload.json b/kbase-extension/static/kbase/config/staging_upload.json index 354a633f17..487795bb38 100644 --- a/kbase-extension/static/kbase/config/staging_upload.json +++ b/kbase-extension/static/kbase/config/staging_upload.json @@ -52,6 +52,10 @@ "id": "import_specification", "name": "Import Specification" }, + { + "id": "dts_manifest", + "name": "Data Transfer Service Manifest" + }, { "id": "decompress", "name": "Decompress/Unpack" @@ -62,6 +66,7 @@ "fastq_reads_interleaved", "fastq_reads_noninterleaved", "gff_metagenome", + "gff_genome", "assembly", "genbank_genome" ], @@ -69,6 +74,7 @@ "web_upload": { "app_id": "kb_uploadmethods/upload_web_file" }, + "dts_manifest": { }, "import_specification": { }, "test_fastq_reads": { "app_id": "NarrativeTest/example_reads_upload", diff --git a/kbase-extension/static/kbase/js/api/StagingServiceClient.js b/kbase-extension/static/kbase/js/api/StagingServiceClient.js index 1d9fbfe17a..7872a131af 100644 --- a/kbase-extension/static/kbase/js/api/StagingServiceClient.js +++ b/kbase-extension/static/kbase/js/api/StagingServiceClient.js @@ -21,7 +21,10 @@ define(['RestAPIClient'], (RestAPIClient) => { rename: { method: 'post', path: 'rename/${path}' }, decompress: { method: 'patch', path: 'decompress/${path}' }, importer_mappings: { method: 'get', path: 'importer_mappings/?${file_list}' }, - bulkSpecification: { method: 'get', path: 'bulk_specification/?files=${files}' }, + bulkSpecification: { + method: 'get', + path: 'bulk_specification/?files=${files}&${flag}', + }, write_bulk_specification: { method: 'post', path: 'write_bulk_specification/' }, }, }); diff --git a/kbase-extension/static/kbase/js/kbaseNarrative.js b/kbase-extension/static/kbase/js/kbaseNarrative.js index 313221df6d..4eca43de89 100644 --- a/kbase-extension/static/kbase/js/kbaseNarrative.js +++ b/kbase-extension/static/kbase/js/kbaseNarrative.js @@ -360,6 +360,12 @@ define([ shareWidget.refresh(); } shareDialog.show(); + + // After a few seconds, focus the share field. + setTimeout(() => { + $('.select2-search__field').focus(); + }, 2000); + }); }; diff --git a/kbase-extension/static/kbase/js/widgets/narrative_core/kbaseNarrativeWorkspace.js b/kbase-extension/static/kbase/js/widgets/narrative_core/kbaseNarrativeWorkspace.js index 2b85c74d39..32c716b3aa 100644 --- a/kbase-extension/static/kbase/js/widgets/narrative_core/kbaseNarrativeWorkspace.js +++ b/kbase-extension/static/kbase/js/widgets/narrative_core/kbaseNarrativeWorkspace.js @@ -358,7 +358,7 @@ define([ // mechanism should be disabled (and the button hidden as well.) const icon = $('#kb-view-mode span'); icon.toggleClass('fa-eye', this.uiMode === 'view'); - icon.toggleClass('fa-pencil', this.uiMode === 'edit'); + icon.toggleClass('fa-eye-slash', this.uiMode === 'edit'); Jupyter.narrative.readonly = this.uiMode === 'view'; // Warning, do not look for the code for this ... it will burn your diff --git a/kbase-extension/static/kbase/js/widgets/narrative_core/upload/importSetup.js b/kbase-extension/static/kbase/js/widgets/narrative_core/upload/importSetup.js index aa2772c1c7..d93317c7d5 100644 --- a/kbase-extension/static/kbase/js/widgets/narrative_core/upload/importSetup.js +++ b/kbase-extension/static/kbase/js/widgets/narrative_core/upload/importSetup.js @@ -14,7 +14,7 @@ define([ /** * This makes a call to the Staging Service to fetch information from bulk specification files. - * This then gets processed through `processSpreadsheetFileData` before being returned. + * This then gets processed through `processBulkImportSpecData` before being returned. * @param {Array[string]} files - array of file path names to treat as import specifications * @returns Promise that resolves into information that can be used to open a bulk import cell. * This has the format: @@ -32,45 +32,18 @@ define([ * } * } * @throws Errors.ImportSetupError if an error occurs in either data fetching from the Staging - * Service, or in the initial parsing done by `processSpreadsheetFileData` + * Service, or in the initial parsing done by `processBulkImportSpecData` */ - function getSpreadsheetFileInfo(files) { - if (!files || files.length === 0) { - return Promise.resolve({}); - } - const stagingUrl = Config.url('staging_api_url'); - const stagingServiceClient = new StagingServiceClient({ - root: stagingUrl, - token: Runtime.make().authToken(), - }); - - // This is overkill, but a little future proofing. We have to make a GET call with an - // undetermined number of files, so if there are more than we can allow in the URL, gotta break that - // into multiple calls. + function getBulkImportFileInfo(xsvFiles, dtsFiles) { + // dtsFiles gets wiped out by the spec requester. + const dtsFileList = [...dtsFiles]; - // a little cheating here to figure out the length allowance. Maybe it should be in the client? - const maxQueryLength = 2048 - stagingUrl.length - '/bulk_specification/?files='.length; - const bulkSpecProms = []; - - while (files.length) { - const fileBatch = []; - let remainingLength = maxQueryLength; - while ( - files.length && - remainingLength - files[0].length - 1 >= 0 // -1 is for the comma - ) { - const nextFile = files.shift(); - fileBatch.push(nextFile); - remainingLength -= nextFile.length + 1; - } - bulkSpecProms.push( - stagingServiceClient.bulkSpecification({ - files: encodeURIComponent(fileBatch.join(',')), - }) - ); - } + // noting here that these are effectively jQuery promises, so we can't just + // make this an async/await function, but need to wrap with Promise.all. + const xsvFileProms = requestBulkImportSpec(xsvFiles); + const dtsFileProms = requestBulkImportSpec(dtsFiles, 'dts'); - return Promise.all(bulkSpecProms) + return Promise.all([...xsvFileProms, ...dtsFileProms]) .then((result) => { // join results of all calls together const errors = []; @@ -92,6 +65,13 @@ define([ } else { allCalls.types[dataType] = callResult.types[dataType]; allCalls.files[dataType] = callResult.files[dataType]; + // These files have the username in there. We don't want that. + // So need to compare after stripping them out. + const fileName = allCalls.files[dataType].file; + const pathIdx = fileName.indexOf('/'); + const strippedFile = + pathIdx !== -1 ? fileName.substring(pathIdx + 1) : fileName; + allCalls.files[dataType].isDts = dtsFileList.includes(strippedFile); } }); return allCalls; @@ -123,10 +103,54 @@ define([ ); }) .then((result) => { - return processSpreadsheetFileData(result); + return processBulkImportSpecData(result); }); } + function requestBulkImportSpec(files, flag = '') { + /** + * This returns an array of jQuery Promises, which is what + * the staging service client uses, so it can't be (easily) + * cast into async/await. + */ + if (!files || files.length === 0) { + return []; + } + const stagingUrl = Config.url('staging_api_url'); + const stagingServiceClient = new StagingServiceClient({ + root: stagingUrl, + token: Runtime.make().authToken(), + }); + // This is overkill, but a little future proofing. We have to make a GET call with an + // undetermined number of files, so if there are more than we can allow in the URL, gotta break that + // into multiple calls. + + // a little cheating here to figure out the length allowance. Maybe it should be in the client? + const path = '/bulk_specification/?' + flag + 'files=&'; + const maxQueryLength = 2048 - stagingUrl.length - path.length; + const bulkSpecProms = []; + + while (files.length) { + const fileBatch = []; + let remainingLength = maxQueryLength; + while ( + files.length && + remainingLength - files[0].length - 1 >= 0 // -1 is for the comma + ) { + const nextFile = files.shift(); + fileBatch.push(nextFile); + remainingLength -= nextFile.length + 1; + } + bulkSpecProms.push( + stagingServiceClient.bulkSpecification({ + files: encodeURIComponent(fileBatch.join(',')), + flag, + }) + ); + } + return bulkSpecProms; + } + /** * This function does some preprocessing on the spreadsheet file data. Specifically, * those parameters that are static dropdowns or checkboxes need to translate their input @@ -153,10 +177,14 @@ define([ * TODO: also return the fetched app specs to avoid fetching them twice? * @param {Object} data */ - async function processSpreadsheetFileData(data) { + async function processBulkImportSpecData(data) { // map from given datatype to app id. // if any data types are missing, record that // if any data types are not bulk import ready, record that, too. + + if (Object.keys(data.types).length === 0 && Object.keys(data.files).length === 0) { + return data; + } const appIdToType = {}; const dataTypeErrors = []; Object.keys(data.types).forEach((dataType) => { @@ -253,19 +281,58 @@ define([ {} ); + /* + * Map from datatype to all file parameters. These are found (as in the bulk import cell) + * by looking for those params that are dynamic dropdowns that look at ftp_staging. + */ + const typeToFileParams = Object.entries(appIdToType).reduce( + (_typeToFileParams, [appId, dataType]) => { + const spec = appIdToSpec[appId].appSpec; + const specParams = spec.parameters.filter((param) => { + return ( + param.dynamic_dropdown_options && + param.dynamic_dropdown_options.data_source === 'ftp_staging' + ); + }); + _typeToFileParams[dataType] = specParams.map((param) => param.id); + return _typeToFileParams; + }, + {} + ); + /* * Now, update all parameters in place. * For each set of parameters in each type, look at the translated spec parameters. * If any of those are in the given parameter set, do the translation. + * + * If the datatype comes from a DTS manifest file, adjust the file paths to always be + * relative to the subdirectory of that file. */ Object.values(appIdToType).forEach((dataType) => { const specParams = typeToAlteredParams[dataType]; + const fileParams = typeToFileParams[dataType]; + let filePrefix = ''; + if (data.files[dataType].isDts) { + const file = data.files[dataType].file; + const parts = file.split('/'); + if (parts.length > 2) { + filePrefix = parts.slice(1, -1).join('/') + '/'; + } + } + data.types[dataType] = data.types[dataType].map((parameterSet) => { Object.keys(parameterSet).forEach((paramId) => { const value = parameterSet[paramId]; if (specParams[paramId] && value in specParams[paramId]) { parameterSet[paramId] = specParams[paramId][value]; } + if ( + data.files[dataType].isDts && + fileParams.includes(paramId) && + parameterSet[paramId] !== null + ) { + parameterSet[paramId] = filePrefix + parameterSet[paramId]; + } }); return parameterSet; }); @@ -390,6 +457,7 @@ define([ const bulkFiles = {}; const singleFiles = []; const xsvFiles = []; + const dtsFiles = []; fileInfo.forEach((file) => { const importType = file.type; if (bulkIds.has(importType)) { @@ -404,11 +472,13 @@ define([ bulkFiles[importType].files.push(file.name); } else if (importType === 'import_specification') { xsvFiles.push(file.name); + } else if (importType === 'dts_manifest') { + dtsFiles.push(file.name); } else { singleFiles.push(file); } }); - return getSpreadsheetFileInfo(xsvFiles) + return getBulkImportFileInfo(xsvFiles, dtsFiles) .then((result) => { if (result.types) { Object.keys(result.types).forEach((dataType) => { diff --git a/package-lock.json b/package-lock.json index 440255c5e9..17deff69bd 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "kbase-narrative-core", - "version": "5.4.3", + "version": "5.5.0", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "kbase-narrative-core", - "version": "5.4.3", + "version": "5.5.0", "dependencies": { "bluebird": "3.7.2", "bootstrap": "3.4.1", @@ -18,10 +18,10 @@ "datatables.net-bs": "1.13.4", "datatables.net-buttons": "2.3.6", "datatables.net-buttons-bs": "2.4.1", - "dompurify": "3.2.4", + "dompurify": "3.2.6", "dropzone": "5.9.3", "file-saver": "1.3.4", - "follow-redirects": "1.15.9", + "follow-redirects": "1.15.11", "font-awesome": "4.7.0", "google-code-prettify": "1.0.5", "handlebars": "^4.7.8", @@ -35,7 +35,7 @@ "kbase-service-clients-js": "https://github.com/kbase/kbase-service-clients-js/archive/refs/tags/v3.3.4.tar.gz", "kbase-ui-plugin-catalog": "https://github.com/kbase/kbase-ui-plugin-catalog/archive/refs/tags/v2.2.5.tar.gz", "numeral": "2.0.6", - "plotly.js-dist-min": "2.35.3", + "plotly.js-dist-min": "3.1.0", "pure-uuid": "1.8.1", "require-css": "0.1.10", "require-yaml": "github:m90/require-yaml", @@ -50,29 +50,29 @@ "word-wrap": "1.2.5" }, "devDependencies": { - "@babel/traverse": "^7.26.9", - "@eslint/eslintrc": "^3.3.0", - "@eslint/js": "^9.21.0", + "@babel/traverse": "7.28.0", + "@eslint/eslintrc": "3.3.1", + "@eslint/js": "9.33.0", "@lodder/grunt-postcss": "^3.1.1", - "@wdio/browserstack-service": "^9.10.1", - "@wdio/cli": "^9.10.1", + "@wdio/browserstack-service": "9.19.1", + "@wdio/cli": "9.19.1", "@wdio/local-runner": "^9.10.1", - "@wdio/mocha-framework": "^9.10.1", + "@wdio/mocha-framework": "9.19.1", "@wdio/selenium-standalone-service": "^8.15.0", - "@wdio/spec-reporter": "^9.10.1", - "autoprefixer": "^10.4.20", - "axios": "^1.8.1", + "@wdio/spec-reporter": "9.19.1", + "autoprefixer": "10.4.21", + "axios": "1.11.0", "bootstrap-sass": "^3.4.3", - "chrome-launcher": "^1.1.2", - "chromedriver": "^133.0.3", - "commander": "^13.1.0", - "cssnano": "^7.0.6", + "chrome-launcher": "^1.2.0", + "chromedriver": "139.0.0", + "commander": "14.0.0", + "cssnano": "7.1.0", "ejs": "^3.1.10", - "eslint": "^9.21.0", - "eslint-config-prettier": "^10.0.2", + "eslint": "9.33.0", + "eslint-config-prettier": "10.1.8", "expect-webdriverio": "^5.0.5", - "glob": "^11.0.1", - "globals": "^16.0.0", + "glob": "11.0.3", + "globals": "16.3.0", "grunt": "^1.6.1", "grunt-cli": "^1.5.0", "grunt-contrib-concat": "^2.1.0", @@ -83,7 +83,7 @@ "grunt-stylelint": "^0.20.1", "husky": "^9.1.7", "jasmine-ajax": "^4.0.0", - "jasmine-core": "^5.6.0", + "jasmine-core": "^5.8.0", "jasmine-jquery": "^2.1.1", "jquery-migrate": "^1.4.1", "karma": "^6.4.4", @@ -98,29 +98,29 @@ "karma-mocha-reporter": "^2.2.5", "karma-requirejs": "^1.1.0", "karma-safari-launcher": "^1.0.0", - "lint-staged": "^15.4.3", + "lint-staged": "16.1.5", "load-grunt-tasks": "^5.1.0", "msw": "^0.40.2", - "postcss": "^8.5.3", - "postcss-cli": "^11.0.0", + "postcss": "8.5.6", + "postcss-cli": "11.0.1", "postcss-discard-comments": "^7.0.0", "postcss-scss": "^4.0.9", "postcss-unprefix": "^2.1.4", - "prettier": "^3.5.2", - "puppeteer": "^24.3.0", + "prettier": "3.6.2", + "puppeteer": "24.16.1", "requirejs": "^2.3.7", - "sass": "^1.85.1", - "selenium-standalone": "^10.0.1", - "selenium-webdriver": "^4.29.0", + "sass": "1.90.0", + "selenium-standalone": "10.0.2", + "selenium-webdriver": "4.35.0", "string-template": "^1.0.0", "string.prototype.endswith": "^1.0.2", "string.prototype.startswith": "^1.0.1", - "stylelint": "^16.15.0", + "stylelint": "16.23.1", "stylelint-color-format": "^1.1.0", - "stylelint-config-recommended": "^15.0.0", + "stylelint-config-recommended": "17.0.0", "stylelint-config-sass-guidelines": "^12.0.0", - "stylelint-config-standard": "^37.0.0", - "terser": "^5.39.0", + "stylelint-config-standard": "39.0.0", + "terser": "5.43.1", "webdriverio": "^9.0.0" }, "engines": { @@ -141,13 +141,13 @@ } }, "node_modules/@babel/code-frame": { - "version": "7.26.2", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.26.2.tgz", - "integrity": "sha512-RJlIHRueQgwWitWgF8OdFYGZX328Ax5BCemNGlqHfplnRT9ESi8JkFlvaVYbS+UubVY6dpv87Fs2u5M29iNFVQ==", + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.27.1.tgz", + "integrity": "sha512-cjQ7ZlQ0Mv3b47hABuTevyTuYN4i+loJKGeV9flcCgIK37cCXRh+L1bd3iBHlynerhQ7BhCkn2BPbQUL+rGqFg==", "dependencies": { - "@babel/helper-validator-identifier": "^7.25.9", + "@babel/helper-validator-identifier": "^7.27.1", "js-tokens": "^4.0.0", - "picocolors": "^1.0.0" + "picocolors": "^1.1.1" }, "engines": { "node": ">=6.9.0" @@ -202,15 +202,15 @@ } }, "node_modules/@babel/generator": { - "version": "7.26.9", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.26.9.tgz", - "integrity": "sha512-kEWdzjOAUMW4hAyrzJ0ZaTOu9OmpyDIQicIh0zg0EEcEkYXZb2TjtBhnHi2ViX7PKwZqF4xwqfAm299/QMP3lg==", + "version": "7.28.0", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.28.0.tgz", + "integrity": "sha512-lJjzvrbEeWrhB4P3QBsH7tey117PjLZnDbLiQEKjQ/fNJTjuq4HSqgFA+UNSwZT8D7dxxbnuSBMsa1lrWzKlQg==", "dev": true, "dependencies": { - "@babel/parser": "^7.26.9", - "@babel/types": "^7.26.9", - "@jridgewell/gen-mapping": "^0.3.5", - "@jridgewell/trace-mapping": "^0.3.25", + "@babel/parser": "^7.28.0", + "@babel/types": "^7.28.0", + "@jridgewell/gen-mapping": "^0.3.12", + "@jridgewell/trace-mapping": "^0.3.28", "jsesc": 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"node_modules/tinyglobby/node_modules/fdir": { + "version": "6.4.6", + "resolved": "https://registry.npmjs.org/fdir/-/fdir-6.4.6.tgz", + "integrity": "sha512-hiFoqpyZcfNm1yc4u8oWCf9A2c4D3QjCrks3zmoVKVxpQRzmPNar1hUJcBG2RQHvEVGDN+Jm81ZheVLAQMK6+w==", + "dev": true, + "peerDependencies": { + "picomatch": "^3 || ^4" + }, + "peerDependenciesMeta": { + "picomatch": { + "optional": true + } + } + }, + "node_modules/tinyglobby/node_modules/picomatch": { + "version": "4.0.3", + "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.3.tgz", + "integrity": "sha512-5gTmgEY/sqK6gFXLIsQNH19lWb4ebPDLA4SdLP7dsWkIXHWlG66oPuVvXSGFPppYZz8ZDZq0dYYrbHfBCVUb1Q==", + "dev": true, + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/sponsors/jonschlinkert" + } + }, "node_modules/tinyrainbow": { "version": "1.2.0", "resolved": "https://registry.npmjs.org/tinyrainbow/-/tinyrainbow-1.2.0.tgz", @@ -20892,9 +21916,9 @@ "dev": true }, "node_modules/undici": { - "version": 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true, "funding": [ { @@ -20972,8 +21996,8 @@ } ], "dependencies": { - "escalade": "^3.1.2", - "picocolors": "^1.0.1" + "escalade": "^3.2.0", + "picocolors": "^1.1.1" }, "bin": { "update-browserslist-db": "cli.js" @@ -21127,16 +22151,16 @@ } }, "node_modules/uuid": { - "version": "10.0.0", - "resolved": "https://registry.npmjs.org/uuid/-/uuid-10.0.0.tgz", - "integrity": "sha512-8XkAphELsDnEGrDxUOHB3RGvXz6TeuYSGEZBOjtTtPm2lwhGBjLgOzLHB63IUWfBpNucQjND6d3AOudO+H3RWQ==", + "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==", "dev": true, "funding": [ "https://github.com/sponsors/broofa", "https://github.com/sponsors/ctavan" ], "bin": { - "uuid": "dist/bin/uuid" + "uuid": "dist/esm/bin/uuid" } }, "node_modules/v8-compile-cache": { @@ -21772,9 +22796,9 @@ } }, "node_modules/ws": { - "version": "8.18.1", - "resolved": 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diff --git a/package.json b/package.json index f4ae47ff94..e827002f1a 100644 --- a/package.json +++ b/package.json @@ -1,36 +1,36 @@ { "name": "kbase-narrative-core", "description": "Core components for the KBase Narrative Interface", - "version": "5.4.3", + "version": "5.5.0", "private": true, "repository": "github.com/kbase/narrative", "engines": { "node": ">=20" }, "devDependencies": { - "@babel/traverse": "^7.26.9", - "@eslint/eslintrc": "^3.3.0", - "@eslint/js": "^9.21.0", + "@babel/traverse": "7.28.0", + "@eslint/eslintrc": "3.3.1", + "@eslint/js": "9.33.0", "@lodder/grunt-postcss": "^3.1.1", - "@wdio/browserstack-service": "^9.10.1", - "@wdio/cli": "^9.10.1", + "@wdio/browserstack-service": "9.19.1", + "@wdio/cli": "9.19.1", "@wdio/local-runner": "^9.10.1", - "@wdio/mocha-framework": "^9.10.1", + "@wdio/mocha-framework": "9.19.1", "@wdio/selenium-standalone-service": "^8.15.0", - "@wdio/spec-reporter": "^9.10.1", - "autoprefixer": "^10.4.20", - "axios": "^1.8.1", + "@wdio/spec-reporter": "9.19.1", + "autoprefixer": "10.4.21", + "axios": "1.11.0", "bootstrap-sass": "^3.4.3", - "chrome-launcher": "^1.1.2", - "chromedriver": "^133.0.3", - "commander": "^13.1.0", - "cssnano": "^7.0.6", + "chrome-launcher": "^1.2.0", + "chromedriver": "139.0.0", + "commander": "14.0.0", + "cssnano": "7.1.0", "ejs": "^3.1.10", - "eslint": "^9.21.0", - "eslint-config-prettier": "^10.0.2", + "eslint": "9.33.0", + "eslint-config-prettier": "10.1.8", "expect-webdriverio": "^5.0.5", - "glob": "^11.0.1", - "globals": "^16.0.0", + "glob": "11.0.3", + "globals": "16.3.0", "grunt": "^1.6.1", "grunt-cli": "^1.5.0", "grunt-contrib-concat": "^2.1.0", @@ -41,7 +41,7 @@ "grunt-stylelint": "^0.20.1", "husky": "^9.1.7", "jasmine-ajax": "^4.0.0", - "jasmine-core": "^5.6.0", + "jasmine-core": "^5.8.0", "jasmine-jquery": "^2.1.1", "jquery-migrate": "^1.4.1", "karma": "^6.4.4", @@ -56,29 +56,29 @@ "karma-mocha-reporter": "^2.2.5", "karma-requirejs": "^1.1.0", "karma-safari-launcher": "^1.0.0", - "lint-staged": "^15.4.3", + "lint-staged": "16.1.5", "load-grunt-tasks": "^5.1.0", "msw": "^0.40.2", - "postcss": "^8.5.3", - "postcss-cli": "^11.0.0", + "postcss": "8.5.6", + "postcss-cli": "11.0.1", "postcss-discard-comments": "^7.0.0", "postcss-scss": "^4.0.9", "postcss-unprefix": "^2.1.4", - "prettier": "^3.5.2", - "puppeteer": "^24.3.0", + "prettier": "3.6.2", + "puppeteer": "24.16.1", "requirejs": "^2.3.7", - "sass": "^1.85.1", - "selenium-standalone": "^10.0.1", - "selenium-webdriver": "^4.29.0", + "sass": "1.90.0", + "selenium-standalone": "10.0.2", + "selenium-webdriver": "4.35.0", "string-template": "^1.0.0", "string.prototype.endswith": "^1.0.2", "string.prototype.startswith": "^1.0.1", - "stylelint": "^16.15.0", + "stylelint": "16.23.1", "stylelint-color-format": "^1.1.0", - "stylelint-config-recommended": "^15.0.0", + "stylelint-config-recommended": "17.0.0", "stylelint-config-sass-guidelines": "^12.0.0", - "stylelint-config-standard": "^37.0.0", - "terser": "^5.39.0", + "stylelint-config-standard": "39.0.0", + "terser": "5.43.1", "webdriverio": "^9.0.0" }, "dependencies": { @@ -92,10 +92,10 @@ "datatables.net-bs": "1.13.4", "datatables.net-buttons": "2.3.6", "datatables.net-buttons-bs": "2.4.1", - "dompurify": "3.2.4", + "dompurify": "3.2.6", "dropzone": "5.9.3", "file-saver": "1.3.4", - "follow-redirects": "1.15.9", + "follow-redirects": "1.15.11", "font-awesome": "4.7.0", "google-code-prettify": "1.0.5", "handlebars": "^4.7.8", @@ -109,7 +109,7 @@ "kbase-service-clients-js": "https://github.com/kbase/kbase-service-clients-js/archive/refs/tags/v3.3.4.tar.gz", "kbase-ui-plugin-catalog": "https://github.com/kbase/kbase-ui-plugin-catalog/archive/refs/tags/v2.2.5.tar.gz", "numeral": "2.0.6", - "plotly.js-dist-min": "2.35.3", + "plotly.js-dist-min": "3.1.0", "pure-uuid": "1.8.1", "require-css": "0.1.10", "require-yaml": "github:m90/require-yaml", diff --git a/src/biokbase/narrative/__init__.py b/src/biokbase/narrative/__init__.py index a14bfe299f..560d2ae107 100644 --- a/src/biokbase/narrative/__init__.py +++ b/src/biokbase/narrative/__init__.py @@ -1,5 +1,5 @@ __all__ = ["magics", "common", "handlers", "contents", "services", "widgetmanager"] -__version__ = "5.4.3" +__version__ = "5.5.0" def version(): diff --git a/src/config.json b/src/config.json index ef77531c66..d164d0b76b 100644 --- a/src/config.json +++ b/src/config.json @@ -168,8 +168,8 @@ "google_analytics_id": "G-GW0WBP8HJS" }, "dev_mode": true, - "git_commit_hash": "3f9ee0617", - "git_commit_time": "Thu Nov 19 08:33:21 2020 -0800", + "git_commit_hash": "27fda32ec", + "git_commit_time": "Tue Sep 13 16:03:25 2022 -0400", "loading_gif": "/narrative/static/kbase/images/ajax-loader.gif", "name": "KBase Narrative", "next": { @@ -202,7 +202,7 @@ "protein_info": "", "provenance_view": "/#objgraphview", "reset_password": "https://gologin.kbase.us/ResetPassword", - "sample_service": "https://next.kbase.us/services/sampleservice", + "sample_service": "https://kbase.us/services/sampleservice", "search": "https://kbase.us/services/search/getResults", "searchapi2": "https://next.kbase.us/services/searchapi2/rpc", "service_wizard": "https://next.kbase.us/services/service_wizard", @@ -231,7 +231,7 @@ "cdn": "https://kbase.us/cdn/files", "compound_img_url": "http://minedatabase.mcs.anl.gov/compound_images/ModelSEED/", "data_panel_sources": "/data_source_config.json", - "execution_engine2": "https://kbase.us/services/ee2-nr", + "execution_engine2": "https://kbase.us/services/ee2", "fba": "https://kbase.us/services/KBaseFBAModeling/", "ftp_api_root": "/data/bulk", "ftp_api_url": "https://kbase.us/services/kb-ftp-api/v0", @@ -374,7 +374,7 @@ "uploader": "", "user_and_job_state": "https://narrative-refactor.kbase.us/services/userandjobstate", "user_profile": "https://narrative-refactor.kbase.us/services/user_profile/rpc", - "version_check": "{{ .Env.VERSION_CHECK }}", + "version_check": "/narrative_version", "workspace": "https://narrative-refactor.kbase.us/services/ws", "ws_browser": "https://narrative-refactor.kbase.us/#ws", "google_analytics_id": "G-GSSGYX2WB8" @@ -391,5 +391,5 @@ "globus_upload_url": "https://app.globus.org/file-manager?destination_id=c3c0a65f-5827-4834-b6c9-388b0b19953a" }, "use_local_widgets": true, - "version": "5.4.3" + "version": "5.5.0" } diff --git a/src/config.json.templ b/src/config.json.templ index edf5d6964c..c69106ffaf 100644 --- a/src/config.json.templ +++ b/src/config.json.templ @@ -391,5 +391,5 @@ "globus_upload_url": "https://app.globus.org/file-manager?destination_id=c3c0a65f-5827-4834-b6c9-388b0b19953a" }, "use_local_widgets": true, - "version": "5.4.3" + "version": "5.5.0" } diff --git a/src/requirements-dev.txt b/src/requirements-dev.txt index eaf0f3a922..1a9986c3f0 100644 --- a/src/requirements-dev.txt +++ b/src/requirements-dev.txt @@ -1,7 +1,7 @@ -coverage==7.6.12 -pytest==8.3.4 -pytest-cov==6.0.0 -pytest-recording==0.13.2 +coverage==7.10.1 +pytest==8.4.1 +pytest-cov==6.2.1 +pytest-recording==0.13.4 requests-mock==1.12.1 -ruff==0.9.9 +ruff==0.12.7 vcrpy==7.0.0 diff --git a/src/requirements.txt b/src/requirements.txt index f57d4fbb42..7fc7d9ddad 100644 --- a/src/requirements.txt +++ b/src/requirements.txt @@ -1,52 +1,52 @@ appdirs==1.4.4 -beautifulsoup4==4.13.3 +beautifulsoup4==4.13.4 biopython==1.85 bokeh==3.6.2 -certifi==2025.1.31 +certifi==2025.7.14 chardet==5.2.0 chart_studio==1.1.0 -cryptography==44.0.1 +cryptography==45.0.5 decorator==5.2.1 ete3==3.1.3 html5lib==1.1 idna==3.10 -jsonschema==4.23.0 -markdown==3.7 +jsonschema==4.25.0 +markdown==3.8.2 markupsafe==3.0.2 ndg-httpsclient==0.5.1 networkx==3.4.2 numpy==2.2.3 pexpect==4.9.0 pickleshare==0.7.5 -pillow==11.1.0 -plotly==5.24.1 +pillow==11.3.0 +plotly==6.2.0 pyasn1==0.6.1 -pycurl==7.45.4 -pygments==2.19.1 -pyopenssl==25.0.0 +pycurl==7.45.6 +pygments==2.19.2 +pyopenssl==25.1.0 python-daemon==3.1.2 python-dateutil==2.9.0.post0 qgrid==1.3.1 -rsa==4.9 +rsa==4.9.1 scipy==1.15.2 seaborn==0.13.2 -setuptools==75.8.2 +setuptools==80.9.0 six==1.17.0 -sympy==1.13.3 +sympy==1.14.0 terminado==0.18.1 wordcloud==1.9.4 # Narrative/Jupyter requirements clustergrammer2==0.18.0 ipython==8.33.0 -ipywidgets==8.1.5 -jinja2==3.1.5 +ipywidgets==8.1.7 +jinja2==3.1.6 # N.b. notebook version must stay under 7 notebook==6.5.7 -pandas==2.2.3 -pymongo==4.11.1 +pandas==2.3.1 +pymongo==4.13.2 pyyaml==6.0.2 -requests==2.32.3 +requests==2.32.4 scikit-learn==1.6.1 -statsmodels==0.14.4 -tornado==6.4.2 +statsmodels==0.14.5 +tornado==6.5.1 diff --git a/test/unit/spec/narrative_core/upload/importSetup-spec.js b/test/unit/spec/narrative_core/upload/importSetup-spec.js index 5e7b40bcb6..216dfcafc9 100644 --- a/test/unit/spec/narrative_core/upload/importSetup-spec.js +++ b/test/unit/spec/narrative_core/upload/importSetup-spec.js @@ -101,10 +101,13 @@ define([ }; } - function stubBulkSpecificationRequest(status, statusText, response) { - jasmine.Ajax.stubRequest( - new RegExp(`${stagingServiceUrl}/bulk_specification`) - ).andReturn({ + function stubBulkSpecificationRequest(status, statusText, response, isDts) { + let requestRegex = `${stagingServiceUrl}/bulk_specification/\\?files=.+&`; + if (isDts) { + requestRegex += 'dts'; + } + requestRegex += '$'; + jasmine.Ajax.stubRequest(new RegExp(requestRegex)).andReturn({ status, statusText, contentType: 'text/plain', @@ -193,31 +196,113 @@ define([ expect(Jupyter.narrative.insertBulkImportCell).not.toHaveBeenCalled(); }); - it('should load a happy path bulk specification file into a bulk import cell', async () => { - const readsDataType = 'fastq_reads_interleaved', - assemblyDataType = 'assembly', - importReadsData = [ + [ + { type: 'import_specification', name: 'bulk specification' }, + { type: 'dts_manifest', name: 'DTS manifest' }, + ].forEach((bulkInfoType) => { + it(`should load a happy path ${bulkInfoType.name} file into a bulk import cell`, async () => { + const isDts = bulkInfoType.type === 'dts_manifest', + readsDataType = 'fastq_reads_interleaved', + assemblyDataType = 'assembly', + importReadsData = [ + { + fastq_fwd_staging_file_name: 'some_reads.fasta', + name: 'some_reads', + sequencing_tech: 'PacBio CLR', + single_genome: '1', + read_orientation_outward: '0', + insert_size_std_dev: 6.66, + insert_size_mean: 66.66, + }, + ], + processedReadsData = [ + { + fastq_fwd_staging_file_name: 'some_reads.fasta', + name: 'some_reads', + sequencing_tech: 'PacBio CLR', + single_genome: 1, + read_orientation_outward: 0, + insert_size_std_dev: 6.66, + insert_size_mean: 66.66, + }, + ], + importAssemblyData = [ + { + staging_file_subdir_path: 'some_assembly.fasta', + assembly_name: 'some_assembly', + type: 'Single amplified genome (SAG)', + min_contig_length: 1000, + }, + ], + processedAssemblyData = [ + { + staging_file_subdir_path: 'some_assembly.fasta', + assembly_name: 'some_assembly', + type: 'sag', + min_contig_length: 1000, + }, + ], + readsFile = 'some_reads_file.' + (isDts ? 'json' : 'csv'), + assemblyFile = 'some_assembly_file.' + (isDts ? 'json' : 'csv'); + + stubBulkSpecificationRequest( + 200, + 'success', { - fastq_fwd_staging_file_name: 'some_reads.fasta', - name: 'some_reads', - sequencing_tech: 'PacBio CLR', - single_genome: '1', - read_orientation_outward: '0', - insert_size_std_dev: 6.66, - insert_size_mean: 66.66, + types: { + [readsDataType]: importReadsData, + [assemblyDataType]: importAssemblyData, + }, + files: { + [readsDataType]: { file: readsFile, tab: null }, + [assemblyDataType]: { file: assemblyFile, tab: null }, + }, }, - ], - processedReadsData = [ + bulkInfoType.type === 'dts_manifest' + ); + + Mocks.mockJsonRpc1Call({ + url: Config.url('narrative_method_store'), + body: /get_method_spec/, + response: [ImportFastqSpec, ImportAssemblySpec], + }); + + Mocks.mockJsonRpc1Call({ + url: Config.url('narrative_method_store'), + body: /get_method_full_info/, + response: [{}, {}], + }); + + await ImportSetup.setupImportCells([ { - fastq_fwd_staging_file_name: 'some_reads.fasta', - name: 'some_reads', - sequencing_tech: 'PacBio CLR', - single_genome: 1, - read_orientation_outward: 0, - insert_size_std_dev: 6.66, - insert_size_mean: 66.66, + name: readsFile, + type: bulkInfoType.type, }, - ], + { + name: assemblyFile, + type: bulkInfoType.type, + }, + ]); + expect(Jupyter.narrative.insertBulkImportCell).toHaveBeenCalledWith({ + [readsDataType]: { + files: [], + appId: uploaders.app_info[readsDataType].app_id, + outputSuffix: uploaders.app_info[readsDataType].app_output_suffix, + appParameters: processedReadsData, + }, + [assemblyDataType]: { + files: [], + appId: uploaders.app_info[assemblyDataType].app_id, + outputSuffix: uploaders.app_info[assemblyDataType].app_output_suffix, + appParameters: processedAssemblyData, + }, + }); + }); + }); + + it('should properly adjust the paths of any files in a DTS manifest to be relative to the DTS manifest file', async () => { + const assemblyDataType = 'assembly', + subDir = 'some/deep/subdirectory', importAssemblyData = [ { staging_file_subdir_path: 'some_assembly.fasta', @@ -228,55 +313,47 @@ define([ ], processedAssemblyData = [ { - staging_file_subdir_path: 'some_assembly.fasta', + staging_file_subdir_path: `${subDir}/some_assembly.fasta`, assembly_name: 'some_assembly', type: 'sag', min_contig_length: 1000, }, ], - readsCsv = 'some_reads_file.csv', - assemblyCsv = 'some_assembly_file.csv'; + manifestPath = `${subDir}/manifest.json`; - stubBulkSpecificationRequest(200, 'success', { - types: { - [readsDataType]: importReadsData, - [assemblyDataType]: importAssemblyData, - }, - files: { - [readsDataType]: { file: readsCsv, tab: null }, - [assemblyDataType]: { file: assemblyCsv, tab: null }, + stubBulkSpecificationRequest( + 200, + 'success', + { + types: { + [assemblyDataType]: importAssemblyData, + }, + files: { + [assemblyDataType]: { file: `a_user/${manifestPath}`, tab: null }, + }, }, - }); + true + ); Mocks.mockJsonRpc1Call({ url: Config.url('narrative_method_store'), body: /get_method_spec/, - response: [ImportFastqSpec, ImportAssemblySpec], + response: [ImportAssemblySpec], }); Mocks.mockJsonRpc1Call({ url: Config.url('narrative_method_store'), body: /get_method_full_info/, - response: [{}, {}], + response: [{}], }); await ImportSetup.setupImportCells([ { - name: 'some_reads_file.csv', - type: 'import_specification', - }, - { - name: 'some_assembly_file.csv', - type: 'import_specification', + name: manifestPath, + type: 'dts_manifest', }, ]); expect(Jupyter.narrative.insertBulkImportCell).toHaveBeenCalledWith({ - [readsDataType]: { - files: [], - appId: uploaders.app_info[readsDataType].app_id, - outputSuffix: uploaders.app_info[readsDataType].app_output_suffix, - appParameters: processedReadsData, - }, [assemblyDataType]: { files: [], appId: uploaders.app_info[assemblyDataType].app_id, @@ -379,7 +456,7 @@ define([ }; jasmine.Ajax.stubRequest( - `${stagingServiceUrl}/bulk_specification/?files=${file1}` + `${stagingServiceUrl}/bulk_specification/?files=${file1}&` ).andReturn({ status: 200, statusText: 'ok', @@ -388,7 +465,7 @@ define([ responseText: JSON.stringify(response1), }); jasmine.Ajax.stubRequest( - `${stagingServiceUrl}/bulk_specification/?files=${file2}` + `${stagingServiceUrl}/bulk_specification/?files=${file2}&` ).andReturn({ status: 200, statusText: 'ok',