diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 15a11211..312c5a16 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,7 +31,7 @@ jobs: env: CI: true - name: Upload Test Coverage - uses: actions/upload-artifact@v1 + uses: actions/upload-artifact@v4 with: name: app-coverage-report path: app/coverage diff --git a/.github/workflows/prodci.yml b/.github/workflows/prodci.yml index f34f05d2..5ba2f0ca 100644 --- a/.github/workflows/prodci.yml +++ b/.github/workflows/prodci.yml @@ -37,7 +37,7 @@ jobs: mkdir app_asset_artifacts && mv app-src_code.zip app_asset_artifacts && mv app-test-coverage-report.zip app_asset_artifacts - name: Upload App Assets if: github.event_name == 'push' - uses: actions/upload-artifact@v1 + uses: actions/upload-artifact@v4 with: name: app-assets path: app_asset_artifacts @@ -73,7 +73,7 @@ jobs: mkdir backend_asset_artifacts && mv backend-src_code.zip backend_asset_artifacts && mv backend-test-coverage-report.zip backend_asset_artifacts - name: Upload Backend Assets if: github.event_name == 'push' - uses: actions/upload-artifact@v1 + uses: actions/upload-artifact@v4 with: name: backend-assets path: backend_asset_artifacts diff --git a/.gitignore b/.gitignore index 629302a3..a852304b 100644 --- a/.gitignore +++ b/.gitignore @@ -40,10 +40,13 @@ mockDB/fuseki/log4j2.properties mockDB/materialsmine_backup/ mockDB/fuseki/files/ mockDB/fuseki/ +sparqlqueries.html #Sync DB mockDB/restore/mongodump/ mockDB/materialsmine_backup/ +whyis/materialsmine/whyis-init.sh +mockDB/whyis-init.sh #Elastic Search mockDB/es/ diff --git a/app/package-lock.json b/app/package-lock.json index 8c3c0d6a..9dddcfbf 100644 --- a/app/package-lock.json +++ b/app/package-lock.json @@ -12,6 +12,8 @@ "@triply/yasgui": "^4.2.21", "apollo-boost": "^0.4.9", "core-js": "^3.6.5", + "cytoscape-dagre": "^2.5.0", + "cytoscape-fcose": "^2.2.0", "d3": "^7.3.0", "datavoyager": "^2.0.0-alpha.24", "graphql": "^15.8.0", @@ -35,6 +37,7 @@ "vue": "^2.7.14", "vue-advanced-cropper": "^1.10.1", "vue-apollo": "^3.1.0", + "vue-cytoscape": "^1.0.8", "vue-json-csv": "^1.2.12", "vue-material": "^1.0.0-beta-15", "vue-mathjax": "^0.0.11", @@ -104,7 +107,6 @@ "version": "7.18.6", "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.18.6.tgz", "integrity": "sha512-TDCmlK5eOvH+eH7cdAFlNXeVJqWIQ7gW9tY1GJIpUtFb6CmjVyq2VM3u71bOyR8CRihcCgMUYoDNyLXao3+70Q==", - "dev": true, "dependencies": { "@babel/highlight": "^7.18.6" }, @@ -472,7 +474,6 @@ "version": "7.19.1", "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.19.1.tgz", "integrity": "sha512-awrNfaMtnHUr653GgGEs++LlAvW6w+DcPrOliSMXWCKo597CwL5Acf/wWdNkf/tfEQE3mjkeD1YOVZOUV/od1w==", - "dev": true, "engines": { "node": ">=6.9.0" } @@ -519,7 +520,6 @@ "version": "7.18.6", "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.18.6.tgz", "integrity": "sha512-u7stbOuYjaPezCuLj29hNW1v64M2Md2qupEKP1fHc7WdOA3DgLh37suiSrZYY7haUB7iBeQZ9P1uiRF359do3g==", - "dev": true, "dependencies": { "@babel/helper-validator-identifier": "^7.18.6", "chalk": "^2.0.0", @@ -3018,6 +3018,11 @@ "@types/node": "*" } }, + "node_modules/@types/cytoscape": { + "version": "3.21.6", + "resolved": "https://registry.npmjs.org/@types/cytoscape/-/cytoscape-3.21.6.tgz", + "integrity": "sha512-kJjnDvtXm/bAOUlcIxPBkqCd5vevCsVQKprwOyVihy8mktEcN5QeUqo/6VRniAxp6YqCTgkIdQUfy1ZrWHsp6g==" + }, "node_modules/@types/estree": { "version": "0.0.50", "resolved": "https://registry.npmjs.org/@types/estree/-/estree-0.0.50.tgz", @@ -3233,6 +3238,11 @@ "source-map": "^0.6.1" } }, + "node_modules/@types/uuid": { + "version": "3.4.13", + "resolved": "https://registry.npmjs.org/@types/uuid/-/uuid-3.4.13.tgz", + "integrity": "sha512-pAeZeUbLE4Z9Vi9wsWV2bYPTweEHeJJy0G4pEjOA/FSvy1Ad5U5Km8iDV6TKre1mjBiVNfAdVHKruP8bAh4Q5A==" + }, "node_modules/@types/webpack": { "version": "4.41.33", "resolved": "https://registry.npmjs.org/@types/webpack/-/webpack-4.41.33.tgz", @@ -4300,7 +4310,6 @@ "version": "5.3.2", "resolved": "https://registry.npmjs.org/acorn-jsx/-/acorn-jsx-5.3.2.tgz", "integrity": "sha512-rq9s+JNhf0IChjtDXxllJ7g41oZk5SlXtp0LHwyA5cejwn7vKmKp4pPri6YEePv2PU65sAsegbXtIinmDFDXgQ==", - "dev": true, "peerDependencies": { "acorn": "^6.0.0 || ^7.0.0 || ^8.0.0" } @@ -4449,7 +4458,6 @@ "version": "4.3.2", "resolved": "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-4.3.2.tgz", "integrity": "sha512-gKXj5ALrKWQLsYG9jlTRmR/xKluxHV+Z9QEwNIgCfM1/uwPMCuzVVnh5mwTd+OuBZcwSIMbqssNWRm1lE51QaQ==", - "dev": true, "dependencies": { "type-fest": "^0.21.3" }, @@ -4476,7 +4484,6 @@ "version": "4.1.1", "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-4.1.1.tgz", "integrity": "sha512-ILlv4k/3f6vfQ4OoP2AGvirOktlQ98ZEL1k9FaQjxa3L1abBgbuTDAdPOpvbGncC0BTVQrl+OM8xZGK6tWXt7g==", - "dev": true, "engines": { "node": ">=6" } @@ -4687,7 +4694,6 @@ "version": "1.0.10", "resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.10.tgz", "integrity": "sha512-o5Roy6tNG4SL/FOkCAN6RzjiakZS25RLYFrcMttJqbdd8BWrnA+fGz57iN5Pb06pvBGvl5gQ0B48dJlslXvoTg==", - "dev": true, "dependencies": { "sprintf-js": "~1.0.2" } @@ -4952,7 +4958,6 @@ "version": "1.0.0", "resolved": "https://registry.npmjs.org/astral-regex/-/astral-regex-1.0.0.tgz", "integrity": "sha512-+Ryf6g3BKoRc7jfp7ad8tM4TtMiaWvbF/1/sQcZPkkS7ag3D5nMBCe2UfOTONtAkaG0tO0ij3C5Lwmf1EiyjHg==", - 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"integrity": "sha512-l8lCEmLcLYZh4nbunNZvQCJc5pv7+RCwa8q/LdUx8u7lsWvPDKmpodJAJNwkAhJC//dFY48KuIEmjtd4RViDrA==", - "dev": true + "integrity": "sha512-l8lCEmLcLYZh4nbunNZvQCJc5pv7+RCwa8q/LdUx8u7lsWvPDKmpodJAJNwkAhJC//dFY48KuIEmjtd4RViDrA==" }, "validate-npm-package-license": { "version": "3.0.4", @@ -56151,6 +56233,35 @@ } } }, + "vue-class-component": { + "version": "7.2.6", + "resolved": "https://registry.npmjs.org/vue-class-component/-/vue-class-component-7.2.6.tgz", + "integrity": "sha512-+eaQXVrAm/LldalI272PpDe3+i4mPis0ORiMYxF6Ae4hyuCh15W8Idet7wPUEs4N4YptgFHGys4UrgNQOMyO6w==", + "requires": {} + }, + "vue-cytoscape": { + "version": "1.0.8", + "resolved": "https://registry.npmjs.org/vue-cytoscape/-/vue-cytoscape-1.0.8.tgz", + "integrity": "sha512-wSdGzUwLLC5THTx2XncOG16Ym2bMm19Z0hEsmC5bZ01pU+KfMhQjx6oGSfHhhDL4EeDbtN6+ym2zQSSCytqa/A==", + "requires": { + "@types/cytoscape": "^3.8.0", + "@types/uuid": "^3.4.6", + "core-js": "^2.6.5", + "cytoscape": "^3.8.1", + "eslint-plugin-prettier": "^3.1.0", + "uuid": "^3.3.3", + "vue": "^2.6.10", + "vue-class-component": "^7.0.2", + "vue-property-decorator": "^8.1.0" + }, + "dependencies": { + "core-js": { + "version": "2.6.12", + "resolved": "https://registry.npmjs.org/core-js/-/core-js-2.6.12.tgz", + "integrity": "sha512-Kb2wC0fvsWfQrgk8HU5lW6U/Lcs8+9aaYcy4ZFc6DDlo4nZ7n70dEgE5rtR0oG6ufKDUnrwfWL1mXR5ljDatrQ==" + } + } + }, "vue-eslint-parser": { "version": "7.11.0", "resolved": "https://registry.npmjs.org/vue-eslint-parser/-/vue-eslint-parser-7.11.0.tgz", @@ -56385,6 +56496,14 @@ "resolved": "https://registry.npmjs.org/vue-mathjax/-/vue-mathjax-0.0.11.tgz", "integrity": "sha512-s2P4OatDmzBZD/gm+/FHl5Idd43gxzSIdXOkMq/MiWrNsdOvMMzNFrirfQp0agqbCiNuA8/It/sXsgCDeh5FfA==" }, + "vue-property-decorator": { + "version": "8.5.1", + "resolved": "https://registry.npmjs.org/vue-property-decorator/-/vue-property-decorator-8.5.1.tgz", + "integrity": "sha512-O6OUN2OMsYTGPvgFtXeBU3jPnX5ffQ9V4I1WfxFQ6dqz6cOUbR3Usou7kgFpfiXDvV7dJQSFcJ5yUPgOtPPm1Q==", + "requires": { + "vue-class-component": "^7.1.0" + } + }, "vue-router": { "version": "3.6.5", "resolved": "https://registry.npmjs.org/vue-router/-/vue-router-3.6.5.tgz", @@ -57726,7 +57845,6 @@ "version": "1.0.3", "resolved": "https://registry.npmjs.org/write/-/write-1.0.3.tgz", "integrity": "sha512-/lg70HAjtkUgWPVZhZcm+T4hkL8Zbtp1nFNOn3lRrxnlv50SRBv7cR7RqR+GMsd3hUXy9hWBo4CHTbFTcOYwig==", - "dev": true, "requires": { "mkdirp": "^0.5.1" } diff --git a/app/package.json b/app/package.json index 9ba998cb..9370257a 100644 --- a/app/package.json +++ b/app/package.json @@ -25,6 +25,8 @@ "@triply/yasgui": "^4.2.21", "apollo-boost": "^0.4.9", "core-js": "^3.6.5", + "cytoscape-dagre": "^2.5.0", + "cytoscape-fcose": "^2.2.0", "d3": "^7.3.0", "datavoyager": "^2.0.0-alpha.24", "graphql": "^15.8.0", @@ -48,6 +50,7 @@ "vue": "^2.7.14", "vue-advanced-cropper": "^1.10.1", "vue-apollo": "^3.1.0", + "vue-cytoscape": "^1.0.8", "vue-json-csv": "^1.2.12", "vue-material": "^1.0.0-beta-15", "vue-mathjax": "^0.0.11", diff --git a/app/src/assets/css/modules/_utility.scss b/app/src/assets/css/modules/_utility.scss index a241a914..b1394e00 100644 --- a/app/src/assets/css/modules/_utility.scss +++ b/app/src/assets/css/modules/_utility.scss @@ -161,6 +161,9 @@ margin-left: 1.2rem !important; } } + &xs { + margin-left: 1.2rem !important; + } &-auto { margin-left: auto !important; } @@ -192,6 +195,9 @@ &--max { width: 100% !important; } + &--auto { + width: auto !important; + } } &--padding-lg { @@ -688,14 +694,14 @@ &-gridicon { position: absolute; right: 4.5rem; - top: 16rem; + top: 6rem; z-index: 10000000; @include respond(tab-land) { right: 2.5rem; - top: 19rem; + top: 5rem; } @include respond(phone) { - top: 15rem; + top: 3.7rem; } & > div { display: inline-block; diff --git a/app/src/components/ChartGallery.vue b/app/src/components/ChartGallery.vue index ccecb823..37014545 100644 --- a/app/src/components/ChartGallery.vue +++ b/app/src/components/ChartGallery.vue @@ -3,7 +3,7 @@
-
+
diff --git a/app/src/components/Drawer.vue b/app/src/components/Drawer.vue index cc58498b..145c205c 100644 --- a/app/src/components/Drawer.vue +++ b/app/src/components/Drawer.vue @@ -1,9 +1,19 @@ diff --git a/app/src/components/ns/classes/NamespaceAccordion.vue b/app/src/components/ns/classes/NamespaceAccordion.vue new file mode 100644 index 00000000..09c8e492 --- /dev/null +++ b/app/src/components/ns/classes/NamespaceAccordion.vue @@ -0,0 +1,121 @@ + + + diff --git a/app/src/components/ns/home/OntologyDetails.vue b/app/src/components/ns/home/OntologyDetails.vue new file mode 100644 index 00000000..b5d1dba2 --- /dev/null +++ b/app/src/components/ns/home/OntologyDetails.vue @@ -0,0 +1,47 @@ + + + diff --git a/app/src/components/ns/home/OntologyMetrics.vue b/app/src/components/ns/home/OntologyMetrics.vue new file mode 100644 index 00000000..383a02f7 --- /dev/null +++ b/app/src/components/ns/home/OntologyMetrics.vue @@ -0,0 +1,36 @@ + + + diff --git a/app/src/components/ns/home/SearchComponent.vue b/app/src/components/ns/home/SearchComponent.vue new file mode 100644 index 00000000..52b709d8 --- /dev/null +++ b/app/src/components/ns/home/SearchComponent.vue @@ -0,0 +1,121 @@ + + + diff --git a/app/src/main.js b/app/src/main.js index 83283daf..c6d157c1 100644 --- a/app/src/main.js +++ b/app/src/main.js @@ -9,6 +9,7 @@ import './registerServiceWorker' import store from './store' import router from './router' import apollo from './modules/gql/apolloClient' +import VueCytoscape from 'vue-cytoscape' const apolloProvider = new VueApollo({ defaultClient: apollo @@ -16,11 +17,12 @@ const apolloProvider = new VueApollo({ Vue.use(VueApollo) Vue.use(VueMaterial) +Vue.use(VueCytoscape) Vue.config.productionTip = false new Vue({ store, router, apolloProvider, - render: h => h(App) + render: (h) => h(App) }).$mount('#app') diff --git a/app/src/modules/nav-routes.js b/app/src/modules/nav-routes.js new file mode 100644 index 00000000..5a99c2a3 --- /dev/null +++ b/app/src/modules/nav-routes.js @@ -0,0 +1,62 @@ +const HEADER_ROUTES = { + explorer: [ + { + path: '/explorer', + label: 'Search', + name: 'home', + exact: true + }, + { + path: '/explorer/visualization', + label: 'Visualization', + exact: false + }, + { + path: '/explorer/curate', + label: 'Curate', + exact: false + }, + { + path: '/explorer/parameterized_query', + label: 'Parameterized Query', + name: 'parameterized_query', + exact: true + }, + { + path: '/explorer/sparql', + label: 'SPARQL Query', + name: 'sparql', + exact: true + } + ], + ns: [ + { + path: '/ns', + label: 'Search', + name: 'home', + exact: true + }, + { + path: '/ns/classes', + label: 'Classes', + exact: true + }, + // { + // path: '/ns/properties', + // label: 'Properties', + // exact: true + // }, + { + path: '/ns/visualize', + label: 'Visualize', + exact: true + }, + { + path: '/ns/submissions', + label: 'Submissions', + exact: true + } + ] +} + +export { HEADER_ROUTES } diff --git a/app/src/modules/vega-chart.js b/app/src/modules/vega-chart.js index 867d7828..a28f5be5 100644 --- a/app/src/modules/vega-chart.js +++ b/app/src/modules/vega-chart.js @@ -104,9 +104,9 @@ function buildXmlLd (xmlData, xmlId) { const dataset = tileArray[1] const dsSeq = tileArray[2] - return { + return `{ '@context': { - '@base': `${nmRdfLodPrefix}`, + '@base': ${nmRdfLodPrefix}, schema: 'http://schema.org/', xsd: 'http://www.w3.org/2001/XMLSchema#', whyis: 'http://vocab.rpi.edu/whyis/', @@ -117,39 +117,35 @@ function buildXmlLd (xmlData, xmlId) { prov: 'http://www.w3.org/ns/prov#', mt: 'https://www.iana.org/assignments/media-types/' }, - '@id': `urn:${whyisId}`, + '@id': urn:${whyisId}, '@graph': { - '@id': `urn:${whyisId}`, + '@id': urn:${whyisId}, '@type': 'np:Nanopublication', 'np:hasAssertion': { - '@id': `urn:${whyisId}_assertion`, + '@id': urn:${whyisId}_assertion, '@type': 'np:Assertion', '@graph': [ { - '@id': `${nmRdfLodPrefix}/explorer/xml/visualizer/${xmlData.id}?isNewCuration=${xmlData.isNewCuration}`, + '@id': ${nmRdfLodPrefix}/api/xml/${xmlData.title}?format=xml, '@type': [ 'schema:DataDownload', 'mt:text/xml', 'http://nanomine.org/ns/NanomineXMLFile' ], - 'whyis:hasContent': `data:text/xml;charset=UTF-8;base64,${b64XmlData}`, + 'whyis:hasContent': data:text/xml;charset=UTF-8;base64,${b64XmlData}, 'dc:conformsTo': { - '@id': `${nmRdfLodPrefix}/api/curate/schema?getXSD=true` + '@id': ${nmRdfLodPrefix}/api/curate/schema?isFile=true } }, { - '@id': `${nmRdfLodPrefix}/api/curate/${dataset}/${dsSeq}`, - '@type': 'schema:Dataset', - 'schema:distribution': [ - { - '@id': `${nmRdfLodPrefix}/explorer/xml/visualizer/${xmlData.id}?isNewCuration=${xmlData.isNewCuration}` - } - ] + '@id': ${nmRdfLodPrefix}/api/curate/${dataset}/${dsSeq}, + "@type" : "schema:Dataset", + "schema:distribution" : [ {"@id" : "${nmRdfLodPrefix}/api/xml/${xmlData.title}"} ] } ] } } - } + }` } function buildXsdLd (xsdData, xsdId, schemaName) { diff --git a/app/src/modules/whyis-dataset.js b/app/src/modules/whyis-dataset.js index 1e1481c5..38ddc6f1 100644 --- a/app/src/modules/whyis-dataset.js +++ b/app/src/modules/whyis-dataset.js @@ -35,7 +35,7 @@ const defaultDataset = { } } -const dcat = 'http://w3.org/ns/dcat#' +const dcat = 'http://www.w3.org/ns/dcat#' const dct = 'http://purl.org/dc/terms/' const vcard = 'http://www.w3.org/2006/vcard/ns#' const foaf = 'http://xmlns.com/foaf/0.1/' @@ -258,7 +258,7 @@ async function saveDatasetFiles (fileList) { body: formData, redirect: 'follow', headers: { - Authorization: store.getters['auth/token'] + Authorization: 'Bearer ' + store.getters['auth/token'] } }) return await result.json() @@ -296,7 +296,20 @@ function buildDistrLd (fileList) { '@type': 'http://purl.org/net/provenance/ns#File', 'http://www.w3.org/2000/01/rdf-schema#label': fileName } - if (fileList[x]?.status === 'complete') { distrLDs[x]['@id'] = fileList[x].uri } else { distrLDs[x]['@id'] = `${window.location.origin}${fileList[x].filename}` } + if (fileList[x]?.status === 'complete') { + distrLDs[x]['@id'] = fileList[x].uri + } else { + distrLDs[x]['@id'] = `${window.location.origin}${fileList[x].filename}` + } + + // Note: When testing SDD linking locally enable below logic and comment above if statement + // if (fileList[x]?.status === 'complete') { + // distrLDs[x]['@id'] = fileList[x].uri + // } else { + // distrLDs[x]['@id'] = `http://restful:3001/${ + // fileList[x].filename?.split('/api/')?.[1] + // }` + // } }) return distrLDs } @@ -307,7 +320,7 @@ function buildDepictionLd (file, uri) { '@type': 'http://purl.org/net/provenance/ns#File', 'http://www.w3.org/2000/01/rdf-schema#label': file?.swaggerFilename ?? file.originalname, - 'http://w3.org/ns/dcat#accessURL': + 'http://www.w3.org/ns/dcat#accessURL': file?.accessUrl ?? `${window.location.origin}${file.filename}` } return depictionLd diff --git a/app/src/pages/explorer/Home.vue b/app/src/pages/explorer/Home.vue index d630e8a1..1a316d7f 100644 --- a/app/src/pages/explorer/Home.vue +++ b/app/src/pages/explorer/Home.vue @@ -85,10 +85,7 @@
-
+
© {{ new Date().getFullYear() }} MaterialsMine Project diff --git a/app/src/pages/explorer/curate/sdd/SddLinking.vue b/app/src/pages/explorer/curate/sdd/SddLinking.vue new file mode 100644 index 00000000..9c731b9f --- /dev/null +++ b/app/src/pages/explorer/curate/sdd/SddLinking.vue @@ -0,0 +1,630 @@ + + diff --git a/app/src/pages/explorer/dataset/Dataset.vue b/app/src/pages/explorer/dataset/Dataset.vue index 20d6beef..688300d4 100644 --- a/app/src/pages/explorer/dataset/Dataset.vue +++ b/app/src/pages/explorer/dataset/Dataset.vue @@ -1,158 +1,310 @@ diff --git a/app/src/pages/ns/Classes.vue b/app/src/pages/ns/Classes.vue new file mode 100644 index 00000000..d631f6d3 --- /dev/null +++ b/app/src/pages/ns/Classes.vue @@ -0,0 +1,120 @@ + + diff --git a/app/src/pages/ns/Home.vue b/app/src/pages/ns/Home.vue new file mode 100644 index 00000000..414437b5 --- /dev/null +++ b/app/src/pages/ns/Home.vue @@ -0,0 +1,76 @@ + + diff --git a/app/src/pages/ns/Properties.vue b/app/src/pages/ns/Properties.vue new file mode 100644 index 00000000..6df57ee8 --- /dev/null +++ b/app/src/pages/ns/Properties.vue @@ -0,0 +1,20 @@ + + diff --git a/app/src/pages/ns/Submissions.vue b/app/src/pages/ns/Submissions.vue new file mode 100644 index 00000000..a0ba5121 --- /dev/null +++ b/app/src/pages/ns/Submissions.vue @@ -0,0 +1,66 @@ + + diff --git a/app/src/pages/ns/Visualize.vue b/app/src/pages/ns/Visualize.vue new file mode 100644 index 00000000..af3c83c1 --- /dev/null +++ b/app/src/pages/ns/Visualize.vue @@ -0,0 +1,367 @@ + + + diff --git a/app/src/pages/ns/cytoscape.js b/app/src/pages/ns/cytoscape.js new file mode 100644 index 00000000..641228d8 --- /dev/null +++ b/app/src/pages/ns/cytoscape.js @@ -0,0 +1,74 @@ +const styleObj = { + style: [ + { + selector: 'node', + style: { + 'background-color': '#2b65ec', + label: 'data(id)', + 'text-valign': 'center', + 'text-halign': 'center', + 'text-outline-color': '#2b65ec', + 'text-outline-width': '1px', + 'font-weight': 150, + color: '#ffffff', + width: 'data(width)', + height: 'data(height)' + } + }, + { + selector: 'edge', + style: { + width: 1, + 'line-color': '#08233c', + 'target-arrow-color': '#08233c', + 'curve-style': 'bezier', + 'target-arrow-shape': 'chevron', + label: 'data(description)', // Display the edge description + 'font-size': 14, // Adjust the font size for the description label + 'text-rotation': 'autorotate', // Ensure the label follows the edge line + color: '#000' + } + }, + { + selector: 'node:selected', + style: { + 'background-color': '#F08080', + 'border-color': 'red' + } + }, + { + selector: 'edge:selected', + style: { + 'line-color': '#F08080', + 'target-arrow-color': '#F08080' + } + } + ] +} + +const fcoseLayout = { + name: 'fcose', + fit: true, + padding: 10, + animate: false, // Enable animation + randomize: true, // Randomize initial positions + nodeDimensionsIncludeLabels: true, // Include node labels in dimension calculations + idealEdgeLength: 1000, // Ideal length of edges + edgeElasticity: 0.5, // Elasticity of edges + nestingFactor: 0.3, // Factor for nesting of compound nodes + gravity: 0.5 // Gravity to pull nodes towards center +} + +const modifiedLayout = { + name: 'dagre', + fit: true, // Fit the viewport to the graph + padding: 10, // Padding around the graph + animate: true, // Disable animation + nodeDimensionsIncludeLabels: true, // Include labels in the layout dimensions + rankDir: 'BT', // Direction of the tree (TB = Top to Bottom, LR = Left to Right) + rankSep: 100, // Vertical separation between nodes + edgeSep: 50, // Separation between edges + nodeSep: 50 // Separation between nodes +} + +export { styleObj, fcoseLayout, modifiedLayout } diff --git a/app/src/router/index.js b/app/src/router/index.js index 8a50ae68..9a100a79 100644 --- a/app/src/router/index.js +++ b/app/src/router/index.js @@ -12,6 +12,7 @@ import metamineRoutes from '@/router/module/metamine' import explorerRoutes from '@/router/module/explorer' import portalRoutes from '@/router/module/portal' import xsdRoutes from '@/router/module/xsd' +import nsRoutes from './module/ns' Vue.use(VueRouter) const routes = [ @@ -25,6 +26,11 @@ const routes = [ component: NanomineBase, children: [...nanomineRoutes] }, + { + path: '/ns', + component: () => import('@/pages/ns/Base.vue'), + children: [...nsRoutes] + }, { path: '/mm', component: MetamineBase, diff --git a/app/src/router/module/explorer.js b/app/src/router/module/explorer.js index 7945cdb4..399c9a3c 100644 --- a/app/src/router/module/explorer.js +++ b/app/src/router/module/explorer.js @@ -134,7 +134,9 @@ const explorerRoutes = [ { path: '', name: 'validList', - component: () => import('@/pages/explorer/curate/validlist/XlsList.vue') + component: () => + import('@/pages/explorer/curate/validlist/XlsList.vue'), + meta: { requiresAuth: true } }, { path: 'update', @@ -170,13 +172,13 @@ const explorerRoutes = [ component: () => import('@/pages/explorer/curate/sdd/SddForm.vue'), meta: { requiresAuth: true } }, - // { - // path: 'curate/sdd/link/:datasetId', - // name: 'LinkSDD', - // props: true, - // component: () => import('@/pages/explorer/curate/sdd/SddLinking.vue'), - // meta: { requiresAuth: true } - // }, + { + path: 'curate/sdd/link/:datasetId', + name: 'LinkSDD', + props: true, + component: () => import('@/pages/explorer/curate/sdd/SddLinking.vue'), + meta: { requiresAuth: true } + }, { path: 'chart', component: ChartBase, diff --git a/app/src/router/module/ns.js b/app/src/router/module/ns.js new file mode 100644 index 00000000..0df6d8ca --- /dev/null +++ b/app/src/router/module/ns.js @@ -0,0 +1,40 @@ +const nsRoutes = [ + { + path: '', + name: 'Namespace', + component: () => import('@/pages/ns/Home.vue'), + meta: { requiresAuth: false } + }, + { + path: 'classes', + name: 'Classes', + component: () => import('@/pages/ns/Classes.vue'), + meta: { requiresAuth: false } + }, + { + path: 'properties', + name: 'Properties', + component: () => import('@/pages/ns/Properties.vue'), + meta: { requiresAuth: false } + }, + { + path: 'submissions', + name: 'Submissions', + component: () => import('@/pages/ns/Submissions.vue'), + meta: { requiresAuth: false } + }, + { + path: 'visualize', + name: 'Visualize', + component: () => import('@/pages/ns/Visualize.vue'), + meta: { requiresAuth: false } + }, + { + path: ':namespace(.*)*', + name: 'Namespaces', + component: () => import('@/pages/ns/Home.vue'), + meta: { requiresAuth: false } + } +] + +export default nsRoutes diff --git a/app/src/store/index.js b/app/src/store/index.js index 8a2d0c38..b5abcd71 100644 --- a/app/src/store/index.js +++ b/app/src/store/index.js @@ -8,6 +8,7 @@ import nanomine from './modules/nanomine/index.js' import metamineNU from './modules/metamineNU/index.js' import contact from './modules/contact/index.js' import portal from './modules/portal/index.js' +import ns from './modules/ns/index.js' Vue.use(Vuex) @@ -20,6 +21,7 @@ export default new Vuex.Store({ nanomine, metamineNU, contact, - portal + portal, + ns } }) diff --git a/app/src/store/modules/explorer/actions.js b/app/src/store/modules/explorer/actions.js index 775e423b..952772b0 100644 --- a/app/src/store/modules/explorer/actions.js +++ b/app/src/store/modules/explorer/actions.js @@ -90,8 +90,14 @@ export default { const responseData = await response.json() let accessURL if (Array.isArray(responseData)) { - accessURL = responseData[0]['http://w3.org/ns/dcat#accessURL'] - } else accessURL = responseData['http://w3.org/ns/dcat#accessURL'] + accessURL = responseData[0]['http://www.w3.org/ns/dcat#accessURL'] + // Note: Initial sets of SDD curations are missing 'www' + if (!accessURL) { accessURL = responseData[0]['http://w3.org/ns/dcat#accessURL'] } + } else { + accessURL = responseData['http://www.w3.org/ns/dcat#accessURL'] + // Note: Initial sets of SDD curations are missing 'www' + if (!accessURL) { accessURL = responseData['http://w3.org/ns/dcat#accessURL'] } + } context.commit('setCurrentDatasetThumbnail', accessURL) return accessURL }, diff --git a/app/src/store/modules/explorer/curation/actions.js b/app/src/store/modules/explorer/curation/actions.js index 779d06bd..f2d4746f 100644 --- a/app/src/store/modules/explorer/curation/actions.js +++ b/app/src/store/modules/explorer/curation/actions.js @@ -80,7 +80,7 @@ export default { datasetObject['http://purl.org/dc/terms/title']?.['@value'], thumbnail: datasetObject['http://xmlns.com/foaf/0.1/depiction']?.[ - 'http://w3.org/ns/dcat#accessURL' + 'http://www.w3.org/ns/dcat#accessURL' ], doi: datasetObject['http://purl.org/dc/terms/isReferencedBy']?.['@value'], organization: datasetObject[ @@ -88,7 +88,7 @@ export default { ]?.map((org) => { return org?.['http://xmlns.com/foaf/0.1/name']?.['@value'] }), - distribution: datasetObject['http://w3.org/ns/dcat#distribution']?.map( + distribution: datasetObject['http://www.w3.org/ns/dcat#distribution']?.map( (dist) => { return dist?.['@id'] } diff --git a/app/src/store/modules/ns/actions.js b/app/src/store/modules/ns/actions.js new file mode 100644 index 00000000..ba273566 --- /dev/null +++ b/app/src/store/modules/ns/actions.js @@ -0,0 +1,106 @@ +export default { + async fetchNsData ( + { commit, getters, dispatch }, + { forceFetch = false } = {} + ) { + commit('setLoading', true) + const metrics = getters.getMetrics + const details = getters.getDetails + const classes = getters.getClasses + + if ( + !Object.keys(metrics).length || + !Object.keys(details).length || + !classes.length || + forceFetch + ) { + try { + const url = '/api/mn/ontology' + + const req = await fetch(url, { + headers: { + Accept: 'application/json' + } + }) + + if (req.status !== 200) { + throw new Error( + req.statusText || 'Server error, cannot fetch namespace error' + ) + } + const res = await req.json() + const { metrics, details, data, submissions } = res + commit('setMetrics', metrics) + commit('setDetails', details) + commit('setClasses', data) + commit('setSubmissions', submissions) + } catch (error) { + const snackbar = { + message: error?.message ?? 'Something went wrong fetching namespace', + action: () => dispatch('fetchNsData', { forceFetch }) + } + commit('setSnackbar', snackbar, { root: true }) + } finally { + commit('setLoading', false) + } + } + }, + async searchNSData ( + { getters, commit }, + { query = '', singleResult = true } = {} + ) { + commit('clearSearchQueries') + if (!query) return + + commit('showErrorResponse', false) + const classes = getters.getClasses + + let response = singleResult ? '' : [] + + const searchArray = (arr, query, exactMatch = false) => { + let result = [] + const queryLower = query.toLowerCase() + const regex = new RegExp(query, 'i') // Case-insensitive regex for partial matching + + for (let i = 0; i < arr.length; i++) { + const element = arr[i] + const elementID = element.ID.split('/') + .pop() + .split('#') + .pop() + .toLowerCase() + + // Check for exact match or partial match based on the third argument + if (exactMatch) { + if (elementID === queryLower) { + return element // Return the found element immediately for exact match + } + } else { + if (elementID.search(regex) !== -1) { + result.push(element) // Push matching element to the result for partial match + } + } + + // If the element has subClasses, search recursively + if (element.subClasses && element.subClasses.length) { + const foundInSub = searchArray(element.subClasses, query, exactMatch) + if (exactMatch && foundInSub) { + return foundInSub // Return the found element immediately for exact match in subClasses + } else if (!exactMatch && foundInSub.length) { + result = [...result, ...foundInSub] // Merge found elements from subClasses for partial match + } + } + } + + // Return the result based on exact match or partial match + return exactMatch ? null : result + } + + response = searchArray(classes, query, singleResult) + const isError = + (singleResult && !response) || (!singleResult && !response.length) + + commit('setSearchResult', response) + commit('showErrorResponse', isError) + } +} diff --git a/app/src/store/modules/ns/getters.js b/app/src/store/modules/ns/getters.js new file mode 100644 index 00000000..79c1fb3f --- /dev/null +++ b/app/src/store/modules/ns/getters.js @@ -0,0 +1,37 @@ +export default { + isLoading (state) { + return state.loading + }, + getDetails (state) { + return state.details + }, + getMetrics (state) { + return state.metrics + }, + getClasses (state) { + return state.classes + }, + getSelectedId (state) { + return state.selectedId + }, + getCurrentClass (state) { + return state.currentClass + }, + getSearchResults (state) { + return state.queryGroup + }, + getLastUpdatedDate (state) { + const options = { year: 'numeric', month: 'long', day: 'numeric' } + const date = state.submissions[0]?.uploaded + if (date) { + return new Date(date).toLocaleDateString(undefined, options) + } + return '-- -- --' + }, + getSubmissions (state) { + return state.submissions + }, + checkError (state) { + return state.searchError + } +} diff --git a/app/src/store/modules/ns/index.js b/app/src/store/modules/ns/index.js new file mode 100644 index 00000000..6c740042 --- /dev/null +++ b/app/src/store/modules/ns/index.js @@ -0,0 +1,24 @@ +import mutations from './mutations.js' +import actions from './actions.js' +import getters from './getters.js' + +export default { + namespaced: true, + state () { + return { + loading: true, + queryGroup: [], + singleQuery: '', + classes: [], + currentClass: {}, + metrics: {}, + details: {}, + submissions: [], + selectedId: null, + searchError: false + } + }, + mutations, + actions, + getters +} diff --git a/app/src/store/modules/ns/mutations.js b/app/src/store/modules/ns/mutations.js new file mode 100644 index 00000000..83ab383f --- /dev/null +++ b/app/src/store/modules/ns/mutations.js @@ -0,0 +1,43 @@ +export default { + setLoading (state, payload) { + state.loading = payload + }, + setMetrics (state, payload) { + state.metrics = payload + }, + setDetails (state, payload) { + state.details = payload + }, + setClasses (state, arr) { + state.classes = arr + }, + setSubmissions (state, obj) { + state.submissions = obj + }, + setLastUpdade (state, obj) { + state.lastUpdated = obj + }, + setSelectedId (state, id) { + state.selectedId = id + }, + setCurrentClass (state, payload) { + state.currentClass = payload + }, + clearCurrentClass (state) { + state.currentClass = {} + }, + setSearchResult (state, payload) { + if (Array.isArray(payload)) { + state.queryGroup = payload + } else { + state.currentClass = payload + } + }, + clearSearchQueries (state) { + state.queryGroup = [] + state.singleQuery = '' + }, + showErrorResponse (state, payload) { + state.searchError = payload + } +} diff --git a/app/tests/jest/__mocks__/nsMock.js b/app/tests/jest/__mocks__/nsMock.js new file mode 100644 index 00000000..1045f198 --- /dev/null +++ b/app/tests/jest/__mocks__/nsMock.js @@ -0,0 +1,50 @@ +const classes = [ + { + subClasses: [ + { + subClasses: [], + ID: 'http://materialsmine.org/ns/Beam', + prefixIRI: 'materialsmine:Beam', + prefLabel: 'Beam', + Label: 'Beam', + 'Preferred Name': 'Beam', + Definitions: + 'A slender 1d structural element that primarily bears lateral loads.', + subClassOf: 'http://materialsmine.org/ns/1DSolidMechanicsModel' + } + ], + ID: 'http://materialsmine.org/ns/1DSolidMechanicsModel', + prefixIRI: 'materialsmine:1DSolidMechanicsModel', + prefLabel: '1D Solid Mechanics Model', + Label: '1D Solid Mechanics Model', + 'Preferred Name': '1D Solid Mechanics Model', + Definitions: + 'A one-dimensional model of a solid relating stress with strain.', + subClassOf: 'http://www.w3.org/2002/07/owl#Thing' + }, + { + ID: 'http://materialsmine.org/ns/2DSolidMechanicsModel', + subClasses: [ + { + subClasses: [], + ID: 'http://materialsmine.org/ns/SolidMechanicsModel', + prefixIRI: 'materialsmine:SolidMechanicsModel', + subClassOf: 'http://materialsmine.org/ns/2DSolidMechanicsModel', + prefLabel: 'Solid Mechanics Model', + Label: 'Solid Mechanics Model', + 'Preferred Name': 'Solid Mechanics Model', + Definitions: + 'A model of a material/system that models interactions caused by forces resulting in stresses and strains.' + } + ], + prefixIRI: 'materialsmine:2DSolidMechanicsModel', + Definitions: + 'A two-dimensional mathematical model that assumes either out of plane strain or out of plane stress component is zero.', + prefLabel: '2D Solid Mechanics Model', + Label: '2D Solid Mechanics Model', + 'Preferred Name': '2D Solid Mechanics Model', + subClassOf: 'http://www.w3.org/2002/07/owl#Thing' + } +] + +export { classes } diff --git a/app/tests/jest/__mocks__/sddDatasetMock.js b/app/tests/jest/__mocks__/sddDatasetMock.js new file mode 100644 index 00000000..db6a17f8 --- /dev/null +++ b/app/tests/jest/__mocks__/sddDatasetMock.js @@ -0,0 +1,21 @@ +export const testDataset = { + '@id': 'http://materialsmine.org/explorer/dataset/test-id', + 'http://purl.org/dc/terms/description': [{ '@value': 'This is a descriptive description' }], + 'http://purl.org/dc/terms/title': [{ '@value': 'Test Dataset' }], + 'http://purl.org/dc/terms/issued': [{ '@value': '2023-06-19' }], + 'http://www.w3.org/ns/dcat#contactpoint': [{ '@id': 'http://orcid.org/0000-0000-0000-0000' }], + 'http://www.w3.org/ns/dcat#distribution': [ + { '@id': 'http://materialsmine.org/files/test_file1.csv?isStore=true' }, + { '@id': 'http://materialsmine.org/files/test_file2.csv?isStore=true' }, + { '@id': 'http://materialsmine.org/files/test_sdd.xlsx?isStore=true' } + ], + 'http://xmlns.com/foaf/0.1/depiction': [{ '@id': 'http://materialsmine.org/explorer/dataset/test-id/depiction' }] +} +export const testThumbnail = [{ '@value': 'http://materialsmine.org/files/test_image.png?isStore=true' }] +export const testOrcid = { + '@id': 'http://orcid.org/0000-0000-0000-0000', + '@type': ['http://schema.org/Person', 'http://localhost/schemaPerson'], + 'http://schema.org/familyName': [{ '@value': 'Person' }], + 'http://schema.org/givenName': [{ '@value': 'Fake' }], + 'http://www.w3.org/2006/vcard/ns#email': [{ '@value': 'test@mail.com' }] +} diff --git a/app/tests/unit/components/explorer/Header.spec.js b/app/tests/unit/components/explorer/Header.spec.js index 9a8a50f4..ad7aaaf7 100644 --- a/app/tests/unit/components/explorer/Header.spec.js +++ b/app/tests/unit/components/explorer/Header.spec.js @@ -1,5 +1,7 @@ import createWrapper from '../../../jest/script/wrapper' import ExpHeader from '@/components/explorer/Header.vue' +import { HEADER_ROUTES } from '@/modules/nav-routes' + describe('Header.vue', () => { let wrapper const toggler = jest.fn() @@ -21,10 +23,58 @@ describe('Header.vue', () => { expect(menuBtn.exists()).toBe(true) }) - it('renders Menu tabs correctly', async () => { - expect.assertions(1) - const menuItems = wrapper.findAll('._menutabs') - expect(menuItems.length).toBe(6) + describe('Header.vue on the explorer route', () => { + beforeAll(async () => { + await wrapper.vm.$router.push({ path: '/explorer/' }) + }) + + it('renders correct number of Menu tabs on explorer routr', async () => { + expect.assertions(1) + const menuItems = wrapper.findAll('._menutabs') + expect(menuItems.length).toBe(HEADER_ROUTES.explorer.length) + }) + + it('renders the correct Menu routes and label on explorer routr', async () => { + const menuItems = wrapper.findAll('._menutabs') + const ExplorerRoutes = HEADER_ROUTES.explorer + + for (let i = 0; i < menuItems.length; i++) { + const element = menuItems.at(i) + expect(element.attributes().to).toEqual(ExplorerRoutes[i].path) + expect(element.attributes().mdlabel).toEqual(ExplorerRoutes[i].label) + expect(!!element.attributes().exact).toEqual(ExplorerRoutes[i].exact) + expect(element.attributes().id).toEqual( + `tab-${ExplorerRoutes[i]?.name ?? ExplorerRoutes[i]?.label}` + ) + } + }) + }) + + describe('Header.vue on the ns route', () => { + beforeAll(async () => { + await wrapper.vm.$router.push({ path: '/ns/' }) + }) + + it('renders correct number of Menu tabs on ns route', async () => { + expect.assertions(1) + const menuItems = wrapper.findAll('._menutabs') + expect(menuItems.length).toBe(HEADER_ROUTES.ns.length) + }) + + it('renders the correct Menu routes and label on ns route', async () => { + const menuItems = wrapper.findAll('._menutabs') + const ExplorerRoutes = HEADER_ROUTES.ns + + for (let i = 0; i < menuItems.length; i++) { + const element = menuItems.at(i) + expect(element.attributes().to).toEqual(ExplorerRoutes[i].path) + expect(element.attributes().mdlabel).toEqual(ExplorerRoutes[i].label) + expect(!!element.attributes().exact).toEqual(ExplorerRoutes[i].exact) + expect(element.attributes().id).toEqual( + `tab-${ExplorerRoutes[i]?.name ?? ExplorerRoutes[i]?.label}` + ) + } + }) }) it('renders Menu tabs only on desktop', async () => { diff --git a/app/tests/unit/components/ns/ClassesList.spec.js b/app/tests/unit/components/ns/ClassesList.spec.js new file mode 100644 index 00000000..eb85ff00 --- /dev/null +++ b/app/tests/unit/components/ns/ClassesList.spec.js @@ -0,0 +1,124 @@ +import createWrapper from '../../../jest/script/wrapper' +import ClassesList from '@/components/ns/classes/ClassesList.vue' + +describe('Classeslist.vue', () => { + let wrapper + describe('Classeslist mounted behaviour', () => { + const highlightClass = jest.spyOn(ClassesList.methods, 'toggleClass') + beforeEach(() => { + wrapper = createWrapper(ClassesList, {}, false) + }) + + afterAll(async () => { + await wrapper.destroy() + }) + + it('highlights selected class', () => { + expect.assertions(2) + expect(wrapper.exists()).toBe(true) + expect(highlightClass).toHaveBeenCalled() + }) + }) + + describe('Classeslist with mock data', () => { + beforeEach(() => { + wrapper = createWrapper(ClassesList, {}, false) + // Set classes + wrapper.vm.$store.commit('ns/setClasses', classes) + }) + + afterAll(async () => { + await wrapper.destroy() + }) + + it('renders Namespace Componenet ', () => { + expect.assertions(5) + const accordion = wrapper.findAllComponents('namespaceaccordion-stub') + expect(accordion.length).toBe(classes.length) + for (let i = 0; i < accordion.length; i++) { + expect(accordion.at(i).props().id).toBe(classes[i].ID) + expect(accordion.at(i).props().summary).toBe( + classes[i]['Preferred Name'] + ) + } + }) + + it('renders toggles height of list ', async () => { + expect.assertions(7) + const button = wrapper.find('[data-test="toggle-list"]') + + expect(wrapper.vm.isListVisible).toBe(true) + expect(button.find('.utility-color').text()).toBe('keyboard_arrow_up') + expect(wrapper.find('div').attributes().class).not.toContain( + 'utility-roverflow' + ) + + await button.trigger('click.prevent') + + expect(wrapper.vm.isListVisible).toBe(false) + expect(wrapper.find('.utility-color').text()).toBe('keyboard_arrow_down') + expect(wrapper.find('div').attributes().class).toContain( + 'utility-roverflow' + ) + expect(wrapper.find('div').attributes().style).toBe('max-height: 6rem;') + }) + + it('filters classes data into dropdown if search is successful ', async () => { + expect.assertions(2) + expect(wrapper.find('.search-dropdown-menu').exists()).toBe(false) + + await wrapper.setData({ searchKeyword: '1DSolidMechanicsModel' }) + + expect(wrapper.find('.search-dropdown-menu').exists()).toBe(true) + }) + }) +}) + +const classes = [ + { + subClasses: [ + { + subClasses: [], + ID: 'http://materialsmine.org/ns/Beam', + prefixIRI: 'materialsmine:Beam', + prefLabel: 'Beam', + Label: 'Beam', + 'Preferred Name': 'Beam', + Definitions: + 'A slender 1d structural element that primarily bears lateral loads.', + subClassOf: 'http://materialsmine.org/ns/1DSolidMechanicsModel' + } + ], + ID: 'http://materialsmine.org/ns/1DSolidMechanicsModel', + prefixIRI: 'materialsmine:1DSolidMechanicsModel', + prefLabel: '1D Solid Mechanics Model', + Label: '1D Solid Mechanics Model', + 'Preferred Name': '1D Solid Mechanics Model', + Definitions: + 'A one-dimensional model of a solid relating stress with strain.', + subClassOf: 'http://www.w3.org/2002/07/owl#Thing' + }, + { + ID: 'http://materialsmine.org/ns/2DSolidMechanicsModel', + subClasses: [ + { + subClasses: [], + ID: 'http://materialsmine.org/ns/SolidMechanicsModel', + prefixIRI: 'materialsmine:SolidMechanicsModel', + subClassOf: 'http://materialsmine.org/ns/2DSolidMechanicsModel', + prefLabel: 'Solid Mechanics Model', + Label: 'Solid Mechanics Model', + 'Preferred Name': 'Solid Mechanics Model', + Definitions: + 'A model of a material/system that models interactions caused by forces resulting in stresses and strains.' + } + ], + prefixIRI: 'materialsmine:2DSolidMechanicsModel', + Definitions: + 'A two-dimensional mathematical model that assumes either out of plane strain or out of plane stress component is zero.', + prefLabel: '2D Solid Mechanics Model', + Label: '2D Solid Mechanics Model', + 'Preferred Name': '2D Solid Mechanics Model', + subClassOf: 'http://www.w3.org/2002/07/owl#Thing' + } +] diff --git a/app/tests/unit/pages/explorer/SddDataset.spec.js b/app/tests/unit/pages/explorer/SddDataset.spec.js index 4368d8b5..5febeeac 100644 --- a/app/tests/unit/pages/explorer/SddDataset.spec.js +++ b/app/tests/unit/pages/explorer/SddDataset.spec.js @@ -12,8 +12,8 @@ const testDataset = { 'http://purl.org/dc/terms/creator': [{ '@id': 'https://materialsmine.org/api/user/123' }], 'http://purl.org/dc/terms/description': [{ '@value': 'A dataset of generated materials' }], 'http://purl.org/dc/terms/title': [{ '@value': 'Test Dataset' }], - 'http://w3.org/ns/dcat#contactpoint': [{ '@id': 'http://orcid.org/0000-0001-0002-0003' }], - 'http://w3.org/ns/dcat#distribution': [ + 'http://www.w3.org/ns/dcat#contactpoint': [{ '@id': 'http://orcid.org/0000-0001-0002-0003' }], + 'http://www.w3.org/ns/dcat#distribution': [ { '@id': 'http://materialsmine.org/api/files/fake_file.csv?isStore=true' }, { '@id': 'http://materialsmine.org/api/files/another_file.txt?isStore=true' } ], @@ -104,10 +104,10 @@ describe('Dataset.vue', () => { expect(dists.length).toBe(2) for (let i = 0; i < dists.length; i++) { expect(dists.at(i).text()).toContain( - parseFileName(testDataset['http://w3.org/ns/dcat#distribution'][i]['@id'])) + parseFileName(testDataset['http://www.w3.org/ns/dcat#distribution'][i]['@id'])) expect(dists.at(i).find('a').exists()).toBe(true) expect(dists.at(i).find('a').attributes('href')) - .toBe(testDataset['http://w3.org/ns/dcat#distribution'][i]['@id']) + .toBe(testDataset['http://www.w3.org/ns/dcat#distribution'][i]['@id']) } }) diff --git a/app/tests/unit/pages/explorer/SddLinking.spec.js b/app/tests/unit/pages/explorer/SddLinking.spec.js new file mode 100644 index 00000000..d4da2e1d --- /dev/null +++ b/app/tests/unit/pages/explorer/SddLinking.spec.js @@ -0,0 +1,79 @@ +import createWrapper from '../../../jest/script/wrapper' +import { testDataset, testOrcid, testThumbnail } from '../../../jest/__mocks__/sddDatasetMock' +import { enableAutoDestroy } from '@vue/test-utils' +import SddLinking from '@/pages/explorer/curate/sdd/SddLinking.vue' +import store from '@/store/index' + +// Mock store since we just to return test data +const dispatch = jest.spyOn(store, 'dispatch').mockImplementation(() => { + store.commit('explorer/setCurrentDataset', testDataset) + store.commit('explorer/setCurrentDatasetThumbnail', testThumbnail) + store.commit('explorer/curation/setOrcidData', testOrcid) +}) + +describe('SddLinking.vue', () => { + let wrapper + beforeEach(async () => { + // Reset store so watchers trigger + store.commit('explorer/setCurrentDataset', null) + store.commit('explorer/setCurrentDatasetThumbnail', null) + store.commit('explorer/curation/setOrcidData', null) + + wrapper = await createWrapper(SddLinking, { + stubs: { + MdPortal: { template: '
' } + }, + props: { + datasetId: 'test-id' + } + }, true) + }) + + enableAutoDestroy(afterEach) + + it('fills page with data from store ', () => { + expect(dispatch).toHaveBeenCalledWith('explorer/fetchSingleDataset', 'http://localhost/explorer/dataset/test-id') + expect(wrapper.vm.dataset).toEqual(testDataset) + }) + + it('renders steppers after page loads', () => { + const steppers = wrapper.findAll('.md-stepper') + expect(steppers.length).toBe(4) + }) + + it('renders loaded data', () => { + const step1 = wrapper.findAll('.md-stepper').at(0) + expect(step1.text()).toContain(testDataset['http://purl.org/dc/terms/title'][0]['@value']) + expect(step1.text()).toContain(testDataset['http://purl.org/dc/terms/description'][0]['@value']) + expect(step1.text()).toContain(testOrcid['http://schema.org/familyName'][0]['@value']) + expect(step1.text()).toContain(testOrcid['http://schema.org/givenName'][0]['@value']) + }) + + it('prompts for uri space', () => { + const step2 = wrapper.findAll('.md-stepper').at(1) + expect(step2.text()).toContain('namespace') + const radios = step2.findAll('.md-radio') + expect(radios.length).toBe(2) + expect(radios.at(0).text()).toContain('default') + expect(radios.at(1).text()).toContain('custom') + }) + + it('asks for delimiters for csv files', () => { + const step3 = wrapper.findAll('.md-stepper').at(2) + expect(step3.text()).toContain('delimiter') + const numCsvs = testDataset['http://www.w3.org/ns/dcat#distribution'] + .filter(file => file['@id'].includes('csv')).length + const inputFields = step3.findAll('.md-field') + expect(inputFields.length).toBe(numCsvs) + }) + + it('asks about SDD files', async () => { + const step4 = wrapper.findAll('.md-stepper').at(3) + expect(step4.text()).toContain('SDD') + const numFiles = testDataset['http://www.w3.org/ns/dcat#distribution'].length + expect(step4.findAll('.md-checkbox').length).toBe(numFiles + 2) + await step4.findAll('input').at(2).trigger('click') + wrapper.vm.$nextTick() + expect(step4.findAll('.md-checkbox').length).toBe(numFiles + 3) + }) +}) diff --git a/app/tests/unit/pages/ns/Visualize.spec.js b/app/tests/unit/pages/ns/Visualize.spec.js new file mode 100644 index 00000000..30e3f1d9 --- /dev/null +++ b/app/tests/unit/pages/ns/Visualize.spec.js @@ -0,0 +1,136 @@ +import createWrapper from '../../../jest/script/wrapper' +import { enableAutoDestroy } from '@vue/test-utils' +import { classes } from '../../../jest/__mocks__/nsMock' +import Visualize from '@/pages/ns/Visualize.vue' + +const classMock = [...classes] + +const totalNodeLength = () => { + let count = classMock.length + + for (let i = 0; i < count; i++) { + const element = classMock[i] + const childCount = element?.subClasses.length ?? 0 // Get the length of subClasses for each element + count += childCount // Add the number of subClasses to the count + } + + return count +} + +describe('Visualize.vue', async () => { + let wrapper + const mountMethod = jest.spyOn(Visualize.methods, 'formatClassData') + const createNode = jest.spyOn(Visualize.methods, 'createNode') + beforeEach(async () => { + wrapper = createWrapper( + Visualize, + { + stubs: { + Cytoscape: { + template: '
' + }, + CyElement: { + template: '
' + } + } + }, + false + ) + await wrapper.setData({ loading: false }) + }) + + enableAutoDestroy(afterEach) + + describe('Visualize.vue without class Data', async () => { + it('call attempts to format the classes data on mount', () => { + expect.assertions(4) + // Expect store data to be empty + expect(wrapper.vm.classes.length).toBe(0) + + // Attempts to format empty data + expect(mountMethod).toHaveBeenCalledTimes(1) + expect(createNode).toHaveBeenCalledTimes(0) + + // Results + expect(wrapper.vm.elements.length).toBe(0) + }) + + it('mount header text properly', () => { + expect.assertions(3) + + const titleContainer = wrapper.find('div.wrapper.viz-u-postion__rel') + expect(titleContainer.exists()).toBe(true) + + const h1 = titleContainer.find('h1') + expect(h1.attributes('class')).toEqual( + 'visualize_header-h1 article_title u_centralize_text' + ) + expect(h1.text()).toMatch('Ontology Visualization') + }) + + it('mount empty text on empty state', () => { + expect.assertions(4) + const emptyDiv = wrapper.find('div.md-empty-state') + expect(emptyDiv.exists()).toBe(true) + + const containter = emptyDiv.find('div.md-empty-state-container') + expect(containter.exists()).toBe(true) + + expect(containter.find('strong.md-empty-state-label').text()).toBe( + 'No Data' + ) + expect(containter.find('p.md-empty-state-description').text()).toBe( + 'No Ontology Data Found' + ) + }) + }) + + describe('Visualize.vue with classes Data', () => { + const createNodeObj = jest.spyOn(Visualize.methods, 'createNodeObj') + const createLineObj = jest.spyOn(Visualize.methods, 'createLineObj') + const nodeLength = totalNodeLength() + + beforeAll(async () => { + // 1. Set the class data from store + await wrapper.vm.$store.commit('ns/setClasses', classMock) + // 2. Call the Mounted method + await wrapper.vm.formatClassData() + }) + it('calls the right methods to format the class data', () => { + // expect.assertions(4) + expect(createNode).toHaveBeenNthCalledWith(1, wrapper.vm.classes) + expect(createNodeObj).toHaveBeenCalledTimes(nodeLength) + expect(createLineObj).toHaveBeenCalled() + }) + + it('still renders header text properly', () => { + expect.assertions(3) + + const titleContainer = wrapper.find('div.wrapper.viz-u-postion__rel') + expect(titleContainer.exists()).toBe(true) + + const h1 = titleContainer.find('h1') + expect(h1.text()).toMatch('Ontology Visualization') + expect(h1.attributes('class')).toEqual( + 'visualize_header-h1 article_title u_centralize_text' + ) + }) + + it('does not render empty', () => { + expect.assertions(3) + expect(wrapper.find('div.md-empty-state').exists()).toBe(false) + + expect(wrapper.find('strong.md-empty-state-label').exists()).toBe(false) + expect(wrapper.find('p.md-empty-state-description').exists()).toBe(false) + }) + + it('renders canvas and node object', () => { + expect.assertions(3) + expect(wrapper.find('[data-test="cytoscape"]').exists()).toBe(true) + expect(wrapper.find('[data-test="cy-element"]').exists()).toBe(true) + expect(wrapper.findAll('[data-test="cy-element"]').length).toBe( + wrapper.vm.elements.length + ) + }) + }) +}) diff --git a/docker-compose.yml b/docker-compose.yml index cbe1f694..d4dcc248 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -151,32 +151,12 @@ services: - AUTH_API_TOKEN_EMAIL=${MANAGED_SERVICES_AUTH_API_TOKEN_EMAIL} - AUTH_API_REFRESH_EMAIL=${MANAGED_SERVICES_AUTH_API_REFRESH_EMAIL} - API_URL=${API_URL} - # managedservices: - # container_name: managedservices - # depends_on: - # - mongo - # restart: always - # build: - # dockerfile: Dockerfile.dev - # context: ./services - # ports: - # - '5050:5050' - # volumes: - # - ./services:/services - # - ./resfulservice/mm_files:/usr/src/files - # environment: - # - MM_RUNTIME_ENV=${MM_RUNTIME_ENV} - # - SECRET_KEY=${TKNS} - # - MM_MONGO_USER=${MM_MONGO_USER} - # - MM_MONGO_PWD=${MM_MONGO_PWD} - # - MANAGED_SERVICES_USER=${MANAGED_SERVICES_USER} - # - MANAGED_SERVICES_PWD=${MANAGED_SERVICES_PWD} - # - MANAGED_SERVICES_DB=${MANAGED_SERVICES_DB} - # - MONGO_ADDRESS=${MONGO_ADDRESS} - # - MONGO_PORT=${MONGO_PORT} - # - FILES_WORKING_DIR=${MANAGED_SERVICES_FILES_WORKING_DIR} - # - AUTH_API_TOKEN_EMAIL=${MANAGED_SERVICES_AUTH_API_TOKEN_EMAIL} - # - AUTH_API_REFRESH_EMAIL=${MANAGED_SERVICES_AUTH_API_REFRESH_EMAIL} + - GITHUB_USERNAME=${GITHUB_USERNAME} + - GITHUB_TOKEN=${GITHUB_TOKEN} + - REPO_OWNER=${REPO_OWNER} + - REPO_NAME=${REPO_NAME} + - FILE_PATH=${FILE_PATH} + - BRANCH=${BRANCH} redis: image: 'redis:alpine' command: redis-server @@ -217,6 +197,10 @@ services: command: /opt/venv/bin/gunicorn wsgi:application --workers ${WEB_CONCURRENCY:-8} --timeout 0 -b :8000 + # entrypoint: + # /bin/sh -c "chmod +x ./whyis-init.sh && /opt/venv/bin/gunicorn + # wsgi:application --workers ${WEB_CONCURRENCY:-8} --timeout 0 -b :8000 & + # sleep 10 && ./whyis-init.sh" environment: - CHOKIDAR_USEPOLLING=true - NM_GRAPH_AUTH_SECRET=${TKNS} @@ -224,10 +208,11 @@ services: volumes: - ./whyis/materialsmine:/app - ./mockDB/fuseki:/app/run + - ./mockDB/whyis-init.sh:/app/whyis-init.sh ports: - '8000:8000' - mem_limit: 2048m - cpus: '0.25' + # mem_limit: 2048m + # cpus: '0.25' fuseki: build: whyis command: /opt/venv/bin/fuseki-server --mem /ds diff --git a/resfulservice/config/constant.js b/resfulservice/config/constant.js index 4edb7fd0..115d1bc2 100644 --- a/resfulservice/config/constant.js +++ b/resfulservice/config/constant.js @@ -152,7 +152,8 @@ module.exports = { }, ManagedServiceRegister: { dynamfit: '/dynamfit/extract/', - chemprops: '/chemprops/call/' + chemprops: '/chemprops/call/', + ontology: '/ontology/extract/' }, MGD_SVC_ERR_CODE: { default: { @@ -160,5 +161,9 @@ module.exports = { description: `This upload has been identified as potentially untrusted. We were unable to verify its origin from the anticipated source` } + }, + SEARCH_FIELD: { + label: 'label', + description: 'description' } }; diff --git a/resfulservice/config/xlsx.json b/resfulservice/config/xlsx.json index 65f97bb3..63aaf169 100644 --- a/resfulservice/config/xlsx.json +++ b/resfulservice/config/xlsx.json @@ -3514,6 +3514,42 @@ "type": "String", "required": false } + }, + "DeflectionAtBreak": { + "description": { + "cellValue": "5.1 Properties-Mechanical|[30,1]", + "type": "String", + "required": false + }, + "value": { + "cellValue": "5.1 Properties-Mechanical|[30,2]", + "type": "String", + "required": false + }, + "unit": { + "cellValue": "5.1 Properties-Mechanical|[30,3]", + "type": "List", + "required": false, + "validList": "pressure" + }, + "uncertainty": { + "uncertaintytype": { + "cellValue": "5.1 Properties-Mechanical|[30,4]", + "type": "List", + "required": false, + "validList": "uncertainty_type" + }, + "value": { + "cellValue": "5.1 Properties-Mechanical|[30,5]", + "type": "String", + "required": false + } + }, + "data": { + "cellValue": "5.1 Properties-Mechanical|[30,6]", + "type": "File", + "required": false + } } }, "Compression": { @@ -6632,11 +6668,7 @@ "File": { "cellValue": "6. Microstructure|[4,1]", "type": "File", - "validTypes": [ - "jpg", - "png", - "gif" - ] + "validTypes": ["jpg", "png", "gif"] }, "Description": { "cellValue": "6. Microstructure|[5,1]", @@ -6946,7 +6978,7 @@ "required": false, "unitofmeasurement": "nm/pi(vo)xel" }, - "2D_RVE": { + "TwoD_RVE": { "Width": { "cellValue": "7. Simulation - FEA|[38,2]", "type": "String", @@ -6960,7 +6992,7 @@ "unitofmeasurement": "pixel" } }, - "3D_RVE": { + "ThreeD_RVE": { "Width": { "cellValue": "7. Simulation - FEA|[41,2]", "type": "String", @@ -8091,4 +8123,4 @@ ] } } -} \ No newline at end of file +} diff --git a/resfulservice/spec/controllers/curationController.spec.js b/resfulservice/spec/controllers/curationController.spec.js index c42a45fc..880d367e 100644 --- a/resfulservice/spec/controllers/curationController.spec.js +++ b/resfulservice/spec/controllers/curationController.spec.js @@ -77,7 +77,7 @@ describe('Curation Controller', function () { header: () => {}, status: () => {}, json: () => {}, - send: () => {}, + send: (value) => value, setHeader: () => {} }; @@ -314,7 +314,7 @@ describe('Curation Controller', function () { const nextSpy = sinon.spy(); sinon.stub(res, 'status').returnsThis(); sinon.stub(res, 'json').returnsThis(); - sinon.stub(DatasetId, 'findOne').throws(); + sinon.stub(XlsxObject, 'find').throws(); await XlsxController.getControlSampleId(req, res, nextSpy); sinon.assert.calledOnce(nextSpy); @@ -820,6 +820,61 @@ describe('Curation Controller', function () { }); }); + context('Download curation XML', () => { + it('should return a 404 if curation is not found', async () => { + req.params = { controlID: 'L5_S4_Hareesh_2023' }; + sinon.stub(res, 'status').returnsThis(); + sinon.stub(res, 'json').returns(); + sinon.stub(res, 'setHeader').returns(true); + sinon.stub(XlsxObject, 'findOne').returns(null); + sinon.stub(XmlData, 'findOne').returns(null); + sinon.stub(latency, 'latencyCalculator').returns(true); + + const result = await XlsxController.getCurationXml(req, res, next); + expect(result).to.have.property('message'); + expect(result.message).to.equal('Curation sample not found'); + }); + it('should return a xml file for new curation', async () => { + req.params = { controlID: 'L5_S4_Hareesh_2023' }; + sinon.stub(res, 'status').returnsThis(); + sinon.stub(res, 'json').returns(); + sinon.stub(res, 'setHeader').returns(true); + sinon.stub(res, 'send').returns(mockXmlData.xml_str); + sinon.stub(XlsxObject, 'findOne').returns(fetchedCuratedXlsxObject); + sinon.stub(XmlData, 'findOne').returns(null); + sinon.stub(latency, 'latencyCalculator').returns(true); + + const result = await XlsxController.getCurationXml(req, res, next); + expect(result).to.be.a('String'); + }); + + it('should return the xml file for old curation', async () => { + req.params = { controlID: 'L5_S4_Hareesh_2023' }; + sinon.stub(res, 'status').returnsThis(); + sinon.stub(res, 'json').returns(); + sinon.stub(res, 'setHeader').returns(true); + sinon.stub(res, 'send').returns(mockXmlData.xml_str); + sinon.stub(XmlData, 'findOne').returns(mockXmlData); + sinon.stub(XlsxObject, 'findOne').returns(null); + sinon.stub(latency, 'latencyCalculator').returns(true); + + const result = await XlsxController.getCurationXml(req, res, next); + expect(result).to.be.a('String'); + }); + + it('should return a 500 server error when database throws an error', async function () { + req.params = { controlID: 'L5_S4_Hareesh_2023' }; + const nextSpy = sinon.spy(); + sinon.stub(res, 'status').returnsThis(); + sinon.stub(res, 'json').returnsThis(); + sinon.stub(XlsxObject, 'findOne').throws(); + sinon.stub(XmlData, 'findOne').throws(); + + await XlsxController.getCurationXml(req, res, nextSpy); + sinon.assert.called(nextSpy); + }); + }); + context('Update Curations', () => { it('should return 404 not found error if ID is invalid and isNew curation', async () => { req.body = { payload: mockCuratedXlsxObject }; diff --git a/resfulservice/spec/controllers/managedServiceController.spec.js b/resfulservice/spec/controllers/managedServiceController.spec.js index 059c41cd..37961af8 100644 --- a/resfulservice/spec/controllers/managedServiceController.spec.js +++ b/resfulservice/spec/controllers/managedServiceController.spec.js @@ -82,7 +82,7 @@ describe('Manage Service Controller Unit Tests:', function () { const appName = 'dynamfit'; req.params = { appName }; sinon.stub(latency, 'latencyCalculator').returns(true); - sinon.stub(axios, 'post').returns(dynafitSuccessResponse); + sinon.stub(axios, 'request').returns(dynafitSuccessResponse); sinon.stub(jwt, 'sign').returns('askle90lk.s409sjgl0ad.s0akng40'); const result = await manageServiceRequest(req, res, next); expect(result).to.have.property('appName'); @@ -99,7 +99,7 @@ describe('Manage Service Controller Unit Tests:', function () { req.params = { appName }; sinon.stub(latency, 'latencyCalculator').returns(true); sinon.stub(jwt, 'sign').returns('askle90lk.s409sjgl0ad.s0akng40'); - sinon.stub(axios, 'post').returns(dynamfitErrorResponse); + sinon.stub(axios, 'request').returns(dynamfitErrorResponse); const result = await manageServiceRequest(req, res, next); expect(result).to.have.property('message'); expect(result.message).to.equal(dynamfitErrorResponse.data.message); @@ -109,7 +109,7 @@ describe('Manage Service Controller Unit Tests:', function () { const appName = 'dynamfit'; req.params = { appName }; const nextSpy = sinon.spy(); - sinon.stub(axios, 'post').throws(); + sinon.stub(axios, 'request').throws(); sinon.stub(latency, 'latencyCalculator').returns(true); await manageServiceRequest(req, res, nextSpy); @@ -121,7 +121,7 @@ describe('Manage Service Controller Unit Tests:', function () { it('should return a 500 server error when chemprops server is not accessible', async function () { req.originalUrl = '/nm/chemprops/init'; const nextSpy = sinon.spy(); - sinon.stub(axios, 'post').throws(); + sinon.stub(axios, 'request').throws(); sinon.stub(latency, 'latencyCalculator').returns(true); await chemPropsSeed(req, res, nextSpy); diff --git a/resfulservice/spec/graphql/resolver/comment.spec.js b/resfulservice/spec/graphql/resolver/comment.spec.js index 4468474e..77a02325 100644 --- a/resfulservice/spec/graphql/resolver/comment.spec.js +++ b/resfulservice/spec/graphql/resolver/comment.spec.js @@ -2,71 +2,29 @@ const chai = require('chai'); const sinon = require('sinon'); const Comment = require('../../../src/models/comment'); const graphQlSchema = require('../../../src/graphql'); -const { Mutation: { postComment, editComment }, Query: { loadComment }} = require('../../../src/graphql/resolver'); - +const { + Mutation: { postComment, editComment }, + Query: { loadComment } +} = require('../../../src/graphql/resolver'); +const { + mockCommentList, + mockDBComment, + mockCommentInput, + mockComment, + user +} = require('../../mocks'); const { expect } = chai; -const user = { - _id: 'ai094oja09aw40-o', - displayName: "test" -} -const mockComment = { - "comment": "test comment", - "type": "xml", - "identifier": "64394c8032bc6325505af6f9", - "user": "64394c8032bc6325505af6f9" -} - -const mockCommentInput = { - "id": "64394c8032bc6325505af6f9", - "comment": "test comment", - "type": "xml", - "identifier": "64394c8032bc6325505af6f9" -} - -const mockDBComment = { - "user": { - "givenName": "Test", - "surName": "Test" - }, - ...mockComment, - lean: () => this, - populate: sinon.stub().returnsThis() -} - -const mockCommentList = [ - { - "_id": "64397a5cdffb639553bf62e4", - "comment": "first comment", - "user": { - "givenName": "Test", - "surName": "Test" - }, - "createdAt": "1681488476581", - "updatedAt": "1681489494515" - }, - { - "_id": "64397a5cdffb639553bf62e4", - "comment": "secont comment", - "user": { - "givenName": "Test", - "surName": "Test" - }, - "createdAt": "1681488476581", - "updatedAt": "1681489494515" - } -] describe('Comment Resolver Unit Tests:', function () { - afterEach(() => sinon.restore()); - const req = { logger: { info: (message) => { }, error: (message) => { } } } + const req = { logger: { info: (message) => {}, error: (message) => {} } }; context('postComment', () => { const input = { ...mockCommentInput - } + }; it('should have postComment(...) as a Mutation resolver', async function () { const { postComment } = graphQlSchema.getMutationType().getFields(); @@ -79,24 +37,35 @@ describe('Comment Resolver Unit Tests:', function () { }); it('should create new comment', async () => { - sinon.stub(Comment.prototype, 'save').callsFake(() => (mockDBComment)) + sinon.stub(Comment.prototype, 'save').callsFake(() => mockDBComment); // sinon.stub(MaterialTemplate.prototype, 'save').callsFake(() => ({...input, _id: 'b39ak9qna'})) - const comment = await postComment({}, { input }, { user, req, isAuthenticated: true }); + const comment = await postComment( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(comment).to.have.property('comment'); }); it('should return a 401 unauthenticated error', async () => { - - const result = await postComment({}, { input: { } }, { user, req, isAuthenticated: false }); + const result = await postComment( + {}, + { input: {} }, + { user, req, isAuthenticated: false } + ); expect(result).to.have.property('extensions'); expect(result.extensions.code).to.be.equal(401); }); - it("should throw a 500, server error", async () => { + it('should throw a 500, server error', async () => { sinon.stub(Comment.prototype, 'save').throws(); - const error = await postComment({}, { input }, { user, req, isAuthenticated: true }); + const error = await postComment( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(500); @@ -106,37 +75,52 @@ describe('Comment Resolver Unit Tests:', function () { const { postComment } = graphQlSchema.getMutationType().getFields(); expect(postComment.type.toString()).to.equal('Comment!'); }); - }) + }); context('editComment', () => { - const input = { ...mockCommentInput } - it("should throw a 401, not authenticated error", async () => { - - const error = await editComment({}, { input }, { user, req, isAuthenticated: false }); + const input = { ...mockCommentInput }; + it('should throw a 401, not authenticated error', async () => { + const error = await editComment( + {}, + { input }, + { user, req, isAuthenticated: false } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(401); }); it("should return a 404 error if column doesn't exist", async () => { sinon.stub(Comment, 'findOneAndUpdate').returns(null); - const error = await editComment({}, { input }, { user, req, isAuthenticated: true }); + const error = await editComment( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(404); }); - it("should update column if column exists", async () => { - sinon.stub(Comment, 'findOneAndUpdate').returns({...mockDBComment }); + it('should update column if column exists', async () => { + sinon.stub(Comment, 'findOneAndUpdate').returns({ ...mockDBComment }); - const result = await editComment({}, { input }, { user, req, isAuthenticated: true }); + const result = await editComment( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('comment'); expect(result).to.have.property('user'); }); - it("should throw a 500, server error", async () => { + it('should throw a 500, server error', async () => { sinon.stub(Comment, 'findOneAndUpdate').throws(); - const error = await editComment({}, { input }, { user, req, isAuthenticated: true }); + const error = await editComment( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(500); @@ -144,25 +128,33 @@ describe('Comment Resolver Unit Tests:', function () { }); context('loadComment', () => { - const input = { ...mockComment, pageNumber: 1, pageSize: 10 } + const input = { ...mockComment, pageNumber: 1, pageSize: 10 }; - it("should return paginated lists of comments", async () => { + it('should return paginated lists of comments', async () => { sinon.stub(Comment, 'countDocuments').returns(2); sinon.stub(Comment, 'find').returns({ limit: sinon.stub().returnsThis(), skip: sinon.stub().returns(mockCommentList) }); - const result = await loadComment({}, { input }, { user, req, isAuthenticated: true }); + const result = await loadComment( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('comments'); expect(result.comments).to.be.an('Array'); }); - it("should throw a 500, server error", async () => { - sinon.stub(Comment, 'countDocuments').returns(2) + it('should throw a 500, server error', async () => { + sinon.stub(Comment, 'countDocuments').returns(2); sinon.stub(Comment, 'find').throws(); - const error = await loadComment({}, { input }, { user, req, isAuthenticated: true }); + const error = await loadComment( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(500); diff --git a/resfulservice/spec/graphql/resolver/contact.spec.js b/resfulservice/spec/graphql/resolver/contact.spec.js index cdbc7678..7576f364 100644 --- a/resfulservice/spec/graphql/resolver/contact.spec.js +++ b/resfulservice/spec/graphql/resolver/contact.spec.js @@ -2,6 +2,11 @@ const chai = require('chai'); const sinon = require('sinon'); const Contact = require('../../../src/models/contact'); const graphQlSchema = require('../../../src/graphql'); +const { + mockContact, + mockUserContact, + mockUpdatedContact +} = require('../../mocks'); const { Mutation: { submitContact, updateContact }, Query: { getUserContacts, contacts } @@ -11,23 +16,6 @@ const FileController = require('../../../src/controllers/fileController'); const { expect } = chai; -const mockContact = { - fullName: 'test user', - email: 'test@example.com', - purpose: 'QUESTION', - message: 'test message', - attachments: [ - '/api/files/strategic_beetle_joelle-2024-02-15T09:25:42.264Z-master_template (5).xlsx?isStore=true', - '/api/files/strategic_beetle_joelle-2024-02-15T09:27:07.905Z-master_template.xlsx?isStore=true' - ] -}; - -const mockUpdatedContact = { - ...mockContact, - resolved: true, - response: 'Thanks for reaching out. We are working on it' -}; - describe('Contact Resolver Unit Tests:', function () { afterEach(() => sinon.restore()); @@ -124,15 +112,6 @@ describe('Contact Resolver Unit Tests:', function () { }); context('getUserContacts', () => { - const mockUserContact = { - _id: 'akdn9wqkn', - fullName: 'test user', - email: 'test@example.com', - purpose: 'QUESTION', - message: 'test message', - lean: () => this - }; - it("should return paginated lists of a user's contacts", async () => { sinon.stub(Contact, 'countDocuments').returns(1); sinon.stub(Contact, 'find').returns(mockUserContact); diff --git a/resfulservice/spec/graphql/resolver/dataset.spec.js b/resfulservice/spec/graphql/resolver/dataset.spec.js index e1bebb09..8b428d1a 100644 --- a/resfulservice/spec/graphql/resolver/dataset.spec.js +++ b/resfulservice/spec/graphql/resolver/dataset.spec.js @@ -4,90 +4,19 @@ const DatasetId = require('../../../src/models/datasetId'); const Dataset = require('../../../src/models/dataset'); const User = require('../../../src/models/user'); const graphQlSchema = require('../../../src/graphql'); -const { Mutation: { createDatasetId, createDataset }, Query: { getUserDataset, getFilesets }} = require('../../../src/graphql/resolver'); - +const { + Mutation: { createDatasetId, createDataset }, + Query: { getUserDataset, getFilesets } +} = require('../../../src/graphql/resolver'); +const { user, mockDataset, mockFiles } = require('../../mocks'); const { expect } = chai; - describe('Dataset Resolver Unit Tests:', function () { - afterEach(() => sinon.restore()); - this.timeout(10000) + this.timeout(10000); - const input = { - doi: 'unpublished/doi-tMbKM2ba5aNwo2ZKPVucBS', - datasetId: '62fce36374da548513a38a9b', - files: [ - { - fieldname: 'uploadfile', - originalname: 'Hopetoun_falls.jpg', - encoding: '7bit', - mimetype: 'image/jpeg', - destination: 'mm_files', - filename: 'comparative_aphid_agathe-2022-08-18T10:00:40.910Z-Hopetoun_falls.jpg', - path: 'mm_files/comparative_aphid_agathe-2022-08-18T10:00:40.910Z-Hopetoun_falls.jpg', - size: 2954043, - }, - { - fieldname: 'uploadfile', - originalname: 'flowers-276014__340.jpg', - encoding: '7bit', - mimetype: 'image/jpeg', - destination: 'mm_files', - filename: 'comparative_aphid_agathe-2022-08-18T10:00:41.018Z-flowers-276014__340.jpg', - path: 'mm_files/comparative_aphid_agathe-2022-08-18T10:00:41.018Z-flowers-276014__340.jpg', - size: 56575, - }, - ], - } - - - - const mockDataset = { - _id: "62f11b1328eedaab012d127c", - datasetId: "62f11b1328eedaab012d127c", - userid: "62f119fb28eedaab012d1262", - filesets: [ - { - fileset: 'E109_S2_Huang_2016', - files: [ - { - type: 'blob', - id: '5b51f112e74a1d4cdbad6a1d', - metadata: { - filename: '4.tif', - contentType: 'image/tiff', - }, - }, - { - type: 'blob', - id: '5b51f137e74a1d4cdbad6a3a', - metadata: { - filename: '5.tif', - contentType: 'image/tiff', - }, - }, - ], - }, - ], - skip: sinon.stub().returnsThis(), - limit: sinon.stub().returnsThis(), - lean: sinon.stub().returnsThis() - } - - const user = { - _id: '62dab1b76db8739c8330611d', - alias: 'testalias', - givenName: 'test', - surName: 'test user', - displayName: 'tester', - userid: '62dab1b76db8739c8330611d', - email: 'test@example.com', - roles: 'member' - } - - const req = { logger: { info: (message) => { }, error: (message) => { } } } + const req = { logger: { info: (message) => {}, error: (message) => {} } }; context('createDatasetId', () => { it('should have createDatasetId(...) as a Mutation resolver', async function () { @@ -95,39 +24,61 @@ describe('Dataset Resolver Unit Tests:', function () { expect(createDatasetId.name).to.equal('createDatasetId'); expect(createDatasetId.type.toString()).to.equal('Datasets!'); }); - - it("should throw a 401, not authenticated error", async () => { - const result = await createDatasetId({}, { }, { user, req, isAuthenticated: false }); + + it('should throw a 401, not authenticated error', async () => { + const result = await createDatasetId( + {}, + {}, + { user, req, isAuthenticated: false } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(401) + expect(result.extensions.code).to.be.equal(401); }); it('should create a new datasetId', async () => { sinon.stub(DatasetId, 'findOne').returns(null); - sinon.stub(DatasetId.prototype, 'save').callsFake(() => ({_id: '62d951cb6981a12d136a0a0d', status: 'WORK IN PROGRESS', samples: [] })) - - const datasetId = await createDatasetId({}, {}, { user, req, isAuthenticated: true }); + sinon.stub(DatasetId.prototype, 'save').callsFake(() => ({ + _id: '62d951cb6981a12d136a0a0d', + status: 'WORK IN PROGRESS', + samples: [] + })); + + const datasetId = await createDatasetId( + {}, + {}, + { user, req, isAuthenticated: true } + ); expect(datasetId).to.have.property('datasetGroupId'); - }); - + }); - it("should throw a 409, when an unused datasetId exists", async () => { - sinon.stub(DatasetId, 'findOne').returns({_id: '62d951cb6981a12d136a0a0d', status: 'WORK IN PROGRESS', samples: [] }) - const result = await createDatasetId({}, { }, { user, req, isAuthenticated: true }); + it('should throw a 409, when an unused datasetId exists', async () => { + sinon.stub(DatasetId, 'findOne').returns({ + _id: '62d951cb6981a12d136a0a0d', + status: 'WORK IN PROGRESS', + samples: [] + }); + const result = await createDatasetId( + {}, + {}, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(409) + expect(result.extensions.code).to.be.equal(409); }); - it('should throw a 500 Internal server error when error is thrown', async () => { sinon.stub(DatasetId, 'findOne').throws(); - const result = await createDatasetId({}, { }, { user, req, isAuthenticated: true }); + const result = await createDatasetId( + {}, + {}, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(500) + expect(result.extensions.code).to.be.equal(500); }); it('should return DatasetId! datatype for createDatasetId(...) mutation', () => { @@ -137,33 +88,31 @@ describe('Dataset Resolver Unit Tests:', function () { }); context('getUserDataset', () => { - const mockDatasetId = { - _id: '9q4kn9898ani4a8n49hn49nv49', - dataset: mockDataset, - user, - status: 'WORK_IN_PROGRESS', - lean: () => this, - populate: () => this, - limit: () => this - } const input = { pageNumber: 1, pageSize: 10, status: 'APPROVED' - } + }; it("should return paginated lists of a user's datasets", async () => { sinon.stub(Dataset, 'find').returns(mockDataset); sinon.stub(Dataset, 'countDocuments').returns(1); sinon.stub(User, 'findOne').returns(user); - const datasets = await getUserDataset({}, { input }, { user, req, isAuthenticated: true }); + const datasets = await getUserDataset( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(datasets).to.have.property('datasets'); expect(datasets.totalItems).to.equal(1); }); - it("should throw a 401, not authenticated error", async () => { - - const error = await getUserDataset({}, { input }, { user, req, isAuthenticated: false }); + it('should throw a 401, not authenticated error', async () => { + const error = await getUserDataset( + {}, + { input: mockFiles }, + { user, req, isAuthenticated: false } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(401); }); @@ -171,55 +120,77 @@ describe('Dataset Resolver Unit Tests:', function () { it('should return a 500 error', async () => { sinon.stub(Dataset, 'find').throws(); - const result = await getUserDataset({}, { input }, { user, req, isAuthenticated: true }); + const result = await getUserDataset( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(500) + expect(result.extensions.code).to.be.equal(500); }); }); context('getFilesets', () => { - const mockFilesetAggregate = [{ - count: 1, - filesets: mockDataset.filesets - }]; + const mockFilesetAggregate = [ + { + count: 1, + filesets: mockDataset.filesets + } + ]; const filesetInput = { - ...input, + ...mockFiles, pageSize: 10, pageNumber: 1 - } - it("should return file list of a fileset when both datasetId and filesetName are provided", async () => { + }; + it('should return file list of a fileset when both datasetId and filesetName are provided', async () => { sinon.stub(Dataset, 'aggregate').returns(mockFilesetAggregate); - // sinon.stub(mockDataset, 'lean').returnsThis(); - const fileset = await getFilesets({}, { input: { ...input, filesetName: 'E109_S2_Huang_2016' } }, { user, req, isAuthenticated: true }); + // sinon.stub(mockDataset, 'lean').returnsThis(); + const fileset = await getFilesets( + {}, + { input: { ...mockFiles, filesetName: 'E109_S2_Huang_2016' } }, + { user, req, isAuthenticated: true } + ); expect(fileset).to.have.property('filesetName'); expect(fileset).to.have.property('files'); expect(fileset.files).to.be.an('array'); - }); - it("should return file list of a fileset when only datasetId is provided", async () => { + it('should return file list of a fileset when only datasetId is provided', async () => { sinon.stub(Dataset, 'aggregate').returns(mockFilesetAggregate); - const filesetGroup = await getFilesets({}, { input: filesetInput }, { user, req, isAuthenticated: true }); + const filesetGroup = await getFilesets( + {}, + { input: filesetInput }, + { user, req, isAuthenticated: true } + ); expect(filesetGroup).to.have.property('filesets'); expect(filesetGroup.filesets).to.be.an('array'); expect(filesetGroup).to.have.property('pageSize'); }); - it("should return an aggregated list of a fileset when only filesetName is provided", async () => { - sinon.stub(Dataset, 'aggregate').returns([{filesets: mockDataset.filesets}]); - const fileset = await getFilesets({}, {input: { filesetName: 'E109_S2_Huang_2016' } }, { user, req, isAuthenticated: true }); + it('should return an aggregated list of a fileset when only filesetName is provided', async () => { + sinon + .stub(Dataset, 'aggregate') + .returns([{ filesets: mockDataset.filesets }]); + const fileset = await getFilesets( + {}, + { input: { filesetName: 'E109_S2_Huang_2016' } }, + { user, req, isAuthenticated: true } + ); expect(fileset).to.have.property('filesetName'); expect(fileset).to.have.property('files'); expect(fileset.files).to.be.an('array'); }); - it("should throw a 401, not authenticated error", async () => { - - const error = await getFilesets({}, { input }, { user, req, isAuthenticated: false }); + it('should throw a 401, not authenticated error', async () => { + const error = await getFilesets( + {}, + { input: mockFiles }, + { user, req, isAuthenticated: false } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(401); }); @@ -227,10 +198,14 @@ describe('Dataset Resolver Unit Tests:', function () { it('should return a 500 error', async () => { sinon.stub(Dataset, 'aggregate').throws(); - const result = await getFilesets({}, { input }, { user, req, isAuthenticated: true }); + const result = await getFilesets( + {}, + { input: mockFiles }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(500) + expect(result.extensions.code).to.be.equal(500); }); }); @@ -245,11 +220,19 @@ describe('Dataset Resolver Unit Tests:', function () { const mockCreatedDataset = { _id: '62d951cb6981a12d136a0a0d', ...mockDataset - } - sinon.stub(Dataset, 'findOne').returns({ _id: '62d951cb6981a12d136a0a0d', filesets: [] }) - sinon.stub(Dataset, 'findOneAndUpdate').callsFake(() => (mockCreatedDataset)) - - const dataset = await createDataset({}, { input }, { user, req, isAuthenticated: true }); + }; + sinon + .stub(Dataset, 'findOne') + .returns({ _id: '62d951cb6981a12d136a0a0d', filesets: [] }); + sinon + .stub(Dataset, 'findOneAndUpdate') + .callsFake(() => mockCreatedDataset); + + const dataset = await createDataset( + {}, + { input: mockFiles }, + { user, req, isAuthenticated: true } + ); expect(dataset).to.have.property('filesets'); }); @@ -257,52 +240,79 @@ describe('Dataset Resolver Unit Tests:', function () { const mockCreatedDataset = { _id: '62d951cb6981a12d136a0a0d', ...mockDataset - } - sinon.stub(Dataset, 'findOne').returns({ _id: '62d951cb6981a12d136a0a0d', filesets: [] }) - sinon.stub(Dataset, 'findOneAndUpdate').callsFake(() => (mockCreatedDataset)) - - const dataset = await createDataset({}, { input: {...input, files: [] } }, { user, req, isAuthenticated: true }); + }; + sinon + .stub(Dataset, 'findOne') + .returns({ _id: '62d951cb6981a12d136a0a0d', filesets: [] }); + sinon + .stub(Dataset, 'findOneAndUpdate') + .callsFake(() => mockCreatedDataset); + + const dataset = await createDataset( + {}, + { input: { ...mockFiles, files: [] } }, + { user, req, isAuthenticated: true } + ); expect(dataset).to.have.property('filesets'); }); - it("should throw a 401, not authenticated error", async () => { - const result = await createDataset({}, { input }, { user, req, isAuthenticated: false }); + it('should throw a 401, not authenticated error', async () => { + const result = await createDataset( + {}, + { input: mockFiles }, + { user, req, isAuthenticated: false } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(401) + expect(result.extensions.code).to.be.equal(401); }); it('should return a 404, not found error', async () => { - sinon.stub(Dataset, 'findOne').returns(null) + sinon.stub(Dataset, 'findOne').returns(null); - const result = await createDataset({}, { input }, { user, req, isAuthenticated: true }); + const result = await createDataset( + {}, + { input: mockFiles }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(404) + expect(result.extensions.code).to.be.equal(404); }); it('should return a 409, conflict error', async () => { - sinon.stub(Dataset, 'findOne').returns(mockDataset) + sinon.stub(Dataset, 'findOne').returns(mockDataset); - const result = await createDataset({}, { input }, { user, req, isAuthenticated: true }); + const result = await createDataset( + {}, + { input: mockFiles }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(409) + expect(result.extensions.code).to.be.equal(409); }); it('should throw a 500 error', async () => { - sinon.stub(Dataset, 'findOne').returns({ _id: '62d951cb6981a12d136a0a0d', status: 'WORK IN PROGRESS' }) - sinon.stub(Dataset, 'findOneAndUpdate').throws() + sinon.stub(Dataset, 'findOne').returns({ + _id: '62d951cb6981a12d136a0a0d', + status: 'WORK IN PROGRESS' + }); + sinon.stub(Dataset, 'findOneAndUpdate').throws(); - const result = await createDataset({}, { input }, { user, req, isAuthenticated: true }); + const result = await createDataset( + {}, + { input: mockFiles }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(500) + expect(result.extensions.code).to.be.equal(500); }); it('should return CreatedDataset datatype for createDatasetId(...) mutation', () => { const { createDataset } = graphQlSchema.getMutationType().getFields(); expect(createDataset.type.toString()).to.equal('CreatedDataset!'); }); - }) + }); }); diff --git a/resfulservice/spec/graphql/resolver/material_template.spec.js b/resfulservice/spec/graphql/resolver/material_template.spec.js index 13e2dd6b..e8ea1e99 100644 --- a/resfulservice/spec/graphql/resolver/material_template.spec.js +++ b/resfulservice/spec/graphql/resolver/material_template.spec.js @@ -1,102 +1,60 @@ const chai = require('chai'); const sinon = require('sinon'); -const MaterialTemplate = require('../../../src/models/xlsxCurationList') +const MaterialTemplate = require('../../../src/models/xlsxCurationList'); const graphQlSchema = require('../../../src/graphql'); -const { Mutation: { createXlsxCurationList, updateXlsxCurationList, deleteXlsxCurationList }, Query: { getXlsxCurationList }} = require('../../../src/graphql/resolver'); - +const { + Mutation: { + createXlsxCurationList, + updateXlsxCurationList, + deleteXlsxCurationList + }, + Query: { getXlsxCurationList } +} = require('../../../src/graphql/resolver'); +const { + user, + mockColumnsInput, + mockColumn, + mockDBColumn, + mockConflictError +} = require('../../mocks'); const { expect } = chai; -const user = { - _id: 'ai094oja09aw40-o', - displayName: "test" -} -const mockColumn = { - field: "Flight_width::Uniter", - values: [ - "nm", - "um", - "mm", - "cm", - "m" - ] -} - -const mockColumnsInput = { - columns: [ - { - field: "Flight_width::Units", - values: [ - "nm", - "um", - "mm", - "cm", - "m" - ] - }, - { - field: "Origins", - values: [ - "experiments", - "informatics (data science)", - "simulations", - "theory" - ] - } - ] -} - -const mockDBColumn = { - _id: 'kas2344nlkla', - ...mockColumn, - lean: () => this -} - -const mockConflictError = { - writeErrors: [ - { - err: { - index: 0, - code: 11000, - errmsg: 'E11000 duplicate key error collection: mgi.materialtemplates index: field_1 dup key: { field: "Flight_width::Units" }', - } - }, - { - err: { - index: 1, - code: 11000, - errmsg: 'E11000 duplicate key error collection: mgi.materialtemplates index: field_1 dup key: { field: "Origins" }', - } - } - ] -} describe('Material Template Resolver Unit Tests:', function () { - afterEach(() => sinon.restore()); - const req = { logger: { info: (message) => { }, error: (message) => { } } } + const req = { logger: { info: (message) => {}, error: (message) => {} } }; context('createXlsxCurationList', () => { const input = { ...mockColumnsInput - } + }; it('should have createXlsxCurationList(...) as a Mutation resolver', async function () { - const { createXlsxCurationList } = graphQlSchema.getMutationType().getFields(); + const { createXlsxCurationList } = graphQlSchema + .getMutationType() + .getFields(); expect(createXlsxCurationList.name).to.equal('createXlsxCurationList'); }); it('should create new material colums', async () => { sinon.stub(MaterialTemplate, 'insertMany').returns(true); // sinon.stub(MaterialTemplate.prototype, 'save').callsFake(() => ({...input, _id: 'b39ak9qna'})) - const columns = await createXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const columns = await createXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(columns).to.have.property('columns'); }); it('should return a 401 unauthenticated error', async () => { - - const result = await createXlsxCurationList({}, { input: { } }, { user, req, isAuthenticated: false }); + const result = await createXlsxCurationList( + {}, + { input: {} }, + { user, req, isAuthenticated: false } + ); expect(result).to.have.property('extensions'); expect(result.extensions.code).to.be.equal(401); @@ -104,47 +62,72 @@ describe('Material Template Resolver Unit Tests:', function () { it('should return a 409 conflict error', async () => { sinon.stub(MaterialTemplate, 'insertMany').throws(mockConflictError); - const result = await createXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const result = await createXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('extensions'); expect(result.extensions.code).to.be.equal(409); }); it('should return MaterialColumns!! datatype for createXlsxCurationList(...) mutation', () => { - const { createXlsxCurationList } = graphQlSchema.getMutationType().getFields(); - expect(createXlsxCurationList.type.toString()).to.equal('MaterialColumns!'); + const { createXlsxCurationList } = graphQlSchema + .getMutationType() + .getFields(); + expect(createXlsxCurationList.type.toString()).to.equal( + 'MaterialColumns!' + ); }); - }) + }); context('updateXlsxCurationList', () => { - const input = { ...mockColumn } - it("should throw a 401, not authenticated error", async () => { - - const error = await updateXlsxCurationList({}, { input }, { user, req, isAuthenticated: false }); + const input = { ...mockColumn }; + it('should throw a 401, not authenticated error', async () => { + const error = await updateXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: false } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(401); }); it("should return a 404 error if column doesn't exist", async () => { sinon.stub(MaterialTemplate, 'findOneAndUpdate').returns(null); - const error = await updateXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const error = await updateXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(404); }); - it("should update column if column exists", async () => { - sinon.stub(MaterialTemplate, 'findOneAndUpdate').returns({...mockDBColumn, ...input, user}); + it('should update column if column exists', async () => { + sinon + .stub(MaterialTemplate, 'findOneAndUpdate') + .returns({ ...mockDBColumn, ...input, user }); - const result = await updateXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const result = await updateXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('field'); expect(result).to.have.property('values'); }); - it("should throw a 500, server error", async () => { + it('should throw a 500, server error', async () => { sinon.stub(MaterialTemplate, 'findOneAndUpdate').throws(); - const error = await updateXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const error = await updateXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(500); @@ -152,9 +135,13 @@ describe('Material Template Resolver Unit Tests:', function () { }); context('deleteXlsxCurationList', () => { - const input = { field: mockColumn.field } - it("should throw a 401, not authenticated error", async () => { - const error = await deleteXlsxCurationList({}, { input }, { user, req, isAuthenticated: false }); + const input = { field: mockColumn.field }; + it('should throw a 401, not authenticated error', async () => { + const error = await deleteXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: false } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(401); @@ -162,29 +149,41 @@ describe('Material Template Resolver Unit Tests:', function () { it("should return a 404 error if column doesn't exist", async () => { sinon.stub(MaterialTemplate, 'findOneAndDelete').returns({ - lean: sinon.stub().returns(null), + lean: sinon.stub().returns(null) }); - const error = await deleteXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const error = await deleteXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(404); }); - it("should delete a curation list", async () => { + it('should delete a curation list', async () => { sinon.stub(MaterialTemplate, 'findOneAndDelete').returns({ - lean: sinon.stub().returns(mockDBColumn), + lean: sinon.stub().returns(mockDBColumn) }); - const result = await deleteXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const result = await deleteXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('field'); expect(result).to.have.property('values'); }); - it("should throw a 500, server error", async () => { + it('should throw a 500, server error', async () => { sinon.stub(MaterialTemplate, 'findOneAndDelete').returns({ - lean: sinon.stub().throws(), + lean: sinon.stub().throws() }); - const error = await deleteXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const error = await deleteXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(500); @@ -192,45 +191,60 @@ describe('Material Template Resolver Unit Tests:', function () { }); context('getXlsxCurationList', () => { - const input = { pageNumber: 1, pageSize: 10 } - it("should throw a 401, not authenticated error", async () => { - - const error = await getXlsxCurationList({}, { input }, { user, req, isAuthenticated: false }); + const input = { pageNumber: 1, pageSize: 10 }; + it('should throw a 401, not authenticated error', async () => { + const error = await getXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: false } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(401); }); - it("should return paginated lists of columns", async () => { + it('should return paginated lists of columns', async () => { sinon.stub(MaterialTemplate, 'countDocuments').returns(2); sinon.stub(MaterialTemplate, 'find').returns({ limit: sinon.stub().returnsThis(), skip: sinon.stub().returns(mockColumnsInput.columns) }); - const result = await getXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const result = await getXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('columns'); expect(result.columns).to.be.an('Array'); }); - it("should return paginated lists of columns", async () => { + it('should return paginated lists of columns', async () => { const input = { field: mockColumn.field }; - sinon.stub(MaterialTemplate, 'countDocuments').returns(2) + sinon.stub(MaterialTemplate, 'countDocuments').returns(2); sinon.stub(MaterialTemplate, 'find').returns({ limit: sinon.stub().returnsThis(), skip: sinon.stub().returns(mockColumnsInput.columns) }); - const result = await getXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const result = await getXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(result).to.have.property('columns'); expect(result.columns).to.be.an('Array'); }); - it("should throw a 500, server error", async () => { - sinon.stub(MaterialTemplate, 'countDocuments').returns(2) + it('should throw a 500, server error', async () => { + sinon.stub(MaterialTemplate, 'countDocuments').returns(2); sinon.stub(MaterialTemplate, 'find').throws(); - const error = await getXlsxCurationList({}, { input }, { user, req, isAuthenticated: true }); + const error = await getXlsxCurationList( + {}, + { input }, + { user, req, isAuthenticated: true } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(500); diff --git a/resfulservice/spec/graphql/resolver/pixelated.spec.js b/resfulservice/spec/graphql/resolver/pixelated.spec.js index f5633610..acd7a943 100644 --- a/resfulservice/spec/graphql/resolver/pixelated.spec.js +++ b/resfulservice/spec/graphql/resolver/pixelated.spec.js @@ -1,68 +1,58 @@ const chai = require('chai'); const sinon = require('sinon'); -const PixelData = require('../../../src/models/pixelated') -const graphQlSchema = require('../../../src/graphql'); -const { Query: { pixelData } } = require('../../../src/graphql/resolver'); - +const PixelData = require('../../../src/models/pixelated'); +const { + Query: { pixelData } +} = require('../../../src/graphql/resolver'); +const { mockPixelData, pixelatedDataInput } = require('../../mocks'); const { expect } = chai; describe('PixelData Resolver Unit Tests:', function () { - afterEach(() => sinon.restore()); - this.timeout(10000) + this.timeout(10000); - const input = { - unitCell: 'TEN', - pageNumber: 1, - pageSize: 1 - } - - const req = { logger: { info: (_message) => { }, error: (_message) => { } } } + const req = { logger: { info: (_message) => {}, error: (_message) => {} } }; context('pixelData', () => { it('should return paginated lists of pixelData', async () => { - const mockPixelData = { - _id: 'akdn9wqknd90uaoikn9ahoi4489i', - symmetry: 'C4v', - unit_cell_x_pixels: '10', - unit_cell_y_pixels: '10', - geometry_condensed: '000000000001001', - geometry_full: '1010000101000000000010000000010000000000000000000000000000000000000000100000000100000000001010000101', - condition: 'Plane Strain', - C11: '2963290579', - C12: '1459531181', - C22: '2963290579', - skip: () => ({_id: 'akdn9wqkn', ...input }), - lean: () => ({_id: 'akdn9wqkn', ...input }), - limit: () => ({_id: 'akdn9wqkn', ...input }) - } sinon.stub(PixelData, 'countDocuments').returns(1); sinon.stub(PixelData, 'find').returns(mockPixelData); sinon.stub(mockPixelData, 'skip').returnsThis(); sinon.stub(mockPixelData, 'limit').returnsThis(); sinon.stub(mockPixelData, 'lean').returns([mockPixelData]); - const pixelatedData = await pixelData({}, { input }, { req }); + const pixelatedData = await pixelData( + {}, + { input: pixelatedDataInput }, + { req } + ); expect(pixelatedData).to.have.property('data'); expect(pixelatedData.totalItems).to.equal(1); }); - it("should throw a 400, input error", async () => { - - const error = await pixelData({}, { input: { unitCell: "BOTH" } }, { req }); + it('should throw a 400, input error', async () => { + const error = await pixelData( + {}, + { input: { unitCell: 'BOTH' } }, + { req } + ); expect(error).to.have.property('extensions'); expect(error.extensions.code).to.be.equal(400); }); it('should return a 500 error', async () => { sinon.stub(PixelData, 'countDocuments').returns(1); - sinon.stub(PixelData, 'find').throws() + sinon.stub(PixelData, 'find').throws(); - const result = await pixelData({}, { input }, { req, isAuthenticated: true }); + const result = await pixelData( + {}, + { input: pixelatedDataInput }, + { req, isAuthenticated: true } + ); expect(result).to.have.property('extensions'); - expect(result.extensions.code).to.be.equal(500) + expect(result.extensions.code).to.be.equal(500); }); - }) -}); + }); +}); diff --git a/resfulservice/spec/graphql/resolver/xml.spec.js b/resfulservice/spec/graphql/resolver/xml.spec.js index 98112d6b..422fdd76 100644 --- a/resfulservice/spec/graphql/resolver/xml.spec.js +++ b/resfulservice/spec/graphql/resolver/xml.spec.js @@ -7,6 +7,7 @@ const { Query: { xmlFinder, xmlViewer } } = require('../../../src/graphql/resolver'); const CuratedSamples = require('../../../src/models/curatedSamples'); +const { mockDBXmlDataList, mockDBXmlData } = require('../../mocks'); const { expect } = chai; @@ -18,25 +19,6 @@ const mockXmlData = { entityState: 'EditedValid' }; -const mockXmlDataList = [ - { - id: '6622848a808bdbee354f96d3', - title: 'L311_S10_Lou_2009.xml', - status: 'Not Approved', - isNewCuration: false, - sequence: 311, - user: '65b8ec85c3d3b2ed82fe4029' - }, - { - id: '65cf719860df704a1ca74428', - title: 'E0_S1_Uthdev_2003.xml', - status: 'Approved', - isNewCuration: true, - sequence: null, - user: '65b8ec85c3d3b2ed82fe4029' - } -]; - describe('XmlData Resolver Unit Tests:', function () { afterEach(() => sinon.restore()); @@ -58,33 +40,35 @@ describe('XmlData Resolver Unit Tests:', function () { sinon.stub(CuratedSamples, 'countDocuments').returns(1); sinon .stub(XmlData, 'aggregate') - .returns([{ count: mockXmlDataList.length, xmlData: mockXmlDataList }]); + .returns([ + { count: mockDBXmlDataList.length, xmlData: mockDBXmlDataList } + ]); const result = await xmlFinder({}, { input }, { req }); expect(result).to.have.property('xmlData'); expect(result.xmlData).to.be.an('Array'); - expect(result.xmlData[0]).to.have.property('id', mockXmlDataList[0].id); + expect(result.xmlData[0]).to.have.property('id', mockDBXmlDataList[0].id); expect(result.xmlData[0]).to.have.property( 'title', - mockXmlDataList[0].title + mockDBXmlDataList[0].title ); expect(result.xmlData[0]).to.have.property( 'status', - mockXmlDataList[0].status + mockDBXmlDataList[0].status ); expect(result.xmlData[0]).to.have.property( 'isNewCuration', - mockXmlDataList[0].isNewCuration + mockDBXmlDataList[0].isNewCuration ); expect(result.xmlData[0]).to.have.property( 'sequence', - mockXmlDataList[0].sequence + mockDBXmlDataList[0].sequence ); expect(result.xmlData[0]).to.have.property( 'user', - mockXmlDataList[0].user + mockDBXmlDataList[0].user ); }); @@ -94,33 +78,35 @@ describe('XmlData Resolver Unit Tests:', function () { sinon .stub(XmlData, 'aggregate') - .returns([{ count: mockXmlDataList.length, xmlData: mockXmlDataList }]); + .returns([ + { count: mockDBXmlDataList.length, xmlData: mockDBXmlDataList } + ]); const result = await xmlFinder({}, { input }, { req }); expect(result).to.have.property('xmlData'); expect(result.xmlData).to.be.an('Array'); - expect(result.xmlData[1]).to.have.property('id', mockXmlDataList[1].id); + expect(result.xmlData[1]).to.have.property('id', mockDBXmlDataList[1].id); expect(result.xmlData[1]).to.have.property( 'title', - mockXmlDataList[1].title + mockDBXmlDataList[1].title ); expect(result.xmlData[1]).to.have.property( 'status', - mockXmlDataList[1].status + mockDBXmlDataList[1].status ); expect(result.xmlData[1]).to.have.property( 'isNewCuration', - mockXmlDataList[1].isNewCuration + mockDBXmlDataList[1].isNewCuration ); expect(result.xmlData[1]).to.have.property( 'sequence', - mockXmlDataList[1].sequence + mockDBXmlDataList[1].sequence ); expect(result.xmlData[1]).to.have.property( 'user', - mockXmlDataList[1].user + mockDBXmlDataList[1].user ); }); @@ -148,7 +134,7 @@ describe('XmlData Resolver Unit Tests:', function () { }); it('should return an xmldata', async () => { - sinon.stub(XmlData, 'findOne').returns(mockXmlData); + sinon.stub(XmlData, 'findOne').returns(mockDBXmlData); const result = await xmlViewer({}, { input }, { req }); @@ -159,7 +145,9 @@ describe('XmlData Resolver Unit Tests:', function () { it('should return a curated sample data', async () => { sinon.stub(CuratedSamples, 'findOne').returns(fetchedCuratedXlsxObject); - sinon.stub(XlsxFileManager, 'xmlGenerator').returns(mockXmlData.xml_str); + sinon + .stub(XlsxFileManager, 'xmlGenerator') + .returns(mockDBXmlData.xml_str); const result = await xmlViewer( {}, { input: { ...input, isNewCuration: true } }, diff --git a/resfulservice/spec/mocks/graphqlMock.js b/resfulservice/spec/mocks/graphqlMock.js new file mode 100644 index 00000000..b6a443ed --- /dev/null +++ b/resfulservice/spec/mocks/graphqlMock.js @@ -0,0 +1,267 @@ +const sinon = require('sinon'); + +const mockComment = { + comment: 'test comment', + type: 'xml', + identifier: '64394c8032bc6325505af6f9', + user: '64394c8032bc6325505af6f9' +}; + +const mockCommentInput = { + id: '64394c8032bc6325505af6f9', + comment: 'test comment', + type: 'xml', + identifier: '64394c8032bc6325505af6f9' +}; + +const mockDBComment = { + user: { + givenName: 'Test', + surName: 'Test' + }, + ...mockComment, + lean: () => this, + populate: sinon.stub().returnsThis() +}; + +const mockCommentList = [ + { + _id: '64397a5cdffb639553bf62e4', + comment: 'first comment', + user: { + givenName: 'Test', + surName: 'Test' + }, + createdAt: '1681488476581', + updatedAt: '1681489494515' + }, + { + _id: '64397a5cdffb639553bf62e4', + comment: 'secont comment', + user: { + givenName: 'Test', + surName: 'Test' + }, + createdAt: '1681488476581', + updatedAt: '1681489494515' + } +]; + +const mockContact = { + fullName: 'test user', + email: 'test@example.com', + purpose: 'QUESTION', + message: 'test message', + attachments: [ + '/api/files/strategic_beetle_joelle-2024-02-15T09:25:42.264Z-master_template (5).xlsx?isStore=true', + '/api/files/strategic_beetle_joelle-2024-02-15T09:27:07.905Z-master_template.xlsx?isStore=true' + ] +}; + +const mockUserContact = { + _id: 'akdn9wqkn', + fullName: 'test user', + email: 'test@example.com', + purpose: 'QUESTION', + message: 'test message', + lean: () => this +}; + +const mockUpdatedContact = { + ...mockContact, + resolved: true, + response: 'Thanks for reaching out. We are working on it' +}; + +const user = { + _id: '62dab1b76db8739c8330611d', + alias: 'testalias', + givenName: 'test', + surName: 'test user', + displayName: 'tester', + userid: '62dab1b76db8739c8330611d', + email: 'test@example.com', + roles: 'member' +}; + +const mockDataset = { + _id: '62f11b1328eedaab012d127c', + datasetId: '62f11b1328eedaab012d127c', + userid: '62f119fb28eedaab012d1262', + filesets: [ + { + fileset: 'E109_S2_Huang_2016', + files: [ + { + type: 'blob', + id: '5b51f112e74a1d4cdbad6a1d', + metadata: { + filename: '4.tif', + contentType: 'image/tiff' + } + }, + { + type: 'blob', + id: '5b51f137e74a1d4cdbad6a3a', + metadata: { + filename: '5.tif', + contentType: 'image/tiff' + } + } + ] + } + ], + skip: sinon.stub().returnsThis(), + limit: sinon.stub().returnsThis(), + lean: sinon.stub().returnsThis() +}; + +const mockFiles = { + doi: 'unpublished/doi-tMbKM2ba5aNwo2ZKPVucBS', + datasetId: '62fce36374da548513a38a9b', + files: [ + { + fieldname: 'uploadfile', + originalname: 'Hopetoun_falls.jpg', + encoding: '7bit', + mimetype: 'image/jpeg', + destination: 'mm_files', + filename: + 'comparative_aphid_agathe-2022-08-18T10:00:40.910Z-Hopetoun_falls.jpg', + path: 'mm_files/comparative_aphid_agathe-2022-08-18T10:00:40.910Z-Hopetoun_falls.jpg', + size: 2954043 + }, + { + fieldname: 'uploadfile', + originalname: 'flowers-276014__340.jpg', + encoding: '7bit', + mimetype: 'image/jpeg', + destination: 'mm_files', + filename: + 'comparative_aphid_agathe-2022-08-18T10:00:41.018Z-flowers-276014__340.jpg', + path: 'mm_files/comparative_aphid_agathe-2022-08-18T10:00:41.018Z-flowers-276014__340.jpg', + size: 56575 + } + ] +}; + +const mockColumn = { + field: 'Flight_width::Uniter', + values: ['nm', 'um', 'mm', 'cm', 'm'] +}; + +const mockColumnsInput = { + columns: [ + { + field: 'Flight_width::Units', + values: ['nm', 'um', 'mm', 'cm', 'm'] + }, + { + field: 'Origins', + values: [ + 'experiments', + 'informatics (data science)', + 'simulations', + 'theory' + ] + } + ] +}; + +const mockDBColumn = { + _id: 'kas2344nlkla', + ...mockColumn, + lean: () => this +}; + +const mockConflictError = { + writeErrors: [ + { + err: { + index: 0, + code: 11000, + errmsg: + 'E11000 duplicate key error collection: mgi.materialtemplates index: field_1 dup key: { field: "Flight_width::Units" }' + } + }, + { + err: { + index: 1, + code: 11000, + errmsg: + 'E11000 duplicate key error collection: mgi.materialtemplates index: field_1 dup key: { field: "Origins" }' + } + } + ] +}; + +const pixelatedDataInput = { + unitCell: 'TEN', + pageNumber: 1, + pageSize: 1 +}; + +const mockPixelData = { + _id: 'akdn9wqknd90uaoikn9ahoi4489i', + symmetry: 'C4v', + unit_cell_x_pixels: '10', + unit_cell_y_pixels: '10', + geometry_condensed: '000000000001001', + geometry_full: + '1010000101000000000010000000010000000000000000000000000000000000000000100000000100000000001010000101', + condition: 'Plane Strain', + C11: '2963290579', + C12: '1459531181', + C22: '2963290579', + skip: () => ({ _id: 'akdn9wqkn', ...pixelatedDataInput }), + lean: () => ({ _id: 'akdn9wqkn', ...pixelatedDataInput }), + limit: () => ({ _id: 'akdn9wqkn', ...pixelatedDataInput }) +}; + +const mockDBXmlData = { + _id: '64394c8032bc6325505af6f9', + title: 'L183_53_Portschke_2003.xml', + xml_str: + ' Empire BurlesqueBob Dylan USA Columbia 10.90 1985 ', + entityState: 'EditedValid' +}; + +const mockDBXmlDataList = [ + { + id: '6622848a808bdbee354f96d3', + title: 'L311_S10_Lou_2009.xml', + status: 'Not Approved', + isNewCuration: false, + sequence: 311, + user: '65b8ec85c3d3b2ed82fe4029' + }, + { + id: '65cf719860df704a1ca74428', + title: 'E0_S1_Uthdev_2003.xml', + status: 'Approved', + isNewCuration: true, + sequence: null, + user: '65b8ec85c3d3b2ed82fe4029' + } +]; + +module.exports = { + mockComment, + mockCommentInput, + mockDBComment, + mockCommentList, + mockContact, + mockUserContact, + mockUpdatedContact, + mockDataset, + mockFiles, + mockColumn, + mockColumnsInput, + mockDBColumn, + mockConflictError, + mockPixelData, + pixelatedDataInput, + mockDBXmlDataList, + mockDBXmlData, + user +}; diff --git a/resfulservice/spec/mocks/index.js b/resfulservice/spec/mocks/index.js index c5e2b1d6..0beacf77 100644 --- a/resfulservice/spec/mocks/index.js +++ b/resfulservice/spec/mocks/index.js @@ -2,6 +2,7 @@ const curation = require('./curationMock'); const user = require('./userMock'); const files = require('./fileMock'); const tasks = require('./taskMock'); +const graphql = require('./graphqlMock'); // It is re-useable across all tests files const next = function (fn) { @@ -13,5 +14,6 @@ module.exports = { ...user, ...files, ...tasks, + ...graphql, next }; diff --git a/resfulservice/src/api-docs/swagger-service.yaml b/resfulservice/src/api-docs/swagger-service.yaml index a136c511..ea2d7818 100644 --- a/resfulservice/src/api-docs/swagger-service.yaml +++ b/resfulservice/src/api-docs/swagger-service.yaml @@ -47,11 +47,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' post: security: - BearerAuth: [] @@ -89,11 +85,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' put: tags: - Admin @@ -185,11 +177,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' delete: security: - BearerAuth: [] @@ -288,11 +276,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' /admin/es/delete-index/{type}: delete: security: @@ -343,12 +327,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - description: Error message - example: Internal Server Error + $ref: '#/components/schemas/Server-Error' /knowledge/charts/favorites: get: security: @@ -407,11 +386,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' post: summary: Add a favorite chart security: @@ -447,11 +422,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' delete: security: - BearerAuth: [] @@ -487,7 +458,7 @@ paths: content: application/json: schema: - $ref: '#/components/schemas/ErrorResponse' + $ref: '#/components/schemas/Server-Error' /curate: get: security: @@ -529,11 +500,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' post: security: - BearerAuth: [] @@ -623,11 +590,8 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' + put: tags: - Curation @@ -704,11 +668,8 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' + delete: security: - BearerAuth: [] @@ -782,11 +743,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' /curate/get/{curationId}: get: @@ -839,11 +796,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' /curate/duplicate/{curationId}: post: @@ -898,11 +851,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' /curate/bulk: post: @@ -983,16 +932,10 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: An error occurred + $ref: '#/components/schemas/Server-Error' /curate/schema: get: - security: - - BearerAuth: [] summary: Gets XSD Schema description: This route provides access to retrieving the XSD Schema. If the isFile query parameter is specified it returns the XSD schema as a downloadable file. Alternatively, if the isJson query parameter is specified, it returns a valid Base JSON Schema. Finally, if the getXSD query parameter is included, it returns the XSD schema as JSON. tags: @@ -1025,14 +968,71 @@ paths: '500': description: Internal Server Error + content: + application/json: + schema: + $ref: '#/components/schemas/Server-Error' + + /xml/{controlID}: + get: + summary: Gets Curation XMl + description: This route downloads a curation xml + tags: + - Xml + parameters: + - in: path + required: true + name: controlID + description: The Control_ID of the xml to be fetched. + schema: + type: string + example: L5_S4_Hareesh_2023 + + - in: query + name: format + schema: + type: string + example: xml + default: xml + description: Set to xml + responses: + '200': + description: Returns the curation XML, either rendered directly or as a downloadable file. + content: + application/xml: + schema: + type: string + example: | + + + <2D_RVE> + 500 + 500 + + <3D_RVE> + 500 + 500 + + + + + '404': + description: Curation not found content: application/json: schema: type: object properties: - message: - type: string - example: An error occurred + message: + type: string + example: 'Curation sample not found' + '500': + description: Internal Server Error + content: + application/json: + schema: + $ref: '#/components/schemas/Server-Error' + /files/{fileId}: get: summary: Download files from the server @@ -1087,11 +1087,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: 'Error fetching file' + $ref: '#/components/schemas/Server-Error' delete: security: @@ -1139,11 +1135,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: 'Error deleting files' + $ref: '#/components/schemas/Server-Error' /files/image_migration/{imageType}: get: @@ -1196,11 +1188,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: 'Error fetching file' + $ref: '#/components/schemas/Server-Error' /files/upload: post: @@ -1265,11 +1253,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: Error uploading files + $ref: '#/components/schemas/Server-Error' /files/metamine: get: @@ -1290,11 +1274,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: error listing metamine objects + $ref: '#/components/schemas/Server-Error' /files/metamine/{fileName}: get: @@ -1323,11 +1303,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: 'error fetching metamine csv object' + $ref: '#/components/schemas/Server-Error' /mn/dynamfit: post: @@ -1400,11 +1376,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: This response indicates an unexpected server-side issue. + $ref: '#/components/schemas/Server-Error' /mn/chemprops: post: @@ -1445,9 +1417,9 @@ paths: schema: type: object properties: - message: - type: string - enum: ["Invalid Polymer Name", "Invalid Request: Ignore if not; it will be added to the database.", "polfil is required", "ChemicalName is required", "polfil must be either pol or fil"] + message: + type: string + enum: ["Invalid Polymer Name", "Invalid Request: Ignore if not; it will be added to the database.", "polfil is required", "ChemicalName is required", "polfil must be either pol or fil"] '401': description: Unauthorized access to this service. @@ -1471,11 +1443,7 @@ paths: content: application/json: schema: - type: object - properties: - message: - type: string - example: This response indicates an unexpected server-side issue. + $ref: '#/components/schemas/Server-Error' /mn/chemprops/init: post: @@ -1513,14 +1481,59 @@ paths: '500': description: Internal Server Error + content: + application/json: + schema: + $ref: '#/components/schemas/Server-Error' + + /mn/ontology: + get: + summary: A route to Extract Ontology Information + description: This route processes an RDF Turtle file to extract ontology details, compute statistical metrics, and build a hierarchical structure of ontology classes. + tags: + - Managed Services + + responses: + '200': + description: Materialsmine Managed Service data + content: + application/json: + schema: + $ref: '#/components/schemas/Successful-Materialsmine-Data' + + '400': + description: Invalid Request Payload content: application/json: schema: type: object properties: - message: - type: string - example: This response indicates an unexpected server-side issue. + message: + type: string + example: Failed to download file from GitHub + '401': + description: Unauthorized access to this service. + content: + application/json: + schema: + $ref: '#/components/schemas/Unauthorized-Error' + + '404': + description: Not Found + content: + application/json: + schema: + type: object + example: + error: Not Found + message: The requested URL was not found on the server. If you entered the URL manually please check your spelling and try again. + + '500': + description: Internal Server Error + content: + application/json: + schema: + $ref: '#/components/schemas/Server-Error' components: securitySchemes: BearerAuth: @@ -1542,6 +1555,12 @@ components: message: type: string example: User is forbidden + Server-Error: + type: object + properties: + message: + type: string + enum: ['An error occurred', 'Internal Server Error', 'This response indicates an unexpected server-side issue.', 'Error fetching file', 'Error deleting files', 'Error uploading files', 'error listing metamine objects', 'error fetching metamine csv object'] Missing-Input-Error: type: object properties: @@ -2170,6 +2189,77 @@ components: StandardName: Polystyrene density: '1.04' uSMILES: C(C(C1=CC=CC=C1)[*])[*] + + Successful-Materialsmine-Data: + type: object + example: + appName: materialsmine + data: + details: + Acronyms: MATERIALSMINE + Visibility: Public + Description: A materials ontology to support data publication involving nanomaterials and metamaterials. + Status: Alpha + Format: OWL + Contact: Sabbir Rashid, rashidsabbir@gmail.com + Categories: Chemical, Development, Physicochemical + OntologyVersion: http://materialsmine.org/ns/1.0 + metrics: + classes: 543 + individuals: 224 + properties: 0 + maximum_depth: 5 + maximum_number_of_children: 21 + average_number_of_children: 1 + classes_with_a_single_child: 216 + classes_with_more_than_25_children: 0 + classes_with_no_definition: 248 + data: + - ID: http://www.w3.org/2002/07/owl#Thing + Preferred Name: Thing + prefixIRI: owl:Thing + prefLabel: Thing + subClasses: + - ID: obo:ID_0000061 + subClasses: + - subClasses: + - subClasses: [] + ID: http://materialsmine.org/ns/TemperatureSweep + prefixIRI: materialsmine:TemperatureSweep + prefLabel: Temperature Sweep + Label: Temperature Sweep + Preferred Name: Temperature Sweep + subClassOf: http://materialsmine.org/ns/DMA_Mode + Definitions: A continuous variation of temperature within a pre-defined range. + ID: http://materialsmine.org/ns/DMA_Mode + prefixIRI: materialsmine:DMA_Mode + subClassOf: http://materialsmine.org/ns/DynamicProperties + prefLabel: Dynamic Mechanical Analysis + Label: Dynamic Mechanical Analysis + Preferred Name: Dynamic Mechanical Analysis + Definitions: The type of condition (e.g., temperature sweep or frequency sweep) under which a material's dynamic mechanical response is measured. + Preferred Name: obo:ID_0000061 + prefLabel: obo:ID_0000061 + prefixIRI: ns2:ID_0000061 + subClassOf: http://www.w3.org/2002/07/owl#Thing + subClassOf: http://www.w3.org/2002/07/owl#Thing + - subClasses: + - subClasses: [] + ID: http://materialsmine.org/ns/Beam + prefixIRI: materialsmine:Beam + subClassOf: http://materialsmine.org/ns/1DSolidMechanicsModel + Definitions: A slender 1d structural element that primarily bears lateral loads. + prefLabel: Beam + Label: Beam + Preferred Name: Beam + ID: http://materialsmine.org/ns/1DSolidMechanicsModel + prefixIRI: materialsmine:1DSolidMechanicsModel + Definitions: A one-dimensional model of a solid relating stress with strain. + prefLabel: 1D Solid Mechanics Model + Label: 1D Solid Mechanics Model + Preferred Name: 1D Solid Mechanics Model + subClassOf: http://www.w3.org/2002/07/owl#Thing + Sample-Files: diff --git a/resfulservice/src/controllers/curationController.js b/resfulservice/src/controllers/curationController.js index 1059ee0f..bd765bec 100644 --- a/resfulservice/src/controllers/curationController.js +++ b/resfulservice/src/controllers/curationController.js @@ -782,6 +782,56 @@ exports.getCurationXSD = async (req, res, next) => { } }; +exports.getCurationXml = async (req, res, next) => { + const { logger, params } = req; + + logger.info('getCurationXml Function Entry:'); + + const { controlID } = params; + + try { + const regex = new RegExp(controlID, 'i'); + + // Perform searches on both collections simultaneously using Promise.all + const [curatedSample, xmlData] = await Promise.all([ + CuratedSamples.findOne({ 'object.Control_ID': { $regex: regex } }, null, { + lean: true + }), + XmlData.findOne({ title: { $regex: regex } }, null, { lean: true }) + ]); + + // Determine which result to use based on availability + const curation = curatedSample || xmlData; + + if (!curation) { + return next( + errorWriter(req, 'Curation sample not found', 'getCurationXml', 404) + ); + } + + let xml; + if (curatedSample) { + xml = XlsxFileManager.xmlGenerator( + JSON.stringify({ PolymerNanoComposite: curatedSample.object }) + ); + xml = `\n${xml}`; + } else { + xml = xmlData.xml_str; + } + + xml = xml.replace(/2D_RVE/g, 'TwoD_RVE').replace(/3D_RVE/g, 'ThreeD_RVE'); + + // Set headers for file download + res.setHeader('Content-Type', 'application/xml'); + + // Send the XML content as a file response + latency.latencyCalculator(res); + return res.send(xml); + } catch (error) { + next(errorWriter(req, error, 'getCurationXml', 500)); + } +}; + const getKeyCaseInsensitive = (obj, key) => { if (typeof obj !== 'object' || obj === null) { return undefined; diff --git a/resfulservice/src/controllers/kgWrapperController.js b/resfulservice/src/controllers/kgWrapperController.js index c248f3d1..b2076f24 100644 --- a/resfulservice/src/controllers/kgWrapperController.js +++ b/resfulservice/src/controllers/kgWrapperController.js @@ -5,6 +5,7 @@ const { setInternal } = require('../middlewares/isInternal'); const elasticSearch = require('../utils/elasticSearch'); const { errorWriter, successWriter } = require('../utils/logWriter'); const { cacheKnowledge } = require('../middlewares/knowledge-cache'); +const { stringifyError } = require('../utils/exit-utils'); const httpsAgent = { rejectUnauthorized: false @@ -216,8 +217,8 @@ exports.getSparql = async (req, res, next) => { await cacheKnowledge(req, res, next, response?.data); } else { log.info( - `getSparql = () => Empty knowledge response (${JSON.stringify( - response.data + `getSparql = () => Empty knowledge response (${stringifyError( + response.data?.results )})` ); } diff --git a/resfulservice/src/controllers/managedServiceController.js b/resfulservice/src/controllers/managedServiceController.js index fea26561..2b9cf31e 100644 --- a/resfulservice/src/controllers/managedServiceController.js +++ b/resfulservice/src/controllers/managedServiceController.js @@ -34,7 +34,7 @@ exports.manageServiceRequest = async (req, res, next) => { `${ appName[0].toUpperCase() + appName.slice(1) } service not available`, - 'getDynamfitChartData', + 'manageServiceRequest', 422 ) ); @@ -53,7 +53,7 @@ exports.manageServiceRequest = async (req, res, next) => { error?.message ?? 'This response indicates an unexpected server-side issue' }`, - 'getDynamfitChartData', + 'manageServiceRequest', statusCode ) ); @@ -87,7 +87,7 @@ exports.chemPropsSeed = async (req, res, next) => { error?.message ?? 'This response indicates an unexpected server-side issue' }`, - 'getDynamfitChartData', + 'chemPropsSeed', statusCode ) ); @@ -100,6 +100,7 @@ const _managedServiceCall = async (req, res) => { url, body, params: { appName }, + method = 'post', logger } = req; req.timer = '1m'; @@ -114,7 +115,10 @@ const _managedServiceCall = async (req, res) => { reqBody.file_name = req.env.DYNAMFIT_TEST_FILE; } - const response = await axios.post(url, reqBody, { + const response = await axios.request({ + method, + url, + data: reqBody, headers: { Authorization: `Bearer ${token}` } diff --git a/resfulservice/src/middlewares/knowledge-cache.js b/resfulservice/src/middlewares/knowledge-cache.js index 16cf07d1..af6c043e 100644 --- a/resfulservice/src/middlewares/knowledge-cache.js +++ b/resfulservice/src/middlewares/knowledge-cache.js @@ -1,3 +1,4 @@ +const { SEARCH_FIELD } = require('../../config/constant'); const Task = require('../sw/models/task'); const elasticSearch = require('../utils/elasticSearch'); @@ -24,54 +25,65 @@ exports.isKnowledgeCached = async (req, res, next) => { req.logger.info(':::middleware.isKnowledgeCached Function Entry'); - // TODO: (Redo) There is an existing search implementation in ES. This new one is not required - const cacheResult = await elasticSearch.searchType( - req, - query, - 'label', - 'knowledge' - ); + let kgResponse = {}; + let knowledgeId = null; + try { + // TODO: (Redo) There is an existing search implementation in ES. This new one is not required + const cacheResult = await elasticSearch.searchType( + req, + query, + SEARCH_FIELD.label, + 'knowledge' + ); - if (cacheResult.data.hits.hits.length) { - const { - _id, - _source: { response, date } - } = cacheResult.data.hits.hits[0]; + if (cacheResult.data.hits.hits.length) { + const { + _id, + _source: { response, date } + } = cacheResult.data.hits.hits[0]; + kgResponse = response; + knowledgeId = _id; - // Get today's date in string format (YYYY-MM-DD); - const todayDate = new Date().toISOString().slice(0, 10); + // Get today's date in string format (YYYY-MM-DD); + const todayDate = new Date().toISOString().slice(0, 10); - // check if date is today's date - if (date === todayDate) { - return res.status(200).json(response); - } + // check if date is today's date + if (date === todayDate) { + return res.status(200).json(response); + } - // check if Task with same elasticsearch _id has already been created - const task = await Task.findOne({ 'info.knowledgeId': _id }); - if (task) { - return res.status(200).json(response); + // check if Task with same elasticsearch _id has already been created + const task = await Task.findOne({ 'info.knowledgeId': _id }); + if (task) { + return res.status(200).json(response); + } } + } catch (error) { + return next(); + } - // create a nightly run task that runs at midnight + // Mongo DB insert failure at this point doesn't matter and can be skipped + // create a nightly run task that runs at midnight + if (knowledgeId) { Task.create({ serviceName: 'knowledgeRequest', whenToRun: 'Nightly', info: { - knowledgeId: _id, + knowledgeId, req: { query: { query } } } }); req.logger.info( - `Middleware.isKnowledgeCached - Created a new nightly task with id: ${_id}` + `Middleware.isKnowledgeCached - Created a new nightly task with id: ${knowledgeId}` ); - return res.status(200).json(response); + return res.status(200).json(kgResponse); } - next(); + return next(); }; -exports.cacheKnowledge = async (req, res, next, data) => { +exports.cacheKnowledge = async (req, _res, _next, data) => { req.logger.info('cacheKnowledge Function Entry'); const query = req.query.query ?? req.body?.query; // 1. NOT caching curation submissions @@ -83,29 +95,35 @@ exports.cacheKnowledge = async (req, res, next, data) => { // 3. NOT Caching empty query strings if (!query) return; - if (req.isBackendCall) { - const response = await elasticSearch.searchType( - req, - query, - 'label', - 'knowledge' - ); - if (response.data.hits.hits.length) { - const result = await elasticSearch.deleteSingleDoc( + // 4. Cache, and if caching fails its okay to return null and try again next time + // Caching may fail if Elastic search is unavailable/unreacheable + try { + if (req.isBackendCall) { + const response = await elasticSearch.searchType( req, - 'knowledge', - response.data.hits.hits[0]._id - ); - req.logger.info( - `Middleware.cacheKnowledge - Deleted document: ${result.deleted}` + query, + 'label', + 'knowledge' ); + if (response.data.hits.hits.length) { + const result = await elasticSearch.deleteSingleDoc( + req, + 'knowledge', + response.data.hits.hits[0]._id + ); + req.logger.info( + `Middleware.cacheKnowledge - Deleted document: ${result.deleted}` + ); + } } - } - const cacheItem = { - label: query, - response: data, - date: new Date().toISOString().slice(0, 10) - }; - return await elasticSearch.indexDocument(req, 'knowledge', cacheItem); + const cacheItem = { + label: query, + response: data, + date: new Date().toISOString().slice(0, 10) + }; + return await elasticSearch.indexDocument(req, 'knowledge', cacheItem); + } catch (_error) { + return null; + } }; diff --git a/resfulservice/src/routes/managed-service.js b/resfulservice/src/routes/managed-service.js index ea2bdd02..87ced044 100644 --- a/resfulservice/src/routes/managed-service.js +++ b/resfulservice/src/routes/managed-service.js @@ -11,6 +11,7 @@ router router .route('/:appName') + .get(latencyTimer, manageServiceController.manageServiceRequest) .post(isAuth, latencyTimer, manageServiceController.manageServiceRequest); router diff --git a/resfulservice/src/routes/xml.js b/resfulservice/src/routes/xml.js new file mode 100644 index 00000000..67d9a7d3 --- /dev/null +++ b/resfulservice/src/routes/xml.js @@ -0,0 +1,10 @@ +const express = require('express'); +const { latencyTimer } = require('../middlewares/latencyTimer'); +const curationController = require('../controllers/curationController'); +const router = express.Router(); + +router + .route('/:controlID') + .get(latencyTimer, curationController.getCurationXml); + +module.exports = router; diff --git a/resfulservice/src/server.js b/resfulservice/src/server.js index e044bca6..1cc1fc0c 100644 --- a/resfulservice/src/server.js +++ b/resfulservice/src/server.js @@ -12,13 +12,14 @@ const { globalMiddleWare, log, swaggerService } = require('./middlewares'); const adminRoutes = require('./routes/admin'); const authRoutes = require('./routes/authService'); const curationRoutes = require('./routes/curation'); -const elasticSearch = require('./utils/elasticSearch'); +// const elasticSearch = require('./utils/elasticSearch'); const fileRoutes = require('./routes/files'); const invalidRoutes = require('./routes/invalid'); const knowledgeRoutes = require('./routes/kg-wrapper'); const pixelatedRoutes = require('./routes/pixelated'); const searchRoutes = require('./routes/search'); const managedServiceRoutes = require('./routes/managed-service'); +const xmlRoutes = require('./routes/xml'); const resolvers = require('./graphql/resolver'); const typeDefs = require('./graphql'); const getHttpContext = require('./graphql/context/getHttpContext'); @@ -31,7 +32,8 @@ if (cluster.isMaster) { // Main process const app = express(); globalMiddleWare(app); - elasticSearch.ping(log); + // TODO: Check - temporarily stopping this error from blowing up the server + // elasticSearch.ping(log); const httpServer = createHttpServer(app); const wsServer = new WebSocketServer({ @@ -54,6 +56,7 @@ if (cluster.isMaster) { app.use('/search', searchRoutes); app.use('/pixelated', pixelatedRoutes); app.use('/mn', managedServiceRoutes); + app.use('/xml', xmlRoutes); app.use('/*', invalidRoutes); const schema = makeExecutableSchema({ typeDefs, resolvers }); @@ -65,7 +68,8 @@ if (cluster.isMaster) { if (!err.extensions) { return err; } - const message = err.extensions.message || 'An error occurred.'; + const message = + err.message ?? err.extensions.exception.message ?? 'An error occurred.'; const code = err.extensions.code || 500; log.error(`GQL Error: ${JSON.stringify(err)}`); return { message, status: code }; diff --git a/resfulservice/src/sw/utils/worker-services.js b/resfulservice/src/sw/utils/worker-services.js index bd75ad92..da018e43 100644 --- a/resfulservice/src/sw/utils/worker-services.js +++ b/resfulservice/src/sw/utils/worker-services.js @@ -10,6 +10,7 @@ const { MinioBucket, TaskStatusMap } = require('../../../config/constant'); +const { stringifyError } = require('../../utils/exit-utils'); const env = process.env; const BUCKETNAME = env.MINIO_BUCKET ?? MinioBucket; @@ -51,7 +52,7 @@ async function workerManager (logger) { logInfo.date = startDate[0]; logInfo.time = startDate[1].split('.')[0]; if (task.whenToRun === 'Nightly') logInfo.runtime = task.whenToRun; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); const { status, isSuccess } = await service.operation(task, logger); @@ -60,7 +61,7 @@ async function workerManager (logger) { logInfo.isSuccess = isSuccess; logInfo.date = endDate[0]; logInfo.time = endDate[1].split('.')[0]; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); if (isSuccess) { await Task.findOneAndDelete({ _id: task._id }); @@ -98,7 +99,7 @@ async function convertImageToPng ({ _id, info: { ref, sampleID } }, logger) { date: date[0], time: date[1].split('.')[0] }; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); if (isFileExist) { try { await sharp(tiffImagePath).png().toFile(pngFilePath); @@ -107,7 +108,7 @@ async function convertImageToPng ({ _id, info: { ref, sampleID } }, logger) { logInfo.status = 'Worker-services.Image Conversion:: Completed'; logInfo.date = date[0]; logInfo.time = date[1].split('.')[0]; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); } catch (error) { tempFile = prefixFile(ref); logger.error(error); @@ -121,7 +122,7 @@ async function convertImageToPng ({ _id, info: { ref, sampleID } }, logger) { 'Worker-services.Update curation with converted file:: Started'; logInfo.date = date[0]; logInfo.time = date[1].split('.')[0]; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); tempFile = generateTempFileName(pngFile); const isPngTempFileExist = await checkFileExistence(tempFile); @@ -159,7 +160,7 @@ async function convertImageToPng ({ _id, info: { ref, sampleID } }, logger) { 'Worker-services.Update curation with converted file:: Completed'; logInfo.date = date[0]; logInfo.time = date[1].split('.')[0]; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); } catch (error) { logger.error(error); prefixFile(pngFilePath); @@ -173,7 +174,7 @@ async function convertImageToPng ({ _id, info: { ref, sampleID } }, logger) { 'Worker-services.Uploading converted file to object store:: Started'; logInfo.date = date[0]; logInfo.time = date[1].split('.')[0]; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); try { if (!(await isObjectExistInMinio(BUCKETNAME, pngFile)) && !isPngFileExist) { return { @@ -205,7 +206,7 @@ async function convertImageToPng ({ _id, info: { ref, sampleID } }, logger) { 'Worker-services.Uploading converted file to object store:: Completed'; logInfo.date = date[0]; logInfo.time = date[1].split('.')[0]; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); return { status: TaskStatusMap.COMPLETED, isSuccess: true }; } catch (error) { prefixFile(pngFilePath); @@ -227,7 +228,7 @@ async function knowledgeRequest ( date: date[0], time: date[1].split('.')[0] }; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); // attach request body and query if not set if (!req.body) req.body = { query: undefined }; @@ -242,7 +243,7 @@ async function knowledgeRequest ( logInfo.status = 'Worker-services.knowledgeRequest:: Completed'; logInfo.date = date[0]; logInfo.time = date[1].split('.')[0]; - logger.info(JSON.stringify(logInfo)); + logger.info(stringifyError(logInfo)); return result ? { diff --git a/resfulservice/src/utils/elasticSearch.js b/resfulservice/src/utils/elasticSearch.js index 6c4b618a..ee97f252 100644 --- a/resfulservice/src/utils/elasticSearch.js +++ b/resfulservice/src/utils/elasticSearch.js @@ -305,25 +305,40 @@ class ElasticSearch { from: (page - 1) * size, query: { bool: { - should: [ - { - match_phrase: { - label: phrase + ...(!searchField && { + should: [ + { + match_phrase: { + label: phrase + } + }, + { + match_phrase: { + description: phrase + } } - }, - { - match_phrase: { - description: phrase + ] + }), + ...(!!searchField && { + should: [ + { + match_phrase: { + [searchField]: phrase + } } - } - ] + ] + }) } } }) }); return response; } catch (err) { - log.error(`elasticsearch.searchType(): ${err.status || 500} - ${err}`); + log.error( + `elasticsearch.searchType(): ${err.status || 500} - ${stringifyError( + err + )}` + ); throw err; } } diff --git a/resfulservice/src/utils/logWriter.js b/resfulservice/src/utils/logWriter.js index 9f552719..af8ed61b 100644 --- a/resfulservice/src/utils/logWriter.js +++ b/resfulservice/src/utils/logWriter.js @@ -1,3 +1,5 @@ +const { stringifyError } = require('./exit-utils'); + /** * Writes error to logger and return the error * @param {*} req @@ -13,8 +15,8 @@ exports.errorWriter = (req, error, fnName = 'N/A', code, type) => { return new Error('Server Error'); } - if (type) req.logger[type](`[${fnName}]: error - ${error}`); - else req.logger?.error(`[${fnName}]: error - ${error}`); + if (type) req.logger[type](`[${fnName}]: error - ${stringifyError(error)}`); + else req.logger?.error(`[${fnName}]: error - ${stringifyError(error)}`); const err = new Error(error); if (code) err.statusCode = code; return err; diff --git a/services/app/__init__.py b/services/app/__init__.py index af9751fd..c63f87ba 100644 --- a/services/app/__init__.py +++ b/services/app/__init__.py @@ -2,6 +2,7 @@ from flask_cors import CORS # type: ignore from app.config import Config import logging +import sys # TODO (@Tee): Enable the ones we need @@ -9,29 +10,40 @@ # mail = Mail() def create_app(config_class = Config): - app = Flask(__name__) - app.config.from_object(config_class) - CORS(app) - - # Configure logging - app.logger.setLevel(logging.INFO) + try: + app = Flask(__name__) + app.config.from_object(config_class) + CORS(app) - # Add a file handler - file_handler = logging.FileHandler('/services/services_app.log') # Log to a file - formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') - file_handler.setFormatter(formatter) - file_handler.setLevel(logging.INFO) # Set log level for the file handler - app.logger.addHandler(file_handler) + # Configure logging + app.logger.setLevel(logging.INFO) + + # Add a file handler + file_handler = logging.FileHandler('/services/services_app.log') # Log to a file + formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') + file_handler.setFormatter(formatter) + file_handler.setLevel(logging.INFO) # Set log level for the file handler + app.logger.addHandler(file_handler) + + try: + from app.chemprops.routes import chemprops + from app.dynamfit.routes import dynamfit + from app.main.routes import main + from app.ontology.routes import ontology + from app.errors.handlers import error + + app.register_blueprint(chemprops) + app.register_blueprint(dynamfit) + app.register_blueprint(main) + app.register_blueprint(ontology) + app.register_blueprint(error) - from app.errors.handlers import error - from app.chemprops.routes import chemprops - from app.dynamfit.routes import dynamfit - from app.main.routes import main + except (ImportError, ModuleNotFoundError) as e: + app.logger.critical(f"Failed to import a module: {str(e)}") + sys.exit(1) # Exit gracefully - app.register_blueprint(error) - app.register_blueprint(chemprops) - app.register_blueprint(dynamfit) - app.register_blueprint(main) - + return app - return app \ No newline at end of file + except Exception as e: + logging.critical(f"Application failed to start due to an unexpected error: {str(e)}", exc_info=True) + sys.exit(1) # Exit gracefully \ No newline at end of file diff --git a/services/app/config.py b/services/app/config.py index 59827959..cd1a4eec 100644 --- a/services/app/config.py +++ b/services/app/config.py @@ -14,4 +14,10 @@ class Config: EMAIL_REFRESH_TOKEN = os.environ.get('AUTH_API_REFRESH_EMAIL', '') FILES_DIRECTORY = os.environ.get('FILES_WORKING_DIR', '/usr/src/files') ALLOWED_EXTENSIONS = set(['tsv', 'csv']) - API_SERVICES = os.environ.get('API_URL', 'http://restful:3001') \ No newline at end of file + API_SERVICES = os.environ.get('API_URL', 'http://restful:3001') + GITHUB_USERNAME = os.environ.get('GITHUB_USERNAME') + GITHUB_TOKEN = os.environ.get('GITHUB_TOKEN') + REPO_OWNER = os.environ.get('REPO_OWNER') + REPO_NAME = os.environ.get('REPO_NAME') + FILE_PATH = os.environ.get('FILE_PATH') + BRANCH = os.environ.get('BRANCH') \ No newline at end of file diff --git a/services/app/ontology/__init__.py b/services/app/ontology/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/services/app/ontology/cache_service.py b/services/app/ontology/cache_service.py new file mode 100644 index 00000000..555ccff3 --- /dev/null +++ b/services/app/ontology/cache_service.py @@ -0,0 +1,45 @@ +import json +import os +import datetime + +# Define the cache file path and name. +CACHE_FILE = '/usr/src/files/mgs_materialsmin_data.json' + +def check_cache(app, serve_out_dated=False): + """Check if mgs_materialsmin_data.json exists and is not empty. Return the content if available.""" + app.logger.info("[check_cache]: Checking if mgs_materialsmin_data.json exists and is not empty.") + if os.path.exists(CACHE_FILE) and os.path.getsize(CACHE_FILE) > 0: + with open(CACHE_FILE, 'r', encoding='utf-8') as f: + data = json.load(f) + app.logger.info("[check_cache]: mgs_materialsmin_data.json exists and is not empty.") + + # Check if the cache has the 'lastUpdateDate' key + if 'lastUpdateDate' not in data: + app.logger.info("[check_cache]: lastUpdateDate not found in the mgs_materialsmin_data.json file.") + return None + + # Parse the lastUpdateDate + last_update_str = data['lastUpdateDate'] + last_update_date = datetime.datetime.strptime(last_update_str, "%Y-%m-%d").date() + today = datetime.date.today() + + # Check if lastUpdateDate is less than today + if last_update_date < today: + app.logger.info("[check_cache]: lastUpdateDate is older than today. Cache is outdated.") + if serve_out_dated: + app.logger.info("[check_cache]: Communication with github failed, Serving outdated data") + return data + return None + else: + # app.logger.info("[check_cache]: lastUpdateDate is the same as today. Returning cached data.") + return data + else: + app.logger.info("[check_cache]: mgs_materialsmin_data.json does not exist or is empty.") + return None + +def save_to_cache(app, data): + """Save the data to mgs_materialsmin_data.json.""" + app.logger.info("[save_to_cache]: Saving data to cache.") + with open(CACHE_FILE, 'w', encoding='utf-8') as f: + json.dump(data, f, indent=4) + app.logger.info('[save_to_cache]: Data cached successfully.') \ No newline at end of file diff --git a/services/app/ontology/github_flow.py b/services/app/ontology/github_flow.py new file mode 100644 index 00000000..3e138264 --- /dev/null +++ b/services/app/ontology/github_flow.py @@ -0,0 +1,115 @@ +import requests +import base64 +from app.config import Config + +GITHUB_USERNAME = Config.GITHUB_USERNAME +GITHUB_TOKEN = Config.GITHUB_TOKEN +REPO_OWNER = Config.REPO_OWNER +REPO_NAME = Config.REPO_NAME +FILE_PATH = Config.FILE_PATH +BRANCH = Config.BRANCH + +# Construct the URL to get the file content +file_url = f'https://api.github.com/repos/{REPO_OWNER}/{REPO_NAME}/contents/{FILE_PATH}?ref={BRANCH}' +# Construct the URL to get the commits for the file +commits_url = f'https://api.github.com/repos/{REPO_OWNER}/{REPO_NAME}/commits?path={FILE_PATH}&sha={BRANCH}' + +def make_github_request(url, app): + """ + This function sends a GET request to the specified URL with GitHub authentication. + It handles different HTTP status codes and logs relevant information using the provided app logger. + + Parameters: + url (str): The URL to send the GET request to. + app: The application instance that provides logging functionality. + + Returns: + dict or None: The JSON response from the GitHub API if the request is successful (status code 200). + None if the request fails or encounters a rate limit (status code 429). + None if there is a network error. + """ + try: + response = requests.get(url, auth=(GITHUB_USERNAME, GITHUB_TOKEN)) + if response.status_code == 200: + return response.json() + elif response.status_code == 429: + app.logger.error(f'[make_github_request]: Rate limit exceeded. Please try again later.') + return None + else: + app.logger.error(f'[make_github_request]: Failed request ({response.status_code}): {response.text}') + return None + except requests.RequestException as e: + app.logger.error(f'[make_github_request]: Network error - {str(e)}') + return None + +def download_file(app): + """ + This function connects to GitHub, retrieves the content of a specified file, decodes it, and saves it locally. + + Parameters: + app: The application instance that provides logging functionality. + + Returns: + bool: True if the file is downloaded and saved successfully. + False if there is an error during the download or saving process. + """ + app.logger.info("[download_file]: Connecting to GitHub to download file") + + file_content_json = make_github_request(file_url, app) + if file_content_json and 'content' in file_content_json: + try: + file_content_decoded = base64.b64decode(file_content_json['content']).decode('utf-8') + + # Save the file locally + with open('/usr/src/files/mgs_materialsmine.ttl', 'w', encoding='utf-8') as file: + file.write(file_content_decoded) + app.logger.info("[download_file]: File downloaded successfully.") + return True + except Exception as e: + app.logger.error(f'[download_file]: Error decoding or saving file content - {str(e)}') + return False + else: + app.logger.error('[download_file]: Failed to retrieve or decode file content.') + return False + +def get_commit_dates(app): + """ + Fetches the last commit dates for a specified file from a GitHub repository. + Constructs a list of dictionaries, each representing a commit with version, description, released, and uploaded dates. + + Parameters: + app: The application instance that provides logging functionality. + + Returns: + list: A list of dictionaries, where each dictionary represents a commit with the following keys: + - version: The version number of the commit. + - description: A brief description of the commit. + - released: The date and time of the commit in ISO 8601 format. + - uploaded: The date and time of the commit in ISO 8601 format. + """ + app.logger.info("[get_commit_dates]: Fetching last commit dates.") + + commits_json = make_github_request(commits_url, app) + if commits_json: + submissions = [] + total_commits = len(commits_json) + # Start from the oldest commit, so the oldest gets 1.0 and newer commits get incremented versions + for i, commit in enumerate(reversed(commits_json)): + version_number = "1.0" if i == 0 else f"1.{i}" + description = "Parsed, Indexed, Metrics, Annotator, Error Diff" if i == (total_commits - 1) else "Archived" + + submission = { + "version": version_number, + "description": description, + "released": commit['commit']['committer']['date'], + "uploaded": commit['commit']['committer']['date'] + } + + submissions.append(submission) + + submissions.reverse() + + return submissions + else: + app.logger.error('[get_commit_dates]: No commits found for this file.') + return [] \ No newline at end of file diff --git a/services/app/ontology/helper.py b/services/app/ontology/helper.py new file mode 100644 index 00000000..76b95707 --- /dev/null +++ b/services/app/ontology/helper.py @@ -0,0 +1,262 @@ +import os +from typing import Tuple, Dict, List +from collections import defaultdict +from rdflib import Graph, URIRef, RDFS, OWL, RDF, BNode, SKOS + +OWL_THING = URIRef("http://www.w3.org/2002/07/owl#Thing") + +# Function to extract prefix for URIs +def extract_prefix(graph, uri): + try: + # Extract the namespace from the URI + namespace_info = graph.namespace_manager.compute_qname(uri) + # Combine the prefix with the local name + return f"{namespace_info[0]}:{namespace_info[2]}" + except Exception as e: + raise ValueError + return None + +# Function to extract ontology details (format, description, version) +def extract_ontology_info(graph): + format_info = None + description = None + version = None + + for s, p, o in graph.triples((None, RDF.type, OWL.Ontology)): + format_info = "OWL" + description = str(graph.value(s, RDFS.comment)) if graph.value(s, RDFS.comment) else None + version = str(graph.value(s, OWL.versionIRI)) if graph.value(s, OWL.versionIRI) else None + + return format_info, description, version + +# Recursive function to sort subclasses +def sort_subclasses(classes): + for class_data in classes.values(): + if class_data["subClasses"]: + class_data["subClasses"] = sorted( + class_data["subClasses"], + key=lambda item: item.get("Preferred Name") + ) + sort_subclasses({sub["ID"]: sub for sub in class_data["subClasses"]}) + +def extract_preferred_name(iri): + return iri.split("#")[-1].split("/")[-1] + +def initialize_statistics() -> Dict[str, int]: + return { + "Classes": 0, + "Individuals": 0, + "Properties": 0, + "Maximum Depth": 0, + "Maximum number of children": 0, + "Average number of children": 0, + "Classes with a single child": 0, + "Classes with more than 25 children": 0, + "Classes with no definition": 0 + } + +def populate_class_with_details(classes, g): + # Populate root classes with their own details + for class_id, class_data in classes.items(): + if "Preferred Name" not in class_data: + class_data["Preferred Name"] = extract_preferred_name(class_id) + if "prefLabel" not in class_data: + class_data["prefLabel"] = extract_preferred_name(class_id) + if "prefixIRI" not in class_data: + class_data["prefixIRI"] = extract_prefix(g, class_id) + if "subClassOf" not in class_data: + class_data["subClassOf"] = str(OWL_THING) + return classes + +def build_hierarchy(classes: Dict, g: Graph) -> Dict: + root_classes = {} + + for class_id, class_data in classes.items(): + sub_class_of = class_data.get("subClassOf", str(OWL_THING)) + if sub_class_of in classes: + if class_data not in classes[sub_class_of]["subClasses"]: + classes[sub_class_of]["subClasses"].append(class_data) + else: + root_classes[sub_class_of] = create_root_class_entry(sub_class_of, class_data, g) + + return root_classes + +def create_root_class_entry(sub_class_of: str, class_data: Dict, g: Graph) -> Dict: + return { + "ID": sub_class_of, + "Preferred Name": extract_preferred_name(sub_class_of), + "prefixIRI": extract_prefix(g, sub_class_of), # Pass the graph object here + "prefLabel": extract_preferred_name(sub_class_of), + "subClasses": [class_data], + "subClassOf": str(OWL_THING), + } + +def process_graph(g: Graph): + attribute_mapping = define_attribute_mapping() + stats = initialize_statistics() + classes = defaultdict(lambda: {"subClasses": []}) + class_children_count = defaultdict(int) + classes_with_definitions = set() + + unique_properties = set() + for s, p, o in g: + unique_properties.add(p) + update_stats_based_on_type(stats, p, o) + track_definitions(s, p, o, classes_with_definitions) + track_child_counts(p, o, class_children_count) + if should_process_triple(s, p, o, g): + process_triple(s, p, o, g, classes, attribute_mapping) + + properties = extract_properties_to_list(unique_properties) + stats["Properties"] += len(properties) + return stats, classes, class_children_count, classes_with_definitions, properties + +def extract_properties_to_list(unique_properties): + # Create a list to store the properties in the desired format + properties = [] + + # Populate the properties list with property names and their URIs + for prop in sorted(unique_properties, key=lambda x: str(x)): + prop_name = str(prop).split('#')[-1].split("/")[-1] # Extract the property name from the URI + properties.append({ + "property_name": prop_name, + "ID": str(prop) + }) + + return properties + +def define_attribute_mapping() -> Dict[str, str]: + return { + "rdfs:subClassOf": "subClassOf", + "rdfs:label": "prefLabel", + "owl:sameAs": "Synonyms", + "skos:altLabel": "altLabel", + "skos:definition": "Definitions", + "prov:wasQuotedFrom": "wasQuotedFrom", + "materialsmine:hasSelector": "hasSelector", + "materialsmine:hasPreferredUnit": "hasPreferredUnit" + } + +def update_stats_based_on_type(stats: Dict[str, int], p: URIRef, o: URIRef) -> None: + if p == RDF.type: + if o == OWL.Class: + stats["Classes"] += 1 + elif o in (OWL.ObjectProperty, OWL.DatatypeProperty): + stats["Properties"] += 1 + else: + stats["Individuals"] += 1 + + +def track_definitions(s: URIRef, p: URIRef, o: URIRef, classes_with_definitions: set) -> None: + if p in (RDFS.comment, SKOS.definition): + classes_with_definitions.add(str(s)) + +def track_child_counts(p: URIRef, o: URIRef, class_children_count: defaultdict) -> None: + if p == RDFS.subClassOf: + class_children_count[str(o).strip('<>')] += 1 + +def should_process_triple(s: URIRef, p: URIRef, o: URIRef, g: Graph) -> bool: + if p == RDF.type and str(o) == "http://www.w3.org/2002/07/owl#Class": + return False + return (s, RDF.type, OWL.Class) in g + +def process_triple(s: URIRef, p: URIRef, o: URIRef, g: Graph, + classes: defaultdict, attribute_mapping: Dict[str, str]) -> None: + class_id = str(s) + classes[class_id]["ID"] = class_id + classes[class_id]["prefixIRI"] = extract_prefix(g, class_id) + + qname = g.namespace_manager.qname(p) + if qname in attribute_mapping: + handle_attribute(qname, o, class_id, classes, attribute_mapping[qname], g) + else: + classes[class_id][qname] = str(o).strip() + +def handle_attribute(qname: str, o: URIRef, class_id: str, + classes: defaultdict, attr_name: str, g: Graph) -> None: + if attr_name == "subClassOf": + handle_subclass_of(o, class_id, classes, g) + elif attr_name == "Synonyms": + classes[class_id]["Synonyms"] = classes[class_id].get("Synonyms", []) + [str(o).strip()] + elif attr_name == "prefLabel": + classes[class_id]["prefLabel"] = str(o).strip() + classes[class_id]["Label"] = str(o).strip() + classes[class_id]["Preferred Name"] = str(o).strip() + else: + classes[class_id][attr_name] = str(o).strip() + +def handle_subclass_of(o: URIRef, class_id: str, classes: defaultdict, g: Graph) -> None: + if isinstance(o, BNode): + return # Skip restrictions + subclass_of = str(o).strip('<>') + classes[class_id]["subClassOf"] = subclass_of + if subclass_of in classes: + classes[subclass_of]["subClasses"].append(classes[class_id]) + else: + classes[subclass_of] = {"ID": subclass_of, "subClasses": [classes[class_id]]} + +def combine_root_class_with_initial_structure(sorted_classes, root_classes): + for class_id, class_data in sorted_classes.items(): + if "subClassOf" not in class_data or class_data["subClassOf"] == str(OWL_THING): + root_classes[class_id] = class_data + +def calculate_additional_statistics(stats, classes, class_children_count, classes_with_definitions, g): + # Calculate additional statistics based on the constructed hierarchy + total_children = 0 + for class_id, count in class_children_count.items(): + total_children += count + stats["Maximum number of children"] = max(stats["Maximum number of children"], count) + if count == 1: + stats["Classes with a single child"] += 1 + if count > 25: + stats["Classes with more than 25 children"] += 1 + + # Calculate average number of children + if stats["Classes"] > 0: + stats["Average number of children"] = round(total_children / stats["Classes"]) + + # Calculate maximum depth and classes with no definitions + for class_id, class_data in classes.items(): + current_depth = 0 + s = URIRef(class_id) + while (s, RDFS.subClassOf, None) in g: + current_depth += 1 + s = g.value(s, RDFS.subClassOf) + stats["Maximum Depth"] = max(stats["Maximum Depth"], current_depth) + + if class_id not in classes_with_definitions: + stats["Classes with no definition"] += 1 + return stats + +def details_from_turtle(app): + app.logger.info('[details_from_turtle]: Extract Details from the turtle file') + turtle_file = "/usr/src/files/mgs_materialsmine.ttl" + + if not os.path.isfile(turtle_file): + raise FileNotFoundError(f"The file {turtle_file} does not exist in the current directory.") + + # Load the Turtle file + g = Graph() + g.parse(turtle_file, format="turtle") + + # Extract ontology details + ontology_info = extract_ontology_info(g) + + # Extract information from the Turtle file + stats, classes, class_children_count, classes_with_definitions, properties = process_graph(g) + final_stats = calculate_additional_statistics(stats, classes, class_children_count, classes_with_definitions, g) + + resolved_classes = populate_class_with_details(classes, g) + + # Sort classes by "Preferred Name" + sorted_classes = dict(sorted(resolved_classes.items(), key=lambda item: item[1].get("Preferred Name"))) + + # Initialize root classes + root_classes = build_hierarchy(sorted_classes, g) + + # Combine root classes with the initial structure + combine_root_class_with_initial_structure(sorted_classes, root_classes) + # Recursively sort all subclasses + sort_subclasses(root_classes) + app.logger.info('[details_from_turtle]: Details retrieved successfully from the turtle file') + return final_stats, ontology_info, list(root_classes.values()), properties \ No newline at end of file diff --git a/services/app/ontology/routes.py b/services/app/ontology/routes.py new file mode 100644 index 00000000..c6b74bf3 --- /dev/null +++ b/services/app/ontology/routes.py @@ -0,0 +1,92 @@ +from flask import Blueprint, jsonify, Response, current_app as app +import json +import datetime +from app.utils.util import token_required, request_logger, log_errors +from app.ontology.github_flow import get_commit_dates, download_file +from app.ontology.helper import details_from_turtle +from app.ontology.cache_service import check_cache, save_to_cache + +ontology = Blueprint("ontology", __name__, url_prefix="/ontology") + +@ontology.route('/extract/', methods=['GET']) +@log_errors +@request_logger +@token_required +def get_data_from_file(request_id): + try: + start_time = datetime.datetime.now() + + # Check if data is available in cache + cached_data = check_cache(app) + if cached_data: + # If cached data is found, return it to the frontend + app.logger.info("Returning cached data.") + response = create_response(request_id, cached_data, start_time) + return response + + # If cache is not found or empty, proceed with the existing logic + if download_file(app): + submission_details = get_commit_dates(app) + metrics, ontology_info, turtle_data, properties = details_from_turtle(app) + + # Constructing the data dictionary + data = construct_data_dictionary(metrics, ontology_info, submission_details, turtle_data, properties) + + # Save the constructed data to cache + save_to_cache(app, data) + + response = create_response(request_id, data, start_time) + + return response + else: + # If download from GitHub fails, serve outdated cache if available + app.logger.error("Failed to download file from GitHub. Serving from existing cache if available.") + cached_data = check_cache(app, serve_out_dated=True) # Check cache again (for fallback) + if cached_data: + app.logger.info("Serving outdated cached data as fallback.") + response = create_response(request_id, cached_data, start_time) + return response + else: + return jsonify({'message': "Failed to download file from GitHub and no cache available."}), 500 + + except ValueError as ve: + app.logger.error(f"ValueError: {str(ve)}", exc_info=True) + return jsonify({'message': str(ve)}), 400 + except Exception as e: + app.logger.error(f"Internal Server Error: {str(e)}", exc_info=True) + return jsonify({'message': "Internal Server error"}), 500 + + +def create_response(request_id, data, start_time): + """Helper function to create a Flask response with headers.""" + json_data = json.dumps(data, indent=4) + + response = Response(json_data, content_type='application/json; charset=utf-8', status=200) + + end_time = datetime.datetime.now() + latency = f"{(end_time - start_time).total_seconds()} seconds" + + response.headers['startTime'] = start_time + response.headers['endTime'] = end_time + response.headers['latency'] = latency + response.headers['responseId'] = request_id + return response + +def construct_data_dictionary(metrics, ontology_info, submission_details, turtle_data, properties): + """Helper function to construct the data dictionary.""" + return { + "details": { + "Acronyms": "MATERIALSMINE", + "Visibility": "Public", + "Description": ontology_info[1], + "Status": "Alpha", + "Format": ontology_info[0], + "Contact": "Marc Palmeri, Ph.D., marc.j.palmeri@duke.eduw", + "Categories": "Chemical, Development, Physicochemical", + }, + "metrics": metrics, + "data": turtle_data, + "submissions": submission_details, + "properties": properties, + "lastUpdateDate": str(datetime.date.today()) + } \ No newline at end of file diff --git a/services/app/utils/util.py b/services/app/utils/util.py index 4aa7814e..394eb739 100644 --- a/services/app/utils/util.py +++ b/services/app/utils/util.py @@ -6,7 +6,7 @@ from flask import request, jsonify, current_app as app # type: ignore import jwt # type: ignore import pandas as pd # type: ignore -import datetime +from datetime import datetime, timedelta, timezone import functools import jwt # type: ignore import uuid @@ -107,21 +107,34 @@ def decorated_function(*args, **kwargs): jwt.ExpiredSignatureError: If the token has expired. jwt.InvalidTokenError: If the token is invalid. """ - token = request.headers.get('Authorization')[7:] + header = request.headers.get('Authorization') + + if not header or not header.startswith('Bearer '): + app.logger.warning("Authorization header is missing or invalid") + return jsonify({'message': 'Authorization header is missing or invalid'}), 401 + + token = header[7:].strip() + if not token: return jsonify({'message': 'Token is missing'}), 401 try: decoded = jwt.decode(token, Config.SECRET_KEY, algorithms=['HS256']) request_id = decoded.get('reqId') if not request_id: + app.logger.warning("Invalid token or missing request_id field") return jsonify({'message': 'Invalid token or missing field'}), 401 # Pass the request_id field value to the function response = f(request_id, *args, **kwargs) return response except jwt.ExpiredSignatureError: + app.logger.warning("Token has expired") return jsonify({'message': 'Token has expired'}), 401 except jwt.InvalidTokenError: + app.logger.warning("Invalid token") return jsonify({'message': 'Invalid token'}), 401 + except Exception as e: + app.logger.error(f"An unexpected error occurred: {str(e)}") + return jsonify({'message': 'An unexpected error occurred'}), 500 return decorated_function @@ -148,14 +161,14 @@ def decorated_function(*args, **kwargs): Returns: Any: The response from the decorated function. """ - start_time = datetime.datetime.now() + start_time = datetime.now() try: json_payload = request.get_json() except Exception: json_payload = None app.logger.info(f"[START]: Entering {func.__name__} function at {start_time}. Request payload: {json_payload}") response = func(*args, **kwargs) - end_time = datetime.datetime.now() + end_time = datetime.now() execution_time = ((end_time - start_time).total_seconds()) * 1000 # Check if a response is sent back if response: @@ -181,7 +194,7 @@ def generate_jwt(expires_in: int = 600): # Add expiration time to the payload request_id = str(uuid.uuid4()) data = {"requestid": request_id} - data.update({"exp": datetime.datetime.utcnow() + datetime.timedelta(seconds=expires_in)}) + data.update({"exp": datetime.now(timezone.utc) + timedelta(seconds=expires_in)}) return jwt.encode(data, Config.SECRET_KEY, algorithm='HS256'), request_id @@ -201,4 +214,4 @@ def decode_jwt(token: str): except jwt.ExpiredSignatureError: return "Token has expired" except jwt.InvalidTokenError: - return "Invalid token" + return "Invalid token" \ No newline at end of file diff --git a/services/requirements/prod_requirements.txt b/services/requirements/prod_requirements.txt index afe944ad..59e75e83 100644 --- a/services/requirements/prod_requirements.txt +++ b/services/requirements/prod_requirements.txt @@ -33,6 +33,7 @@ pymongo==3.8.0 python-dateutil==2.8.2 python-dotenv==1.0.1 pytz==2023.3.post1 +rdflib==7.0.0 requests==2.31.0 six==1.16.0 soupsieve==2.5