From 28056fdc90e6a2dedd61ff575f1bced0cc91220d Mon Sep 17 00:00:00 2001 From: mihailefter Date: Tue, 2 Nov 2021 15:48:27 +0100 Subject: [PATCH] Develop (#4) * Redirect unknown to main * Add GitHub link * API icon * Switch to using map instead of lift * Run name checker from main * Description extractor access link * Add feedback overlay (#3) * Start adding progress indicators (#2) * Related references progress indicator fix (#2) * Add some RNA support in the name checker * Normalized colors and no reference information when ERETR * Start exon numbering from 1 and no index for CDS * Reference sequence information panel title * Switch to affected protein link * View backtranslated variants * Extend and integrate the batch checker * Add copy to clipboard button for multiple descriptions * Update batch checker * Update info messages section * Batch checker file download name * Add algebra * Some updates * Better error visualisation in algebra * Name checker with sequence and variants * Extend related * Specific acknowledgement. * Add recommended by links * Integrate new viewer in the name checker * Add strand orientation * Mapper integration * Update mapper example * Name checker related link to mapper * Error handling Co-authored-by: Jeroen F.J. Laros --- package-lock.json | 235 +++++++-- package.json | 3 +- src/App.vue | 89 ++++ src/assets/hvp_recommended_system.png | Bin 0 -> 3630 bytes src/assets/irdirc_recognized_resource.jpg | Bin 0 -> 16915 bytes src/assets/main.css | 85 ++- src/components/AffectedProtein.vue | 15 +- src/components/Description.vue | 65 +++ src/components/LiftOver.vue | 144 ----- src/components/ReferenceInformation.vue | 170 +++--- src/components/Related.vue | 248 +++++++++ src/components/SelectorShort.vue | 12 +- src/components/ViewVariants.vue | 122 +++++ src/components/ViewVariantsCore.vue | 441 ++++++++++++++++ src/router/index.js | 21 + src/services/MutalyzerService.js | 24 +- src/services/NcbiEutils.js | 18 + src/views/About.vue | 53 +- src/views/Algebra.vue | 575 ++++++++++++++++++++ src/views/BatchChecker.vue | 327 ++++++++++++ src/views/DescriptionExtractor.vue | 67 ++- src/views/Home.vue | 98 +++- src/views/Mapper.vue | 514 ++++++++++++++++++ src/views/NameChecker.vue | 612 +++++++++++++++++----- src/views/PositionConverter.vue | 40 +- 25 files changed, 3503 insertions(+), 475 deletions(-) create mode 100644 src/assets/hvp_recommended_system.png create mode 100644 src/assets/irdirc_recognized_resource.jpg create mode 100644 src/components/Description.vue delete mode 100644 src/components/LiftOver.vue create mode 100644 src/components/Related.vue create mode 100644 src/components/ViewVariants.vue create mode 100644 src/components/ViewVariantsCore.vue create mode 100644 src/services/NcbiEutils.js create mode 100644 src/views/Algebra.vue create mode 100644 src/views/BatchChecker.vue create mode 100644 src/views/Mapper.vue diff --git a/package-lock.json b/package-lock.json index d3f56da..b197bb5 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,14 +1,15 @@ { "name": "mutalyzer_website", - "version": "0.1.0", + "version": "0.1.3", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "mutalyzer_website", - "version": "0.1.0", + 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a/package.json b/package.json index 1482050..ed6d6b7 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "mutalyzer_website", - "version": "0.1.2", + "version": "0.1.3", "private": true, "scripts": { "serve": "vue-cli-service serve", @@ -9,6 +9,7 @@ }, "dependencies": { "core-js": "^3.9.1", + "postgresql-client": "^1.16.4", "v-clipboard": "^2.2.3", "vue": "^2.6.12", "vue-json-pretty": "^1.7.1", diff --git a/src/App.vue b/src/App.vue index 2deab1d..2689d6c 100644 --- a/src/App.vue +++ b/src/App.vue @@ -9,6 +9,14 @@ Alpha + + + Feedback + @@ -89,6 +177,7 @@ export default { data: () => ({ drawer: false, apiBaseUrl: apiBaseUrl, + feedback: false, }), }; diff --git a/src/assets/hvp_recommended_system.png b/src/assets/hvp_recommended_system.png new file mode 100644 index 0000000000000000000000000000000000000000..828232e1685affd1dc168cd5dade4c5cde26ff97 GIT binary patch literal 3630 zcmV+}4$<+6P)%q#i;%mUp2exI&bqwV$jsr_+w1=S{8ieduK)l50d!JM 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Affected Protein Description
-
- {{ protein.description }} +
+
Affected Protein Reference Sequence
@@ -20,8 +25,13 @@ + diff --git a/src/components/LiftOver.vue b/src/components/LiftOver.vue deleted file mode 100644 index 32fa706..0000000 --- a/src/components/LiftOver.vue +++ /dev/null @@ -1,144 +0,0 @@ - - - - - diff --git a/src/components/ReferenceInformation.vue b/src/components/ReferenceInformation.vue index 25eea0e..92a8598 100644 --- a/src/components/ReferenceInformation.vue +++ b/src/components/ReferenceInformation.vue @@ -1,83 +1,96 @@ @@ -100,6 +113,8 @@ export default { record: null, gene: null, selector: null, + progress: true, + no_response: true, }; }, created: function () { @@ -122,19 +137,20 @@ export default { }; } MutalyzerService.referenceModel(params).then((response) => { + this.progress = false; if (response.data) { this.reference_model = response.data; this.record = this.getRecord(this.reference_model); this.gene = this.getGene(this.reference_model); this.selector = this.getSelector(this.reference_model); + this.no_response = false; + } else { + this.no_response = true; } }); }, methods: { getRecord(annotations) { - if (annotations.type != "record") { - return; - } let output = { id: annotations.id }; if (annotations.qualifiers) { output.details = this.extractQualifiers(annotations.qualifiers); diff --git a/src/components/Related.vue b/src/components/Related.vue new file mode 100644 index 0000000..d85387b --- /dev/null +++ b/src/components/Related.vue @@ -0,0 +1,248 @@ + + + + + diff --git a/src/components/SelectorShort.vue b/src/components/SelectorShort.vue index a88bd53..ea6bc72 100644 --- a/src/components/SelectorShort.vue +++ b/src/components/SelectorShort.vue @@ -65,7 +65,7 @@ export default { for (var i = 0; i < this.selector.exon.g.length; i++) { if (this.selector.exon.c) { output.push({ - name: i, + name: i + 1, g_s: this.selector.exon.g[i][0], g_e: this.selector.exon.g[i][1], c_s: this.selector.exon.c[i][0], @@ -73,7 +73,7 @@ export default { }); } else if (this.selector.exon.n) { output.push({ - name: i, + name: i + 1, g_s: this.selector.exon.g[i][0], g_e: this.selector.exon.g[i][1], n_s: this.selector.exon.n[i][0], @@ -81,7 +81,7 @@ export default { }); } else { output.push({ - name: i, + name: i + 1, g_s: this.selector.exon.g[i][0], g_e: this.selector.exon.g[i][1], }); @@ -94,7 +94,6 @@ export default { var output = []; if (this.selector.cds) { output.push({ - name: "0", g_s: this.selector.cds.g[0][0], g_e: this.selector.cds.g[0][1], c_s: this.selector.cds.c[0][0], @@ -143,11 +142,6 @@ export default { if (this.selector.exon.c) { output.push( ...[ - { - text: "Number", - value: "name", - sortable: false, - }, { text: "Start (g.)", value: "g_s", sortable: false }, { text: "End (g.)", value: "g_e", sortable: false }, { text: "Start (c.)", value: "c_s", sortable: false }, diff --git a/src/components/ViewVariants.vue b/src/components/ViewVariants.vue new file mode 100644 index 0000000..d2d3d1e --- /dev/null +++ b/src/components/ViewVariants.vue @@ -0,0 +1,122 @@ + + + + + + diff --git a/src/components/ViewVariantsCore.vue b/src/components/ViewVariantsCore.vue new file mode 100644 index 0000000..e2326c7 --- /dev/null +++ b/src/components/ViewVariantsCore.vue @@ -0,0 +1,441 @@ + + + + + + diff --git a/src/router/index.js b/src/router/index.js index 0d775ff..e1a0c7d 100644 --- a/src/router/index.js +++ b/src/router/index.js @@ -5,6 +5,9 @@ import About from "../views/About.vue"; import NameChecker from "../views/NameChecker.vue"; import PositionConverter from "../views/PositionConverter.vue"; import DescriptionExtractor from "../views/DescriptionExtractor.vue"; +import Mapper from "../views/Mapper.vue"; +import BatchChecker from "../views/BatchChecker.vue"; +import Algebra from "../views/Algebra.vue"; Vue.use(VueRouter); @@ -36,6 +39,24 @@ const routes = [ name: "DescriptionExtractor", component: DescriptionExtractor, }, + { + path: "/mapper", + props: true, + name: "Mapper", + component: Mapper, + }, + { + path: "/batchchecker", + props: true, + name: "BatchChecker", + component: BatchChecker, + }, + { + path: "/algebra", + props: true, + name: "Algebra", + component: Algebra, + }, { path: "/api", }, diff --git a/src/services/MutalyzerService.js b/src/services/MutalyzerService.js index 06dc7d8..92bb900 100644 --- a/src/services/MutalyzerService.js +++ b/src/services/MutalyzerService.js @@ -12,9 +12,17 @@ const apiClient = axios.create({ }); export default { - nameCheck(description) { + compare(params) { + return apiClient.get("/compare/", { params }); + }, + nameCheckHgvs(description) { return apiClient.get("/name_check/" + encodeURIComponent(description)); }, + nameCheckSequence(description, params) { + return apiClient.get("/name_check/" + encodeURIComponent(description), { + params, + }); + }, positionConvert(params) { return apiClient.get("/position_convert/", { params }); }, @@ -27,7 +35,17 @@ export default { getSelectors(referenceId) { return apiClient.get("/get_selectors/" + encodeURIComponent(referenceId)); }, - lift(params) { - return apiClient.get("/lift/", { params }); + map(params) { + return apiClient.get("/map/", { params }); + }, + view(description, params) { + return apiClient.get("/view_variants/" + encodeURIComponent(description), { + params, + }); + }, + relatedReferences(reference_id) { + return apiClient.get( + "/related_references/" + encodeURIComponent(reference_id) + ); }, }; diff --git a/src/services/NcbiEutils.js b/src/services/NcbiEutils.js new file mode 100644 index 0000000..05e5729 --- /dev/null +++ b/src/services/NcbiEutils.js @@ -0,0 +1,18 @@ +import axios from "axios"; + +const ncbiDatasetsBaseUrl = `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/`; + +const apiClient = axios.create({ + baseURL: ncbiDatasetsBaseUrl, + withCredentials: false, // This is the default + headers: { + Accept: "application/json", + "Content-Type": "application/json", + }, +}); + +export default { + get_gene_summary(id) { + return apiClient.get("/esummary.fcgi?db=gene&id=" + id + "&retmode=json"); + }, +}; diff --git a/src/views/About.vue b/src/views/About.vue index 3cc3ad9..5e4750f 100644 --- a/src/views/About.vue +++ b/src/views/About.vue @@ -2,9 +2,56 @@ -

About Page

-
-

Website version: {{ version }}

+

About Mutalyzer

+

Website version: {{ version }}

+ +

Contact

+

+ If you have a private question or a security related issue to discuss, + please use the private address + info@mutalyzer.nl. +

+ +

Funding

+

+ This project was supported by the Fair Genomes project as financed in + the Personalised Medicine program from the the Netherlands + Organization for Health Research and Development (ZonMw) under grant + number + 846003201. +

+

Recommended by

+ + + + HVP + + + + IRDiRC + + diff --git a/src/views/Algebra.vue b/src/views/Algebra.vue new file mode 100644 index 0000000..94cc853 --- /dev/null +++ b/src/views/Algebra.vue @@ -0,0 +1,575 @@ + + + + + + diff --git a/src/views/BatchChecker.vue b/src/views/BatchChecker.vue new file mode 100644 index 0000000..2e44337 --- /dev/null +++ b/src/views/BatchChecker.vue @@ -0,0 +1,327 @@ + + + + + diff --git a/src/views/DescriptionExtractor.vue b/src/views/DescriptionExtractor.vue index 766b5ce..afb63eb 100644 --- a/src/views/DescriptionExtractor.vue +++ b/src/views/DescriptionExtractor.vue @@ -40,7 +40,13 @@ class="mt-5" color="primary" :disabled="!valid" - @click.prevent="descriptionExtract()" + :to="{ + name: 'DescriptionExtractor', + query: { + reference: reference, + observed: observed, + }, + }" > Extract @@ -52,7 +58,7 @@ - {{ summary }} + @@ -61,8 +67,12 @@ diff --git a/src/views/Mapper.vue b/src/views/Mapper.vue new file mode 100644 index 0000000..89ceeba --- /dev/null +++ b/src/views/Mapper.vue @@ -0,0 +1,514 @@ + + + + + diff --git a/src/views/NameChecker.vue b/src/views/NameChecker.vue index ae7d505..f8080fe 100644 --- a/src/views/NameChecker.vue +++ b/src/views/NameChecker.vue @@ -7,44 +7,101 @@ The Name Checker takes the variant description as input and checks whether it is correct.

- - + + + + + + + + {{ + getSwitchText() + }} + + + + + + + + + +
+ Examples: + {{ example }} +
+ + + + + + + + + + + + - -
- Examples: - {{ example }} -
- - - Normalize - + Normalize + + + + Example + + @@ -63,30 +120,30 @@ prominent tile v-if="isNormalized()" + :color="getNormalizedColor()" type="success" > - {{ response.normalized_description }} - - - - - - Copy - + - +