mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Standard naming for components. TODO: organization, and re-add citations (working around case-insensitivity here)
This commit is contained in:
Dannon Baker
@@ -10,7 +10,7 @@ import Router from "layout/router";
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import Utils from "utils/utils";
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import Page from "layout/page";
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import Vue from "libs/vue";
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import UserAPIKeys from "components/user_api_keys.vue";
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import UserAPIKeys from "components/UserAPIKeys.vue";
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window.app = function app(options, bootstrapped) {
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window.Galaxy = new GalaxyApp.GalaxyApp(options, bootstrapped);
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@@ -13,7 +13,7 @@ import Tours from "mvc/tours";
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import GridView from "mvc/grid/grid-view";
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import GridShared from "mvc/grid/grid-shared";
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import Workflows from "mvc/workflow/workflow";
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import HistoryImport from "components/history-import.vue";
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import HistoryImport from "components/HistoryImport.vue";
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import HistoryList from "mvc/history/history-list";
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import ToolFormComposite from "mvc/tool/tool-form-composite";
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import QueryStringParsing from "utils/query-string-parsing";
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@@ -21,7 +21,7 @@ import Utils from "utils/utils";
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import Ui from "mvc/ui/ui-misc";
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import DatasetError from "mvc/dataset/dataset-error";
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import DatasetEditAttributes from "mvc/dataset/dataset-edit-attributes";
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import Citations from "components/citations.vue";
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import Citations from "components/Citations.vue";
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import Vue from "libs/vue";
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/** define the 'Analyze Data'/analysis/main/home page for Galaxy
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@@ -1,202 +0,0 @@
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<template>
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<div class="toolForm">
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<div class="toolFormTitle">
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Citations
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<button v-if="viewRender" v-on:click="toggleViewRender" type="button" class="btn btn-xs" title="Show all in BibTeX format.">
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<i class="fa fa-pencil-square-o"></i>
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Show BibTeX
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</button>
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<button v-else type="button" v-on:click="toggleViewRender" class="btn btn-xs" title="Return to formatted citation list.">
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<i class="fa fa-times"></i>
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Hide BibTeX
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</button>
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</div>
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<div class="citations-bibtex toolFormBody citation-padding">
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<div v-if="source === 'histories'" class="infomessage">
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When writing up your analysis, remember to include all references that should be cited in order
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to completely describe your work. Also, please remember to <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.
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</div>
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<span v-if="viewRender" class="citations-formatted">
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<p v-html="formattedReferences">
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</p>
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</span>
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<textarea v-else class="citations-bibtex-text">
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{{ content }}
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</textarea>
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</div>
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</div>
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</template>
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<script>
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import axios from "axios";
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import * as bibtexParse from "libs/bibtexParse";
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import { convertLaTeX } from "latex-to-unicode-converter";
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import { stringifyLaTeX } from "latex-parser";
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export default {
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props: {
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source: {
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type: String,
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required: true
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},
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id: {
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type: String,
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required: true
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},
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viewRender: {
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type: Boolean,
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requried: false,
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default: true
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}
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},
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data() {
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return {
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citations: [],
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content: "",
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errors: []
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};
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},
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computed: {
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formattedReferences: function() {
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return this.citations.reduce((a, b) => a.concat(`<p class="formatted-reference">${this.formattedReference(b)}</p>`), "");
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}
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},
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created: function() {
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axios
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.get(`${Galaxy.root}api/${this.source}/${this.id}/citations`)
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.then(response => {
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this.content = "";
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for (var rawCitation of response.data) {
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try {
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var citation = {
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fields: {},
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entryType: undefined
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};
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var parsed = bibtexParse.toJSON(rawCitation.content);
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if (parsed) {
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parsed = _.first(parsed);
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citation.entryType = parsed.entryType || undefined;
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for (var key in parsed.entryTags) {
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citation.fields[key.toLowerCase()] = parsed.entryTags[key];
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}
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}
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this.citations.push(citation);
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this.content += rawCitation.content;
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} catch (err) {
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console.warn("Error parsing bibtex: " + err);
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}
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}
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})
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.catch(e => {
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console.error(e);
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});
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},
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methods: {
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formattedReference: function(citation) {
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var entryType = citation.entryType;
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var fields = citation.fields;
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var ref = "";
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var authorsAndYear = `${this._asSentence(
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(fields.author ? fields.author : "") + (fields.year ? ` (${fields.year})` : "")
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)} `;
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var title = fields.title || "";
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var pages = fields.pages ? `pp. ${fields.pages}` : "";
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var address = fields.address;
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if (entryType == "article") {
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var volume =
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(fields.volume ? fields.volume : "") +
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(fields.number ? ` (${fields.number})` : "") +
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(pages ? `, ${pages}` : "");
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ref = `${authorsAndYear +
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this._asSentence(title) +
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(fields.journal ? `In <em>${fields.journal}, ` : "") +
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this._asSentence(volume) +
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this._asSentence(fields.address)}</em>`;
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} else if (entryType == "inproceedings" || entryType == "proceedings") {
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ref = `${authorsAndYear +
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this._asSentence(title) +
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(fields.booktitle ? `In <em>${fields.booktitle}, ` : "") +
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(pages ? pages : "") +
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(address ? `, ${address}` : "")}.</em>`;
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} else if (entryType == "mastersthesis" || entryType == "phdthesis") {
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ref =
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authorsAndYear +
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this._asSentence(title) +
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(fields.howpublished ? `${fields.howpublished}. ` : "") +
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(fields.note ? `${fields.note}.` : "");
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} else if (entryType == "techreport") {
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ref =
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authorsAndYear +
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this._asSentence(title) +
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this._asSentence(fields.institution) +
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this._asSentence(fields.number) +
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this._asSentence(fields.type);
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} else if (entryType == "book" || entryType == "inbook" || entryType == "incollection") {
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ref = `${authorsAndYear} ${this._formatBookInfo(fields)}`;
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} else {
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ref = `${authorsAndYear} ${this._asSentence(title)}${this._asSentence(
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fields.howpublished
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)}${this._asSentence(fields.note)}`;
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}
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var doiUrl = "";
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if (fields.doi) {
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doiUrl = `http://dx.doi.org/${fields.doi}`;
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ref += `[<a href="${doiUrl}" target="_blank">doi:${fields.doi}</a>]`;
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}
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var url = fields.url || doiUrl;
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if (url) {
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ref += `[<a href="${url}" target="_blank">Link</a>]`;
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}
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return convertLaTeX({ onError: (error, latex) => `{${stringifyLaTeX(latex)}}` }, ref);
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},
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_formatBookInfo: function(fields) {
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var info = "";
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if (fields.chapter) {
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info += `${fields.chapter} in `;
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}
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if (fields.title) {
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info += `<em>${fields.title}</em>`;
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}
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if (fields.editor) {
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info += `, Edited by ${fields.editor}, `;
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}
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if (fields.publisher) {
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info += `, ${fields.publisher}`;
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}
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if (fields.pages) {
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info += `, pp. ${fields.pages}`;
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}
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if (fields.series) {
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info += `, <em>${fields.series}</em>`;
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}
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if (fields.volume) {
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info += `, Vol.${fields.volume}`;
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}
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if (fields.issn) {
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info += `, ISBN: ${fields.issn}`;
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}
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return `${info}.`;
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},
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_asSentence: function(str) {
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return str && str.trim() ? `${str}. ` : "";
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},
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toggleViewRender: function() {
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this.viewRender = !this.viewRender;
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}
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}
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};
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</script>
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<style>
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.citations-formatted{
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word-wrap: break-word;
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}
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.citations-bibtex-text{
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width: 100%;
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height: 500px;
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}
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.citation-padding{
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padding:5px 10px;
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}
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</style>
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@@ -5,7 +5,7 @@ import Utils from "utils/utils";
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import Deferred from "utils/deferred";
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import Ui from "mvc/ui/ui-misc";
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import FormBase from "mvc/form/form-view";
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import Citations from "components/citations.vue";
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import Citations from "components/Citations.vue";
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import Vue from "libs/vue";
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export default FormBase.extend({
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initialize: function(options) {
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