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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,197 @@ | ||
| <template> | ||
| <div class="toolForm"> | ||
| <div class="toolFormTitle"> | ||
| Citations | ||
| <button v-if="viewRender" v-on:click="toggleViewRender" type="button" class="btn btn-xs citations-to-bibtex" title="Show all in BibTeX format."> | ||
| <i class="fa fa-pencil-square-o"></i> | ||
| Show BibTeX | ||
| </button> | ||
| <button v-else type="button" v-on:click="toggleViewRender" class="btn btn-xs citations-to-formatted" title="Return to formatted citation list."> | ||
| <i class="fa fa-times"></i> | ||
| Hide BibTeX | ||
| </button> | ||
| </div> | ||
| <div class="toolFormBody" style="padding:5px 10px"> | ||
| <div v-if="source == 'history'" style="padding:5px 10px"> | ||
| <b>Warning: This is a experimental feature.</b> Most Galaxy | ||
| tools will not annotate citations explicitly at this time. When | ||
| writing up your analysis, please manually review your histories | ||
| and find all references that should be cited in order to | ||
| completely describe your work. Also, please remember to <a | ||
| href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>. | ||
| </div> | ||
| </div> | ||
| <div class="citations-bibtex toolFormBody" style="padding:5px 10px"> | ||
| <span v-if="viewRender" class="citations-formatted" style="word-wrap: break-word;"> | ||
| <p v-html="formattedReferences"> | ||
| </p> | ||
| </span> | ||
| <textarea v-else style="width: 100%; height: 500px;" class="citations-bibtex-text"> | ||
| {{ content }} | ||
| </textarea> | ||
| </div> | ||
| </div> | ||
| </template> | ||
| <script> | ||
| import axios from "axios"; | ||
| import * as bibtexParse from "libs/bibtexParse"; | ||
| import { convertLaTeX } from "latex-to-unicode-converter"; | ||
| import { stringifyLaTeX } from "latex-parser"; | ||
| export default { | ||
| props: { | ||
| source: { | ||
| type: String, | ||
| required: true | ||
| }, | ||
| id: { | ||
| type: String, | ||
| required: true | ||
| }, | ||
| viewRender: { | ||
| type: Boolean, | ||
| requried: false, | ||
| default: true | ||
| } | ||
| }, | ||
| data() { | ||
| return { | ||
| citations: [], | ||
| content: "", | ||
| errors: [] | ||
| }; | ||
| }, | ||
| computed: { | ||
| formattedReferences: function() { | ||
| return this.citations.reduce((a, b) => a.concat(`<p>${this.formattedReference(b)}</p>`), ""); | ||
| } | ||
| }, | ||
| created: function() { | ||
| axios | ||
| .get(`${Galaxy.root}api/${this.source}/${this.id}/citations`) | ||
| .then(response => { | ||
| this.content = ""; | ||
| for (var rawCitation of response.data) { | ||
| try { | ||
| var citation = { | ||
| fields: {}, | ||
| entryType: undefined | ||
| }; | ||
| var parsed = bibtexParse.toJSON(rawCitation.content); | ||
| if (parsed) { | ||
| parsed = _.first(parsed); | ||
| citation.entryType = parsed.entryType || undefined; | ||
| for (var key in parsed.entryTags) { | ||
| citation.fields[key.toLowerCase()] = parsed.entryTags[key]; | ||
| } | ||
| } | ||
| this.citations.push(citation); | ||
| this.content += rawCitation.content; | ||
| } catch (err) { | ||
| console.warn("Error parsing bibtex: " + err); | ||
| } | ||
| } | ||
| }) | ||
| .catch(e => { | ||
| console.error(e); | ||
| }); | ||
| }, | ||
| methods: { | ||
| formattedReference: function(citation) { | ||
| var entryType = citation.entryType; | ||
| var fields = citation.fields; | ||
| var ref = ""; | ||
| var authorsAndYear = `${this._asSentence( | ||
| (fields.author ? fields.author : "") + (fields.year ? ` (${fields.year})` : "") | ||
| )} `; | ||
| var title = fields.title || ""; | ||
| var pages = fields.pages ? `pp. ${fields.pages}` : ""; | ||
| var address = fields.address; | ||
| if (entryType == "article") { | ||
| var volume = | ||
| (fields.volume ? fields.volume : "") + | ||
| (fields.number ? ` (${fields.number})` : "") + | ||
| (pages ? `, ${pages}` : ""); | ||
| ref = `${authorsAndYear + | ||
| this._asSentence(title) + | ||
| (fields.journal ? `In <em>${fields.journal}, ` : "") + | ||
| this._asSentence(volume) + | ||
| this._asSentence(fields.address)}</em>`; | ||
| } else if (entryType == "inproceedings" || entryType == "proceedings") { | ||
| ref = `${authorsAndYear + | ||
| this._asSentence(title) + | ||
| (fields.booktitle ? `In <em>${fields.booktitle}, ` : "") + | ||
| (pages ? pages : "") + | ||
| (address ? `, ${address}` : "")}.</em>`; | ||
| } else if (entryType == "mastersthesis" || entryType == "phdthesis") { | ||
| ref = | ||
| authorsAndYear + | ||
| this._asSentence(title) + | ||
| (fields.howpublished ? `${fields.howpublished}. ` : "") + | ||
| (fields.note ? `${fields.note}.` : ""); | ||
| } else if (entryType == "techreport") { | ||
| ref = | ||
| authorsAndYear + | ||
| this._asSentence(title) + | ||
| this._asSentence(fields.institution) + | ||
| this._asSentence(fields.number) + | ||
| this._asSentence(fields.type); | ||
| } else if (entryType == "book" || entryType == "inbook" || entryType == "incollection") { | ||
| ref = `${authorsAndYear} ${this._formatBookInfo(fields)}`; | ||
| } else { | ||
| ref = `${authorsAndYear} ${this._asSentence(title)}${this._asSentence( | ||
| fields.howpublished | ||
| )}${this._asSentence(fields.note)}`; | ||
| } | ||
| var doiUrl = ""; | ||
| if (fields.doi) { | ||
| doiUrl = `http://dx.doi.org/${fields.doi}`; | ||
| ref += `[<a href="${doiUrl}" target="_blank">doi:${fields.doi}</a>]`; | ||
| } | ||
| var url = fields.url || doiUrl; | ||
| if (url) { | ||
| ref += `[<a href="${url}" target="_blank">Link</a>]`; | ||
| } | ||
| return convertLaTeX({ onError: (error, latex) => `{${stringifyLaTeX(latex)}}` }, ref); | ||
| }, | ||
| _formatBookInfo: function(fields) { | ||
| var info = ""; | ||
| if (fields.chapter) { | ||
| info += `${fields.chapter} in `; | ||
| } | ||
| if (fields.title) { | ||
| info += `<em>${fields.title}</em>`; | ||
| } | ||
| if (fields.editor) { | ||
| info += `, Edited by ${fields.editor}, `; | ||
| } | ||
| if (fields.publisher) { | ||
| info += `, ${fields.publisher}`; | ||
| } | ||
| if (fields.pages) { | ||
| info += `, pp. ${fields.pages}`; | ||
| } | ||
| if (fields.series) { | ||
| info += `, <em>${fields.series}</em>`; | ||
| } | ||
| if (fields.volume) { | ||
| info += `, Vol.${fields.volume}`; | ||
| } | ||
| if (fields.issn) { | ||
| info += `, ISBN: ${fields.issn}`; | ||
| } | ||
| return `${info}.`; | ||
| }, | ||
| _asSentence: function(str) { | ||
| return str && str.trim() ? `${str}. ` : ""; | ||
| }, | ||
| toggleViewRender: function() { | ||
| this.viewRender = !this.viewRender; | ||
| console.debug(this.viewRender); | ||
| } | ||
| } | ||
| }; | ||
| </script> | ||
| <style> | ||
| </style> |
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