From 15053783bf52b914830d9afdf4fa1435ec4d8b28 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 29 Nov 2017 13:24:15 -0500
Subject: [PATCH] Case insensitive filesystems are a terrible idea.

---
 .../galaxy/scripts/components/Citations.vue   | 202 ++++++++++++++++++
 1 file changed, 202 insertions(+)
 create mode 100644 client/galaxy/scripts/components/Citations.vue

diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
new file mode 100644
index 00000000000..ab4ea97b5a1
--- /dev/null
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -0,0 +1,202 @@
+<template>
+    <div class="toolForm">
+        <div class="toolFormTitle">
+            Citations
+            <button v-if="viewRender" v-on:click="toggleViewRender" type="button" class="btn btn-xs" 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" title="Return to formatted citation list.">
+                <i class="fa fa-times"></i>
+                Hide BibTeX
+            </button>
+        </div>
+        <div class="citations-bibtex toolFormBody citation-padding">
+            <div v-if="source === 'histories'" class="infomessage">
+                When writing up your analysis, remember to include 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>
+            <span v-if="viewRender" class="citations-formatted">
+                <p v-html="formattedReferences">
+                </p>
+            </span>
+            <textarea v-else 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 class="formatted-reference">${this.formattedReference(b)}</p>`), "");
+        }
+    },
+    created: function() {
+        axios
+            .get(`${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;
+        }
+    }
+};
+</script>
+<style>
+.citations-formatted{
+    word-wrap: break-word;
+}
+
+.citations-bibtex-text{
+    width: 100%;
+    height: 500px;
+}
+
+.citation-padding{
+    padding:5px 10px;
+}
+</style>