From d074b22f296c8ce76a1c982fa63eab60ed74a1e2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 29 Nov 2017 13:23:51 -0500
Subject: [PATCH] Standard naming for components.  TODO: organization, and
 re-add citations (working around case-insensitivity here)

---
 client/galaxy/scripts/apps/admin.js           |   2 +-
 client/galaxy/scripts/apps/analysis.js        |   4 +-
 .../{history-import.vue => HistoryImport.vue} |   0
 .../{user_api_keys.vue => UserAPIKeys.vue}    |   0
 .../galaxy/scripts/components/citations.vue   | 202 ------------------
 .../galaxy/scripts/mvc/tool/tool-form-base.js |   2 +-
 6 files changed, 4 insertions(+), 206 deletions(-)
 rename client/galaxy/scripts/components/{history-import.vue => HistoryImport.vue} (100%)
 rename client/galaxy/scripts/components/{user_api_keys.vue => UserAPIKeys.vue} (100%)
 delete mode 100644 client/galaxy/scripts/components/citations.vue

diff --git a/client/galaxy/scripts/apps/admin.js b/client/galaxy/scripts/apps/admin.js
index bbbfb3cc5c2..ea2926d7c68 100644
--- a/client/galaxy/scripts/apps/admin.js
+++ b/client/galaxy/scripts/apps/admin.js
@@ -10,7 +10,7 @@ import Router from "layout/router";
 import Utils from "utils/utils";
 import Page from "layout/page";
 import Vue from "libs/vue";
-import UserAPIKeys from "components/user_api_keys.vue";
+import UserAPIKeys from "components/UserAPIKeys.vue";
 
 window.app = function app(options, bootstrapped) {
     window.Galaxy = new GalaxyApp.GalaxyApp(options, bootstrapped);
diff --git a/client/galaxy/scripts/apps/analysis.js b/client/galaxy/scripts/apps/analysis.js
index 230266a5f51..f4b6ab3ac19 100644
--- a/client/galaxy/scripts/apps/analysis.js
+++ b/client/galaxy/scripts/apps/analysis.js
@@ -13,7 +13,7 @@ import Tours from "mvc/tours";
 import GridView from "mvc/grid/grid-view";
 import GridShared from "mvc/grid/grid-shared";
 import Workflows from "mvc/workflow/workflow";
-import HistoryImport from "components/history-import.vue";
+import HistoryImport from "components/HistoryImport.vue";
 import HistoryList from "mvc/history/history-list";
 import ToolFormComposite from "mvc/tool/tool-form-composite";
 import QueryStringParsing from "utils/query-string-parsing";
@@ -21,7 +21,7 @@ import Utils from "utils/utils";
 import Ui from "mvc/ui/ui-misc";
 import DatasetError from "mvc/dataset/dataset-error";
 import DatasetEditAttributes from "mvc/dataset/dataset-edit-attributes";
-import Citations from "components/citations.vue";
+import Citations from "components/Citations.vue";
 import Vue from "libs/vue";
 
 /** define the 'Analyze Data'/analysis/main/home page for Galaxy
diff --git a/client/galaxy/scripts/components/history-import.vue b/client/galaxy/scripts/components/HistoryImport.vue
similarity index 100%
rename from client/galaxy/scripts/components/history-import.vue
rename to client/galaxy/scripts/components/HistoryImport.vue
diff --git a/client/galaxy/scripts/components/user_api_keys.vue b/client/galaxy/scripts/components/UserAPIKeys.vue
similarity index 100%
rename from client/galaxy/scripts/components/user_api_keys.vue
rename to client/galaxy/scripts/components/UserAPIKeys.vue
diff --git a/client/galaxy/scripts/components/citations.vue b/client/galaxy/scripts/components/citations.vue
deleted file mode 100644
index ab4ea97b5a1..00000000000
--- a/client/galaxy/scripts/components/citations.vue
+++ /dev/null
@@ -1,202 +0,0 @@
-<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>
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index 0129154a33e..21faf772987 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -5,7 +5,7 @@ import Utils from "utils/utils";
 import Deferred from "utils/deferred";
 import Ui from "mvc/ui/ui-misc";
 import FormBase from "mvc/form/form-view";
-import Citations from "components/citations.vue";
+import Citations from "components/Citations.vue";
 import Vue from "libs/vue";
 export default FormBase.extend({
     initialize: function(options) {