├── .gitignore ├── LICENCE.md ├── README.md ├── config.js ├── copy-reference.js ├── get-current-pdf-page.js ├── package-lock.json ├── package.json ├── phd-protocol-handler.js └── utils.js /.gitignore: -------------------------------------------------------------------------------- 1 | node_modules 2 | ids.json 3 | *.xoj 4 | shortcut 5 | -------------------------------------------------------------------------------- /LICENCE.md: -------------------------------------------------------------------------------- 1 | Copyright 2022 Gilles Castel 2 | 3 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: 4 | 5 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 6 | 7 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 8 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Instant Reference 2 | 3 | This repository complements [my blog post on my Mathematics PhD research workflow](https://castel.dev/post/research-workflow). 4 | 5 | Pdf reference: 6 | 7 | ![pdf-reference](https://user-images.githubusercontent.com/7069691/162628728-099034c5-378b-421b-bbac-4cf35ab089aa.gif) 8 | 9 | Url reference: 10 | 11 | ![url-reference](https://user-images.githubusercontent.com/7069691/162628882-309c98d0-5e66-4565-a9ed-a60975337317.gif) 12 | 13 | 14 | ## Installing 15 | 16 | First install dependencies by running 17 | 18 | ``` 19 | sudo apt install xclip exiftool xdotool x11-utils zenity xsel 20 | ``` 21 | 22 | Then clone this repository into a directory. 23 | ```bash 24 | cd directory 25 | git clone https://github.com/gillescastel/instant-reference 26 | cd instant-reference 27 | npm install 28 | ``` 29 | 30 | 31 | Then add this directory to your PATH by adding the following line to the bottom of your `~/.profile` file: 32 | 33 | ```bash 34 | export PATH="/home/username/path/to/directory/instant-reference:$PATH" 35 | ``` 36 | 37 | You might need to log out and log in for this to work. 38 | 39 | ### Installing the protocol 40 | 41 | Install the `phd` protocol by creating a file located at `~/.local/share/applications/phd.desktop` containing: 42 | 43 | ```ini 44 | [Desktop Entry] 45 | Name=Phd helper 46 | Exec=phd-protocol-handler.js %u 47 | Icon=emacs-icon 48 | Type=Application 49 | Terminal=false 50 | MimeType=x-scheme-handler/phd; 51 | ``` 52 | 53 | Then run the following to register it 54 | ```bash 55 | sudo update-desktop-database 56 | xdg-mime default phd.desktop x-scheme-handler/phd 57 | ``` 58 | 59 | In `config.js` located in `instant-reference`, change the `pdfViewer` to the one you use (in Ubuntu, the default is evince). 60 | 61 | ### Installing the 'Add to library button' (optional) 62 | 63 | ![arxiv2](https://user-images.githubusercontent.com/7069691/162634543-b7d6b4ee-e102-4799-8207-16e3cd1db865.png) 64 | 65 | Install a userscripts manager add-on for your browser, for example Tampermonkey ([Chrome](https://chrome.google.com/webstore/detail/tampermonkey/dhdgffkkebhmkfjojejmpbldmpobfkfo?hl=en), [Firefox](https://addons.mozilla.org/en-US/firefox/addon/tampermonkey/)). 66 | Then add the following userscript: 67 | ```javascript 68 | // ==UserScript== 69 | // @name ArXiv add to library 70 | // @version 0.1 71 | // @description Add a button to ArXiv to add a paper to your library 72 | // @match https://arxiv.org/* 73 | 74 | // ==/UserScript== 75 | 76 | (function() { 77 | 'use strict'; 78 | const download = document.querySelector('.download-pdf').href 79 | const title = document.querySelector('.title').textContent.replace(/^Title:/, '') 80 | const authors = [...document.querySelectorAll('.authors a')].map(a => a.textContent) 81 | const query = new URLSearchParams({title, download, authors}); 82 | const url = 'phd://download-arxiv/download?' + query 83 | const list = document.querySelector('.extra-services .full-text ul') 84 | const li = document.createElement('li') 85 | const a = document.createElement('a') 86 | a.target = '_blank' 87 | a.innerHTML = 'Add to library' 88 | a.href = url 89 | li.appendChild(a) 90 | list.appendChild(li) 91 | })(); 92 | ``` 93 | 94 | So this simply adds a link to ArXiv with url `phd://download-arxiv/download?title=Title&authors=&Authors&download=pdfUrl`. When you click on it the custom protocol handler takes over and downloads the file. 95 | 96 | **Change download location by editing `config.js` (located in the `instant-reference` directory) and changing the value of `papersDirectory`.** Be sure to create the directory. 97 | 98 | If you get errors using Firefox, try this. 99 | Go to `about:config` and add the following settings: 100 | 101 | ``` 102 | network.protocol-handler.app.phd /home/username/path/to/directory/phd-protocol-handler.js 103 | network.protocol-handler.expose.phd false 104 | network.protocol-handler.external.phd true 105 | ``` 106 | 107 | Then once you click a `phd://` link it will ask you to how to open these kind of links. Specify the protocol handler located at `/home/username/path/to/directory/phd-protocol-handler.js` and click on 'Don't ask next time'. 108 | 109 | 110 | ### Setting up the shortcut 111 | 112 | Using your preferred shortcut manager (E.g. Settings > Keyboard Shortcuts in Ubuntu), add a shortcut that executes 113 | `/home/username/path/to/directory/copy-reference.js`. 114 | 115 | When you press this shortcut, the script will copy a bit of LaTeX code for you to paste in your editor. 116 | By adding the following definition of `\pdfref` to your preamble, the copied LaTeX snippet will transform in a clickable link, and upon clicking on it, the custom protocol handler will open the document at the correct page. 117 | 118 | ```tex 119 | \usepackage{hyperref} 120 | \hypersetup{hidelinks} 121 | \usepackage{xifthen} 122 | \usepackage{fontawesome} 123 | 124 | \newcommand\urlref[2]{% 125 | \href{#1}{\raisebox{0.15ex}{\scriptsize \faLink}\:\textup{\textbf{#2}}}% 126 | } 127 | 128 | \newcommand\pdfref[3]{% 129 | \href{phd://open-paper?id=#1&page=#2}{% 130 | \textup{[\textbf{\ifthenelse{\isempty{#3}}{here}{#3}}]}}% 131 | } 132 | ``` 133 | 134 | The first argument of `\pdfref` is the id of the document, the second the page number and the third the title, which is by default the title of the pdf, which you can change by running 135 | 136 | ```bash 137 | exiftool -overwrite_original_in_place -Title="New title" document.pdf 138 | ``` 139 | 140 | 141 | ## Supported Pdf readers 142 | 143 | ### Zathura 144 | 145 | Zathura is supported out of the box. 146 | 147 | ### Evince 148 | 149 | Evince is also supported, but beware of the following. 150 | First, you need to have gvfs installed and running (the filesystem metadata framework Evince uses to save current page number.) This is by default on Ubuntu. 151 | 152 | The snap version of Ubuntu has [some problems](https://gitlab.gnome.org/GNOME/evince/-/issues/1642#note_1409663) with talking to gvfs, so this doesn't work. To fix this, remove it and install a deb-based version: 153 | 154 | ```bash 155 | sudo snap remove evince 156 | sudo apt install evince 157 | ``` 158 | 159 | You'll probably also need to disable App Armor for Evince to allow it to talk to gvfs. Do this by running: 160 | 161 | ``` 162 | sudo apt install apparmor-utils 163 | sudo aa-complain /usr/bin/evince 164 | ``` 165 | 166 | ### Other pdf viewers 167 | 168 | Interested in adding support for other pdf viewers? Feel free to add a pull request. Have a look at `get-current-pdf-page.js` to get started. 169 | 170 | 171 | ## Debugging 172 | 173 | To debug the protocol handler, run the following and have a look at the output. This should download 'Ricci flow with surgery on three-manifolds' to your preferred download location. 174 | 175 | ```bash 176 | ./phd-protocol-handler.js "phd://download-arxiv/test?title=Ricci+flow+with+surgery+on+three-manifolds&download=https%3A%2F%2Farxiv.org%2Fpdf%2Fmath%2F0303109&authors=Grisha+Perelman" 177 | ``` 178 | 179 | For the reference shortcut, run 180 | 181 | ```bash 182 | sleep 2; ./copy-reference.js 183 | ``` 184 | 185 | Within two second, move activate your pdf reader and have a look at the output. 186 | -------------------------------------------------------------------------------- /config.js: -------------------------------------------------------------------------------- 1 | export const papersDirectory = '/home/gilles/phd/papers/' 2 | export const pdfReader = 'zathura' 3 | -------------------------------------------------------------------------------- /copy-reference.js: -------------------------------------------------------------------------------- 1 | #!/usr/bin/node 2 | 3 | import {execa, execaCommand, execaCommandSync} from "execa"; 4 | import {copy, wait, press, notify, pathToId} from "./utils.js"; 5 | import {getCurrentPdfPage} from "./get-current-pdf-page.js"; 6 | 7 | async function getFirefoxReference(name) { 8 | const [titleRaw, _] = name.split("—"); 9 | const title = titleRaw.trim(); 10 | 11 | await wait(200); 12 | await press("ctrl+l"); 13 | await press("ctrl+c"); 14 | await wait(200); 15 | await press("F6"); 16 | const {stdout: url} = await execaCommand("xclip -selection clipboard -o"); 17 | 18 | await notify(`${title}, url:${url}`); 19 | await copy("\\urlref{" + url + "}{" + title + "}"); 20 | } 21 | 22 | async function getPdfReference() { 23 | const {path, page} = await getCurrentPdfPage(); 24 | 25 | const {stdout: metadataStr} = await execa("exiftool", ["-j", path]); 26 | const metadata = JSON.parse(metadataStr); 27 | 28 | const fileName = path.split("/").pop().replace(".pdf", ""); 29 | const title = metadata[0].Title || fileName; 30 | const pageNumber = page + 1; 31 | 32 | console.log(fileName, title, pageNumber); 33 | 34 | await notify(`${title}, p. ${pageNumber}`); 35 | await copy( 36 | [ 37 | "\\pdfref{", 38 | await pathToId(path), 39 | "}{", 40 | pageNumber, 41 | "}{", 42 | title, 43 | "}", 44 | ].join("") 45 | ); 46 | } 47 | 48 | async function main() { 49 | const {stdout: name} = await execaCommand( 50 | "xdotool getactivewindow getwindowname" 51 | ); 52 | 53 | if (name.includes("Firefox")) { 54 | await getFirefoxReference(name); 55 | process.exit(0); 56 | } 57 | 58 | // maybe pdf reference 59 | await getPdfReference(); 60 | process.exit(0); 61 | } 62 | 63 | main(); 64 | -------------------------------------------------------------------------------- /get-current-pdf-page.js: -------------------------------------------------------------------------------- 1 | import {execa, execaCommand} from "execa"; 2 | 3 | import dbus from "dbus-next"; 4 | 5 | export async function getCurrentPdfPage() { 6 | try { 7 | var {stdout: windowId} = await execaCommand("xdotool getactivewindow"); 8 | } catch (e) { 9 | console.log('Could not find active window. Is xdotool installed?'); 10 | } 11 | 12 | try { 13 | var {stdout: xClassStr} = await execa("xprop", [ 14 | "-id", 15 | windowId, 16 | "WM_CLASS", 17 | ]); 18 | } catch (e) { 19 | console.log('Could not get X window Class. Is xprop installed?'); 20 | } 21 | 22 | const xClass = xClassStr.split(" = ")[1]; 23 | const {stdout: pid} = await execaCommand( 24 | "xdotool getactivewindow getwindowpid" 25 | ); 26 | 27 | if (xClass.includes("zathura")) 28 | return await getZathuraMetadata(pid) 29 | 30 | if (xClass.includes("evince")) 31 | return await getEvinceMetadata(pid) 32 | 33 | return null; 34 | } 35 | 36 | 37 | async function getZathuraMetadata(pid) { 38 | console.log('Found zathura window'); 39 | const bus = dbus.sessionBus(); 40 | const obj = await bus.getProxyObject( 41 | `org.pwmt.zathura.PID-${pid}`, 42 | "/org/pwmt/zathura" 43 | ); 44 | const properties = obj.getInterface("org.freedesktop.DBus.Properties"); 45 | 46 | const page = (await properties.Get("org.pwmt.zathura", "pagenumber")).value; 47 | const path = (await properties.Get("org.pwmt.zathura", "filename")).value; 48 | bus.disconnect(); 49 | return {page, path}; 50 | } 51 | 52 | async function getEvinceMetadata(pid) { 53 | console.log('Found evince window'); 54 | const {stdout: paths} = await execaCommand(`realpath /proc/${pid}/fd/*`, {shell: true}); 55 | const path = paths.split('\n').find(p => p.endsWith('.pdf')).trim(); 56 | const {stdout: metadata} = await execa("gio", [ 57 | "info", 58 | "-a", 59 | "metadata::evince::page", 60 | path, 61 | ]); 62 | 63 | try { 64 | const {groups: {page} = {page: null}} = metadata.match( 65 | /metadata::evince::page:\s*(?\d+)/ 66 | ); 67 | return {page: parseInt(page), path}; 68 | } catch (e) { 69 | console.log('Could not find evince metadata. 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-------------------------------------------------------------------------------- 1 | { 2 | "name": "test", 3 | "version": "1.0.0", 4 | "description": "", 5 | "main": "index.js", 6 | "scripts": { 7 | "test": "echo \"Error: no test specified\" && exit 1" 8 | }, 9 | "type": "module", 10 | "keywords": [], 11 | "author": "", 12 | "license": "ISC", 13 | "dependencies": { 14 | "dbus-next": "^0.10.2", 15 | "execa": "^6.0.0" 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /phd-protocol-handler.js: -------------------------------------------------------------------------------- 1 | #!/usr/bin/node 2 | 3 | import {papersDirectory, pdfReader} from "./config.js"; 4 | import {execa} from "execa"; 5 | import {join} from "node:path"; 6 | import fs from "node:fs"; 7 | import url from "node:url"; 8 | import {idToPath, downloadFile, notify} from "./utils.js"; 9 | 10 | async function openPdf({id, page = 0}) { 11 | const path = await idToPath(id); 12 | console.log(id, path); 13 | if (pdfReader == 'zathura') 14 | return await execa(pdfReader, [path, "-P", page]); 15 | if (pdfReader == 'evince') 16 | return await execa(pdfReader, ["--page-index", page, path]); 17 | 18 | try { 19 | await execa(pdfReader, [path, "-p", page]); 20 | } catch (e) { 21 | try { 22 | await execa(pdfReader, [path, "-p", page]); 23 | } catch (e) {} 24 | } 25 | } 26 | 27 | async function downloadArxiv({authors: authorsStr, title, download}) { 28 | notify('Downloading ' + title); 29 | const allAuthors = authorsStr.split(",").map(lastNameFirst); 30 | const authors = allAuthors.slice(0, 5); 31 | 32 | const path = join( 33 | papersDirectory, 34 | title + " -- " + authors + ".pdf" 35 | ); 36 | 37 | // check if file exists. 38 | 39 | // only if it exists! 40 | await downloadFile(download + ".pdf", path); 41 | await execa("exiftool", [ 42 | "-overwrite_original_in_place", 43 | `-Title=${title}`, 44 | `-Author=${allAuthors.join(", ")}`, 45 | path, 46 | ]); 47 | 48 | execa(pdfReader, [path]); 49 | } 50 | 51 | function lastNameFirst(author) { 52 | const splitted = author.split(" "); 53 | const last = splitted[splitted.length - 1]; 54 | const rest = splitted.slice(0, -1); 55 | return [last, ...rest].join(" ").replace(".", ""); 56 | } 57 | 58 | async function handle(host, query) { 59 | if (host == "open-paper") { 60 | openPdf(query); 61 | } 62 | 63 | if (host == "download-arxiv") { 64 | downloadArxiv(query); 65 | } 66 | } 67 | 68 | const args = process.argv; 69 | const parsed = url.parse(args[2], true); 70 | const {host, query} = parsed; 71 | 72 | handle(host, query); 73 | 74 | // or follow: 75 | // https://askubuntu.com/questions/514125/url-protocol-handlers-in-basic-ubuntu-desktop 76 | // go to .local/share/applications 77 | // Add to phd.desktop: 78 | // [Desktop Entry] 79 | // Name=Phd helper 80 | // Exec=phd-protocol-handler 81 | // Icon=emacs-icon 82 | // Type=Application 83 | // Terminal=false 84 | // MimeType=x-scheme-handler/phd; 85 | // 86 | // xdg-mime default phd.desktop x-scheme-handler/phd 87 | //sudo update-desktop-database 88 | // 89 | // In firefox, maybe have to go to settings and then select 'use phd-protocol-handler for dealing with phd protocol 90 | // 91 | // 92 | // 93 | // 94 | // ==UserScript== 95 | // @name ArXiv add to library 96 | // @namespace http://tampermonkey.net/ 97 | // @version 0.1 98 | // @description try to take over the world! 99 | // @author You 100 | // @match https://arxiv.org/* 101 | // @icon data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw== 102 | // @grant none 103 | // ==/UserScript== 104 | // 105 | // (function() { 106 | // 'use strict'; 107 | // const download = document.querySelector('.download-pdf').href 108 | // const title = document.querySelector('.title').textContent.replace(/^Title:/, '') 109 | // const authors = [...document.querySelectorAll('.authors a')].map(a => a.textContent) 110 | // const query = new URLSearchParams({title, download, authors}); 111 | // const url = 'phd://download-arxiv/test?' + query 112 | // const list = document.querySelector('.extra-services .full-text ul') 113 | // const li = document.createElement('li') 114 | // const a = document.createElement('a') 115 | // a.target = '_blank' 116 | // a.innerHTML = 'Add to library' 117 | // a.href = url 118 | // li.appendChild(a) 119 | // list.appendChild(li) 120 | // })(); 121 | -------------------------------------------------------------------------------- /utils.js: -------------------------------------------------------------------------------- 1 | import https from "node:https"; 2 | import fs from "node:fs/promises"; 3 | import fsn from "node:fs"; 4 | import {join} from "node:path"; 5 | import {execa, execaCommand, execaCommandSync} from "execa"; 6 | 7 | export const copy = (str) => 8 | execaCommand("xsel --input --clipboard", { 9 | input: str, 10 | }); 11 | 12 | export const wait = async (ms) => new Promise((res) => setTimeout(res, ms)); 13 | export const press = async (key) => execa("xdotool", ["key", key]); 14 | export const notify = (str) => execa("notify-send", [str]); 15 | 16 | export const ask = async (question) => { 17 | try { 18 | const {stdout} = await execa('zenity', ['--entry', '--text', question]); 19 | return stdout.trim() 20 | } catch (e) {} 21 | 22 | console.log('Please install zenity'); 23 | return null 24 | } 25 | 26 | export const downloadFile = (url, path) => { 27 | return new Promise((done, rej) => { 28 | https.get( 29 | url, 30 | { 31 | headers: { 32 | "User-Agent": 33 | "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:94.0) Gecko/20100101 Firefox/94.0", 34 | }, 35 | }, 36 | (res) => { 37 | const writeStream = fsn.createWriteStream(path); 38 | res.pipe(writeStream); 39 | 40 | writeStream.on("finish", () => { 41 | writeStream.close(); 42 | done(); 43 | }); 44 | } 45 | ); 46 | }); 47 | }; 48 | 49 | export const idToPath = async (id) => { 50 | const db = new URL("./ids.json", import.meta.url); 51 | let ids = []; 52 | try { 53 | ids = JSON.parse(await fs.readFile(db)); 54 | } catch (e) {} 55 | const result = ids.find(([i, p]) => i == id); 56 | return result ? result[1] : null; 57 | }; 58 | 59 | export const pathToId = async (path) => { 60 | const db = new URL("./ids.json", import.meta.url); 61 | let ids = []; 62 | try { 63 | ids = JSON.parse(await fs.readFile(db)); 64 | } catch (e) {} 65 | 66 | const existing = ids.find(([id, p]) => p === path); 67 | if (existing) return existing[0]; 68 | 69 | const unique = (option) => !ids.find(([id, p]) => id === option); 70 | let id; 71 | while (!id || !unique(id)) { 72 | id = await ask('New file. Please give it a unique id.') 73 | if (!id) return null; 74 | } 75 | 76 | ids.push([id, path]); 77 | await fs.writeFile(db, JSON.stringify(ids, null, 2)); 78 | return id; 79 | }; 80 | --------------------------------------------------------------------------------