Table of Contents
Description of all the files in the github repository
(about researchr)
All files can be downloaded from github. Because I constantly change the files to suit my own workflow and experiments, and because this has grown quite organic, rather than being planned, it's a bit of a mishmash. This is an attempt at documenting which files do what, and show how it all “hangs together”.
I have attached links to the source in github, and also shown which keyboard shortcuts I have assigned the various scripts (see keyboard shortcuts). These have nothing to do with the programs themselves, of course, and can be freely assigned. Unless something else is indicated, my shortcuts start with CTRL+ALT+CMD to avoid conflicting with existing program shortcuts.
Also see my design patterns, where I have documented some neat ways of coding, and a list of the Appscript strings I have used.
BibDesk
Read more about BibDesk hacks in general
| bibdesk-copy.rb | src | Copies all the selected publications onto the clipboard, in the format citekey, which are understood by DokuWiki and WordPress renders, as well as PanDoc. | C |
| bibdesk-linkfile.rb | src | Automatically attaches the most recent PDF file in the Download directory to the currently selected publication | L |
| bibdesk-qlook.rb | src | Launches quicklook to quickly preview currently selected file | ALT+SPACE |
| bibdesk-kindle.rb | src | Reformats and sends the selected files to Kindle, either by copying, or through e-mail (if Kindle is not connected) | K |
| bibdesk.rb | src | Opens selected citations from BibDesk in Chrome, creating metadata pages if they don't already exist | CMD+E |
| bibdesk.app | src | App-wrapper for an AppleScript that launches bibdesk-url.rb, and is connected to the bibdesk: URL scheme | |
| bibdesk-url.rb | src | Launched by a bibdesk: URL through bibdesk.app, opens the citation given in BibDesk | |
| gscholar.rb | src | Looks up the title of the currently selected publication on Google Scholar, and displays a list of the top hits with PDFs available for download (for use with gscholar-y.rb) | G |
| gscholar-y.rb | src | Takes a number argument, reads the file generated by gscholar.rb, downloads the correct file, and autolinks it to the selected publication | 1..8 |
Skim
| skim.rb | src | Exports all highlights, notes and images from open PDF file to wikipage, also generating citations (see anatomy of a publication page) | CMD+E |
| skim-screenshots.rb | src | Adds path of most recent screenshot in Desktop folder to a temp file, used when skim.rb exports notes to wiki. First use Shift+CMD+2 or Shift+CMD+3 to take screenshot, then this to add to cache | C |
| skimx.app | src | App-wrapper for an AppleScript that launches skim-url.rb, and is connected to the skimx: URL scheme | |
| skim-url.rb | src | Launched by a skimx: URL through skimx.app, opens the PDF given in Skim (on the page given, if specified) |
DokuWiki
Although these scripts are written to interact with DokuWiki, they interact directly with Chrome.
| dokuwiki-bulletlist.rb | src | Converts the selected text to a DokuWiki bullet list, splitting on LF, comma, semicolon or space (trying to determine intelligently which one to use) | P |
| dokuwiki-clip.rb | src | Asks for a page name, and appends selected text on current page to that wiki page, with proper citation | I |
| dokuwiki-go.rb | src | Presents a wiki page selector and opens the selected page | ' |
| dokuwiki-image.rb | src | Moves the most recent screenshot to the DokuWiki media folder, and inserts a proper DokuWiki image tag | C |
| dokuwiki-sbs.rb | src | Asks for the name of a page, and presents it side-by-side with the existing page, in editing mode if it's a wiki page, and run through Instapaper to clean it up, if it's a normal page | : |
| newauthor.rb | src | Launched through a ruby: link in the DokuWiki sidebar, asks for the name of an author, and creates a new author page according to template. Wouldn't be necessary if 404redirect plugin enabled templates when opening a new file for editing automatically | |
| sbibtex.php | src | Plugin for DokuWiki which renders citekey as Author, Author2 (year), linked to the main publication page, and shows the full citation on mouse-over. Gets its data from the json file generated by bibtex-batch.rb |
Chrome
| imfeelinglucky.rb | src | Script similar to gscholar.rb, searches for currently selected phrase in Google, gives you top hits, let's you choose one (through imfeelinglucky-y.rb) and then inserts a fully formatted links, depending on whether you are currently browsing a wikipage, WordPress, or any other page. Currently doesn't work, because Google blocked the API | L |
| imfeelinglucky-y.rb | src | See above | 1..4 |
| ruby.app | src | App-wrapper for an AppleScript that launches ruby.rb, and is connected to the ruby: URL scheme | |
| ruby.rb | src | Launches whatever ruby script was specified by a ruby: URL, through ruby.app, used for newauthor.rb |
Kindle
Other apps
| qlmanage-doc2pdf.rb | src | Uses quicklook to generate a PDF of Word doc, RTF etc currently selected in Finder | P |
| devonthink.rb | src | Opens currently selected publication in DevonThink in DokuWiki (used for importing entire BibDesk PDF folder into DevonThink for full-text search | CMD+E |
| convert-doc.rb | src | Takes a text file as argument, and converts it into HTML formatted for opening in Word, converting all citekeys into proper citations, and adding a reference list. Inspired by Pandoc, still very early days. Should eventually be able to output to different formats. |
Utility scripts
| bibtex-batch.rb | src | Runs through Bibliography.bib (generated by BibDesk) and generates main bibliography, bibliography pages by author and by keyword, and json bibliography cache for WordPress and DokuWiki plugins |
| utility-functions.rb | src | A number of useful functions used by other scripts, such as wrapper for growl, File.write and File.append, wrappers for pbcopy and pbpaste, clean_pagename (see below), GUI wikipage selector, wrapper for dwpage (insert page in DokuWiki), etc. |
| clean_id.php | src | Extracted from DokuWiki source code, takes a title and turns it into a DokuWiki filename (ü → ue etc). Used by clean_pagename() in utility-functions.rb |
| utf8.php | src | Helper script for clean_id.php, from DokuWiki source code |
| wiki-lib.rb | src | Functions for DokuWiki, mainly ensure_refpage() which generates the main publication page (see anatomy of a publication page) |
| mail-lib.rb | src | Helper function for e-mail, used by bibdesk-kindle.rb |
| config.yaml.distribution | src | Rename to config.yaml and modify, used by mail-lib.rb |
| update_refpage.rb | src | Command-line script to force updating of main publication page (citation info), usually ensure_refpage() only does this if file doesn't already exist |
| Pashua.rb | src | Helper script for using Pashua, GUI library used by wiki page selector |
| keyboard_maestro.kmmacros | src | Dump of Keyboard Maestro shortcuts, see keyboard shortcuts |
| wiki.sh | src | Bash-script using rsync to update server-version of DokuWiki. Updates all files, including plugins etc, and generates sitemap for Google |
| wikilite.sh | src | Version of wiki.sh that only updates data-files (not plugins and config), should usually be used |
Legacy
These are scripts that I were working on, but are not part of the key researchr workflow, some of the code I still use, other I keep around in case I want to keep hacking on it.
| convert.rb | src | Imports a Kindle My Clippings file to DevonThink |
| folders.rb | src | Converts a hierarchy of folders and files to a website with index, can process output of Scrivener and DevonThink “export to HTML” |
| library.rb | src | Helper functions for folders.rb |
| amatch.rb | src | Experiment with matching Kindle clippings with PDFs in Skim, not functional |
| make-clippings-nice.rb | src | Tool to reformat some legacy clippings |
| testskim.rb | src | Related to amatch.rb |
| teststrip.rb | src | Related to amatch.rb |
