Jodi Schneider jodischneider

Using Homebrew on OS X?

Want Apache Jena's command-line tools, including the incredibly useful sparql command, but can't be bothered endlessly messing with Jena's environment variables to get them to work?

Try the command below, which installs Jena via a formula made by my colleague Kevin Lyda:

brew install https://raw.github.com/lyda/homebrew/jena/Library/Formula/jena.rb

If it worked, you can now do:

	# a messy hack written by Edd Dumbill. http://twitter.com/edd

	# You may need to rerun this script if you hit a Twitter Error because you
	# use up API rate limiting. That's why we pickle the results, so we can resume
	# where we left off.

	# get the twitter module using 'easy_install twitter'

	from twitter.api import Twitter, TwitterError
	from twitter.oauth import OAuth

	(function() {
	// Change `silent` to true to invoke the promptless, self-closing
	// version of the bookmarklet.
	var silent = false;

	var url = location.href;
	var title = document.title;

	// Look for a single hAtom entry on the page, and iff one is found, extract
	// the entry-title in place of the document title:

	1. Go to the app directory

	cd /Applications/Google\ Chrome.app/Contents/MacOS/

	2. Rename the app to app.orig

	mv Google\ Chrome Google\ Chrome.orig

	3. Create a shell script with the original name that uses the args you want

	# Inputs
	feature_names <- c("Feature 5", "Feature 4", "Feature 3", "Feature 2", "Feature 1")
	num_features <- length(feature_names)
	y <- array(c(10,4,1,0, 3,4,2,0, 1,2,8,1, 0,0,5,1, 1,2,5,3), dim=c(4,num_features))

	# Calculate plot
	num_neg_ratings <- 0
	num_pos_ratings <- 0
	for(i in 1:num_features) {
	num_neg_ratings = max(num_neg_ratings, sum(y[1:2,i]), sum(y[3:4,i]))

	Search PubMed for articles in the PMC Open Access Subset for which free full text (i.e. XML) is available:
	http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmode=xml&term=pubmed+pmc+open+access%5Bfilter%5D+AND+free+full+text%5Bfilter%5D

	Find the PMCID for an article by PMID:
	http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pmc&retmode=xml&linkname=pubmed_pmc&id=24191168

	Fetch full text article XML from PMC by PMCID:
	http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=3804407

	A PMC article for which the full text XML is not available:

	#!/bin/bash

	# tika2text.sh - given a directory, recursively extract text frome files

	# Eric Lease Morgan <emorgan@nd.edu>
	# (c) University of Notre Dame, distributed under a GNU Public License

	# March 27, 2017 - a second cut; works with a directory