palexander’s gists

palexander / ThickboxFromJS.js

Created October 28, 2009 05:49

	jQuery(document).ready(function(){
	var url = "/#TB_inline?height=400&width=600&inlineId=not_browsable_content&modal=true"
	tb_show("", url);
	});

palexander / ThickboxFromJS.html

Created October 28, 2009 05:57

	<div id="not_browsable_content" style="display:none;">
	<p>Text for display in modal Thickbox.</p>
	</div>

palexander / search_term_context.rb

Created October 30, 2009 17:08

	##
	# Get the context for a search term and highlight the term itself
	# text: string containing the search term and additional information
	# term: string with the term you're looking for
	# words: int for how many words to include total
	# padding_left: int for characters to the left of the search term
	# padding_right: int for characters to the right of the search term
	#
	# Only handles the first instance of a given term. Can be modified to take
	# character positions denoting the start and stop of term(s).

palexander / redirect_controller.rb

Created November 3, 2009 21:06

	# The redirect controller allows for routes-based redirects
	# as we move old content to new URL locations.

	class RedirectController < ApplicationController
	def index
	if params[:url] # We were provided with a url to redirect to
	params_string = ""
	# Trigger to switch the placeholders
	first_param = true
	# Loop through the given params, ignore ones we know about or are provided by default

palexander / jquery_autocomplete_footer.js

Created February 27, 2010 08:39

	function showResults() {
	// get the position of the input field right now (in case the DOM is shifted)
	var pos = findPos(input);
	// either use the specified width, or autocalculate based on form element
	var iWidth = (options.width > 0) ? options.width : $input.width();
	// add any footer information
	if (options.footer != undefined) $results.append(options.footer);
	// reposition
	$results.css({
	width: parseInt(iWidth) + "px",

palexander / jquery_autocomplete_setup.js

Created February 27, 2010 08:59

	jQuery("#autocomplete").autocomplete(data, {
	onFindValue: jumpToValue,
	onItemSelect: jumpToSelect,
	formatItem: formatItem
	footer: '<div style="color: grey; font-size: 8pt; font-family: Verdana; padding: .8em .5em .3em;">Results provided by <a style="color: grey;" href="http://bioportal.bioontology.org">NCBO BioPortal</a></div>',
	});

palexander / gc overhead limit reached

Created June 28, 2010 16:19

	Jun 27, 2010 10:15:56 PM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor processChildren
	SEVERE: Exception invoking periodic operation:
	java.lang.OutOfMemoryError: GC overhead limit exceeded
	at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:114)
	at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1306)
	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1570)
	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1559)
	at java.lang.Thread.run(Thread.java:619)
	Jun 27, 2010 10:16:42 PM org.apache.tomcat.util.net.AprEndpoint$Acceptor run
	SEVERE: Socket accept failed

palexander / new_bioportal_config_options.rb

Created July 3, 2010 01:06

	# Organization info
	$ORG = "NCBO"
	$ORG_URL = "http://www.bioontology.org"

	# Site name (required)
	$SITE = "BioPortal"

	# The URL for the BioPortal Rails UI (this application)
	$UI_URL = "http://bioportal.bioontology.org"

palexander / new_bioportal_config_options.rb

Created August 11, 2010 21:24 — forked from palexander/new_bioportal_config_options.rb

	# Organization info
	$ORG = "NCBO"
	$ORG_URL = "http://www.bioontology.org"

	# Site name (required)
	$SITE = "BioPortal"

	# The URL for the BioPortal Rails UI (this application)
	$UI_URL = "http://bioportal.bioontology.org"

palexander / sql_connection_error.java

Created August 11, 2010 22:29

	2010-08-11 15:05:08,009 [http-8080-4] ERROR - Could not toggle autocommit
	java.sql.SQLException: Connection com.mysql.jdbc.JDBC4Connection@4067f6d is closed.
	at org.apache.tomcat.dbcp.dbcp.DelegatingConnection.checkOpen(DelegatingConnection.java:354)
	at org.apache.tomcat.dbcp.dbcp.DelegatingConnection.setAutoCommit(DelegatingConnection.java:331)
	at org.apache.tomcat.dbcp.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.setAutoCommit(PoolingDataSource.java:317)
	at org.hibernate.transaction.JDBCTransaction.toggleAutoCommit(JDBCTransaction.java:194)
	at org.hibernate.transaction.JDBCTransaction.commitAndResetAutoCommit(JDBCTransaction.java:142)
	at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:115)
	at org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:655)
	at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:732)

Paul R Alexander palexander