Paul R Alexander palexander
palexander
/ MappingMetadata.java
Created
September 10, 2010 00:40
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| import java.io.Serializable; | |
| import java.util.Date; | |
| import java.util.UUID; | |
| import org.openrdf.model.URI; | |
| import org.openrdf.model.impl.URIImpl; | |
| import org.openrdf.repository.object.annotations.iri; | |
| @iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#Mapping_Metadata") | |
| public class MappingMetadata implements Serializable { |
palexander
/ enable_bioportal_fqdn_lookup.rb
Created
August 24, 2010 18:01
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| 1,5d0 | |
| < # Get the local machine's FQDN -- DO NOT MODIFY | |
| < require 'socket' | |
| < $LOCAL_FQDN = Socket.gethostbyname(Socket.gethostname).first | |
| < | |
| < | |
| 14c9 | |
| < $UI_URL = "http://#{$LOCAL_FQDN}" | |
| --- | |
| > $UI_URL = "http://demo.bioontology.org" |
palexander
/ closed_connection_stack_traces.java
Created
August 11, 2010 22:40
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| java.sql.SQLException: Connection com.mysql.jdbc.JDBC4Connection@591227c4 is closed. | |
| at org.apache.tomcat.dbcp.dbcp.DelegatingConnection.checkOpen(DelegatingConnection.java:354) | |
| at org.apache.tomcat.dbcp.dbcp.DelegatingConnection.setAutoCommit(DelegatingConnection.java:331) | |
| at org.apache.tomcat.dbcp.dbcp.PoolingDataSource$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) | |
| at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransacti |
palexander
/ sql_connection_error.java
Created
August 11, 2010 22:29
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| 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) |
palexander
/ new_bioportal_config_options.rb
Created
August 11, 2010 21:24
— forked from palexander/new_bioportal_config_options.rb
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| # 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
July 3, 2010 01:06
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| # Organization info | |
| $ORG = "NCBO" | |
| $ORG_URL = "http://www.bioontology.org" | |
| # Site name (required) | |
| $SITE = "BioPortal" | |
| # The URL for the BioPortal Rails UI (this application) | |
| $UI_URL = "http://bioportal.bioontology.org" |
palexander
/ gc overhead limit reached
Created
June 28, 2010 16:19
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| Jun 27, 2010 10:15:56 PM org.apache.catalina.core.ContainerBase$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
/ jquery_autocomplete_setup.js
Created
February 27, 2010 08:59
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| 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
/ jquery_autocomplete_footer.js
Created
February 27, 2010 08:39
palexander
/ redirect_controller.rb
Created
November 3, 2009 21:06
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| # 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 |