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Paul R Alexander palexander

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palexander / closed_connection_stack_traces.java
Created August 11, 2010 22:40
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
palexander / enable_bioportal_fqdn_lookup.rb
Created August 24, 2010 18:01
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
palexander / MappingMetadata.java
Created September 10, 2010 00:40
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
palexander / bp_parse_errors.txt
Created October 1, 2010 19:52
BioPortal returned an error: Error Deprecating/Deleting Ontologies: [Cereal plant trait (Id: 44265) - No coding scheme could be located for the values you provided Parameter: codingSchemeName Value: null, Phenotypic quality (Id: 44260) - No coding scheme could be located for the values you provided Parameter: codingSchemeName Value: null, C. elegans phenotype (Id: 44267) - No coding scheme could be located for the values you provided Parameter: codingSchemeName Value: null, Human disease (Id: 44262) - No coding scheme could be located for the values you provided Parameter: codingSchemeName Value: null, Human disease (Id: 44240) - No coding scheme could be located for the values you provided Parameter: codingSchemeName Value: null, Mosquito insecticide resistance (Id: 44264) - No coding scheme could be located for the values you provided Parameter: codingSchemeName Value: null, Mosquito insecticide resistance (Id: 44241) - No coding scheme could be located for the values you provided Parameter: codingSchemeNam
@palexander
palexander / RdfParser.java
Created October 6, 2010 03:28
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.Collection;
import java.util.Iterator;
import org.openrdf.model.Statement;
import org.openrdf.rio.RDFHandlerException;
import org.openrdf.rio.RDFParseException;
import org.openrdf.rio.helpers.StatementCollector;
@palexander
palexander / gist:614371
Created October 7, 2010 00:54
[palexand@ncboprod-ridb2 mysql_data]$ sudo mysqldumpslow -a -t 50 /var/lib/mysql/mysql_data/slowlog
Reading mysql slow query log from /var/lib/mysql/mysql_data/slowlog
Count: 1 Time=15434.30s (15434s) Lock=0.00s (0s) Rows=0.0 (0), ri-api[ri-api]@ncbostage-obr1.Stanford.EDU
SELECT ET.local_element_id, T1.local_concept_id, CXT.name, DAT.term_id, TT.name, DAT.position_from, DAT.position_to, IT.score FROM obr_canano_annotation DAT, obr_canano_element ET, obs_concept AS T1, obs_term TT, obr_context CXT, obr_canano_aggregation IT WHERE DAT.element_id=ET.id AND DAT.concept_id=T1.id AND DAT.term_id=TT.id AND DAT.context_id= CXT.id AND DAT.element_id=IT.element_id AND DAT.concept_id=IT.concept_id AND TT.name REGEXP '[^0-9]+' AND T1.local_concept_id IN ('42785/npo:NPO_518', '40402/C7764222590860') AND ET.id IN (SELECT DISTINCT IT1.element_id FROM obr_canano_annotation AS IT1, obs_concept AS CT1, obr_canano_annotation AS IT2, obs_concept AS CT2 WHERE IT1.element_id=IT2.element_id AND IT1.concept_id=CT1.id AND
@palexander
palexander / gist:614374
Created October 7, 2010 00:56
[palexand@ncboprod-ridb2 mysql_data]$ sudo mysqldumpslow -a -s c -t 50 /var/lib/mysql/mysql_data/slowlog
Reading mysql slow query log from /var/lib/mysql/mysql_data/slowlog
Count: 18 Time=14.34s (258s) Lock=0.00s (0s) Rows=1.0 (18), ri-api[ri-api]@ncbostage-obr1.Stanford.EDU
SELECT COUNT(*) FROM obr_rxrd_aggregation IT, obr_rxrd_element ET, obs_concept AS T1 WHERE IT.element_id=ET.id AND IT.concept_id=T1.id AND T1.local_concept_id IN ('42789/108369006', '42838/Neoplasm')
Count: 11 Time=639.36s (7032s) Lock=0.00s (0s) Rows=1.0 (11), ri-api[ri-api]@ncbostage-obr1.Stanford.EDU
SELECT COUNT(*) FROM obr_aers_aggregation IT, obr_aers_element ET, obs_concept AS T1 WHERE IT.element_id=ET.id AND IT.concept_id=T1.id AND T1.local_concept_id='40397/T25'
@palexander
palexander / gist:614375
Created October 7, 2010 00:59
[palexand@ncboprod-ridb2 mysql_data]$ sudo mysqldumpslow -s c -t 50 /var/lib/mysql/mysql_data/slowlog
Reading mysql slow query log from /var/lib/mysql/mysql_data/slowlog
Count: 89 Time=489.59s (43573s) Lock=0.00s (0s) Rows=0.9 (79), ri-api[ri-api]@ncbostage-obr1.Stanford.EDU
SELECT COUNT(*) FROM obr_aers_aggregation IT, obr_aers_element ET, obs_concept AS T1 WHERE IT.element_id=ET.id AND IT.concept_id=T1.id AND T1.local_concept_id='S'
Count: 79 Time=157.57s (12448s) Lock=0.00s (0s) Rows=7.5 (592), ri-api[ri-api]@ncbostage-obr1.Stanford.EDU
SELECT ET.local_element_id, T1.local_concept_id, IT.score FROM obr_ct_aggregation IT, obr_ct_element ET, obs_concept AS T1 WHERE IT.element_id=ET.id AND IT.concept_id=T1.id AND T1.local_concept_id='S' ORDER BY IT.score DESC LIMIT N,N
@palexander
palexander / mapping_sample.xml
Created November 16, 2010 18:33
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#ce89a730-b872-012d-45dd-0026bb635fee>
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#comment> "Mappings created by users through the BioPortal user interface" ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_source_ontology_version> 13578 ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_target_ontology_version> 39521 ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#date> "2009-03-30T13:26:34-07:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source> "Application" ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_algorithm> "" ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_contact_info> "support@bioontology.org" ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_name> "
@palexander
palexander / gist:702235
Created November 16, 2010 18:34
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#ce89a730-b872-012d-45dd-0026bb635fee>
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#comment> "Mappings created by users through the BioPortal user interface" ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_source_ontology_version> 13578 ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_target_ontology_version> 39521 ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#date> "2009-03-30T13:26:34-07:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source> "Application" ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_algorithm> "" ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_contact_info> "support@bioontology.org" ;
<http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_name> "