Paul R Alexander palexander
palexander
/ gist:1212784
Created
September 12, 2011 23:43
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| #bp_nav_tools_active .bp_nav_link, | |
| #bp_nav_tools .bp_nav_link { | |
| width: 62px; | |
| } | |
| #bp_nav_tools_active, #bp_nav_tools:hover { | |
| background: url("/images/layout/bp_nav_sprite.png") -30px -602px; | |
| } | |
| #bp_nav_tools { |
palexander
/ gist:1212780
Created
September 12, 2011 23:42
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| <%if controller.controller_name.eql?('tools')%> | |
| <li id="bp_nav_tools_active"><a href="/tools" title="Tools" class="bp_nav_link"></a></li> | |
| <%else%> | |
| <li id="bp_nav_tools"><a href="/Tools" title="Tools" class="bp_nav_link"></a></li> | |
| <%end%> |
palexander
/ gist:1202209
Created
September 7, 2011 23:55
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| // This is broken | |
| function refreshOntList() { | |
| jQuery("#ontology_ontologyId").trigger("liszt:updated"); | |
| jQuery("#ontology_ontologyId").trigger("change"); | |
| } | |
| var select_groups = { | |
| init: function() { | |
| jQuery("#select_groups").bind("click", function(e){bp_popup_init(e)}); | |
| jQuery(".select_group_link").bind("click", function(e){select_groups.selectGroup(e)}); |
palexander
/ gist:702235
Created
November 16, 2010 18:34
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| <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> "[email protected]" ; | |
| <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_name> " |
palexander
/ mapping_sample.xml
Created
November 16, 2010 18:33
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| <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> "[email protected]" ; | |
| <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_name> " |
palexander
/ gist:614375
Created
October 7, 2010 00:59
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| [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
/ gist:614374
Created
October 7, 2010 00:56
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| [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
/ gist:614371
Created
October 7, 2010 00:54
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| [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
/ RdfParser.java
Created
October 6, 2010 03:28
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| 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
/ bp_parse_errors.txt
Created
October 1, 2010 19:52
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| 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 |