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[Gmod-apollo-cmts] CVS: apollo/conf chado-adapter.xml,1.39,1.40
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From: Scott C. <sco...@us...> - 2007-08-24 15:04:56
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Update of /cvsroot/gmod/apollo/conf In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv22577 Modified Files: chado-adapter.xml Log Message: removing old (not working) configs Index: chado-adapter.xml =================================================================== RCS file: /cvsroot/gmod/apollo/conf/chado-adapter.xml,v retrieving revision 1.39 retrieving revision 1.40 diff -C2 -d -r1.39 -r1.40 *** chado-adapter.xml 21 Jul 2006 14:54:47 -0000 1.39 --- chado-adapter.xml 24 Aug 2007 15:04:56 -0000 1.40 *************** *** 1,206 **** ! <?xml version="1.0" encoding="UTF-8"?> ! <!-- This file is used to config chado database adapter --> ! <chado-adapter> ! ! <chadoInstance id="referenceInstance" default="true"> ! ! <writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTemplateFile> ! ! <featureCV>sequence</featureCV> ! <polypeptideType>polypeptide</polypeptideType> ! <relationshipCV>relationship</relationshipCV> ! <propertyTypeCV>feature_property</propertyTypeCV> ! ! <!-- default is part_of --> ! <partOfCvTerm>part_of</partOfCvTerm> ! <transProtRelationTerm>derives_from</transProtRelationTerm> ! ! <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs> ! ! <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName> ! ! <oneLevelAnnotTypes> ! <type>promoter</type> ! <type>insertion site</type> ! <type>transposable_element</type> ! <type>transposable_element_insertion_site</type> ! <type>remark</type> ! <type>repeat_region</type> ! </oneLevelAnnotTypes> ! ! <threeLevelAnnotTypes> ! <type>gene</type> ! <type>pseudogene</type> ! <type>tRNA</type> ! <type>snRNA</type> ! <type>snoRNA</type> ! <type>ncRNA</type> ! <type>rRNA</type> ! <type>miRNA</type> ! </threeLevelAnnotTypes> ! ! </chadoInstance> ! ! <chadoInstance id="flybaseInstance"> ! ! <inheritsInstance>referenceInstance</inheritsInstance> ! ! <sequenceTypes> ! <type>gene</type> ! <type>golden_path_region</type> ! </sequenceTypes> ! ! <polypeptideType>protein</polypeptideType> ! ! <featureCV>SO</featureCV> ! <relationshipCV>relationship type</relationshipCV> ! <!-- default is part_of --> ! <partOfCvTerm>partof</partOfCvTerm> ! <!-- default is derives_from --> ! <producedByCvTerm>producedby</producedByCvTerm> ! <propertyTypeCV>property type</propertyTypeCV> ! ! <genePredictionPrograms> ! <program>genscan</program> ! <program>piecegenie</program> ! </genePredictionPrograms> ! ! <searchHitPrograms> ! <program>sim4</program> ! <program>%blastx%</program> ! </searchHitPrograms> ! ! <searchHitsHaveFeatLocs>false</searchHitsHaveFeatLocs> ! ! </chadoInstance> ! ! <!-- Indiana public FlyBase server r4.2 --> ! <!-- user is "apollo" password is "flybase930" for all fly svrs --> ! <chadodb> ! <name>FlyBase Chado Indiana public server r4.2</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://flybase.org:5432/dmel_r4.2</url> ! <dbName>dmel_r4.2</dbName> ! <dbInstance>flybaseInstance</dbInstance> ! <style>fly.style</style> ! <dbUser>apollo</dbUser> ! <dbPassword>flybase930</dbPassword> ! <!-- Don't allow user to edit username/password: --> ! <allowDbUserInput>false</allowDbUserInput> ! <allowDbPasswordInput>false</allowDbPasswordInput> ! </chadodb> ! ! <!-- Indiana public FlyBase server r4.1 --> ! <chadodb> ! <name>FlyBase Chado Indiana public server r4.1</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://flybase.org:5432/dmel_r4.1</url> ! <dbName>dmel_r4.1</dbName> ! <dbInstance>flybaseInstance</dbInstance> ! <style>fly.style</style> ! </chadodb> ! ! <!-- Indiana public FlyBase server r3.2 --> ! <chadodb> ! <name>FlyBase Chado Indiana public server r3.2</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://flybase.org:5432/dmel_r3.2</url> ! <dbName>dmel_r3.2</dbName> ! <dbInstance>flybaseInstance</dbInstance> ! <style>fly.style</style> ! </chadodb> ! ! <!-- Indiana public FlyBase dpse server 1.0.4 --> ! <chadodb> ! <name>FlyBase Chado Indiana Dpse public server 1.0.4</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://flybase.org:5432/dpse_r1.0.4</url> ! <dbName>dpse_r1.0.4</dbName> ! <dbInstance>flybaseInstance</dbInstance> ! <style>fly.style</style> ! </chadodb> ! ! <!-- Indiana public FlyBase het server --> ! <chadodb> ! <name>FlyBase Chado Indiana Heterochromatin public server</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://flybase.org:5432/dmelhet_r3.2</url> ! <dbName>dmelhet_r3.2</dbName> ! <dbInstance>flybaseInstance</dbInstance> ! <style>fly.style</style> ! </chadodb> ! ! ! <chadoInstance id="riceInstance" default="true"> ! ! <inheritsInstance>referenceInstance</inheritsInstance> ! ! <sequenceTypes> ! <type>gene</type> ! <!-- bacs are not in rice yet <type>BAC</type> --> ! <!-- useStartAndEnd specifies this is a range so that different GUI ! can be used, queryForValue -> query db for chroms/seqIds --> ! <type> ! <name>chromosome</name> ! <useStartAndEnd>true</useStartAndEnd> ! <queryForValueList>true</queryForValueList> ! <isTopLevel>true</isTopLevel> ! </type> ! </sequenceTypes> ! ! <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXmlTemplateFile> ! <featureCV>Sequence Ontology Feature Annotation</featureCV> ! <relationshipCV>Relationship Ontology</relationshipCV> ! <propertyTypeCV>autocreated</propertyTypeCV> ! ! <genePredictionPrograms> ! <program>FgenesH</program> ! </genePredictionPrograms> ! ! <searchHitPrograms> ! <program>blat</program> ! </searchHitPrograms> ! ! <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs> ! ! <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName> ! ! <oneLevelAnnotTypes> ! <type>promoter</type> ! <type>transposable_element</type> ! <type>remark</type> ! <type>repeat_region</type> ! </oneLevelAnnotTypes> ! ! </chadoInstance> ! ! ! <!-- Test rice database at brebiou.cshl.org --> ! <chadodb> ! <name>RiceDB test server at brebiou</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://brebiou.cshl.org:5432/rice</url> ! <dbName>rice</dbName> ! <dbUser>wgm</dbUser> ! <dbInstance>riceInstance</dbInstance> ! <style>rice.style</style> ! </chadodb> ! ! <!-- Marks Test rice database at brebiou.cshl.org - works with ssh ! tunnel on local host (need to have csh login & change -l mgibson) ! ssh -L15432:brebiou.cshl.org:5432 -l mgibson -N brebiou.cshl.org --> ! <chadodb> ! <name>RiceDB test server at brebiou(Tunneling)</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://localhost:15432/rice</url> ! <dbName>rice</dbName> ! <dbUser>mgibson</dbUser> ! <dbInstance>riceInstance</dbInstance> ! <style>rice.style</style> ! <!-- default database to use for loading and saving from --> ! <!-- command line if none is specified --> ! <default-command-line-db>false</default-command-line-db> ! </chadodb> ! ! </chado-adapter> ! --- 1,154 ---- ! <?xml version="1.0" encoding="UTF-8"?> ! <!-- This file is used to config chado database adapter --> ! <chado-adapter> ! ! <chadoInstance id="flybaseInstance"> ! ! <genePredictionPrograms> ! <program>genscan</program> ! <program>piecegenie</program> ! </genePredictionPrograms> ! ! <searchHitPrograms> ! <program>sim4</program> ! <program>%blastx%</program> ! </searchHitPrograms> ! ! <searchHitsHaveFeatLocs>false</searchHitsHaveFeatLocs> ! ! <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName> ! ! <oneLevelAnnotTypes> ! <type>promoter</type> ! <type>insertion site</type> ! <type>transposable_element</type> ! <type>transposable_element_insertion_site</type> ! <type>remark</type> ! <type>repeat_region</type> ! </oneLevelAnnotTypes> ! ! <threeLevelAnnotTypes> ! <type>gene</type> ! <type>pseudogene</type> ! <type>tRNA</type> ! <type>snRNA</type> ! <type>snoRNA</type> ! <type>ncRNA</type> ! <type>rRNA</type> ! <type>miRNA</type> ! </threeLevelAnnotTypes> ! ! </chadoInstance> ! ! <chadoInstance id="riceInstance" default="true"> ! ! <genePredictionPrograms> ! <program>FgenesH</program> ! </genePredictionPrograms> ! ! <searchHitPrograms> ! <program>blat</program> ! </searchHitPrograms> ! ! <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs> ! ! <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName> ! ! <oneLevelAnnotTypes> ! <type>promoter</type> ! <type>transposable_element</type> ! <type>remark</type> ! <type>repeat_region</type> ! </oneLevelAnnotTypes> ! ! <threeLevelAnnotTypes> ! <type>gene</type> ! <type>pseudogene</type> ! <type>tRNA</type> ! <type>snRNA</type> ! <type>snoRNA</type> ! <type>ncRNA</type> ! <type>rRNA</type> ! <type>miRNA</type> ! </threeLevelAnnotTypes> ! ! </chadoInstance> ! ! <chadoInstance id="riceInstance-no-hits"> ! ! <genePredictionPrograms> ! <program>FgenesH</program> ! </genePredictionPrograms> ! ! <searchHitPrograms> ! </searchHitPrograms> ! ! <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs> ! ! <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName> ! ! <oneLevelAnnotTypes> ! <type>promoter</type> ! <type>transposable_element</type> ! <type>remark</type> ! <type>repeat_region</type> ! </oneLevelAnnotTypes> ! ! <threeLevelAnnotTypes> ! <type>gene</type> ! <type>pseudogene</type> ! <type>tRNA</type> ! <type>snRNA</type> ! <type>snoRNA</type> ! <type>ncRNA</type> ! <type>rRNA</type> ! <type>miRNA</type> ! </threeLevelAnnotTypes> ! ! </chadoInstance> ! ! <!-- Marks Test rice database at brebiou.cshl.org --> ! <chadodb> ! <name>RiceDB test server at brebiou(Tunneling)</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://localhost:15432/rice</url> ! <dbName>rice</dbName> ! <dbUser>mgibson</dbUser> ! <dbInstance>riceInstance</dbInstance> ! <style>rice.style</style> ! <!-- default database to use for loading and saving from --> ! <!-- command line if none is specified --> ! <default-command-line-db>false</default-command-line-db> ! </chadodb> ! ! <chadodb> ! <name>RiceDB test server at brebiou(Tunneling,no hits)</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://localhost:15432/rice</url> ! <dbName>rice</dbName> ! <dbUser>mgibson</dbUser> ! <dbInstance>riceInstance-no-hits</dbInstance> ! <style>rice.style</style> ! <!-- default database to use for loading and saving from --> ! <!-- command line if none is specified --> ! <default-command-line-db>true</default-command-line-db> ! </chadodb> ! ! <!-- Scotts Test rice database at gmod.cshl.org - works with ssh ! tunnel on local host ! ssh -L15432:gmod.cshl.edu:5432 -l cain -N gmod.cshl.edu --> ! <chadodb> ! <name>RiceDB test server at gmod.cshl.edu(Tunneling)</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://localhost:15432/rice</url> ! <dbName>rice</dbName> ! <dbUser>cain</dbUser> ! <dbInstance>riceInstance</dbInstance> ! <style>rice.style</style> ! <!-- default database to use for loading and saving from --> ! <!-- command line if none is specified --> ! <default-command-line-db>true</default-command-line-db> ! </chadodb> ! ! ! </chado-adapter> |