Dear Justin, Please find the chado-adapter.xml at the end of this mail
Regards Joelle -------------------------------------- Joelle Amselem INRA-URGI http://urgi.versailles.inra.fr ------------------------------------ Le 11 mars 2010 à 16:18, Justin Reese a écrit : > Dear Joelle, > Thanks very much for your help. It's a huge help to see how other people have > approached Apollo->chado writebacks. Would you mind if I had a look at your > chado-adapter.xml too? > > I think that the community might indeed be interested in more sophisticated > user handling in Apollo. I guess Ed Lee would know best whether it is > feasible to roll your changes into Apollo. > > Best regards, > Justin > > On Thu, Mar 11, 2010 at 12:36 AM, Joelle Amselem > <[email protected]> wrote: > Dear Justin, > > We use the chado-adapter.xml (delivered in the conf directory, and configured > with our settings). We can send you our chado-adapter.xml configuration (let > us know) > About the user's id, we have modified some classes (Baptiste done it) to > force Apollo to to be connected with a chado user login instead a generic > login/passwd to make writebacks possible. > > By default, it doesn't change anything, it take the computer user as author, > but it's weird when the user is "admin" or work from different computer with > a diffrent login > > At this time we patch each new apollo version. > > If Apollo community is interested by the patch we can send it to Ed Lee to > add it in the next version > > Regards > Joelle
<<inline: ApolloUser.gif>>
> > > > Le 9 mars 10 à 14:55, Justin Reese a écrit : > >> Dear Michael, Joelle and Valentine, >> You don't know me, but I saw your presentation at the GMOD meeting in >> San Diego, which I very much enjoyed. (I presented too, about Chado on >> Rails.) >> >> We at Bovine Genome Database and BeeBase were planning on setting up >> Apollo to Chado writebacks, and I wondered if you would mind giving us >> some advice. In particular, we'd like your advice about how to handle >> "user" information. That is, we'd like for user's id to be saved along >> with the annotations in Chado. >> >> Also, did you write your own Chado adapter? If so, would you mind if >> we had a look at it? >> >> Any advice you could give us would be appreciate. Thanks, >> Justin >> >> -- >> Justin Reese >> Affiliate Research Professor >> Department of Biology | Georgetown University >> [email protected] | [email protected] >> phone +66 813 929167 | +66 042 414065 > <?xml version="1.0" encoding="UTF-8"?> <!-- This file is used to config chado database adapter --> <chado-adapter> <chadoInstance id="MyOrganismInstance" default="true"> <!-- load gene uniquename or contig --> <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>supercontig</name> <useStartAndEnd>true</useStartAndEnd> <queryForValueList>true</queryForValueList> <isTopLevel>true</isTopLevel> <!--<values></values>--> </type> </sequenceTypes> <!-- parameters for PureJDBCTransactionWriter --> <pureJDBCWriteMode>true</pureJDBCWriteMode> <pureJDBCCopyOnWrite>false</pureJDBCCopyOnWrite> <pureJDBCNoCommit>false</pureJDBCNoCommit> <!-- Don't save CDS, the chado bulkloader doesn't use them any more --> <pureJDBCUseCDS>false</pureJDBCUseCDS> <!--<buildCDSFeature>false</buildCDSFeature>--> <!--<writebackXmlTemplateFile>transactionXMLTemplate_paramecium.xml</writebackXmlTemplateFile>--> <!-- use the next Ontology SO, RELA, featureprop ontology--> <featureCV>sequence</featureCV> <relationshipCV>relationship</relationshipCV> <propertyTypeCV>feature_property</propertyTypeCV> <!-- describe relations --> <producedByCvTerm>part_of</producedByCvTerm> <partOfCvTerm>part_of</partOfCvTerm> <polypeptideType>polypeptide</polypeptideType> <transProtRelationTerm>derives_from</transProtRelationTerm> <!-- 3 level prediction programs --> <genePredictionPrograms> <program>fgenesh</program> <program>EuGene</program> </genePredictionPrograms> <!-- one level programs with or without target --> <oneLevelResultPrograms> <program>RepeatMasker</program> <program>MUMmer</program> </oneLevelResultPrograms> <!-- 2 level programs with target--> <searchHitPrograms> <program>blastn</program> <program>sim4</program> <program>blastx</program> <program>blat</program> </searchHitPrograms> <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs> <!-- we currently use ParameciumDBChadoInstance --> <!-- for the datamodel rules --> <clsName>apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance</clsName> <!-- one can add other types if needed --> <oneLevelAnnotTypes> <type>match</type> <type>tandem_repeat</type> </oneLevelAnnotTypes> <!-- manual annotation top level type --> <!-- othertop level type are not managed at this tinme in the ChadoJDBCNameAdapter--> <threeLevelAnnotTypes> <type>gene</type> <type>pseudogene</type> <type>tRNA</type> </threeLevelAnnotTypes> </chadoInstance> <!-- connection to chado DB parameters --> <chadodb> <name>My oprganism Apollo-Chado Annotation Database</name> <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> <url>jdbc:postgresql://host:port/dbname</url> <dbName>dbname</dbName> <dbUser>dbuser</dbUser> <dbPassword>dbpasswd</dbPassword> <dbInstance>MyOrganismInstance</dbInstance> <style>MyOrganismeFile.style</style> <default-command-line-db>true</default-command-line-db> </chadodb> </chado-adapter>
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