[kepler-dev] Private Repository
jing
tao at nceas.ucsb.edu
Mon May 9 10:44:14 PDT 2011
Hi, Scott:
Thank you for sending the information.
The reason there is an additional transformation step on server side
when you query the server from Kepler is that Kepler uses ecogrid web
service and ecogrid will transform the ecogrid query to metacat query.
When you use web page to query metacat, it uses metacata query directly.
The subtle difference results in different behaviors. There was a bug in
xslt style sheet which transforms the ecogrid query to metadata query.
It was fixed in the early of this year. However, I looked the log
information and found you didn't install a version of metacat which
contains the fix code. You may install the metacat from the metacat svn
trunk (or, Ben, do you have a better suggestion?) and i think the issue
will be gone. Please let me know if a new installation of metacat will
fix the problem.
Thanks,
Jing
On 05/05/2011 09:00 PM, Scott Zimmer wrote:
> Hi Jing:
>
> I appreciate your help. I've restarted our DB and it should be up and
> running again. Below are the log file from performing the search
> inside Kepler followed by the log file from performing the search via
> a browser. The main difference I see is that the query from inside
> Kepler seems to be doing a transformation and then performing an
> squery instead of a query. I don't really understand much more of the
> information in the log file. Any insight you have would be appreciated...
>
> Scott
>
> knb 20110506-01:30:54: [WARN]: start authenticated query method in
> grid service
> [org.ecoinformatics.ecogrid.metacat.authenticatedqueryservice.impl.MetacatAuthenticatedQueryServiceImpl]
>
> knb 20110506-01:30:54: [WARN]: before transforming query
> [org.ecoinformatics.ecogrid.metacat.authenticatedqueryservice.impl.MetacatAuthenticatedQueryServiceImpl]
>
> knb 20110506-01:30:54: [INFO]: parsed the ecogrid query xml
> [org.ecoinformatics.ecogrid.metacat.authenticatedqueryservice.impl.EcogridQueryToMetacatQueryTransformer]
>
> knb 20110506-01:30:54: [INFO]: transforming xml node...[query: null]
> [org.ecoinformatics.ecogrid.metacat.authenticatedqueryservice.impl.EcogridQueryToMetacatQueryTransformer]
>
> knb 20110506-01:30:54: [INFO]: transformer is:
> org.apache.xalan.transformer.TransformerImpl at 307b37df
> [org.ecoinformatics.ecogrid.metacat.authenticatedqueryservice.impl.EcogridQueryToMetacatQueryTransformer]
>
> knb 20110506-01:30:54: [INFO]: query: <?xml version="1.0"
> encoding="iso-8859-1"?><pathquery
> version="1.2"><meta_file_id>test.1.1</meta_file_id><querytitle>kepler
> query</querytitle><returndoctype>http://www.kepler-project.org/kar-2.1.0</returndoctype><returndoctype>http://www.kepler-project.org/kar-2.0.0</returndoctype><returnfield>/entity/@name</returnfield><querygroup
> operator="INTERSECT"><queryterm searchmode="contains"
> casesensitive="false"><value>%twittergraph%</value><pathexpr>/</pathexpr></queryterm></querygroup></pathquery>
> [org.ecoinformatics.ecogrid.metacat.authenticatedqueryservice.impl.EcogridQueryToMetacatQueryTransformer]
>
> knb 20110506-01:30:54: [INFO]: transformed the ecogrid query xml to
> pathquery xml
> [org.ecoinformatics.ecogrid.metacat.authenticatedqueryservice.impl.EcogridQueryToMetacatQueryTransformer]
>
> knb 20110506-01:30:54: [WARN]: after transforming query
> [org.ecoinformatics.ecogrid.metacat.authenticatedqueryservice.impl.MetacatAuthenticatedQueryServiceImpl]
>
> knb 20110506-01:30:54: [INFO]: MetaCatServlet.handleGetOrPost - Action
> is: squery [edu.ucsb.nceas.metacat.MetaCatServlet]
>
> knb 20110506-01:30:54: [INFO]: MetaCatServlet.handleGetOrPost - The
> user is : public [edu.ucsb.nceas.metacat.MetaCatServlet]
>
> knb 20110506-01:30:54: [INFO]: DBQuery.findDocuments - SESSIONID: 0
> [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-01:30:54: [INFO]: DBQuery.findDocuments - xmlquery: <?xml
> version="1.0" encoding="iso-8859-1"?><pathquery
> version="1.2"><meta_file_id>test.1.1</meta_file_id><querytitle>kepler
> query</querytitle><returndoctype>http://www.kepler-project.org/kar-2.1.0</returndoctype><returndoctype>http://www.kepler-project.org/kar-2.0.0</returndoctype><returnfield>/entity/@name</returnfield><querygroup
> operator="INTERSECT"><queryterm searchmode="contains"
> casesensitive="false"><value>%twittergraph%</value><pathexpr>/</pathexpr></queryterm></querygroup></pathquery>
> [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-01:30:54: [INFO]: DBQuery.findDocuments - qformat: xml
> [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-01:30:54: [INFO]: QuerySpecification.handleReturnField -
> there are no attributes in the XPATH statement
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-01:30:54: [INFO]: In QueryGroup.printSQL.. found a
> QueryGroup: (SELECT DISTINCT docid FROM xml_nodes WHERE
> UPPER(nodedata) LIKE '%%TWITTERGRAPH%%' ANDparentnodeid IN (SELECT
> nodeid FROM xml_index WHERE path LIKE '/')
> )[edu.ucsb.nceas.metacat.QueryGroup]
>
> knb 20110506-01:30:54: [INFO]: In QueryGroup.printSQL.. final query
> returned is: ((SELECT DISTINCT docid FROM xml_nodes WHERE
> UPPER(nodedata) LIKE '%%TWITTERGRAPH%%' ANDparentnodeid IN (SELECT
> nodeid FROM xml_index WHERE path LIKE '/') ) )
> [edu.ucsb.nceas.metacat.QueryGroup]
>
> knb 20110506-01:30:54: [INFO]: QuerySpecification.printSQL - Query :
> ((SELECT DISTINCT docid FROM xml_nodes WHERE UPPER(nodedata) LIKE
> '%%TWITTERGRAPH%%' ANDparentnodeid IN (SELECT nodeid FROM xml_index
> WHERE path LIKE '/') ) ) [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-01:30:54: [INFO]: QuerySpecification.printSQL -
> percentage number: 0 [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-01:30:54: [INFO]: QuerySpecification.createOwerQuery -
> OwnerQuery: null [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-01:30:54: [INFO]: QuerySpecification.constructAllowString
> - allow string is: (lower(principal_name) = 'public') ANDperm_type =
> 'allow' ANDpermission > 3 [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-01:30:54: [INFO]: QuerySpecification.createAllowRuleQuery
> - allow query is: SELECT docid from xml_access WHERE(
> (lower(principal_name) = 'public') ANDperm_type = 'allow'
> ANDpermission > 3) [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-01:30:54: [INFO]: QuerySpecification.constructDenyString
> - deny string is: (lower(principal_name) = 'public') ANDperm_type =
> 'deny' ANDperm_order ='allowFirst' ANDpermission > 3
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-01:30:54: [INFO]: QuerySpecification.createDenyRuleQuery
> - denyquery is: SELECT docid from xml_access WHERE(
> (lower(principal_name) = 'public') ANDperm_type = 'deny' ANDperm_order
> ='allowFirst' ANDpermission >
> 3)[edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-01:30:54: [INFO]: QuerySpecification.getAccessQuery -
> access query is:AND(docid IN (SELECT docid from xml_access WHERE(
> (lower(principal_name) = 'public') ANDperm_type = 'allow'
> ANDpermission > 3)) ANDdocid NOT IN (SELECT docid from xml_access
> WHERE( (lower(principal_name) = 'public') ANDperm_type = 'deny'
> ANDperm_order ='allowFirst' ANDpermission > 3) ))
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-01:30:54: [INFO]: DBQuery.getResultXMLFromCache - Get
> query from cache [edu.ucsb.nceas.metacat.DBQuery]
>
>
>
>
> knb 20110506-00:58:46: [INFO]: MetaCatServlet.handleGetOrPost - Action
> is: query [edu.ucsb.nceas.metacat.MetaCatServlet]
>
> knb 20110506-00:58:46: [INFO]: MetaCatServlet.handleGetOrPost - The
> user is : public [edu.ucsb.nceas.metacat.MetaCatServlet]
>
> knb 20110506-00:58:46: [INFO]: DBQuery.findDocuments - SESSIONID: 0
> [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-00:58:46: [INFO]: DBQuery.findDocuments - xmlquery: <?xml
> version="1.0"?>
>
> <pathquery version="1.2">
>
> <returndoctype>http://www.kepler-project.org/kar-2.0.0</returndoctype><returndoctype>http://www.kepler-project.org/kar-2.1.0</returndoctype><returnfield>karFileName</returnfield><returnfield>karEntry/karEntryXML/entity/@name</returnfield><returnfield>mainAttributes/lsid</returnfield><returnfield>karEntry/karEntryXML/entity/property[@name='author']/configure</returnfield><returnfield>karEntry/karEntryXML/entity/property[@name='KeplerDocumentation']/property[@name='version']/configure</returnfield><returnfield>karEntry/karEntryXML/entity/property[@name='KeplerDocumentation']/property[@name='description']/configure</returnfield><returnfield>karEntry/karEntryXML/entity/property[@name='KeplerDocumentation']/property[@name='userLevelDocumentation']/configure</returnfield><querygroup
> operator="INTERSECT"><queryterm casesensitive="false"
> searchmode="contains"><value>rssgraph</value></queryterm></querygroup></pathquery>
> [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-00:58:46: [INFO]: DBQuery.findDocuments - qformat: kepler
> [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.handleReturnField -
> there are no attributes in the XPATH statement
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.handleReturnField -
> there are no attributes in the XPATH statement
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.handleReturnField -
> there are no attributes in the XPATH statement
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.handleReturnField -
> there are no attributes in the XPATH statement
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.handleReturnField -
> there are no attributes in the XPATH statement
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.handleReturnField -
> there are no attributes in the XPATH statement
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.handleReturnField -
> there are no attributes in the XPATH statement
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: In QueryGroup.printSQL.. found a
> QueryGroup: (SELECT DISTINCT docid FROM xml_nodes WHERE
> UPPER(nodedata) LIKE '%RSSGRAPH%' )[edu.ucsb.nceas.metacat.QueryGroup]
>
> knb 20110506-00:58:46: [INFO]: In QueryGroup.printSQL.. final query
> returned is: ((SELECT DISTINCT docid FROM xml_nodes WHERE
> UPPER(nodedata) LIKE '%RSSGRAPH%' ) ) [edu.ucsb.nceas.metacat.QueryGroup]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.printSQL - Query :
> ((SELECT DISTINCT docid FROM xml_nodes WHERE UPPER(nodedata) LIKE
> '%RSSGRAPH%' ) ) [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.printSQL -
> percentage number: 0 [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.createOwerQuery -
> OwnerQuery: null [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.constructAllowString
> - allow string is: (lower(principal_name) = 'public') ANDperm_type =
> 'allow' ANDpermission > 3 [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.createAllowRuleQuery
> - allow query is: SELECT docid from xml_access WHERE(
> (lower(principal_name) = 'public') ANDperm_type = 'allow'
> ANDpermission > 3) [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.constructDenyString
> - deny string is: (lower(principal_name) = 'public') ANDperm_type =
> 'deny' ANDperm_order ='allowFirst' ANDpermission > 3
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.createDenyRuleQuery
> - denyquery is: SELECT docid from xml_access WHERE(
> (lower(principal_name) = 'public') ANDperm_type = 'deny' ANDperm_order
> ='allowFirst' ANDpermission >
> 3)[edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: QuerySpecification.getAccessQuery -
> access query is:AND(docid IN (SELECT docid from xml_access WHERE(
> (lower(principal_name) = 'public') ANDperm_type = 'allow'
> ANDpermission > 3)) ANDdocid NOT IN (SELECT docid from xml_access
> WHERE( (lower(principal_name) = 'public') ANDperm_type = 'deny'
> ANDperm_order ='allowFirst' ANDpermission > 3) ))
> [edu.ucsb.nceas.metacat.QuerySpecification]
>
> knb 20110506-00:58:46: [INFO]: DBQuery.findResultDoclist - real
> result: 5439.341 [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-00:58:46: [INFO]: DBQuery.getXmlReturnfieldsTableId -
> ReturnField Query:SELECT returnfield_id, usage_count FROM
> xml_returnfield WHERE returnfield_string LIKE ?
> [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-00:58:46: [INFO]: DBQuery.getXmlReturnfieldsTableId -
> ReturnField Table Update:UPDATE xml_returnfield SET usage_count ='81'
> WHERE returnfield_id ='2' [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-00:58:46: [INFO]: DBQuery.handleSubsetResult - size of
> partOfDoclist before docidsInQueryresultTable(): 1
> [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-00:58:46: [INFO]: DBQuery.docidsInQueryresultTable -
> Query to get docids from xml_queryresult:select docid,
> queryresult_string from xml_queryresult where returnfield_id = 2 and
> docid in ('5439.341') [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-00:58:46: [INFO]: DBQuery.handleSubsetResult - size of
> partOfDoclist after docidsInQueryresultTable(): 0
> [edu.ucsb.nceas.metacat.DBQuery]
>
> knb 20110506-00:58:46: [INFO]: DBTransform.getStyleSystemId - Trying
> style-set file:
> /usr/share/tomcat5.5/webapps/knb/style/skins/kepler/kepler.xml
> [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.getStyleSystemId - style
> system id is:
> http://50.17.219.137:8080/knb/style/skins/kepler/resultset.xsl
> [edu.ucsb.nceas.metacat.DBTransform]
>
> SystemId Unknown; Line #294; Column #36; A location step was expected
> following the '/' or '//' token.
>
> SystemId Unknown; Line #303; Column #39; A location step was expected
> following the '/' or '//' token.
>
> SystemId Unknown; Line #312; Column #36; A location step was expected
> following the '/' or '//' token.
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - qformat:
> kepler [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param:
> pagestart -- 0 [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param:
> anyfield -- rssgraph [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param:
> operator -- INTERSECT [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param:
> qformat -- kepler [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param:
> returnfield -- karFileName [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param: action
> -- query [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param:
> pagesize -- 10 [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param:
> returndoctype -- http://www.kepler-project.org/kar-2.0.0
> [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param:
> enableediting -- false [edu.ucsb.nceas.metacat.DBTransform]
>
> knb 20110506-00:58:47: [INFO]: DBTransform.doTransform - param: query
> -- <?xml version="1.0"?>
>
> <pathquery version="1.2">
>
> <returndoctype>http://www.kepler-project.org/kar-2.0.0</returndoctype><returndoctype>http://www.kepler-project.org/kar-2.1.0</returndoctype><returnfield>karFileName</returnfield><returnfield>karEntry/karEntryXML/entity/@name</returnfield><returnfield>mainAttributes/lsid</returnfield><returnfield>karEntry/karEntryXML/entity/property[@name='author']/configure</returnfield><returnfield>karEntry/karEntryXML/entity/property[@name='KeplerDocumentation']/property[@name='version']/configure</returnfield><returnfield>karEntry/karEntryXML/entity/property[@name='KeplerDocumentation']/property[@name='description']/configure</returnfield><returnfield>karEntry/karEntryXML/entity/property[@name='KeplerDocumentation']/property[@name='userLevelDocumentation']/configure</returnfield><querygroup
> operator="INTERSECT"><queryterm casesensitive="false"
> searchmode="contains"><value>rssgraph</value></queryterm></querygroup></pathquery>
> [edu.ucsb.nceas.metacat.DBTransform]
>
>
>
> On Thu, May 5, 2011 at 5:28 PM, tao <tao at nceas.ucsb.edu
> <mailto:tao at nceas.ucsb.edu>> wrote:
>
> Hi, Soctt:
>
> I looked at the configurations and they look good to me. I tried
> to access the server but got a timeout response.
>
> When you do a search on both kepler and web site, can you monitor
> the tomcat log file? To compare the difference on the output might
> give us some idea why there is no return on kepler search. In
> order to get more information from tomcat log file, you may change
> the default level from WARN to INFO in tomcat log4j property file.
>
> Thanks,
>
> Jing
>
> Scott Zimmer wrote:
>
> I have set up a private knb repository to store KAR files. I
> am able to successfully authenticate and upload KAR files to
> the repository. I can also search for KAR files from a web
> browser, but I get no returns when I search for the KAR files
> from within Kepler. I am able to authenticate to the
> repository, but no search results are returned. I can
> successfully search the Kepler-Dev repository. I've included
> the repository related entries from my configuration.xml
> files. I left the registry path set to the ecogrid one
> because I did not see an easy way to set that up myself. I
> would appreciate any insight you have into why I get no search
> results inside Kepler from the repository---Scott
>
> <repository>
> <name>
> optensity
> </name>
> <repository>
> 50.17.219.137:8080 <http://50.17.219.137:8080>
> <http://50.17.219.137:8080>
>
> </repository>
> <putpath>
> /knb/services/PutService
> </putpath>
> <authprotocol>
> http
> </authprotocol>
> <authdomain>
> OPTENSITY
> </authdomain>
> <lsidpath>
> /knb/services/IdentifierService
> </lsidpath>
> <querypath>
> /knb/services/QueryService
> </querypath>
> <authenticatedquerypath>
> /knb/services/AuthenticatedQueryService
> </authenticatedquerypath>
> <authorizationPath>
> /knb/services/AuthorizationService
> </authorizationPath>
> <registrypath>
> http://ecogrid.ecoinformatics.org/registry/services/RegistryService
> </registrypath>
> <registryauth>
> http://50.17.219.137:8080/knb/services/AuthenticationService
> </registryauth>
> <class>
> org.kepler.objectmanager.repository.EcogridRepository
> </class>
> <lsidAuthority>
> kepler-dev.nceas.ucsb.edu <http://kepler-dev.nceas.ucsb.edu>
> <http://kepler-dev.nceas.ucsb.edu>
>
> </lsidAuthority>
> <searchRepository>
> true
> </searchRepository>
> </repository>
>
> <service>
> <domain>OPTENSITY</domain>
> <serviceOperation>ldap</serviceOperation>
> <serviceURL>http://50.17.219.137:8080/knb/services/AuthenticationService</serviceURL>
> <serviceClass>org.kepler.authentication.LDAPAuthenticationService</serviceClass>
> <username>uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org</username>
> <password>kepler</password>
> </service>
>
> Scott
> --
> Scott Zimmer
> Optensity, Inc.
> 512-299-7218
> ------------------------------------------------------------------------
>
> _______________________________________________
> Kepler-dev mailing list
> Kepler-dev at kepler-project.org
> <mailto:Kepler-dev at kepler-project.org>
> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-dev
>
>
>
>
>
> --
> Scott Zimmer
> Optensity, Inc.
> 512-299-7218
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