Metacat: Issues
https://projects.ecoinformatics.org/ecoinfo/
https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?1469134036
2013-10-12T00:39:33Z
Ecoinformatics Redmine
Redmine
Bug #6142 (Resolved): Metacat.property guid.ezid.unitemplate.metadata includes context
https://projects.ecoinformatics.org/ecoinfo/issues/6142
2013-10-12T00:39:33Z
Lauren Walker
walker@nceas.ucsb.edu
<p>This has been changed to just be the hostname only.</p>
<p>The metacat.properties file on the Gulfwatch server is also now just hostname/#view.. (removed "/metacatui")</p>
Bug #6141 (Closed): Permission denied to update/publish metadata for group member on Gulfwatch
https://projects.ecoinformatics.org/ecoinfo/issues/6141
2013-10-12T00:36:25Z
Lauren Walker
walker@nceas.ucsb.edu
<p>Sarah Clark was unable to publish metadata on Gulfwatch even though she is a member of the evos group which has permission type 7 for that guid.</p>
<p>Jing and I could not replicate the problem on dev2 and were able to publish.</p>
<p>Example: <a class="external" href="http://gulfwatch.nceas.ucsb.edu/gulfwatch/d1/mn/v1/meta/df35a.21.31">http://gulfwatch.nceas.ucsb.edu/gulfwatch/d1/mn/v1/meta/df35a.21.31</a></p>
<p>Tomcat log:<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.31"} hits=0 status=0 QTime=1 <br />SEVERE: SystemMetadataEventListener.itemAdded - could not comit the index into the solr server since Solr index doesn't have the information about the id df35a.21.31 which is a component in the resource map resourceMap_df35a.21.31. Metacat-Index can't process the resource map prior to its components.<br />org.apache.solr.client.solrj.SolrServerException: Solr index doesn't have the information about the id df35a.21.31 which is a component in the resource map resourceMapdf35a.21.31. Metacat-Index can't process the resource map prior to its components.<br />INFO: ===================================adding the document df35a.21.31<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.30"} hits=1 status=0 QTime=4 <br />INFO: {delete=[df35a.21.30]} 0 13<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.29"} hits=0 status=0 QTime=7 <br />INFO: {delete=[df35a.21.29]} 0 5<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.28"} hits=0 status=0 QTime=8 <br />INFO: {delete=[df35a.21.28]} 0 5<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.27"} hits=0 status=0 QTime=7 <br />INFO: {delete=[df35a.21.27]} 0 5<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.26"} hits=0 status=0 QTime=2 <br />INFO: {delete=[df35a.21.26]} 0 13<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.25"} hits=0 status=0 QTime=1 <br />INFO: {delete=[df35a.21.25]} 0 13<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.22"} hits=0 status=0 QTime=2 <br />INFO: {delete=[df35a.21.22]} 0 15<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.21"} hits=0 status=0 QTime=7 <br />INFO: {delete=[df35a.21.21]} 0 5<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.20"} hits=0 status=0 QTime=1 <br />INFO: {delete=[df35a.21.20]} 0 13<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.16"} hits=0 status=0 QTime=1 <br />INFO: {delete=[df35a.21.16]} 0 13<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.15"} hits=0 status=0 QTime=7 <br />INFO: {delete=[df35a.21.15]} 0 5<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.14"} hits=0 status=0 QTime=5 <br />INFO: {delete=[df35a.21.14]} 0 5<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.13"} hits=0 status=0 QTime=8 <br />INFO: {delete=[df35a.21.13]} 0 5<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.12"} hits=0 status=0 QTime=7 <br />INFO: {delete=[df35a.21.12]} 0 6<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.11"} hits=0 status=0 QTime=8 <br />INFO: {delete=[df35a.21.11]} 0 5<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.10"} hits=0 status=0 QTime=2 <br />INFO: {delete=[df35a.21.10]} 0 13<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.9"} hits=0 status=0 QTime=1 <br />INFO: {delete=[df35a.21.9]} 0 13<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.8"} hits=0 status=0 QTime=2 <br />INFO: {delete=[df35a.21.8]} 0 12<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.7"} hits=0 status=0 QTime=1 <br />INFO: {delete=[df35a.21.7]} 0 12<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.5"} hits=0 status=0 QTime=1 <br />INFO: {delete=[df35a.21.5]} 0 12<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.4"} hits=0 status=0 QTime=1 <br />INFO: {delete=[df35a.21.4]} 0 12<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.3"} hits=0 status=0 QTime=1 <br />INFO: {delete=[df35a.21.3]} 0 12<br />INFO: [] webapp=null path=/select params={q=id:"df35a.21.31"} hits=0 status=0 QTime=8 <br />INFO: {add=[df35a.21.31]} 0 58<br />INFO: ============================= insert index for the identifier df35a.21.31<br />original pathInfo: /views/metacatui/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/views/metacatui/df35a.21.31<br />new pathinfo: /views/metacatui/df35a.21.31<br />original pathInfo: /query/solr/fl=id,resourceMap&wt=xml&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:"df35a.21.31" <br />original requestURI: /gulfwatch/d1/mn/v1/query/solr/fl=id,resourceMap&wt=xml&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:%22df35a.21.31%22<br />new pathinfo: /query/solr/fl=id,resourceMap&wt=xml&q=formatType:METADATA -obsoletedBy:* resourceMap:* id:"df35a.21.31" <br />fl=id,resourceMap&wt=xml&q=formatType:METADATA -obsoletedBy:* resourceMap:* id:"df35a.21.31" [edu.ucsb.nceas.metacat.dataone.MNodeService]<br />original pathInfo: /meta/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/meta/df35a.21.31<br />new pathinfo: /meta/df35a.21.31<br />INFO: [] webapp=null path=/select params={{main(fl=id,resourceMap&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:"df35a.21.31"&wt=xml),extra(fq=(readPermission:"cn%3Devos,o%3DNCEAS,dc%3Decoinformatics,dc%3Dorg")<abbr title="rightsHolder:"cn%3Devos,o%3DNCEAS,dc%3Decoinformatics,dc%3Dorg"">OR</abbr><abbr title="readPermission:"authenticatedUser"">OR</abbr><abbr title="readPermission:"public"">OR</abbr><abbr title="readPermission:"uid%3Dsclark,o%3DNCEAS,dc%3Decoinformatics,dc%3Dorg"">OR</abbr><abbr title="rightsHolder:"uid%3Dsclark,o%3DNCEAS,dc%3Decoinformatics,dc%3Dorg"">OR</abbr>)}} hits=0 status=0 QTime=19 <br />original pathInfo: /meta/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/meta/df35a.21.31<br />new pathinfo: /meta/df35a.21.31<br />original pathInfo: /isAuthorized/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/isAuthorized/df35a.21.31<br />new pathinfo: /isAuthorized/df35a.21.31<br />original pathInfo: /publish/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/publish/df35a.21.31<br />new pathinfo: /publish/df35a.21.31<br />metacat 20131011-13:14:13: [DEBUG]: Updating pid df35a.21.31 [edu.ucsb.nceas.metacat.dataone.D1NodeService]<br />metacat 20131011-13:14:13: [DEBUG]: looking in identifier table for pid df35a.21.31 [edu.ucsb.nceas.metacat.dataone.D1NodeService]<br />metacat 20131011-13:14:13: [DEBUG]: localId: df35a.21.31 [edu.ucsb.nceas.metacat.dataone.D1NodeService]<br />metacat 20131011-13:14:13: [DEBUG]: incremented localId: df35a.21.32 [edu.ucsb.nceas.metacat.dataone.D1NodeService]<br />java.lang.Exception: User uid=sclark,o=NCEAS,dc=ecoinformatics,dc=org does not have permission to update XML Document #df35a.21.31<br />metacat 20131011-13:14:13: [ERROR]: D1ResourceHandler: Serializing exception with code 500: Error inserting or updating document: <?xml version="1.0"?><error>User uid=sclark,o=NCEAS,dc=ecoinformatics,dc=org does not have permission to update XML Document #df35a.21.31</error> [edu.ucsb.nceas.metacat.restservice.D1ResourceHandler]<br />org.dataone.service.exceptions.ServiceFailure: Error inserting or updating document: <?xml version="1.0"?><error>User uid=sclark,o=NCEAS,dc=ecoinformatics,dc=org does not have permission to update XML Document #df35a.21.31</error><br />original pathInfo: /views/metacatui/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/views/metacatui/df35a.21.31<br />new pathinfo: /views/metacatui/df35a.21.31<br />original pathInfo: /query/solr/fl=id,resourceMap&wt=xml&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:"df35a.21.31" <br />original requestURI: /gulfwatch/d1/mn/v1/query/solr/fl=id,resourceMap&wt=xml&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:%22df35a.21.31%22<br />new pathinfo: /query/solr/fl=id,resourceMap&wt=xml&q=formatType:METADATA -obsoletedBy:* resourceMap:* id:"df35a.21.31" <br />fl=id,resourceMap&wt=xml&q=formatType:METADATA -obsoletedBy:* resourceMap:* id:"df35a.21.31" [edu.ucsb.nceas.metacat.dataone.MNodeService]<br />original pathInfo: /meta/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/meta/df35a.21.31<br />new pathinfo: /meta/df35a.21.31<br />INFO: [] webapp=null path=/select params={{main(fl=id,resourceMap&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:"df35a.21.31"&wt=xml),extra(fq=(readPermission:"public"))}} hits=0 status=0 QTime=14 <br />original pathInfo: /meta/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/meta/df35a.21.31<br />new pathinfo: /meta/df35a.21.31<br />original pathInfo: /isAuthorized/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/isAuthorized/df35a.21.31<br />new pathinfo: /isAuthorized/df35a.21.31<br />metacat 20131011-13:36:02: [ERROR]: D1ResourceHandler: Serializing exception with code 401: CHANGE_PERMISSION not allowed on df35a.21.31 for subject[s]: public; [edu.ucsb.nceas.metacat.restservice.D1ResourceHandler]<br />org.dataone.service.exceptions.NotAuthorized: CHANGE_PERMISSION not allowed on df35a.21.31 for subject[s]: public; <br />original pathInfo: /views/metacatui/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/views/metacatui/df35a.21.31<br />new pathinfo: /views/metacatui/df35a.21.31<br />original pathInfo: /query/solr/fl=id,resourceMap&wt=xml&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:"df35a.21.31" <br />original requestURI: /gulfwatch/d1/mn/v1/query/solr/fl=id,resourceMap&wt=xml&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:%22df35a.21.31%22<br />new pathinfo: /query/solr/fl=id,resourceMap&wt=xml&q=formatType:METADATA -obsoletedBy:* resourceMap:* id:"df35a.21.31" <br />fl=id,resourceMap&wt=xml&q=formatType:METADATA -obsoletedBy:* resourceMap:* id:"df35a.21.31" [edu.ucsb.nceas.metacat.dataone.MNodeService]<br />original pathInfo: /meta/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/meta/df35a.21.31<br />new pathinfo: /meta/df35a.21.31<br />INFO: [] webapp=null path=/select params={{main(fl=id,resourceMap&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:"df35a.21.31"&wt=xml),extra(fq=(readPermission:"public"))}} hits=0 status=0 QTime=14 <br />original pathInfo: /meta/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/meta/df35a.21.31<br />new pathinfo: /meta/df35a.21.31<br />original pathInfo: /isAuthorized/df35a.21.31<br />original requestURI: /gulfwatch/d1/mn/v1/isAuthorized/df35a.21.31<br />new pathinfo: /isAuthorized/df35a.21.31<br />metacat 20131011-13:36:40: [ERROR]: D1ResourceHandler: Serializing exception with code 401: CHANGE_PERMISSION not allowed on df35a.21.31 for subject[s]: public; [edu.ucsb.nceas.metacat.restservice.D1ResourceHandler]</p>
Bug #6138 (Closed): Metacat-index assumes default "knb" context
https://projects.ecoinformatics.org/ecoinfo/issues/6138
2013-10-10T19:12:13Z
ben leinfelder
leinfelder@nceas.ucsb.edu
Bug #6136 (Closed): files left open causes too many file descriptors on OS
https://projects.ecoinformatics.org/ecoinfo/issues/6136
2013-10-09T20:03:37Z
Matt Jones
jones@nceas.ucsb.edu
<p>Metacat writes temp files to disk, and in the process has been failing to close file handles. Over time, especially with operations that touch many files, the number of file handles in use by Metacat increases and eventually exceeds the operating systems hard limit, causing exceptions when Metacat tries to open any additional files. Need to be sure to close all file handles properly after usage.</p>