Project

General

Profile

Statistics
| Revision:
Name Size Revision Age Author Comment
  accesscontrol 8173 about 11 years ben leinfelder avoid SQL errors when processing very old objec...
  admin 8642 over 10 years ben leinfelder merge recent upgrade changes from 2.4 branch
  advancedsearch 6901 over 12 years Matt Jones Properly initialize the servlet context when st...
  annotation 8718 over 10 years ben leinfelder attribute the datapackage to the creator (using...
  authentication 8575 over 10 years Jing Tao Modified the usage.
  cart 5374 over 14 years berkley refactored the sessionService to use a correct ...
  client 7395 about 12 years ben leinfelder include inverted sendParameters() method that u...
  clientview 7475 almost 12 years ben leinfelder move DocInfo parsing into utilities project so ...
  database 6606 almost 13 years ben leinfelder uses prepared statement instead of plain old st...
  dataone 8647 over 10 years ben leinfelder recursively submit obsoleted objects for indexi...
  dataquery 6000 over 13 years ben leinfelder refactor the names of these Data Manager implem...
  event 6029 over 13 years ben leinfelder add event notification for insert/update/delete...
  harvesterClient 8018 about 11 years ben leinfelder allow running the Harvester client without a so...
  index 8678 over 10 years ben leinfelder allow "+" in solr query syntax. https://project...
  lsid 8265 about 11 years ben leinfelder Refer to metacat.war deployments since those ar...
  oaipmh 8304 almost 11 years Matt Jones Reviewed code for all uses of FileInputStream, ...
  plugin 5518 about 14 years ben leinfelder include MetacatHandlerPlugin interface so that ...
  portal 7737 over 11 years ben leinfelder first pass at integrating CILogon/MyProxy certi...
  properties 7781 over 11 years Jing Tao Solr will be enabled if it is in the db.enabled...
  replication 8689 over 10 years ben leinfelder support content from all serverLocations when s...
  restservice 8715 over 10 years ben leinfelder remove leading '?' in the query parameter for M...
  scheduler 7475 almost 12 years ben leinfelder move DocInfo parsing into utilities project so ...
  service 8588 over 10 years ben leinfelder allow utf-8 user first/last names to be used in...
  shared 7475 almost 12 years ben leinfelder move DocInfo parsing into utilities project so ...
  spatial 8265 about 11 years ben leinfelder Refer to metacat.war deployments since those ar...
  util 8524 over 10 years Jing Tao Add a method to get the user management url.
  workflow 6124 over 13 years Chris Jones Merged in the D1_0_6_2_BRANCH changes that incl...
AccessionNumber.java 10.8 KB 6595 almost 13 years ben leinfelder http://bugzilla.ecoinformatics.org/show_bug.cgi...
AccessionNumberException.java 1.82 KB 3077 almost 18 years Matt Jones Removed the @release@ ant token from all files ...
ArchiveHandler.java 8.4 KB 5030 about 15 years daigle Change location of PropertyService to propertie...
AssociateAccessPolicy.java 16.4 KB 6744 almost 13 years ben leinfelder refactor Metacat access handling to be on a per...
AuthInterface.java 4.25 KB 8476 over 10 years Jing Tao Add the getUserInfo method.
AuthLdap.java 54.3 KB 8704 over 10 years Jing Tao Remove the code to lookup alias dn in the getGr...
AuthSession.java 10.4 KB 8652 over 10 years Jing Tao In the authenticate method, if metacat can't ge...
AuthStub.java 7.64 KB 5030 about 15 years daigle Change location of PropertyService to propertie...
AuthTLSException.java 1.54 KB 5158 almost 15 years daigle Separate code to do tls and non-tls authenticat...
AuthTest.java 9.28 KB 5030 about 15 years daigle Change location of PropertyService to propertie...
BasicNode.java 6.68 KB 3077 almost 18 years Matt Jones Removed the @release@ ant token from all files ...
CatalogMessageHandler.java 2.97 KB 3077 almost 18 years Matt Jones Removed the @release@ ant token from all files ...
CommentNode.java 2.13 KB 3077 almost 18 years Matt Jones Removed the @release@ ant token from all files ...
ContentTypeProvider.java 20.9 KB 6595 almost 13 years ben leinfelder http://bugzilla.ecoinformatics.org/show_bug.cgi...
DBDTDHandler.java 5.38 KB 5015 about 15 years daigle Create database and shared directories for data...
DBEntityResolver.java 17.5 KB 6606 almost 13 years ben leinfelder uses prepared statement instead of plain old st...
DBQuery.java 107 KB 8304 almost 11 years Matt Jones Reviewed code for all uses of FileInputStream, ...
DBSAXHandler.java 30.2 KB 7403 almost 12 years ben leinfelder remove morpho.jar -- moved needed classes into ...
DBSAXNode.java 16.8 KB 6606 almost 13 years ben leinfelder uses prepared statement instead of plain old st...
DBSimpleQuery.java 7.44 KB 5015 about 15 years daigle Create database and shared directories for data...
DBTransform.java 14.7 KB 8664 over 10 years Jing Tao Set the userManagementURL property.
DBUtil.java 27.9 KB 7015 over 12 years ben leinfelder overload getAllDocidsByType() method for backwa...
DBValidate.java 10.8 KB 5030 about 15 years daigle Change location of PropertyService to propertie...
DistributionSection.java 3.07 KB 5090 almost 15 years daigle Move access control source to it's own directory.
DocumentIdQuery.java 4.5 KB 5731 almost 14 years ben leinfelder typo - "dataset/pubDate"
DocumentIdentifier.java 7.53 KB 6595 almost 13 years ben leinfelder http://bugzilla.ecoinformatics.org/show_bug.cgi...
DocumentImpl.java 190 KB 8647 over 10 years ben leinfelder recursively submit obsoleted objects for indexi...
DocumentImplWrapper.java 3.92 KB 7128 over 12 years ben leinfelder add a parameter for optionally writing EML-embe...
EML201DocumentCorrector.java 5.84 KB 6606 almost 13 years ben leinfelder uses prepared statement instead of plain old st...
ElementNode.java 5.45 KB 4080 over 16 years daigle Merge 1.9 changes into Head
Eml200SAXHandler.java 120 KB 8630 over 10 years Peter Slaughter get guid from online id for call to SyncAccessP...
Eml210SAXHandler.java 71.6 KB 8560 over 10 years Peter Slaughter Sync access policy between MN -> CN when access...
ErrorHandledException.java 1.53 KB 4950 over 15 years daigle Add archival read funtionality (jar/kar/war files)
EventLog.java 23.2 KB 8647 over 10 years ben leinfelder recursively submit obsoleted objects for indexi...
EventLogData.java 3.34 KB 6542 almost 13 years ben leinfelder add User-Agent logging to support D1 requirements
IdentifierManager.java 69.7 KB 7639 over 11 years ben leinfelder Allow null SM.submitter (per schema). There wer...
IndexingQueue.java 10.9 KB 8164 about 11 years Jing Tao If the pathquery engine is disabled, the xml pa...
IndexingTimerTask.java 4.47 KB 8164 about 11 years Jing Tao If the pathquery engine is disabled, the xml pa...
McdbDocNotFoundException.java 2.94 KB 5282 over 14 years Matt Jones Added initial support for arbitrary string iden...
McdbException.java 3.49 KB 5752 almost 14 years ben leinfelder use detected XML encoding when reading/writing ...
MetaCatServlet.java 48.3 KB 8588 over 10 years ben leinfelder allow utf-8 user first/last names to be used in...
MetacatHandler.java 156 KB 8647 over 10 years ben leinfelder recursively submit obsoleted objects for indexi...
MetacatProfiler.java 7.6 KB 5607 almost 14 years berkley profiler code for metacat
MetacatResultSet.java 4.69 KB 5363 over 14 years berkley implementing getObjects in CrudService.
MetacatURL.java 9.32 KB 3077 almost 18 years Matt Jones Removed the @release@ ant token from all files ...
MetacatVersion.java 2.06 KB 6124 over 13 years Chris Jones Merged in the D1_0_6_2_BRANCH changes that incl...
NodeComparator.java 3.49 KB 3077 almost 18 years Matt Jones Removed the @release@ ant token from all files ...
NodeRecord.java 6.91 KB 6012 over 13 years ben leinfelder add support for temporal element query in pathq...
PINode.java 2.17 KB 3079 almost 18 years Matt Jones Eliminated unneeded log information in source c...
PathIndexEntry.java 2.87 KB 6012 over 13 years ben leinfelder add support for temporal element query in pathq...
PermissionController.java 35.3 KB 7475 almost 12 years ben leinfelder move DocInfo parsing into utilities project so ...
QueryGroup.java 14.1 KB 7407 almost 12 years ben leinfelder simplify the xml_access query, and instead use ...
QueryResultTableBuilder.java 3.19 KB 3799 over 16 years Jing Tao Add a new class will build query result able in...
QuerySpecification.java 41.3 KB 7495 over 11 years ben leinfelder group user_owner clause as "AND (... OR .... OR...
QueryTerm.java 24.2 KB 6740 almost 13 years ben leinfelder retry: add node name in the correct order for p...
RelationHandler.java 8.24 KB 7403 almost 12 years ben leinfelder remove morpho.jar -- moved needed classes into ...
RemoteDocument.java 17 KB 5030 about 15 years daigle Change location of PropertyService to propertie...
SchemaLocationResolver.java 13 KB 5945 over 13 years Jing Tao Add code to download the included schema.
Sitemap.java 14.4 KB 7766 over 11 years Matt Jones Updated documentation, and added modification d...
SubTree.java 7.7 KB 5311 over 14 years daigle Merge 1.9.2 changes back into the trunk
TextNode.java 2.09 KB 3077 almost 18 years Matt Jones Removed the @release@ ant token from all files ...
Version.java 2.92 KB 4080 over 16 years daigle Merge 1.9 changes into Head
XMLQueryresultAccess.java 3.31 KB 7475 almost 12 years ben leinfelder move DocInfo parsing into utilities project so ...

Latest revisions

# Date Author Comment
8718 03/31/2014 11:11 AM ben leinfelder

attribute the datapackage to the creator (using orcid if we can find it). https://projects.ecoinformatics.org/ecoinfo/issues/6267
https://projects.ecoinformatics.org/ecoinfo/issues/6423

8717 03/31/2014 10:31 AM ben leinfelder

add test for BioPortal annotator service.

8716 03/28/2014 03:51 PM ben leinfelder

refactor web service calls to bioportal and orcid outside of the annotator class. test with orcid sandbox server. include orcid uri for the annotations being generated (we can index these and drive our searches on these values down the road). related to this: https://projects.ecoinformatics.org/ecoinfo/issues/6423 and also some semtools tasks.

8715 03/27/2014 04:54 PM ben leinfelder

remove leading '?' in the query parameter for MN.query() implementation. We want it to match CN behavior/expectations and comply with the DataONE specification for the interface. https://projects.ecoinformatics.org/ecoinfo/issues/6488

8714 03/26/2014 04:05 PM ben leinfelder

Use OBOE-SBC ontology for looking up concepts (it contains subclasses of our OBOE Characteristic and Standard superclasses). Restrict annotations to only subclasses that fit the OBOE model. Correct the xpointer and individual naming conventions so they are unique, but express the exact entity/attribute being annotated.

8713 03/26/2014 03:10 PM ben leinfelder

remove my api key. oops

8712 03/26/2014 03:02 PM ben leinfelder

add comment/pointer to BioPortal annotation service.

8711 03/26/2014 03:00 PM ben leinfelder

Include method to look up annotation classes from BioPortal. We still have OBOE-SBC in there, and theyhave the SWEET ontology. The suggestions returned are not perfect, but they can be better than nothing. Ideally, we'd only query a few ontologies so we don't end up using terms from medical ontologies that aren't really appropriate for our domain. https://projects.ecoinformatics.org/ecoinfo/issues/6256

8710 03/24/2014 04:17 PM ben leinfelder

Add xpointer FragmentSelectors to each annotation.
Split attribute label into tokens to attempt matching to OBOE concepts.

8709 03/23/2014 12:11 AM ben leinfelder

include code to generate random annotations for UI testing. Effective, but can be confusing to see so many unrelated concepts on duplicate EML packages.

View revisions

Also available in: Atom