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  • svn:mergeinfo: /branches/D1_0_6_2_BRANCH:6107-6121

# Date Author Comment
8877 10/06/2014 05:42 PM Jing Tao

dd a new routine to check if the uid has been taken already in the production space during the creation process.

8875 09/25/2014 09:01 AM Lauren Walker

In the EML XSLT - Add classes to the entity details containers so they can be identified easily

8874 09/23/2014 06:27 PM ben leinfelder

add /token endpoint for annotatorJS/annotateIt.org integration. https://github.com/DataONEorg/sem-prov-design/issues/18

8872 09/22/2014 06:29 PM Jing Tao

Add code to determine if a id exists in a solr server.

8871 09/19/2014 04:15 PM ben leinfelder

include resource="#xpointer(...)" attributes for sections that are potential targets for annotation. So far we have the various people (creator, contact, etc) and data table attributes. https://github.com/DataONEorg/sem-prov-design/issues/18

8869 09/18/2014 03:12 PM Jing Tao

Persitence the system metadata object in the memory before deleting it from hazelcast.

8866 09/16/2014 05:18 PM Jing Tao

Add the code to handle the delete of the resource map.

8864 09/16/2014 05:07 PM Jing Tao

Add the code to handle to remove the resource map index.

8862 09/16/2014 04:48 PM Jing Tao

Add codes to handle remove a source map solr index.

8860 09/16/2014 04:36 PM Jing Tao

Add a field to contain the content of resource map.

8859 09/15/2014 06:31 PM Jing Tao

Add a util class to judge if a namespace is a resource map file.

8857 09/15/2014 02:32 PM Lauren Walker

Create a valid URI by using all lowercase letters when creating a name for the triple model in the Rdf Xml Subprocessor. See bug: https://projects.ecoinformatics.org/ecoinfo/issues/6595

8854 09/12/2014 04:17 PM Jing Tao

Make the delete method work.

8852 09/12/2014 04:03 PM Jing Tao

Make the deleteSystemmetadata method really roll-backable.

8850 09/12/2014 03:56 PM Jing Tao

Add the code to delete systemmetadata.

8849 09/11/2014 02:37 PM ben leinfelder

remove semantic annotation proposal - moved to github: https://github.com/DataONEorg/sem-prov-design/blob/master/docs/use-cases/semantics/semantic-annotation.md

8848 09/11/2014 09:26 AM Lauren Walker

In InsertORETest: Set the format ID of the metadata object to an EML formatId so that it gets indexed correctly.

8847 09/10/2014 02:56 PM Jing Tao

Change the d1_cn_index_processor version from 1.3.0 snapshot to 2.0.0 snapshot.

8846 09/04/2014 03:24 PM Jing Tao

Add the code to delete the records in the xml_accesssubtree table.

8844 09/02/2014 02:07 PM ben leinfelder

use configured auth.base rather than hard-coded dc=ecoinformatics,dc=org. https://projects.ecoinformatics.org/ecoinfo/issues/6592

8842 08/22/2014 05:50 PM Jing Tao

Add a code to check if the pathquery engine is enabled in the checkIndexPaths method.

8841 08/21/2014 11:50 AM Jing Tao

Adjust the number of schema fields since new ones were added.

8840 08/19/2014 11:38 AM Lauren Walker

When indexing annotations from RDFs, use the doc id to access the system metadata, not the model name since they are not always the same.

8839 08/18/2014 03:25 PM Lauren Walker

Add PROV relationships to the Solr schema. Populate the fields using the RdfXmlSubprocessor

8837 08/18/2014 10:03 AM Lauren Walker

Add wasDerivedFrom field to the Solr schema and use Sparql query to retrieve the value from the RDF

8836 08/18/2014 09:30 AM Lauren Walker

Replace the /u00A0 character encoding with space character instead since /u00A0 displays literally in browsers

8835 08/15/2014 01:25 PM Lauren Walker

Add a test class that inserts an ORE with PROV relationships

8834 08/07/2014 02:28 PM ben leinfelder

use mock CN for testing metacat implementations

8833 08/07/2014 02:12 PM ben leinfelder

remove unused tests

8832 08/07/2014 11:13 AM ben leinfelder

comment out myproxy servlets. https://redmine.dataone.org/issues/5742

8829 08/06/2014 01:48 PM ben leinfelder

convert v2 SM to v1 SM for the v1 service call response

8828 08/06/2014 01:43 PM Jing Tao

Separate the target and source version for the java compilation.

8827 08/06/2014 01:27 PM ben leinfelder

update to use v2 types for indexing

8826 08/06/2014 01:09 PM ben leinfelder

update to use v2 types for indexing

8825 08/05/2014 09:21 PM Jing Tao

Add target and source attribute to harvester, client and compile-lsid beside the target compile.

8823 08/05/2014 04:17 PM Jing Tao

Add the attribute target="1.6" when it compiles the metacat code.
The metacat.jar file can run in java 1.6 even though it was compiled in java 1.7.

8821 08/04/2014 04:08 PM Jing Tao

For the existing uidnumber, we decrease the size of vector for sorting.

8820 08/04/2014 10:04 AM Lauren Walker

Login automatically via curl rather than manually entering the cookie info for the registry test script

8819 08/01/2014 09:20 AM Jing Tao

Add the code to check if the existing highest uidNumber really exists.

8818 07/31/2014 06:10 PM Jing Tao

In the getNextUidNumber method, a mechanism to look up the highest existing udiNumber was added.

8817 07/30/2014 11:24 AM Lauren Walker

Fix XML validation errors in the metacatui confirmData template for the registry. Add a test script that submits multiple datasets to the registry.

8816 07/29/2014 05:33 PM Lauren Walker

Create a lock file for the registry
if one doesn't exist

8815 07/29/2014 04:35 PM Lauren Walker

Allow the registry form to specify a docid scope

8814 07/29/2014 03:53 PM Lauren Walker

Only lock the local docid file when creating a new docid, not when inserting, for faster upload times. Remove extra debug messages from testing.

8813 07/28/2014 05:22 PM Lauren Walker

Fix bug in the online registry where data files were not using the new docid creation process

8812 07/28/2014 03:57 PM Lauren Walker

Lock a local file while docids are being created so multiple docs can be uploaded at once

8811 07/24/2014 10:25 AM ben leinfelder

remove CN.systemMetadataChanged in favor of the CN.updateSystemMetadata method. Otherwise there's no good way to know where to fetch the auth copy from since the SM change might be to switch the authMN!

8810 07/23/2014 04:19 PM ben leinfelder

add support for v2 DataONE API.

8809 06/09/2014 04:06 PM ben leinfelder

remove old EML jar -- datamanager.jar has the EMLParser now and is pulled in with maven.

8808 06/06/2014 04:54 PM ben leinfelder

use css changes from EML project to render a PDF that fits on a printed page during export. Note that this also changes the default skin slightly (for the better, we think). https://projects.ecoinformatics.org/ecoinfo/issues/6053

8807 06/02/2014 12:16 PM ben leinfelder

remove configxml.jar as the ConfigXML class is now included in the utilities library.

8806 06/01/2014 08:48 AM ben leinfelder

handle login/logout when testing using metacat client (recent refactoring to use more standard http client code)

8805 05/30/2014 05:06 PM ben leinfelder

handle multiple subprocessors (RDF and ORE) before the object gets indexed by making sure to merge the solr doc map before submitting to the index.

8804 05/30/2014 01:58 PM ben leinfelder

use maven for datamanager dependency now that EML project has been [partially] maven-ized.

8803 05/29/2014 03:47 PM ben leinfelder

switch to use utilities from Maven repo instead of pulling from SVN and building locally. Added trunk/SNAPSHOT build to dev-testing Hudson (DataONE) for users who do not actively develop the utilities library. Motivated by the HTML->PDF utility, seemed like as good a time as any to convert Metacat's dependency on the project.

8802 05/29/2014 02:53 PM ben leinfelder

remove dependency on HttpMessage that was in the utilities project but is now removed in favor of newer (standard) http client library code.

8801 05/28/2014 05:19 PM ben leinfelder

add more sections about extending the annotation model, serializations, and permissions.

8800 05/28/2014 11:49 AM ben leinfelder

Include PDF version of the metadata in the package download. https://projects.ecoinformatics.org/ecoinfo/issues/6053

8799 05/28/2014 11:48 AM ben leinfelder

use default "metacat" context name for metacat-index testing.

8798 05/27/2014 04:14 PM ben leinfelder

Added more description for the model. cleaned up a few formatting issues.

8797 05/23/2014 05:29 PM ben leinfelder

draft of semantic model documentation

8796 05/23/2014 03:08 PM Peter Slaughter

Change geohash type to "string" (was "text") so that no Solr analysis or tokenizing happens during indexing.

8795 05/22/2014 01:59 PM ben leinfelder

take advantage of the ezidclient for multi-threaded/asynchronous DOI registration. This will be most useful for doing large batch updates and not so much for the one-at-a-time publish actions but works in either context. https://projects.ecoinformatics.org/ecoinfo/issues/6440

8794 05/21/2014 06:24 PM ben leinfelder

use a member instance of ezid service that only logs in every 24 hours (or other time TBD) instead of every time there is an interaction with the service. Saves us many calls when doing batch updates to ezid but keeps us from trying to use expired sessions. Motivated by https://projects.ecoinformatics.org/ecoinfo/issues/6440

8793 05/21/2014 02:59 PM Lauren Walker

Fixed an error in the ORE model diagrams

8792 05/20/2014 04:11 PM ben leinfelder

prevent js scriptlets from running when we return error messages to the client by escaping any potentially harmful xml blocks. https://projects.ecoinformatics.org/ecoinfo/issues/6224

8791 05/20/2014 04:09 PM ben leinfelder

allow updates to all doi: prefixes - realized we are already restricting to specific replica servers when updating these. worst case is we try to update a registration for which we are not the owner. https://projects.ecoinformatics.org/ecoinfo/issues/6440

8790 05/20/2014 04:08 PM ben leinfelder

show the SM and ORE generation buttons even if they have not registered/configured dataone. many potential MNs want to see their generated SM before registering (and we want them to too!).

8789 05/20/2014 10:40 AM ben leinfelder

restrict DOI updates to DOIs that match our server shoulder -- may consider opening this up to any "doi:" prefix if this is too restrictive. https://projects.ecoinformatics.org/ecoinfo/issues/6440

8788 05/19/2014 02:21 PM ben leinfelder

use separate surName and givenNames to lookup ORCIDs.

8787 05/19/2014 01:17 PM Lauren Walker

Changed errors in the ORE model expansion metacat documentation diagrams

8786 05/16/2014 03:13 PM Lauren Walker

Describe the primary data resource in the derived resource RDF

8785 05/16/2014 10:03 AM Lauren Walker

Create a derived data and metadata in the OrePackageTest

8784 05/15/2014 03:17 PM ben leinfelder

all full-text queries for ORCID, but it isn't that great because we might have a"PISCO" creator that shows us in may different orcid profiles...false matches.

8783 05/15/2014 11:55 AM ben leinfelder

correct glaring erros -- still needs to be honed, but at least it runs without NPE and Jena/foresite errors

8782 05/15/2014 11:29 AM ben leinfelder

stub for testing ORE augmentation - this generates an ORE, adds a "wasDerivedFrom" triple and saves to Metacat MN for indexing. https://projects.ecoinformatics.org/ecoinfo/issues/6548

8781 05/15/2014 10:27 AM ben leinfelder

include ORE formatId as handled by the RDF subprocessor and index prov:wasDerivedFrom field where it exists in the RDF model. https://projects.ecoinformatics.org/ecoinfo/issues/6548

8780 05/15/2014 09:34 AM ben leinfelder

expand the sparql queries to include dcterms:identifier

8779 05/14/2014 02:09 PM Lauren Walker

Text changes to ORE docs

8778 05/14/2014 01:22 PM Lauren Walker

Add documentation for the ORE model expansion for derived data

8777 05/14/2014 12:04 PM ben leinfelder

use HttpClient to query orcid so I can easily set headers and such -- getting 503s from their production server when I test on dev.nceas...odd

8776 05/14/2014 11:43 AM ben leinfelder

adjust tests for production service -- more "real" information shows additional return values from the query.

8775 05/14/2014 09:18 AM ben leinfelder

switch to the production ORCID server for looking up orcid matches for our creators.
add test to summarize how many creator matches we can actually find. https://projects.ecoinformatics.org/ecoinfo/issues/6423

8774 05/13/2014 03:36 PM ben leinfelder

use a non-public rightsHolder for both EML and Annotation test documents now that the RDF subprocessor checks each annotation to see that it came from a user that as write permission for the object being annotated.

8773 05/13/2014 03:34 PM ben leinfelder

test for update using the updated EML file, not the original. Also add the SM to the shared map so that the indexing process can consult SM.accessPolicy when indexing annotations that assert things about those test documents.

8772 05/13/2014 03:32 PM ben leinfelder

ignore the metacat/solr comparator tests - they are one-offs.

8771 05/13/2014 03:31 PM ben leinfelder

change the hazelcast group name to be the default "metacat" instance so that the metacat-index tests pass without additional local configuration, at least when running a default metacat deployment.

8770 05/12/2014 11:31 AM ben leinfelder

do not set archived=false for all CN.create calls. The CN will use create() even harvesting content that is new to it and needs to handle already-archived content. https://projects.ecoinformatics.org/ecoinfo/issues/6475

8769 05/09/2014 01:48 PM ben leinfelder

cache the imported models to avoid timeouts from remote hosts (or being locked out for too many requests in a given time period).

8768 05/08/2014 04:25 PM ben leinfelder

process all the returned annotation suggestions until we find one that is appropriately located in the subclass hierarchy for the given superclass.

8767 05/08/2014 04:23 PM ben leinfelder

use in-memory TDB dataset for querying annotations for indexing -- this comes with the same reasoning capabilities as the directory-based one, but has the benefit of not filling the directory with triples that will not be used again. prepping for d1 AHM

8766 05/07/2014 11:16 PM ben leinfelder

pass around the object file path rather than the data stream so that multiple subprocessors can index the same object and not consume the stream before it gets to the next one. In preparation for extending the assertions stored in OREs. https://projects.ecoinformatics.org/ecoinfo/issues/6548

8765 05/07/2014 11:12 PM ben leinfelder

when indexing annotations directly, just use an in-memory triple store rather than TDB since we remove each graph as it is processed (and my TDB instance would get into the multi-GB range with a few runs, even if I removed the old models)

8764 05/05/2014 05:17 PM ben leinfelder

redirect "short form" metacat read URIs to the the new Metacat UI using the configured UI context. This translates the docid -> pid to use the correct identifier for the correct service. https://projects.ecoinformatics.org/ecoinfo/issues/6546

8763 05/02/2014 04:39 PM ben leinfelder

simplify lookup for classes and orcid. remove the "random" annotation code branches -- just too confusing to look at those bogus classes especially now that we have "real" generated annotations.

8762 04/30/2014 03:47 PM ben leinfelder

add 'test' for indexing annotations without actually storing the RDF of the generated annotation.

8761 04/30/2014 03:46 PM ben leinfelder

only allow multiple values for multi-valued fields....

8760 04/30/2014 01:02 PM Lauren Walker

Add admin service to update DOI registrations by specifying a list of formatIds or DOIs, or update all.

8759 04/29/2014 05:21 PM ben leinfelder

use new method to override the CN URL when constructing a CNode instance. see https://redmine.dataone.org/issues/5142

8758 04/29/2014 04:55 PM ben leinfelder

use newer httpclient library so that Jena's dependency is met - this goes all the way back to d1_common/libclient needing to pull in the newer library.