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# Date Author Comment
9062 01/07/2015 04:03 PM Jing Tao

In the getLogRecords method, the pidFilter is checked if it exists.

9061 01/07/2015 04:02 PM Jing Tao

In the getLogRecords method, the pidFilter is checked if it exists.

9059 01/07/2015 12:01 PM Jing Tao

Fixed a bug that the getLogRecords can't handle the case that the event is null.

9057 01/07/2015 12:00 PM Jing Tao

Fixed a bug that the getLogRecords can't handle the case that the event is null.

9056 01/06/2015 03:32 PM Jing Tao

Add the code to check the if the new series id is legitimate in the systemMetadataChanged method.

9051 12/31/2014 03:49 PM Jing Tao

Add the code to support the sereis id on isAuthorized and systemMetadataChanged method.

9050 12/30/2014 04:34 PM Jing Tao

Add the code to handle the sid in the delete and archive method.

9048 12/30/2014 02:09 PM Jing Tao

Fixed a bug in comparing two identifiers in the update method.

9047 12/30/2014 11:04 AM Jing Tao

Add a check that the sid shouldn't equals the pid in the update and create method.

9046 12/29/2014 05:10 PM Jing Tao

Add the code the check if the format of the sid is valid in the system metadata.

9045 12/29/2014 05:06 PM Jing Tao

Add the enforcement for the sid in the create method.

9044 12/29/2014 04:26 PM Jing Tao

Enforce the sid requirement in the update method.

9043 12/29/2014 03:03 PM Jing Tao

Check if the identifier is a sid for the v1 update.

9041 12/29/2014 12:23 PM Jing Tao

Add the code to handle the deleted identifier in the checking v1 system metadata existing method.

9040 12/29/2014 11:42 AM Jing Tao

Enforce the mn.getChecksum only to handle an PID.

9038 12/24/2014 11:41 AM Jing Tao

Add the series id to the system metadata.

9037 12/24/2014 09:47 AM Jing Tao

Implement the series id in the getSystemMetadata method.

9036 12/23/2014 04:53 PM Jing Tao

Looking for sid for the method describe.

9033 12/22/2014 02:31 PM Jing Tao

Refactor the code to check a pid exists in the v1 api.

9032 12/19/2014 04:59 PM Jing Tao

Modified the get method to handle the sid in the v2 api.

9030 12/19/2014 03:10 PM Jing Tao

Change a method name to use pid rather than guid.

9026 12/17/2014 04:57 PM Jing Tao

Add the code to get the most recent version of a sid which all pids are obsoleted.

9024 12/16/2014 06:50 PM Jing Tao

Fixed a bug that the method getLocalId swallowed an exception incorrectly in the IdentifierManager.

9023 12/12/2014 04:25 PM Jing Tao

Fixed a bug that some service failure exceptions were handled as the NotFound exception.

9017 12/11/2014 03:24 PM Jing Tao

1. In the identifierExists method, the code to check if the identifier exist on the serial-id fields of the system metadata table.
2. Fixed a bug on the identifierExists - it considered an identifier didn't exist when the determining process threw an exception.

9016 12/10/2014 04:33 PM Jing Tao

Add a method to check if a serial id exists.

9015 12/09/2014 05:03 PM Jing Tao

Add a method to get the pid of the head version of a sid.

9014 12/09/2014 01:10 PM ben leinfelder

add Annotator Store implementation -- pass through to D1 API for the AnnotatorJS API

9009 12/02/2014 02:08 PM ben leinfelder

include person's full name in the JWT returned from /token

8991 11/20/2014 09:00 AM Jing Tao

Fixed a bug that the reindex of data objects may index an archived data object.

8986 11/19/2014 04:59 PM Jing Tao

Fixed a bug that the solr index of data files doesn't reflect the change of access control.

8983 11/19/2014 12:52 PM ben leinfelder

[merge from 2.4 branch] use solr schema upgrader for 2.4.2 release -- need to replace the solr schema to include geohash fields

8977 11/19/2014 12:17 PM ben leinfelder

remove AnnotatorService completely - was moved to cn-index-processor

8972 11/17/2014 09:29 PM ben leinfelder

let metacat-index lookup annotations for indexing rather than the metacat "reindex" action.

8971 11/17/2014 04:30 PM Jing Tao

Add delete log for data objects on CNs.

8964 11/14/2014 11:20 AM ben leinfelder

only index non-empty comment text

8963 11/14/2014 11:13 AM ben leinfelder

index both tags and text from annotateit.org

8961 11/13/2014 05:59 PM ben leinfelder

query by consumerKey until the pid search facets are fully supported on annotateit.org

8959 11/10/2014 02:22 PM Jing Tao

During the replication, the remote content will be saved without alteration.

8953 11/05/2014 01:42 PM ben leinfelder

allow per-document reindexing to be initiated by any user (to support third-party annotations)

8948 10/31/2014 05:36 PM Jing Tao

Write the input stream into the file system without alteration in dataone create and update methods.

8946 10/31/2014 05:09 PM ben leinfelder

look up annotations when reindexing a given pid. still very much a prototype in that we are looking up annotations from an external annotator-store. TODO: add pid filtering to query when annotateit.org supports it (pending upgrade on their site).

8910 10/17/2014 05:02 PM ben leinfelder

use http://tools.ietf.org/rfc/rfc3023 spec for conformsTo property. use the full xpath for EML dataTable and attribute selectors

8903 10/15/2014 04:34 PM Jing Tao

Added the code to inform users the pid was deleted in the NotFound exception.

8901 10/14/2014 06:11 PM Jing Tao

Added the code to check if a not-found object was deleted in the isAuthorized method.

8899 10/14/2014 06:01 PM Jing Tao

Move the code to get the object in front of the method to get the system metadata.

8896 10/14/2014 01:44 PM Jing Tao

Add a utility method for determine if there is a delete event for a given id.

8889 10/10/2014 02:16 PM Jing Tao

Removed the method which had the byte array attribute.

8887 10/10/2014 02:10 PM Jing Tao

Remove the system metadata for data objects.

8884 10/10/2014 02:01 PM Jing Tao

change the way to delete the solr index of a resource map.

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

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.

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.

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

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

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

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

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

update to use v2 types for indexing

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.

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.

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

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

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.

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.

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

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

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.

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

8757 04/29/2014 04:54 PM ben leinfelder

first pass at direct EML->semantic index method. Still produces an RDF model, but does not persist it in Metacat, only in the triplestore. Allows us to re-run without adding stale RDF to the MN store.

8749 04/28/2014 03:30 PM Jing Tao

Store the cn url in the backup.

8748 04/24/2014 01:28 PM ben leinfelder

switch to use FIleUpload instead of O'Reilly COS library for handling chunked file uploads. https://projects.ecoinformatics.org/ecoinfo/issues/6517

8747 04/24/2014 01:26 PM ben leinfelder

forgot to check in the actual class: first pass at allowing admins to update DOI registration. This only acts on EML objects at the moment and is meant to illustrate one mechanism for updating the DOIs. https://projects.ecoinformatics.org/ecoinfo/issues/6530

8746 04/23/2014 12:35 PM ben leinfelder

first pass at allowing admins to update DOI registration. This only acts on EML objects at the moment and is meant to illustrate one mechanism for updating the DOIs. https://projects.ecoinformatics.org/ecoinfo/issues/6530

8745 04/23/2014 10:19 AM ben leinfelder

correct the ORE lookup query syntax and add junit assertion to check that it continues to function as expected. https://projects.ecoinformatics.org/ecoinfo/issues/6529

8744 04/22/2014 03:38 PM ben leinfelder

index the ORE after we submit the metadata for indexing. https://projects.ecoinformatics.org/ecoinfo/issues/6520

8743 04/22/2014 11:43 AM ben leinfelder

include BioPortal lookup for Entity matches using the data table description. TODO: only associate measurements to the entity observation if they apply.

8739 04/17/2014 02:19 PM Jing Tao

Index the document after it has been inserted.

8738 04/17/2014 02:18 PM Jing Tao

Index the document after document is written to the db.

8724 04/02/2014 03:36 PM ben leinfelder

check for null entities and/or attributes (typically when otherEntity is being used in EML).

8723 04/02/2014 03:35 PM ben leinfelder

remove extra space in log message

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