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# Date Author Comment
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.

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.

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

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.

8707 03/21/2014 01:21 PM ben leinfelder

include SSLVerify* directives for client certificates and a pointer for getting the DataONE chain files.

8704 03/14/2014 03:33 PM Jing Tao

Remove the code to lookup alias dn in the getGroups method.

8703 03/14/2014 01:16 PM Jing Tao

Rather than directly to modify the env, we use context.addToEnv.
This fixed a bug in non-tls env, the alias log-in doesn't work.

8702 03/14/2014 10:59 AM ben leinfelder

first pass at generating annotations from EML attribute information. uses the OpenAnnotation model that the metacat-index tests assume which allows us to populate dynamic index fields for the annotation class[es]. There is still much to be done with finding appropriate concepts for each attribute. https://projects.ecoinformatics.org/ecoinfo/issues/6256

8700 03/06/2014 03:28 PM Lauren Walker

Edited the replicaPolicies script to print out a list of IDs that have a different authoritative member node, the number of successes, and failures at the end.

8699 03/05/2014 11:46 AM Lauren Walker

Add comments to bash script to explain its function and dependencies

8698 03/05/2014 11:30 AM Lauren Walker

Added a bash script to call /replicaPolicies/{pid} via the DataONE API for all objects in a MN or a list of ids.

8689 03/03/2014 03:41 PM ben leinfelder

support content from all serverLocations when summarizing entity info (semtools)

8678 02/28/2014 04:06 PM ben leinfelder

allow "+" in solr query syntax. https://projects.ecoinformatics.org/ecoinfo/issues/6435

8670 02/26/2014 10:49 PM ben leinfelder

include read events when re-indexing obsoleted objects. https://projects.ecoinformatics.org/ecoinfo/issues/6424

8664 02/26/2014 04:19 PM Jing Tao

Set the userManagementURL property.

8656 02/26/2014 07:55 AM ben leinfelder

update to use 2.4.1 so the trunk has all artifacts for upgrades.

8655 02/26/2014 07:47 AM ben leinfelder

simple upgrade scripts for version 2.4.1

8652 02/25/2014 07:46 PM Jing Tao

In the authenticate method, if metacat can't get user info, the login still can be successful.

8651 02/25/2014 06:39 PM Jing Tao

change a log information.

8650 02/25/2014 06:31 PM Jing Tao

In the getALiasedName method, the referral set to ignore. Since the alias name is the local referral, we need to set it to ignore.

8647 02/25/2014 04:14 PM ben leinfelder

recursively submit obsoleted objects for indexing when instructed. https://projects.ecoinformatics.org/ecoinfo/issues/6424

8646 02/24/2014 04:30 PM ben leinfelder

First pass at a class for summarizing attribute information for analysis. (semtools) https://projects.ecoinformatics.org/ecoinfo/issues/6256

8642 02/21/2014 03:12 PM ben leinfelder

merge recent upgrade changes from 2.4 branch

8634 02/21/2014 11:20 AM ben leinfelder

look up guid when done setting access by docid so we can sync and refresh accesspolicy on MN and CN.

8633 02/21/2014 10:50 AM ben leinfelder

additional logging for set access

8630 02/21/2014 09:05 AM Peter Slaughter

get guid from online id for call to SyncAccessPolicy

8629 02/21/2014 09:02 AM Peter Slaughter

setAccessAction: get guid from passed in id for calls to SyncAccessPolicy, HazelcastService.refreshSystemMetadataEntry

8628 02/20/2014 04:16 PM ben leinfelder

example of how we can look up pid (guid) given a metacat docid.

8626 02/20/2014 01:57 PM ben leinfelder

remove sensorML from the catalog since we don't actually ship it (yet?)

8617 02/19/2014 02:35 PM Chris Jones

Add in Darwin Core schema support into xml_catalog, and insert it on upgrade as well. The schemas are cached in lib/schema/dwc, and Matt and Ben noted that the tdwg_basetypes.xsd and tdwg_dwctypes.xsd are part of the same namespace, but are xs:include'd rather than imported via namespace.

8614 02/19/2014 12:54 PM ben leinfelder

include a few tests for isEqual method. https://projects.ecoinformatics.org/ecoinfo/issues/6407

8610 02/18/2014 02:48 PM Peter Slaughter

Change isEqual to private so it can be used by test suite

8609 02/17/2014 07:11 AM Chris Jones

Add DataONE, Dublin Core, and Dryad schemas during the 2.4.0 upgrade, and be sure to remove the appropriate entries before inserting to avoid duplicate rows.

8608 02/17/2014 06:53 AM Chris Jones

Add schema support for the DataONE, dublin Core, and Dryad schemas. Schemas get downloaded into lib/schema priior to jar and dist targets, and get loaded into xml_catalog on installation.

8607 02/14/2014 03:43 PM ben leinfelder

move the postgres changes to the oracle version -- update note about not attempting to restore because no Oracle MNs exist.

8606 02/14/2014 03:20 PM ben leinfelder

do not include "sm" alias in the SET clause.

8605 02/14/2014 03:19 PM ben leinfelder

allow statements starting with 'WITH'

8604 02/14/2014 02:56 PM ben leinfelder

comment out the select statements so they do not run during real upgrade.

8601 02/13/2014 03:12 PM ben leinfelder

loosen the restriction on which archive flags we set to false -- if we have an obsoleted_by value then it need not be marked as archived.

8600 02/13/2014 02:44 PM ben leinfelder

add [partial] upgrade to the oracle script -- does not look for any records that the CN deleted because there are no Oracle-backed MNs at this time.

8599 02/13/2014 02:08 PM ben leinfelder

add comment (and commented out code) for possibly inspecting the /dirtySysMeta call for archive=true flag. https://projects.ecoinformatics.org/ecoinfo/issues/6417

8596 02/13/2014 12:01 PM ben leinfelder

only index event information for known events. https://projects.ecoinformatics.org/ecoinfo/issues/6346

8595 02/13/2014 11:12 AM Peter Slaughter

call getDescription on cn.setaccesspolicy service failure

8594 02/12/2014 01:56 PM ben leinfelder

make all objects in a package publicly readable when published. https://projects.ecoinformatics.org/ecoinfo/issues/6415

8593 02/11/2014 02:19 PM Jing Tao

Add the code to check if the docid contains the whitespaces in the handleInsertOrUpdate, handleUpload and handleInsertMultipartInsertAction methods.

8592 02/11/2014 02:15 PM Peter Slaughter
8591 02/11/2014 01:43 PM ben leinfelder

make all package contents publicly readable when publishing with a DOI. https://projects.ecoinformatics.org/ecoinfo/issues/6415

8590 02/11/2014 01:29 PM Peter Slaughter

Run syncAll in a single thread so admin config UI doesn't freeze