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

# Date Author Comment
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.

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.

8756 04/29/2014 04:52 PM ben leinfelder

allow multivalued fields to be indexed using the "fields" pass through.

8755 04/29/2014 04:47 PM Jing Tao

Remove the attribute disable from the update button if it has been submitted.

8754 04/29/2014 03:31 PM Jing Tao

The image which has the default values.

8753 04/29/2014 03:13 PM Jing Tao

Add a new screen shot which contains the cn url.

8752 04/28/2014 04:54 PM Jing Tao

Localized the file which doesn't have the bean for dataUrl.

8751 04/28/2014 03:38 PM Jing Tao

Add the cn url.

8750 04/28/2014 03:37 PM Jing Tao

Add the text field for the cn url.

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.

8742 04/21/2014 11:12 AM ben leinfelder

recompile with java 1.6 for compatibility with our servers.

8741 04/18/2014 05:29 PM Jing Tao

Remove the reference to the bean eml.fileID.

8740 04/17/2014 05:22 PM ben leinfelder

use 1.5.1 tag for hudson to build metacat ui (for KNB deployment)

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.

8737 04/16/2014 02:28 PM Jing Tao

Use the ecogrid-1.2.3 branch which will be the next release.

8736 04/15/2014 09:36 AM Jing Tao

Remove the bean named eml.fileID which used the ResolveSolrField class.

8735 04/14/2014 02:58 PM ben leinfelder

calculate geohash_3 to three places (typo)

8734 04/14/2014 02:55 PM ben leinfelder

use NSEW for the bounding box geohash calculation from EML - all versions

8733 04/14/2014 02:50 PM ben leinfelder

up the field count to 111 to include the 9 geohash fields.

8732 04/14/2014 02:07 PM Peter Slaughter

Using 1.3.0-SNAPSHOT from d1_cn_index_processor

8731 04/14/2014 01:34 PM Peter Slaughter

Add fields for geohashes

8730 04/14/2014 01:33 PM Peter Slaughter

Add beans to support geohashes

8729 04/14/2014 01:33 PM Peter Slaughter

Add beans to support geohashes

8728 04/07/2014 01:25 PM Lauren Walker

Check for undefined and null elements to avoid errors in IE 8 and earlier in the registry entry form JS

8727 04/04/2014 12:03 PM Lauren Walker

Close a <span> HTML tag in the entry form MetacatUI template to avoid errors in older browsers

8726 04/03/2014 09:44 AM Jing Tao

The package libdigest-sha1-perl was removed from ubuntu 12.04. We have to install it from cpan.

8725 04/02/2014 03:40 PM ben leinfelder

add "test" for generating annotations based on the entity/attribute details of a datapackage. This iterates through all current EML revisions and either updates or creates annotations based on what it finds. It does add content to your metacat deployment (RDF files) but it can be safely re-run when each time we change our annotation algorithm.

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

8722 04/02/2014 03:35 PM ben leinfelder

handle null Boolean in SM.archived field

8721 03/31/2014 04:04 PM ben leinfelder

include sample data package for generating annotations. This is the classic Datos Meteorologicos set, but with Matthew Jones as the creator so that we can look up his ORCID in their sandbox environment. https://projects.ecoinformatics.org/ecoinfo/issues/6267

8720 03/31/2014 03:25 PM ben leinfelder

use Matthew Jones for test creator since he has an ORCID in their staging environment.

8719 03/31/2014 12:31 PM ben leinfelder

augment annotation indexing test/sample to include orcid annotation. https://projects.ecoinformatics.org/ecoinfo/issues/6267
https://projects.ecoinformatics.org/ecoinfo/issues/6423

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.

8708 03/21/2014 05:07 PM ben leinfelder

include characteristic_sm field with SPARQL query

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

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

8706 03/19/2014 01:26 PM Lauren Walker

Added an explanation of "metacat context" to the Metacat Themes docs based on questions asked by an actual user following our instructions in the docs.

8705 03/18/2014 12:18 PM Lauren Walker

Edited the docs to incude more details about creating a custom theme

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

8701 03/14/2014 10:55 AM ben leinfelder

switch to index standard since it is more likely we will be able to determine this from our existing EML attribute information. https://projects.ecoinformatics.org/ecoinfo/issues/6253

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.

8697 03/04/2014 10:23 AM Jing Tao

Add the test class for the pisco account.

8696 03/04/2014 10:22 AM Jing Tao

Remove the test method for the pisco account since it maybe fails because of the fire wall issue.

8695 03/04/2014 09:48 AM Jing Tao

Add the login test of the pisco account.

8694 03/04/2014 09:47 AM Jing Tao

Add the pisco account.

8693 03/03/2014 04:33 PM ben leinfelder

Do a more thorough check that the characteristic annotation was successfully indexed as expected (semtools)

8692 03/03/2014 03:56 PM ben leinfelder

switch to the OpenAnnotation (OA) model for annotating datapackages with measurements/characteristics (semtools)

8691 03/03/2014 03:55 PM ben leinfelder

switch to the OpenAnnotation (OA) model for annotating datapackages with measurements/characteristics (semtools)

8690 03/03/2014 03:54 PM ben leinfelder

switch to the OpenAnnotation (OA) model for annotating datapackages with measurements/characteristics (semtools)

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

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

8688 03/03/2014 09:30 AM ben leinfelder

bump the poms to 2.4.2

8685 03/02/2014 06:26 PM ben leinfelder

merge from trunk: these open layers resources were not committed!

8682 03/01/2014 03:28 PM ben leinfelder

merge from branch: more notes on 2.4.1 release in the readme

8680 02/28/2014 04:39 PM Jing Tao

Add a pisco test account.

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

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

8677 02/28/2014 01:53 PM Jing Tao

Add a comment to warn the users not to change the password file path to a production one since it will be deleted.

8675 02/28/2014 01:11 PM ben leinfelder

clear test password file so subsequent runs will not fail -- tests assume blank file to begin with.

8673 02/27/2014 12:50 PM ben leinfelder

use local release of OpenLayers api so that it works over https with our secure deployments (openlayers.org does not offer the api from their servers using https).

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

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

8668 02/26/2014 05:05 PM Jing Tao

Change the loginForm attributes which is generated by the logout action.

8665 02/26/2014 04:19 PM Jing Tao

Use the userManagement variable.

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

Set the userManagementURL property.

8662 02/26/2014 03:24 PM Jing Tao

make the loginForm and logoutForm the onSubmit "false" and the method "post".

8659 02/26/2014 10:29 AM ben leinfelder

remove metacarta map layer -- their WMS service is no longer responding.

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.

8649 02/25/2014 05:44 PM Jing Tao

Change the password.

8648 02/25/2014 04:32 PM ben leinfelder

test that obsoleted objects remain indexed, but are marked as obsoleted. https://projects.ecoinformatics.org/ecoinfo/issues/6424

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

8644 02/21/2014 03:33 PM ben leinfelder

add note about archive correction

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

merge recent upgrade changes from 2.4 branch

8636 02/21/2014 01:13 PM ben leinfelder

use UI 1.4 branch pre 2.4 branch

8635 02/21/2014 11:35 AM ben leinfelder

uncomment other tests in suite.

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.