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

# Date Author Comment
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.

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

additional logging for set access

8632 02/21/2014 10:35 AM ben leinfelder

add a few more checks while debugging test

8631 02/21/2014 10:04 AM Peter Slaughter

Use D1client for communication with CN (for integration test)

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.

8627 02/20/2014 03:53 PM Lauren Walker

Changed some of the font and stlyes of the metacat docs for easier reading and fixed a big where the metacat admin "configure" buttons were not working

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

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

8625 02/20/2014 01:37 PM ben leinfelder

add test for invalid dryad content -- should be rejected because it is not schema valid.

8624 02/20/2014 12:42 PM ben leinfelder

clean up dryad test doc - only use D1 api. https://projects.ecoinformatics.org/ecoinfo/issues/6419

8623 02/20/2014 12:25 PM ben leinfelder

add generated diagrams for stats proposal -- seems to be our practice for other documentation pages.

8622 02/20/2014 10:35 AM ben leinfelder

test for inserting dryad instance doc. https://projects.ecoinformatics.org/ecoinfo/issues/6419

8621 02/19/2014 05:04 PM Peter Slaughter

add test to check sync of access policies of data object referenced in EML 2.0.1 docs

8620 02/19/2014 04:43 PM ben leinfelder

initial basic test of inserting dryad metadata. NOTE: uses metacat api, not dataone api. https://projects.ecoinformatics.org/ecoinfo/issues/6419

8619 02/19/2014 03:30 PM ben leinfelder

do not delete the lib/schema directory on fullclean now that we actually have content in there in SVN. https://projects.ecoinformatics.org/ecoinfo/issues/6419

8618 02/19/2014 02:52 PM Chris Jones

Add an example Dryad Metadata Profile instance document to test inserts of this schema type.

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.

8616 02/19/2014 02:14 PM Chris Jones

In lieu of pulling schemas from URL endpoints for dataONE, Darwin core, and Dryad, we're caching them in Metacat so we have stable copies. Remove the ant targets used to pull them.

8615 02/19/2014 02:11 PM Chris Jones

Add the three Darwin Core schemas required by the Dryad Metadata Profile (via imports).

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

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

8613 02/19/2014 08:49 AM Chris Jones

Add cached versions of the DataONE, Dryad, Dublin core, and Darwin Core schemas to Metacat. Remove schemaLocation attributes so that we rely on the local catalog and don't use (potentially changing) URL endpoints.

8612 02/18/2014 04:50 PM Peter Slaughter

Use client.MetacatClient instance for all metacat api calls

8611 02/18/2014 02:49 PM Peter Slaughter

Test syncing of access policies when updated with legacy metacat api

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.

8603 02/14/2014 11:49 AM ben leinfelder

use rangeOfDates | singleDateTime to populate the beginDate and endDate index fields. https://projects.ecoinformatics.org/ecoinfo/issues/6285

8602 02/14/2014 09:46 AM ben leinfelder

switch to ezid 1.0.0 release and pull from dev-testing.dataone.org Maven repo.

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

8598 02/13/2014 01:02 PM ben leinfelder

use '/var/metacat/users/password.xml' as the default password file path to: a) indicate it is for managing users and b) that it uses XML serialization. https://projects.ecoinformatics.org/ecoinfo/issues/6320

8597 02/13/2014 12:58 PM ben leinfelder

add a link to the authentication interface page so users can more easily find information on how to add users to the auth file.

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