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From 02/28/2014 to 03/29/2014

03/28/2014

03:51 PM Revision 8716 (metacat): 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.
ben leinfelder

03/27/2014

04:55 PM Bug #6488 (Feedback): Comply with DataONE MN.query() REST endpoint specifications.
Committed to Metacat trunk for testing. Should support query URLs with and without leading "?" now. ben leinfelder
04:52 PM Bug #6488: Comply with DataONE MN.query() REST endpoint specifications.
The DataONE MN API docs indicate that the {query} parameter should be delimited with a "?". The Metacat MN implementa... ben leinfelder
04:50 PM Bug #6488 (Closed): Comply with DataONE MN.query() REST endpoint specifications.
ben leinfelder
04:54 PM Revision 8715 (metacat): 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
ben leinfelder

03/26/2014

04:05 PM Revision 8714 (metacat): 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.
ben leinfelder
03:10 PM Revision 8713 (metacat): remove my api key. oops
ben leinfelder
03:02 PM Revision 8712 (metacat): add comment/pointer to BioPortal annotation service.
ben leinfelder
03:00 PM Revision 8711 (metacat): 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
ben leinfelder

03/24/2014

04:17 PM Revision 8710 (metacat): Add xpointer FragmentSelectors to each annotation.
Split attribute label into tokens to attempt matching to OBOE concepts. ben leinfelder

03/23/2014

12:11 AM Revision 8709 (metacat): include code to generate random annotations for UI testing. Effective, but can be confusing to see so many unrelated concepts on duplicate EML packages.
ben leinfelder

03/21/2014

05:07 PM Revision 8708 (metacat): include characteristic_sm field with SPARQL query
ben leinfelder
01:21 PM Revision 8707 (metacat): include SSLVerify* directives for client certificates and a pointer for getting the DataONE chain files.
ben leinfelder

03/20/2014

11:48 AM Bug #6475 (Closed): CN.create() implementation sets SystemMetadata.archived=false
ben leinfelder

03/19/2014

04:02 PM Bug #6473 (Closed): Problem in activating a new generated ldap account
"^x" is part of the hash string.
It seem user successfully activated his account:
Hi Jing,
I was able to activ...
Jing Tao
01:08 PM Bug #6473: Problem in activating a new generated ldap account
What is this at the end of the hash?... ben leinfelder
12:41 PM Bug #6473 (Closed): Problem in activating a new generated ldap account
Zach Nelson reported there was an issue to activate his account:
hash string Kv9aZuLOdu$tO3 doesn't match our reco...
Jing Tao
01:26 PM Revision 8706 (metacat): 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.
Lauren Walker

03/18/2014

12:18 PM Revision 8705 (metacat): Edited the docs to incude more details about creating a custom theme
Lauren Walker

03/14/2014

03:35 PM Bug #6466: Groups Assignment after making some accounts aliases
I modified the code so metacat wouldn't change the group assignment after the dn was aliased.
So it will work as ...
Jing Tao
01:31 PM Bug #6466 (Closed): Groups Assignment after making some accounts aliases
Background: the merge of our ldap trees, the groups information wouldn't be touched.
Before the merge, the uid=ben...
Jing Tao
03:33 PM Revision 8704 (metacat): Remove the code to lookup alias dn in the getGroups method.
Jing Tao
01:16 PM Revision 8703 (metacat): 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. Jing Tao
10:59 AM Revision 8702 (metacat): 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
ben leinfelder
10:55 AM Revision 8701 (metacat): 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
ben leinfelder

03/12/2014

12:13 PM Task #6433: Test Metacat on tomcat7
Update: after Aaron downgraded its tomcat to 6, morpho 10.1 still has the frozen issue. Jing Tao

03/06/2014

03:28 PM Revision 8700 (metacat): 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.
Lauren Walker

03/05/2014

11:46 AM Revision 8699 (metacat): Add comments to bash script to explain its function and dependencies
Lauren Walker
11:34 AM Feature #6445 (New): Alter replicaPolicies.sh so that the script will iterate over pages of objects instead of updating the count in the code manually
Lauren Walker
11:30 AM Revision 8698 (metacat): Added a bash script to call /replicaPolicies/{pid} via the DataONE API for all objects in a MN or a list of ids.
Lauren Walker

03/04/2014

12:09 PM Story #6440 (Closed): Keep DOI registrations current and resolvable
We have used a few different DOI registration approaches on the KNB:
* bulk load of all historical content (metadata...
ben leinfelder
10:23 AM Revision 8697 (metacat): Add the test class for the pisco account.
Jing Tao
10:22 AM Revision 8696 (metacat): Remove the test method for the pisco account since it maybe fails because of the fire wall issue.
Jing Tao
09:48 AM Revision 8695 (metacat): Add the login test of the pisco account.
Jing Tao
09:47 AM Revision 8694 (metacat): Add the pisco account.
Jing Tao

03/03/2014

04:33 PM Revision 8693 (metacat): Do a more thorough check that the characteristic annotation was successfully indexed as expected (semtools)
ben leinfelder
03:56 PM Revision 8692 (metacat): switch to the OpenAnnotation (OA) model for annotating datapackages with measurements/characteristics (semtools)
ben leinfelder
03:55 PM Revision 8691 (metacat): switch to the OpenAnnotation (OA) model for annotating datapackages with measurements/characteristics (semtools)
ben leinfelder
03:54 PM Revision 8690 (metacat): switch to the OpenAnnotation (OA) model for annotating datapackages with measurements/characteristics (semtools)
ben leinfelder
03:41 PM Revision 8689 (metacat): support content from all serverLocations when summarizing entity info (semtools)
ben leinfelder
09:30 AM Revision 8688 (metacat): bump the poms to 2.4.2
ben leinfelder
07:03 AM Story #6437: Upgrade to SOLR 4 or 5
Assigning to Peter for now -- seems he will be involved with SOLR for stats service and has already experimented with... ben leinfelder
06:52 AM Story #6437 (New): Upgrade to SOLR 4 or 5
We'd like to make use of new key features in SOLR 4:
* spatial indexing/filters
* geohash (for heatmaps/displaying ...
ben leinfelder

03/02/2014

06:26 PM Revision 8685 (metacat): merge from trunk: these open layers resources were not committed!
ben leinfelder

03/01/2014

03:28 PM Revision 8682 (metacat): merge from branch: more notes on 2.4.1 release in the readme
ben leinfelder

02/28/2014

04:39 PM Revision 8680 (metacat): Add a pisco test account.
Jing Tao
04:30 PM Bug #6424 (Closed): Obsoleted objects not marked in index
Now re-indexing the obsoleted revision[s] of any new objects that are added with update commands. Note that we do not... ben leinfelder
04:08 PM Bug #6435 (Closed): Solr queries with certain URL-encoded characters are decoded twice
Added special case for "+" so that when we use the SOLRJ parser it does not encode the intended "+" into a space. ben leinfelder
02:45 PM Bug #6435 (Closed): Solr queries with certain URL-encoded characters are decoded twice
The one character I know is a problem is + (%2B). When %2B is sent in a Solr query, Metacat seems to decode it twice ... Lauren Walker
04:06 PM Revision 8678 (metacat): allow "+" in solr query syntax. https://projects.ecoinformatics.org/ecoinfo/issues/6435
ben leinfelder
01:53 PM Revision 8677 (metacat): Add a comment to warn the users not to change the password file path to a production one since it will be deleted.
Jing Tao
01:11 PM Revision 8675 (metacat): clear test password file so subsequent runs will not fail -- tests assume blank file to begin with.
ben leinfelder
10:54 AM Task #6433 (Closed): Test Metacat on tomcat7
Aaron from UW installed a Metacat instance on tomcat7 (Ubuntu 12). But a user can't log in when a Morpho connected it... Jing Tao
 

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