From 03/09/2014 to 04/07/2014


01:26 PM Bug #6498 (Resolved): entryForm.js throwing errors in IE 8
Added a check for undefined and null objects in the sortTagWithAttributeName function Lauren Walker
01:25 PM Revision 8728 (metacat): Check for undefined and null elements to avoid errors in IE 8 and earlier in the registry entry form JS
Lauren Walker


04:06 PM Bug #6498 (Resolved): entryForm.js throwing errors in IE 8
I am getting an error in the sortTagWithAttributeName function - "Object is required" and the entry form will not sub... Lauren Walker
12:03 PM Bug #6496 (Resolved): <span> HTML element is never closed in the Registry HTML, causing errors in IE8
Lauren Walker
11:45 AM Bug #6496 (Resolved): <span> HTML element is never closed in the Registry HTML, causing errors in IE8
There is a span element in the Abstract area of the registry HTML sent from Metacat to MetacatUI which does not have ... Lauren Walker
12:03 PM Revision 8727 (metacat): Close a <span> HTML tag in the entry form MetacatUI template to avoid errors in older browsers
Lauren Walker


09:44 AM Revision 8726 (metacat): The package libdigest-sha1-perl was removed from ubuntu 12.04. We have to install it from cpan.
Jing Tao


03:40 PM Revision 8725 (metacat): 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.
ben leinfelder
03:36 PM Revision 8724 (metacat): check for null entities and/or attributes (typically when otherEntity is being used in EML).
ben leinfelder
03:35 PM Revision 8723 (metacat): remove extra space in log message
ben leinfelder
03:35 PM Revision 8722 (metacat): handle null Boolean in SM.archived field
ben leinfelder


04:04 PM Revision 8721 (metacat): 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.
ben leinfelder
03:25 PM Revision 8720 (metacat): use Matthew Jones for test creator since he has an ORCID in their staging environment.
ben leinfelder
12:31 PM Revision 8719 (metacat): augment annotation indexing test/sample to include orcid annotation. ben leinfelder
11:11 AM Revision 8718 (metacat): attribute the datapackage to the creator (using orcid if we can find it). ben leinfelder
10:31 AM Revision 8717 (metacat): add test for BioPortal annotator service.
ben leinfelder


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: and also some semtools tasks.
ben leinfelder


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.
ben leinfelder


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.
ben leinfelder


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


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


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


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


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


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


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.
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.
ben leinfelder


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

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