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# Date Author Comment
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.

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

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.

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.

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

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

allow statements starting with 'WITH'

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

8589 02/11/2014 11:05 AM Chris Jones

Change CnodeService.archive() to no longer broadcast MN.archive() calls to all of the replica MNs of a pid, but rather broadcast MN.systemMetadataChanged().

8588 02/10/2014 04:17 PM ben leinfelder

allow utf-8 user first/last names to be used in responses for: login, logout, validatesession, getprincipals.

8585 02/10/2014 11:52 AM ben leinfelder

Couple modifications:
-use "pid" throughout so as not to confuse docids and pids
-ensure any failures in the set do not prevent synching for other pids in the set

8579 02/07/2014 12:40 PM Peter Slaughter

sync pids of <distribution><online> data objects with CN when their access rules change in EML 2.0.* <additionalMetadata>

8575 02/06/2014 02:42 PM Jing Tao

Modified the usage.

8566 02/05/2014 01:55 PM ben leinfelder

do not set sm.archived=true when generating system metadata for objects that come in via the old Metacat API.

8564 02/05/2014 01:24 PM Jing Tao

Modify the usage message.

8563 02/05/2014 09:43 AM Jing Tao

Use a DN name for the group in the usage message printout.

8561 02/04/2014 02:25 PM Peter Slaughter

Fixed bug where sync'ing not working when CN had more access rules than MN

8560 02/04/2014 02:24 PM Peter Slaughter

Sync access policy between MN -> CN when access rules are updated in EML 2.1+ for data object

8556 02/03/2014 03:35 PM Jing Tao

Remove code to add the organzation in the search filter. This is not necessary since we use the dn as the search base. The code was not actually used but caused some problem.

8553 02/03/2014 02:52 PM ben leinfelder

can only log events with a valid localId.

8548 01/31/2014 02:49 PM Jing Tao

Add a note to let user know he/she should use single quotes to surround the hashed password.

8547 01/31/2014 02:35 PM ben leinfelder

edit some of the user management phrases. use UTF-8 for all returned XML. https://projects.ecoinformatics.org/ecoinfo/issues/6320

8535 01/24/2014 06:56 PM Jing Tao

Fixed a bug that AuthFile constructor didn't read the new value of the password file path from the metacat.properties.

8534 01/24/2014 05:17 PM Jing Tao

Add the code to handle a runtime exception.

8532 01/24/2014 04:29 PM Jing Tao

Add code to persist the properties in the group 3.

8530 01/23/2014 05:20 PM Jing Tao

If the user doesn't exist in the password file, the auth configuration will give an error.

8524 01/22/2014 05:33 PM Jing Tao

Add a method to get the user management url.

8511 01/21/2014 09:58 AM Peter Slaughter

Fixed Exception declaration problem

8510 01/21/2014 08:59 AM Peter Slaughter

minor changes to error msgs

8509 01/21/2014 08:41 AM Peter Slaughter

When a docid's access policy is modified with metacat native api, update CN with the new access policy

8504 01/15/2014 05:33 PM Jing Tao

Add a note to the administrator to tell the name format of groups and users.

8495 01/14/2014 12:49 PM ben leinfelder

fix typos/compilation

8493 01/13/2014 01:41 PM Jing Tao

Change to use AuthFile constructor.

8492 01/13/2014 01:39 PM Jing Tao

Add code to check if groups is null.

8491 01/12/2014 04:48 PM Peter Slaughter

Sync access policy between mn -> cn in case where metacat native ui being used to update ap on mn

8489 01/10/2014 02:35 PM Jing Tao

Consolidate the user/group utitlities code.

8488 01/10/2014 10:50 AM Jing Tao

Change the element name in the user from "group" to "memberof".
Fixed a bug that in groupadd.

8487 01/09/2014 10:31 PM Jing Tao

Add methods to handle modify user's attributes.

8486 01/09/2014 09:16 PM Jing Tao

Complete the method - handleUseradd.

8485 01/09/2014 06:25 PM Jing Tao

Add code to handle useradd command.

8484 01/09/2014 04:39 PM Jing Tao

Fixed a bug that showing illegal options in the groupadd command.

8481 01/09/2014 04:17 PM Jing Tao

Add a main method which will be used in the command line users management tool.

8478 01/09/2014 09:15 AM Jing Tao

Add the code to handle the organization name.

8476 01/08/2014 05:17 PM Jing Tao

Add the getUserInfo method.

8475 01/08/2014 04:33 PM Jing Tao

Add the common name, organization name and email into the getprincipal method.

8474 01/08/2014 04:32 PM Jing Tao

Add some contants.

8473 01/08/2014 04:04 PM Jing Tao

Add the description in the getGroups methods.

8471 01/08/2014 02:58 PM Jing Tao

Add the common name and email address information into the getUsers method.

8469 01/08/2014 11:06 AM Jing Tao

Fixed a bug that the method addUser didn't set password.

8465 01/07/2014 05:03 PM Jing Tao

Change the code to use BCryptHash to protect password.

8464 01/07/2014 01:56 PM ben leinfelder

Unify solr indexing with an IndexTask that is added to the queue -- allows us to send more than just the systemMetadata to the indexer. Initially this is for READ event counts for each document. https://projects.ecoinformatics.org/ecoinfo/issues/6346

8463 01/06/2014 02:57 PM Jing Tao

Add code to get user info and group info for an alias.

8461 12/24/2013 01:48 PM Jing Tao

Add the code to handle the login action if it is an alias.

8460 12/23/2013 01:29 PM Jing Tao

Add the methods to get the aliased dn through non-tls or tls.

8459 12/20/2013 05:03 PM Jing Tao

Add a method to get the aliasedDn.

8454 12/20/2013 07:46 AM Chris Jones

On changes to system metadata in CNodeService and DocumentImpl, increment the serialVersion.

8452 12/19/2013 04:15 PM Peter Slaughter

(task #6297): sync pid(s) access policy between member node and coordinating node

8450 12/19/2013 02:35 PM Chris Jones

Change CNodeService's archive() and delete() methods to only update Member Nodes in the replica list (not CNs!), since calling CN.archive() again would cause an infinite loop. Thanks for catching this Ben.

8444 12/19/2013 09:35 AM Chris Jones

Update CNodeService.delete() and .archive() to handle situations where the pid is of formatType DATA, and therefore are not registered in the identifier table, and caused NotFound exceptions. For DATA objects, we just update the system metadata now, and for all other objects (METADATA, RESOURCE), we continue to use super.{delete()|archive()}. Also, log the delete/archive into the event log....

8439 12/19/2013 08:13 AM Chris Jones

Remove the broadcastSystemMetadataChange() method since it was a duplicate of notifyReplicaNodes(). Consolidated now.

8438 12/17/2013 05:22 PM Jing Tao

Add some log information.

8437 12/17/2013 09:42 AM Lauren Walker

retrieve the given file names (entityName) of the data files from the EML and use those for our file names in the BagIt content.

8436 12/13/2013 03:42 PM Lauren Walker

Change the BagIt file names to the pid+resource type. Create new Files instead of createTempFile to avoid the randomly generated numbers in the name.

8434 12/12/2013 04:43 PM Jing Tao

Add a description element for the group.

8433 12/12/2013 01:49 PM Jing Tao

Change the user id from the name to the uid.

8431 12/11/2013 04:34 PM Jing Tao

Add the method to get the principals.

8429 12/11/2013 11:44 AM Jing Tao

Add the methods about reset and change password.