Metacat

change the hazelcast group name to be the default "metacat" instance so that the metacat-index tests pass without additional local configuration, at least when running a default metacat deployment.

do not set archived=false for all CN.create calls. The CN will use create() even harvesting content that is new to it and needs to handle already-archived content. https://projects.ecoinformatics.org/ecoinfo/issues/6475

cache the imported models to avoid timeouts from remote hosts (or being locked out for too many requests in a given time period).

process all the returned annotation suggestions until we find one that is appropriately located in the subclass hierarchy for the given superclass.

use in-memory TDB dataset for querying annotations for indexing -- this comes with the same reasoning capabilities as the directory-based one, but has the benefit of not filling the directory with triples that will not be used again. prepping for d1 AHM

when indexing annotations directly, just use an in-memory triple store rather than TDB since we remove each graph as it is processed (and my TDB instance would get into the multi-GB range with a few runs, even if I removed the old models)

redirect "short form" metacat read URIs to the the new Metacat UI using the configured UI context. This translates the docid -> pid to use the correct identifier for the correct service. https://projects.ecoinformatics.org/ecoinfo/issues/6546

simplify lookup for classes and orcid. remove the "random" annotation code branches -- just too confusing to look at those bogus classes especially now that we have "real" generated annotations.

Add admin service to update DOI registrations by specifying a list of formatIds or DOIs, or update all.

use new method to override the CN URL when constructing a CNode instance. see https://redmine.dataone.org/issues/5142

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.

Store the cn url in the backup.

switch to use FIleUpload instead of O'Reilly COS library for handling chunked file uploads. https://projects.ecoinformatics.org/ecoinfo/issues/6517

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

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

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

index the ORE after we submit the metadata for indexing. https://projects.ecoinformatics.org/ecoinfo/issues/6520

include BioPortal lookup for Entity matches using the data table description. TODO: only associate measurements to the entity observation if they apply.

Index the document after it has been inserted.

Index the document after document is written to the db.

check for null entities and/or attributes (typically when otherEntity is being used in EML).

remove extra space in log message

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

add test for BioPortal annotator service.

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.

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

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.

remove my api key. oops

add comment/pointer to BioPortal annotation service.

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

Add xpointer FragmentSelectors to each annotation.
Split attribute label into tokens to attempt matching to OBOE concepts.

include code to generate random annotations for UI testing. Effective, but can be confusing to see so many unrelated concepts on duplicate EML packages.

Remove the code to lookup alias dn in the getGroups method.

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.

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

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

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

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

Set the userManagementURL property.

In the authenticate method, if metacat can't get user info, the login still can be successful.

change a log information.

In the getALiasedName method, the referral set to ignore. Since the alias name is the local referral, we need to set it to ignore.

recursively submit obsoleted objects for indexing when instructed. https://projects.ecoinformatics.org/ecoinfo/issues/6424

First pass at a class for summarizing attribute information for analysis. (semtools) https://projects.ecoinformatics.org/ecoinfo/issues/6256

merge recent upgrade changes from 2.4 branch

look up guid when done setting access by docid so we can sync and refresh accesspolicy on MN and CN.

additional logging for set access

get guid from online id for call to SyncAccessPolicy

setAccessAction: get guid from passed in id for calls to SyncAccessPolicy, HazelcastService.refreshSystemMetadataEntry

example of how we can look up pid (guid) given a metacat docid.

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

Change isEqual to private so it can be used by test suite

allow statements starting with 'WITH'

add comment (and commented out code) for possibly inspecting the /dirtySysMeta call for archive=true flag. https://projects.ecoinformatics.org/ecoinfo/issues/6417

only index event information for known events. https://projects.ecoinformatics.org/ecoinfo/issues/6346

call getDescription on cn.setaccesspolicy service failure

make all objects in a package publicly readable when published. https://projects.ecoinformatics.org/ecoinfo/issues/6415

Add the code to check if the docid contains the whitespaces in the handleInsertOrUpdate, handleUpload and handleInsertMultipartInsertAction methods.

make all package contents publicly readable when publishing with a DOI. https://projects.ecoinformatics.org/ecoinfo/issues/6415

Run syncAll in a single thread so admin config UI doesn't freeze

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

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

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

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

Modified the usage.

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

Modify the usage message.

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

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

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

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.

can only log events with a valid localId.

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

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

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

Add the code to handle a runtime exception.

Add code to persist the properties in the group 3.

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

Add a method to get the user management url.

Fixed Exception declaration problem

minor changes to error msgs

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

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

fix typos/compilation

Change to use AuthFile constructor.

Add code to check if groups is null.

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

Consolidate the user/group utitlities code.

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

Add methods to handle modify user's attributes.

Complete the method - handleUseradd.

Add code to handle useradd command.

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

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

Add the code to handle the organization name.

Add the getUserInfo method.

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

Add some contants.

Add the description in the getGroups methods.