Metacat

Fix XML validation errors in the metacatui confirmData template for the registry. Add a test script that submits multiple datasets to the registry.

add support for v2 DataONE API.

handle login/logout when testing using metacat client (recent refactoring to use more standard http client code)

remove dependency on HttpMessage that was in the utilities project but is now removed in favor of newer (standard) http client library code.

take advantage of the ezidclient for multi-threaded/asynchronous DOI registration. This will be most useful for doing large batch updates and not so much for the one-at-a-time publish actions but works in either context. https://projects.ecoinformatics.org/ecoinfo/issues/6440

use separate surName and givenNames to lookup ORCIDs.

Create a derived data and metadata in the OrePackageTest

all full-text queries for ORCID, but it isn't that great because we might have a"PISCO" creator that shows us in may different orcid profiles...false matches.

correct glaring erros -- still needs to be honed, but at least it runs without NPE and Jena/foresite errors

stub for testing ORE augmentation - this generates an ORE, adds a "wasDerivedFrom" triple and saves to Metacat MN for indexing. https://projects.ecoinformatics.org/ecoinfo/issues/6548

adjust tests for production service -- more "real" information shows additional return values from the query.

switch to the production ORCID server for looking up orcid matches for our creators.
add test to summarize how many creator matches we can actually find. https://projects.ecoinformatics.org/ecoinfo/issues/6423

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 'test' for indexing annotations without actually storing the RDF of the generated annotation.

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.

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

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

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

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.

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

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.

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

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

Add the test class for the pisco account.

Remove the test method for the pisco account since it maybe fails because of the fire wall issue.

Add the login test of the pisco account.

Add the pisco account.

Add a comment to warn the users not to change the password file path to a production one since it will be deleted.

clear test password file so subsequent runs will not fail -- tests assume blank file to begin with.

Change the password.

uncomment other tests in suite.

add a few more checks while debugging test

Use D1client for communication with CN (for integration test)

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

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

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

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

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

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

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

Use client.MetacatClient instance for all metacat api calls

Test syncing of access policies when updated with legacy metacat api

Add a method to test an alias account in the ldap server.

Add a group for the testing.

Add users which are needed in the junit tests when the metacat is file-based authentication.
If users have been added, it just print out the exception.

Change the test file according to the change on the constructor.

Made changes according the changes in the AuthFile class.

Add the test method for the getUserInfo method.

Modified the junit test file according to the change in the class.

Change the test file according to the change made in the class.

Change the addGroup method since the API was changed.

Add the test method for the getPrincipals.

Add test methods for changing passwords.

Add method to test the getusers method.

Add a test method to test authentication.

Add an test method for adding a user.

Add a junit test for the AuthFile

Fixed compile error that an ioexception should be caught.

Reviewed code for all uses of FileInputStream, checking to see if the method should be closing the stream, and if so, closing it in the method as well as in the finally clause to ensure we don't leak file descriptors.

Refer to metacat.war deployments since those are now the default. https://projects.ecoinformatics.org/ecoinfo/issues/6082

test that d1 node admin is allowed all permissions. https://projects.ecoinformatics.org/ecoinfo/issues/6086

test for configured target url template on metadata using the default #view url. https://projects.ecoinformatics.org/ecoinfo/issues/6092

implement ORE check method to actually query the MN for OREs that reference the given pid.
https://projects.ecoinformatics.org/ecoinfo/issues/6061

check both previous and current data revisions when updating packages. https://projects.ecoinformatics.org/ecoinfo/issues/5647

default to non-https when testing localhost. If the developer has a hostname configured with https, it will correctly use this configured baseUrl, otherwise it will just use http://localhost.

do not use a URL that could resolve when testing the Metacat inaccessible exception.

use shared metacatContextDir variable for calls to Harvester.loadProperties(metacatContextDir);

MN.getPackage() - test with ORE that includes 2 data files and a "metadata" file (still should be using EML for that test). https://projects.ecoinformatics.org/ecoinfo/issues/6026

First pass at MN.getPackage() implementation using Bagit library from LOC. https://projects.ecoinformatics.org/ecoinfo/issues/6026

add method for publishing existing object (usually assumed to be scimeta) with a DOI. https://projects.ecoinformatics.org/ecoinfo/issues/6014

add Metacat servlet action to force the reindexing of one or more or all pids in the system. https://projects.ecoinformatics.org/ecoinfo/issues/5945

add simple test for the IndexEventDAO class -- adding, removing, listing events in the DB table. https://projects.ecoinformatics.org/ecoinfo/issues/5944

correct regex for whitespace in D1 identifier.

Add code to test title for the query result.

Rewrite some methods, so the query result can be processed many times.

Removed the commented out text cases and add a test for archvied document.

Call setting certificate location to be the test one after getting the MN baseurl.
The method to getting MN baseurl somehow calls CN and it set the certificate location to be /var/metacat/certs/METACAT1.pem.

Add a distrusted certificate for the testing.

Use the MNode to query the server when we use certificates to set up the session.

Add the code to test the user with a distrusted certificate.

Add tests to test group and rightsholder.

Change the delete to archive.

Add a test for testing access control for the solr query.

use maven to manage most jar dependencies in Metacat.
Exceptions include: LSID, Datamamager (EML),

lookup the title for EML files when registering DOIs.
lookup the creator from DataONE CN (if available).
add EML-based test. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

include the create test in the suite

Correctly mint and register DOIs in teh MN API implementation. Add tests to exercise minting and creating. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

remove older lucene library and include ORE test to make sure that change does not prevent us from generating OREs. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5874

move DocInfo parsing into utilities project so that it can be used by Morpho as well as Metacat.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5737

return from test when we encounter the NotImplemented exception for CN.search()

include identifier.guid in the test SQL clause.

CN.search() id not implemented by metacat -- making that explicit and also testing for it.

In migrating to Hazelcast 2.4.x, replace deprecated methods.

simplify the xml_access query, and instead use guid to check for permission. Now the docid/rev join (to get most recent version for search results) happens "higher up" in the query.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

remove use of HttpMessage (in morpho.jar) in favor of standard httpclient methods for calling the servlet in tests

use CDATA for docname field in docInfo so that XML parser ignores the content that can contain characters like "&

sleep before updating and deleting test documents - otherwise their index entries may not be fully written and this causes errors (update and delete first attempt to remove index references, but if they are not in the DB yet then they are not removed but then they do get added and the FK constraints make the delete fail). Since we know indexing occurs in a separate thread with a configured delay, we just use this same delay in our testing.

Use a final static string to replace the hard code.
Search document title rather than id in testReplicateEML_AtoB method.

use CN session when testing getLogRecords() and getOperationStatistics() becuase they are now protecting "sensitive" information