Added the junit tests to test the NotFoundException having the deleted information.
Added the code to inform users the pid was deleted in the NotFound exception.
Added the code to check if a not-found object was deleted in the isAuthorized method.
Move the code to get the object in front of the method to get the system metadata.
Add a test method to test the method determining if there is a delete event for the given id.
Add a utility method for determine if there is a delete event for a given id.
when we remove a slor index of a resource map, we don't need to know the content of the resource map. Instead, we will search the solr index to get information.
Remove the byte array field.
Removed the method which had the byte array attribute.
Remove the system metadata for data objects.
change the way to delete the solr index of a resource map.
Backup the /etc/apache2/site-enabled directory.
Remove the code to stop/start ldap server.Change the script name to stop/start tomcat.Also backup metacat.properties.
Replace the operator "=~' by "eq" in comparing the two password fields.
dd a new routine to check if the uid has been taken already in the production space during the creation process.
In the EML XSLT - Add classes to the entity details containers so they can be identified easily
add /token endpoint for annotatorJS/annotateIt.org integration. https://github.com/DataONEorg/sem-prov-design/issues/18
Add code to determine if a id exists in a solr server.
include resource="#xpointer(...)" attributes for sections that are potential targets for annotation. So far we have the various people (creator, contact, etc) and data table attributes. https://github.com/DataONEorg/sem-prov-design/issues/18
Persitence the system metadata object in the memory before deleting it from hazelcast.
Add the code to handle the delete of the resource map.
Add the code to handle to remove the resource map index.
Add codes to handle remove a source map solr index.
Add a field to contain the content of resource map.
Add a util class to judge if a namespace is a resource map file.
Create a valid URI by using all lowercase letters when creating a name for the triple model in the Rdf Xml Subprocessor. See bug: https://projects.ecoinformatics.org/ecoinfo/issues/6595
Make the delete method work.
Make the deleteSystemmetadata method really roll-backable.
Add the code to delete systemmetadata.
remove semantic annotation proposal - moved to github: https://github.com/DataONEorg/sem-prov-design/blob/master/docs/use-cases/semantics/semantic-annotation.md
In InsertORETest: Set the format ID of the metadata object to an EML formatId so that it gets indexed correctly.
Change the d1_cn_index_processor version from 1.3.0 snapshot to 2.0.0 snapshot.
Add the code to delete the records in the xml_accesssubtree table.
use configured auth.base rather than hard-coded dc=ecoinformatics,dc=org. https://projects.ecoinformatics.org/ecoinfo/issues/6592
Add a code to check if the pathquery engine is enabled in the checkIndexPaths method.
Adjust the number of schema fields since new ones were added.
When indexing annotations from RDFs, use the doc id to access the system metadata, not the model name since they are not always the same.
Add PROV relationships to the Solr schema. Populate the fields using the RdfXmlSubprocessor
Add wasDerivedFrom field to the Solr schema and use Sparql query to retrieve the value from the RDF
Replace the /u00A0 character encoding with space character instead since /u00A0 displays literally in browsers
Add a test class that inserts an ORE with PROV relationships
use mock CN for testing metacat implementations
remove unused tests
comment out myproxy servlets. https://redmine.dataone.org/issues/5742
convert v2 SM to v1 SM for the v1 service call response
Separate the target and source version for the java compilation.
update to use v2 types for indexing
Add target and source attribute to harvester, client and compile-lsid beside the target compile.
Add the attribute target="1.6" when it compiles the metacat code. The metacat.jar file can run in java 1.6 even though it was compiled in java 1.7.
For the existing uidnumber, we decrease the size of vector for sorting.
Login automatically via curl rather than manually entering the cookie info for the registry test script
Add the code to check if the existing highest uidNumber really exists.
In the getNextUidNumber method, a mechanism to look up the highest existing udiNumber was added.
Fix XML validation errors in the metacatui confirmData template for the registry. Add a test script that submits multiple datasets to the registry.
Create a lock file for the registry if one doesn't exist
Allow the registry form to specify a docid scope
Only lock the local docid file when creating a new docid, not when inserting, for faster upload times. Remove extra debug messages from testing.
Fix bug in the online registry where data files were not using the new docid creation process
Lock a local file while docids are being created so multiple docs can be uploaded at once
remove CN.systemMetadataChanged in favor of the CN.updateSystemMetadata method. Otherwise there's no good way to know where to fetch the auth copy from since the SM change might be to switch the authMN!
add support for v2 DataONE API.
remove old EML jar -- datamanager.jar has the EMLParser now and is pulled in with maven.
use css changes from EML project to render a PDF that fits on a printed page during export. Note that this also changes the default skin slightly (for the better, we think). https://projects.ecoinformatics.org/ecoinfo/issues/6053
remove configxml.jar as the ConfigXML class is now included in the utilities library.
handle login/logout when testing using metacat client (recent refactoring to use more standard http client code)
handle multiple subprocessors (RDF and ORE) before the object gets indexed by making sure to merge the solr doc map before submitting to the index.
use maven for datamanager dependency now that EML project has been [partially] maven-ized.
switch to use utilities from Maven repo instead of pulling from SVN and building locally. Added trunk/SNAPSHOT build to dev-testing Hudson (DataONE) for users who do not actively develop the utilities library. Motivated by the HTML->PDF utility, seemed like as good a time as any to convert Metacat's dependency on the project.
remove dependency on HttpMessage that was in the utilities project but is now removed in favor of newer (standard) http client library code.
add more sections about extending the annotation model, serializations, and permissions.
Include PDF version of the metadata in the package download. https://projects.ecoinformatics.org/ecoinfo/issues/6053
use default "metacat" context name for metacat-index testing.
Added more description for the model. cleaned up a few formatting issues.
draft of semantic model documentation
Change geohash type to "string" (was "text") so that no Solr analysis or tokenizing happens during indexing.
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 a member instance of ezid service that only logs in every 24 hours (or other time TBD) instead of every time there is an interaction with the service. Saves us many calls when doing batch updates to ezid but keeps us from trying to use expired sessions. Motivated by https://projects.ecoinformatics.org/ecoinfo/issues/6440
Fixed an error in the ORE model diagrams
prevent js scriptlets from running when we return error messages to the client by escaping any potentially harmful xml blocks. https://projects.ecoinformatics.org/ecoinfo/issues/6224
allow updates to all doi: prefixes - realized we are already restricting to specific replica servers when updating these. worst case is we try to update a registration for which we are not the owner. https://projects.ecoinformatics.org/ecoinfo/issues/6440
show the SM and ORE generation buttons even if they have not registered/configured dataone. many potential MNs want to see their generated SM before registering (and we want them to too!).
restrict DOI updates to DOIs that match our server shoulder -- may consider opening this up to any "doi:" prefix if this is too restrictive. https://projects.ecoinformatics.org/ecoinfo/issues/6440
use separate surName and givenNames to lookup ORCIDs.
Changed errors in the ORE model expansion metacat documentation diagrams
Describe the primary data resource in the derived resource RDF
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
include ORE formatId as handled by the RDF subprocessor and index prov:wasDerivedFrom field where it exists in the RDF model. https://projects.ecoinformatics.org/ecoinfo/issues/6548
expand the sparql queries to include dcterms:identifier
Text changes to ORE docs
Add documentation for the ORE model expansion for derived data
use HttpClient to query orcid so I can easily set headers and such -- getting 503s from their production server when I test on dev.nceas...odd
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
use a non-public rightsHolder for both EML and Annotation test documents now that the RDF subprocessor checks each annotation to see that it came from a user that as write permission for the object being annotated.
test for update using the updated EML file, not the original. Also add the SM to the shared map so that the indexing process can consult SM.accessPolicy when indexing annotations that assert things about those test documents.
ignore the metacat/solr comparator tests - they are one-offs.