Metacat

Fixed a bug that the method getLocalId swallowed an exception incorrectly in the IdentifierManager.

Fixed a bug that some service failure exceptions were handled as the NotFound exception.

add accessors for bean property

use ISolrDataField because RDF subprocessor uses the SparqlField subclass.

use input stream instead of Document for resource map processing test

Change the number of the schema feilds.

update classes and context files that use cn-index-processor classes. allowing document subprocessors to be less tied to XML.

1. In the identifierExists method, the code to check if the identifier exist on the serial-id fields of the system metadata table.
2. Fixed a bug on the identifierExists - it considered an identifier didn't exist when the determining process threw an exception.

Add a method to check if a serial id exists.

Add a method to get the pid of the head version of a sid.

add Annotator Store implementation -- pass through to D1 API for the AnnotatorJS API

remove annotator service test -- this feature has been moved upstream

use 2.5.0 for current DB version

Don't remove postgresql 8.4 and 9.1
Don't remove data directory of postgresql 8.4

use getCookie action now that portal has different getToken action.

include person's full name in the JWT returned from /token

Overwrite the default node id (which value is metacat) from the metacat.properties. Otherwise, the test will fail.

Add the code to install the build-essential package.

Merge the java 1.6 support node for 2.4.2 release.

merge updates from 2.4.2 changes

Merge changes in the 2.4 branch into the trunk for the ORNL Mercury schema support. References https://projects.ecoinformatics.org/ecoinfo/issues/6619.

This schema is maintained by Jim Green (jgreen@iiaweb.com) and Ranjeet Devarakonda (devarakondar@ornl.gov). The schema uses a subset of the FGDC 1998 CSDGM elements, along with custom elements specific to the Mercury Metadata web application. Support is included in Metacat for Coordinating Node operations in the DataONE network.

Fixed a bug that the reindex of data objects may index an archived data object.

Fixed a bug that the solr index of data files doesn't reflect the change of access control.

include schema.xml md5 checksum for 2.4.2 release.

[merge from 2.4 branch] use solr schema upgrader for 2.4.2 release -- need to replace the solr schema to include geohash fields

add 2.4.2 upgrade scripts so they are available in the 2.5.0 release as well

update documentation for trunk to use 2.5.0 release number

remove AnnotatorService completely - was moved to cn-index-processor

add annotation, orcid and orgin_combined fields to the index schema

use sparql field and triple store from cn-index_processor (refactor). include annotatorSubprocessor for testing in metacat-index

let metacat-index lookup annotations for indexing rather than the metacat "reindex" action.

Add delete log for data objects on CNs.

remove dev-testing in favor of maven.dataone.org repo

only index non-empty comment text

index both tags and text from annotateit.org

query by consumerKey until the pid search facets are fully supported on annotateit.org

add JkOptions directive and encoded slash options for dataone and solr query support in the URLs that metacat can get (they were in the -ssl version of this file already)

During the replication, the remote content will be saved without alteration.

Merge change from 2.4 branch to trunk (removed some duplicated links)

Fixed issues for login and logout on Saeon skin:
https://projects.ecoinformatics.org/ecoinfo/issues/6613'

M saeon/SaeonLogin.jspx

allow per-document reindexing to be initiated by any user (to support third-party annotations)

Add junit test method for saving a metadata document with unmatched xml encoding declaration.

Add a test file for unmatched xml encoding declaration.

Write the input stream into the file system without alteration in dataone create and update methods.

look up annotations when reindexing a given pid. still very much a prototype in that we are looking up annotations from an external annotator-store. TODO: add pid filtering to query when annotateit.org supports it (pending upgrade on their site).

add the code to install xmlstarlet.

Find files of which type is link.

Change the urls of dataone and geotools repositories.

Keep /var/lib/postgresql/8.4/main directory.

Add the code to stop tomcat and apache.

Add the "-y" option to force removing the old postgresql without prompting a y/n question.

Restore the database for a gzipped sql file.

Added the code to gzip the output file in the dumpall command. This will save disk space.

Modified the redirect rules which didn't work.

Add the code to add the attribute useHttpOnly='false' to the Context element in the context.xml file.

Fixed a bug the code can get the argument from the command line.

Added the code to change the permission of the backup file so the postgres user can read it.

Added the code to check if the metacat backup file exists.
Added the code "exist 0" at the end of the scripts.

Added the .conf to those site files since the new apache server only loads the sites with the extension.

Add the code to vacuum the db.

Add the code to enable the 8009 port for ajp connection in the server.xml of tomcat7.

Added the code to modify the geo data directory in the metacat.properties file.

Fixed some bugs to restore postgresql data.

Add the code install some components for installing tomcat7

Use a variable to replace the hard code.

Use the version directly.

Fixed a typo.

put the date to an output file.

A script for vacuum the db.

Add a script to move the db from 8.3 to 9.1 base on a dumped file.

Use the pg_dumpall command to back up all information of the database.

Add the code to backup the cerificate/key of the apache server.

Removed the code to write the backup file to a dvd drive.

Added the code to copy Metacat and other web applications from the webapps directory in tomcat6 to tomcat7.
It also update the value of deploy.applicationDir in the metacat.properties file as well.

Only insert new configuration lines once to the /etc/tomcat7/catalina.properties.

Used variables to replace hard code in sed command. Also we have to escape the variables.

include type="party" attribute for the divs that contain contact information (for annotating with ORCIDs)

Used variables to replace the hard code.

Add the code to modify the workers.properties file.

Fixed typo.

use http://tools.ietf.org/rfc/rfc3023 spec for conformsTo property. use the full xpath for EML dataTable and attribute selectors

Add a script to install openjdk 7 and tomcat 7.
It also configures java, javac,keytools and tomcat7.

Remove an import.

Removed an import.

Added the junit tests to test the NotFoundException having the deleted information.

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.