Metacat

Fixed a bug in comparing two identifiers in the update method.

Add a check that the sid shouldn't equals the pid in the update and create method.

Add the code the check if the format of the sid is valid in the system metadata.

Add the enforcement for the sid in the create method.

Enforce the sid requirement in the update method.

Check if the identifier is a sid for the v1 update.

Add the code to test getChecksum.

Add the code to handle the deleted identifier in the checking v1 system metadata existing method.

Enforce the mn.getChecksum only to handle an PID.

Add the test code for getSystemMetadata(sid) and describe(sid).

Add the series id to the system metadata.

Implement the series id in the getSystemMetadata method.

Looking for sid for the method describe.

Add two updates on the testGetSID method.

Add the code to test getting test series ids.

Refactor the code to check a pid exists in the v1 api.

Modified the get method to handle the sid in the v2 api.

Change methods'name base on the change on the source code.

Change a method name to use pid rather than guid.

Add the code to test the methods of determining if a sid or guid exists.

use refactored classes from cn-index-processor. still in flux, but improving to better handle non-xml files

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

Add the code to get the most recent version of a sid which all pids are obsoleted.

Change the test method base on the change of throwing a new sql exception on the getLocalId method.

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.