Metacat

Refactored metacat to use dataone-service-api-0.3.0 jar file, with the new JIBX generated types and serialization. Included JIBX runtime jar in metacat to handle serialization and deserialization of SystemMetadata objects. Removed the old API jar file.

Modifications to support the DataONE service API version 0.1.0. For DataONE, the get() and
create() services are partially complete. Several more functions and checks need to be added to
create() before it is viable. This DataONE support is not complete, and the current support breaks the MetacatRestClientTest for the time being (this client will eventually be removed).

Add a debug statement to show existing doc id

Move all user images into the dev image directory. Remove all but the MetacatAdministratorsGuide from the user dir.

Merge 1.9.2 changes back into the trunk

Updated to use new name of dataone service API module.

Adding commons-io jar for the IOUtils utilities for stream manipulation.

Modified ResourceHandler to return error codes in XML format for the get() method.

Modifications to metacat rest service to use the new DataONE CrudService for
get() operation. Minor issue with permissions errors propagating up the
stack, but otherwise this is the first implementation of a full DataONE
method.

Modified readFromMetacat() to pass most exceptions up the call stack, which
allows creation of new entry points for calling reads. Still need to
continue factoring out the HTTPServletResponse that is passed in in order to
make entrypoints that are not servlet based possible. Problem now is in...

Excluding the Maven ant tasks jar from the metacat war distribution because
it is not needed (its only used to build dataone-service at build time, and
is unused at runtime), and it conflicts with jar files checked in for Spring
as part of the geoserver install. Also updated dataone interface...

Modified the build.xml to include a new task for building the dataone
service api package, which generates a jar file that is put into lib. This
task depends on maven being installed in maven.home, and depends on the
DataONE service_api being checed out in a sibling directory to the build....

Updated the build to properly locate the servlet jar depending on which
version of tomcat is being used, tomcat5 or tomcat6.

when looking up group membership, skip referrals that have errors
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4900

skip referrals that have errors (connection timeout, host down, etc)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4900

Refactored putObject method to separate the create() and update() portions in order to match the method signatures needed for DataONE.

Modified ResourceHandler.deleteObject() to take a globally unique id (guid)
as input rather than a metacat-conformant docid. The guid is translated
into a metacat docid which is then used in the handleDelete() call. So now
Metacat supports use of arbitrary identifiers for delete operations, but...

Added support to ResourceHandler to allow the putObject method to use
arbitrary guid strings as input. These strings are examined, and if they
match the Metacat docid format (scope.id.rev), they are used directly. If
the id is a string in another format, a new localId is generated based on...

Adding a new property to be used as an identifier prefix by default.

Updated MetacatRestClientTest so that the tests are actually calling fail()
when errors occur, and fixed all sixteen tests so that they run successfully
and can be run from any client (i.e., they don't depend on particular
documents being present in Metacat). The 'restfiles' directory can probably ...

Fixed bug in getNextRevision() where "error" documents were not being
detected properly before searching for the next identifier.

Added initial support for arbitrary string identifiers in metacat (referred to as a guid). The new identifier table is used to map arbitrary string identifiers to Metacat's current docid format (referred to as the localId). Added a new IdentifierManager class to manage this table, adding new mappings as objects are added to the system. Modified the MetacatTest service to utilize this mapping table to look up a localId from a guid. IdentiferManagerTest is working with these guids now, as is the MetacatTest service get() method, but other parts of the system are unaware of them (e.g., create, update, delete operations are unaware, and no mapping is created when new documents are created). As a consequence, the MetacatRestClientTest is not working (although it also had lots of hardcoded dependencies that need to be fixed as well).

Added copyright, license, and class documentation.

Modified table structure to change identifiers table (previously unused) to
represent a mapping between arbitrary string identifiers and metacat docids.
More information in https://trac.dataone.org/ticket/361. Modifications to
Oracle schemas were made but not tested.

Fixed typos in metacat documentation.

Removed version as not sure when this will be delivered, so be agnostic.

Adding new documentation section for Metacat design documents in Sphinx/ReStructured Text format. Build this documentation using the
provided Makefile, assuming that both Sphinx and PlantUML are installed and on the local executable path by running 'make plantuml html'....

Fix two issues: Remove State from 'Data Set Contact' section of confirmation form (part of #3922), and make sure when editing a document that email addresses are picked up appropriately (capitalization).

Modified ResourceHandler to change the GET url from /objects to /object to
match the DataONE method name.

Update the filename reference

Merging in REST interface implementation that was created by Serhan Akin. Main change is
a refactored MetaCatServlet.java class, in which all of the handle* methods were moved
into a separate MetacatHandler.java class. This allows both the standard MetaCatServlet...

Adding missing brackets in else clause. Need to verify with Daigle that this is what he meant.

Move the chunking of large test element data to centralized location in DBSAXNode.writeChildNodeToDB(). Beff up logging

Beef up log messages

add delay in insertSpatialDocs test to avoid buildIndex conflict

Add debug log statements

make sure querygroup is not null before trying to print it.

Re-add the build dir property so the lsid server can build

Populate esa home links with skin property value

Get the latest revision from metacat when a modify call docid does not have a revision number.

Send appropriate message when trying to update a docid that was previously deleted.

Reformat file. No code change.

do a quick retry if building path index fails with a SQL error

Make sure buildIndex throws an exception if it has a sqlexception. That way the indexing object will be added to the indexing queue and reprocessed.

PDF version of doc

Pass the doc xml as a string to docImpl.write and writeRepication. This is so a reader can be create for the parsing and for the write to disk. Also created a db access class for xml query result deletion.

Update java version references to java 6

Remove redundant Version information

Add 1.9.2 release notes.

Fixed typo in docs.

Updated index page to hide obsolete documentation and provide a simpler
description of Metacati, as well as links to where Metacat is in use.

Add comments

make constants final

change dropdown select event to work on IE.

Fix the bug of http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4645. handleGetRevisionAndDocTypeAction will search both xml_documents and xml_revisions table.
It also changed some constrain in AccessionNumber when user update a document, of which all previous versions are in xml_revisions table.

Fix main cross browser gui compatibility issues in sanparks tpc skin.

Fix main cross browser gui compatibility issues in sanparks tpc skin.

Remove commas from the end of lists because they break IE

remove the "optional" tip since it is not currently optional

add required authentication exception class so that the scheduler can compile

add properties expected by the DB property service

use workflowscheduler DB

use @class attribute for path queries rather than @name

Add a sleep statement between getting the dtd from source and checking for it via url. Add method names to log output.

Get all eml code from svn instead of cvs

Log doc and rev query counts and times. Fix mis-spellings.

Log doc and rev query counts and times. Fix mis-spellings.

remove extra open paren

remove call to print busy db connections

add xml_revisions docid index

Add debug to show sql

Fix for Bug #4637 - Metacat Harvester fails to catch some insert and update failures. As per comments in the bug entry, the Metacat Harvester logic has been modified to examine the Metacat client return string to confirm that it contains the substring "<success>" following an insert or update operation. It no longer considers just the absence of an exception as indicative of a successful operation.

log connection warnings only when thresholds are exceeded. Add method names to log output

add method name to log statements

fix spelling of word additional

add method name to log messages and create configured thresholds for warning messages

add parc-moderators to config.username

I've added the PARC and PISCO organizations to the delete and confirm form templates for the data registry application.

Change log levels where appropriate and add class/method name to output.

Change warn messages to info

beef up error log messages

Make sure session data exists before extracting information

Separate code to do tls and non-tls authentication. Introduce AuthTLSException to make error handling easier.

Beefed up the logging

remove registry.config.username value

Start to flesh out the eclipse metacat setup document

Create some basic workflow scheduler system installation documents

When comparing lat and long ranges, make sure the values have content first. Perl values with no content = 0.

Change add sql to use a prepared statement. Only try to download a cert if a url was provided.

change unregister error message to be an info message

fix file name reference for skin configuration file

added a commented out line for auth.moderators for the parc system. This will get uncommented on the parc system and the existing auth.moderators will be commented out.

I've removed the value for the PARC registry.config.site property since it isn't appropriate to this skin, and causes the registry CGI to produce two organization creator elements with the same value.

hard code parc home url

Redirect data.palmyraresearch.org to parc skin

I've added the PARC organization to the login form template.

I've replaced hard-coded URL strings in the PARC skin files with their appropriate variables in JSP, TT2, and XSL.

This updates the Registry login form to handle PARC logins. I've changed the template to load the PARC header and footer if the cfg = parc.

added parc to list of available skins.

Fix errors in workflow scheduler unit test