Metacat

refactored the sessionService to use a correct singleton initialization scheme. Added true authentication to ResourceHandler.

new class to handle system metadata tasks in metacat

Commit the change for Madhusudan Gujral from java.net.URL url = new java.net.URL;
to java.net.URL url = new java.net.URL;

added systemMetadata table to the upgrade scripts

listObjects is now working for rest calls as well as crud calls

added some params to the loop that segments the listObjects resultset

allow any nonquote characters in the schemaLocation attribute, otherwise the whole line is matched and this prevents schemaLocation from appearing anywhere but at the end of the line.

Fixed bug the download link didn't work.

finished the crud part of listObjects. need to implement it in the rest interface now.

implementing getObjects in CrudService.

implementing getObjects in CrudService.

implementing getObjects in CrudService.

listObjects is almost working. need to get the result set parsed when returned to CrudService.

Add a mapping between kar xml namespace and karxml.xsl.

Add a style sheet to transform kar xml document.

setting up the framework for the listObjects api call

added the renamed Java classes for ObjectList

Change the search query according to the karxml change.

changed the detailCode for DataOne exceptions to a string

added getSystemMetadata to ResourceHandler and changed the url format to be meta/guid. added a new servlet reponse handler in the web.xml file to handle the new urls and send them to the RestServlet.

Change the return type from kar to the namespace.

implemented update in ResourceHandler and fixed a bug in CrudService where data files were not handled correctly on update

removed system.outs

update works. it was the test that was faulty. all working now

amost have update working. still need to get unit test squared away.

removed old method that didn't do anything

added exception testing to the crud test

added a new target to install the dataone schemas from a loca dir if you don't want svn calls being made during installation

getSystemMetadata is now working. added unit test as well.

adding stax jar. if this is somewhere else, i'll remove it, but i'm unable to find it anywhere in dataone

getting getSystemMetadata to work

adding test for getSystemMetadata. a bit of refactoring.

adding test for getSystemMetadata. a bit of refactoring.

adding test for getSystemMetadata. a bit of refactoring.

refactored XMLSchemaService to not have static methods. made the CrudServiceTest more robust.

removed system.outs

fixed schema location bug. the dataone schemas are now correclty found

removed CrudService dependency on servlet params. CrudService is now a singleton. I'm getting an error from metacat saying it can't find teh systemmetadata schema, even though it is, in fact, registered with metacat. need to identify why this is happening.

Fixed some minor documentation errors regarding the Harvester.

added a test for CrudService and added tests for IdentifierManager for each method

refactoring to remove duplicate code

adding a system to track system metadata documents for dataone

Added initial implementation of getSystemMetadata and its associated REST service. Current implementation is returning a hardcoded system metadata document -- need to look up the real document for each guid and return that.

Completed main parts of CrudService.create(). Now the method writes both data and metadata objects along with their system metadata, and handles the mapping between global identifiers and local identifiers. Access control and logging still need to be dealt with to properly authenticate and then log activities.

Updating build to properly clear temporary export directory before doing svn export.

Modify CrudService to write SystemMetadata to disk with an autogenerated localId and an autogenerated GUID. Validation depends on the DataONE schemas being setup in xml_catalog properly, so still need to check upgrade scripts to be sure these new schemas are added. Still need to handle the metadata document insert, but should be same as system metadata insert.

Add support for getting the DataONE schemas from SVN and copying them into metacat's schema catalog. Still need to update the oracle scripts as well.

Added comment about MIME form processing.

Refactored schema service to call doRefresh() in constructor to eliminate code duplication.

Added note on TODO for access bug.

replication of guids now works. tested this for both forced replication and update/insert/delete triggered replication

fixed bug where guid end tag wasn't getting printed

added a method in IdentifierManager to get a guid from a docid and rev. added fields in the documentinfo replication document to pass the guid. now need to handle the guid and insert it into the table if its found

Add 'metacat/lib/oaipmh' directory to the list of required jar files in the 'Set up Metacat Dependencies' section.

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.