refactored XMLSchemaService to not have static methods. made the CrudServiceTest more robust.
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() andcreate() services are partially complete. Several more functions and checks need to be added tocreate() 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 forget() operation. Minor issue with permissions errors propagating up thestack, but otherwise this is the first implementation of a full DataONEmethod.
Modified readFromMetacat() to pass most exceptions up the call stack, which allows creation of new entry points for calling reads. Still need tocontinue factoring out the HTTPServletResponse that is passed in in order tomake entrypoints that are not servlet based possible. Problem now is in...
Excluding the Maven ant tasks jar from the metacat war distribution becauseit is not needed (its only used to build dataone-service at build time, andis unused at runtime), and it conflicts with jar files checked in for Springas part of the geoserver install. Also updated dataone interface...
Modified the build.xml to include a new task for building the dataoneservice api package, which generates a jar file that is put into lib. Thistask depends on maven being installed in maven.home, and depends on theDataONE service_api being checed out in a sibling directory to the build....
Updated the build to properly locate the servlet jar depending on whichversion of tomcat is being used, tomcat5 or tomcat6.
when looking up group membership, skip referrals that have errorshttp://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 translatedinto a metacat docid which is then used in the handleDelete() call. So nowMetacat supports use of arbitrary identifiers for delete operations, but...
Added support to ResourceHandler to allow the putObject method to usearbitrary guid strings as input. These strings are examined, and if theymatch the Metacat docid format (scope.id.rev), they are used directly. Ifthe 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 successfullyand can be run from any client (i.e., they don't depend on particulardocuments being present in Metacat). The 'restfiles' directory can probably ...
Fixed bug in getNextRevision() where "error" documents were not beingdetected 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 toOracle 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 theprovided 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 tomatch the DataONE method name.
Update the filename reference
Merging in REST interface implementation that was created by Serhan Akin. Main change isa refactored MetaCatServlet.java class, in which all of the handle* methods were movedinto 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 simplerdescription of Metacati, as well as links to where Metacat is in use.
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.
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.
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