Metacat

fix for null session bug

hudson tests are now running. needed date conversions. still more work to do with systemmetadata date format.

updated for date format that supports time zones correctly.

changed date comparison to compare to gmt only

fixed NPE with sessionData

added some new error handling to work around this issue https://trac.dataone.org/ticket/706

fixed bug in access control where the sessionid was not correctly passed along so changes of privileges were not being made

fixed bug where null session data was not treated properly.

Correct log warning message - not "Account" but "Accession" number

fixing date formatting and timezone issues

fixed bug with log processing

fixed some bugs in time handling for listObjects and getLogRecords

bug fix to handle nulls

fixed bug in getLogRecords where the wrong id was getting set as the identifier

added new exception handling to serialize number format exceptions for rest calls

fixed listObject bugs, added params to the listObjects rest interface, consolidated the date format passed in params

fixed query for listObjects so that paging works as advertised.

formatting

fixed error with listObjects and get.

got the crud test to pass on knb-mn, now need to figure out why the rest service still isn't working

still looking for listObjects problem

more debug for another instance

adding some debug info

fixed bug with upper case comparison

changed getSessionData so that it will respond property to public tokens

Added SQL lines for registering D1 schemas in the upgrade process.

Removing drop statements from upgrade scripts because the systemmetadata table
does not exist in 1.9.2, so these objects can't be dropped on upgrade.

MetacatPopulator is now working. It allows you to do a query from one metacat instance, then insert any returned docs into another metacat instance

cleanup of 'fixed' ResourceHandler

tracked down streaming bug. now need to figure out a better way to fix it.

added getValue() to the guid so that it prints the guid and not an object id

added a DataOneLogger for event notifications on the CN. The logger is called DataOneLogger and can be managed in the log4j.properties file

finished getLogRecords. Fixed some date bugs in metacat.

adding getlogrecords to the rest interface.

changed getLogRecords to use new classes for log events

fixed bug in metacat that allowed attribute data to be appended to element data in returnfields

fixed bugs associated with crud access control changes.

implementing getLogRecords

added EventLog statements to all public methods in CrudService in preparation for addin the getLogRecords() method

added better debugging error messages for CN dev errors

added generateMissingSystemMetadata to the ResourceHandler so it is now available via a REST call.

made the test functional so that it checks that missing system metadata will be created.

mostly done with generating systemmetadata from legacy knb docs. need to write a better test and enable this through the ResourceHandler then it will be done.

working on getting systemmetadata creation working for legacy knb objects

working on a function to create dataone system metadata docs for legacy metacat objects that do not have SM.

moved authentication checking out of ResourceHandler and into CrudService

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

new class to handle system metadata tasks in metacat

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.

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.

setting up the framework for the listObjects api call

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.

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

removed system.outs

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

added exception testing to the crud test

getting getSystemMetadata to work

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.

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.

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

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).

Merge 1.9.2 changes back into the trunk

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...

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...

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.

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...