Metacat

use shared getLogRecords method

Remove isAuthorized(), setAccessPolicy(), and getLogRecords() methods since they're implemented in the superclass.

use Permission, not Event for isAuthorized() methods

do not use pisco for referral testing (merge from 1.9.5)

include different (non pisco) referral account (merge from 1.9.5 branch)
include upgrade sql scripts

merge changes from 1.9.5 branch for upgrade process (1.9.3->1.9.4->1.9.5)

merge 1.9.5 changes to trunk (delete now preserves access rules and docs can be read after deletion)

do not delete the access rules when we "archive" the document on "delete" (commented out for now)

allow reading from xml_revision table when we are the doc owner

CNCoreImpl is replaced by CNodeService

implement CNAuthorization

Metacat does not implement CNIdentity - it is a stand-alone service

implement registerSystemMetadata

implement object format methods - using a separate class to do the actual metacat lookup/caching so that teh CN implementation looks cleaner

implement getLogRecords

include latest D1 common/lib changes

On the fullclean target, add code to delete the entired checked-out utilities directory.

add commons-io-2.0.jar dependency to Metacat Client API section

Initial check in of the MNodeService stub methods that implement the D1 MN* interfaces. CrudService methods will be transitioned into this class. The methods follow the D1 0.6.2 API thus far.

Also changed CNodeService to reflect minor changes to the D1NodeService class.

Add a static getInstance() method to CNodeService and make CNodeService a singleton.

Initial check in of the CNodeService stub methods that implement the D1 CN* interfaces. CNCoreImpl methods will be transitioned into this class. The methods follow the D1 0.6.2 API thus far.

CNAuthorization.isAuthorized() and MNAuthorization.isAuthorized() differ. Removed it from the base class.

getChecksum() is intentionally different on the CN vs MN, so I'm removing it as a common method.

Initial check in of the D1NodeService class that provides methods common to both CNodeService and MNodeService implementation classes. The common API methods are:

Methods common to CNCore and MNCore APIs
getLogRecords()

Methods common to CNRead and MNRead APIs...

Get username and password from a property file.

placeholder for setting up certificate manager

remove AuthToken (use session). Remove login() call. Use AccessPolicu object to set public read permission

take getLogRecords impl form CrudService and use in CNCoreImpl

Added NCEAS logo to header.

Begin process of migrating Admin guide to Sphinx. Structure is now set up, but
content needs to be copied.

escape quotes when processing returnfield with predicates. example:
<returnfield>dataset/dataTable/physical/distribution/online/url[@function='download']</returnfield>

Updated MetacatPopulator to now use ObjectFormatCache.getInstance(). Note: problems remain with the authentication API changes - calls to mn.login(), etc. need to be addressed.

New D1 libclient and common 0.6.2 jars with changes to the ObjectFormat schema type (adds isScienceMetadata field).

Removed ObjectFormatService in favor of CNCoreImpl

Updated tests to use ObjectFormatCache.getInstance(), and added tests for CNCoreImpl.listFormats and getFormat().

Added support in ResourceHandler for the /formats collection. Added listFormats() and getFormat() method, both of which call CNCoreImpl methods to handle the call.

Updated CNCoreImpl to implement listFormats() and getFormat(), and changed calls to ObjectFormatCache in IdentifierManager, MetacatHandler to call getInstance(). Removed the ObjectFormatService registration from MetaCatServlet since it is replaced by CNCoreImpl.

Added the /formats collection into the servlet-mappings for D1UrlFilter to handle.

Removed module index from docs because we don't have multiple modules yet.

add option for replicating system metadata (dataone)
https://redmine.dataone.org/issues/1626
also make sure the latest table changes are included in upgrade scripts

add option for replicating system metadata (dataone)
https://redmine.dataone.org/issues/1626

use Data Manager Library to parse EML when needed in DataONE classes.
(augmented DML to parse data format elements in EML to estimate MIME type)
https://redmine.dataone.org/issues/1634

When calling SystemMetadata.getObjectFormat(), return the string value of the ObjectFormatIdentifier rather than ObjectFormat.toString() (which no longer returns the fmtid string).

When calling SystemMetadata.getObjectFormat(), return the string value of the ObjectFormatIdentifier rather than ObjectFormat.toString() (which no longer returns the fmtid string).

When calling SystemMetadata.getObjectFormat(), return the value of the ObjectFormatIdentifier rather than ObjectFormat.toString() (which no longer returns the fmtid string).

organize imports so that it is clearer what dependencies exist on the D1 jars

include create() and reserveIdentifier() methods

include override annotation for register method

use Date not joda's DateTime

expose spatial cache regeneration option in the admin interface

force replication for newly-registered system metadata

Merged in the D1_0_6_2_BRANCH changes that include the transition from ObjectFormat calls to ObjectFormatCache calls.

check system metadata for the id as well (in cases when we only have system metadata)

include GUID column for xml_access and related methods for storing/retrieving access rules

implement the old interface for now (until 0.6.2)

include CNCore implementation - only registerSystemMetadata is implemented at the moment. also - updated d1 jar (0.6.2) should be used since that is where the method is defined.
would like to consider making ResourceHandler more modular - seems like it does A LOT of different things

include System Metadata forced replication - just need to figure out when to call it!

handle timed replication of system metadata. there are still a few outstanding issues:
-track server location of system metadata-only entries
-replication policy flag for system metadata-only entries?
-locking for replicated entries?
-forced replication of entries

read and write D1 access policy rules from metacat xml_access table.
still TBD: which mechanism takes precedence when there are systemMetadata access rules and EML access rules and other access rules?

persist system metadata replication policy and status using db tables

rework SystemMetadata creation when inserting documents via the Metacat servlet api (in which case there was no client-supplued system metadata)

do not look in systemMetadata for a docid->guid mapping

use 1.9.4 version

transfer full System Metadata (as XML) during document and data replication

remove docid and rev from systemMetadata table

-remove system metadata guid -> local id mapping (there is no document for system metadata now)
-include system metadata elements when replicating data objects (TODO: transfer all system metadata structures with the docinfo request).
TODO: remove docid+rev from the systemMetadata table definition

add systemMetadataProvenance table for tracking those relationships

do not use XML files for storing SystemMetadata - use DB tables only.

Committing the change to the utilities tag to pick up fixes in newline handling at the end of the files. With this, the MetacatClientTests pass.

Commenting out these MetacatRestClient tests because the Metacat RestService is no longer registered as a servlet and needs to be removed, along with the associated MetacatRestClient and tests.

Fixed MetaCatServletTest test failures by removing the hardcoded username/passwords used in the tests and replacing those with data from metacat.properties.

Fix AuthLdapTest to use accounts that are more reliable when searching for existing accounts in the getPrincipals output.

Modified Metacat to build against the D1_SCHEMA_0_6_1 branch of the dataone schemas by incorporating the 0.6.1-SNAPSHOT version of d1_common and d1_libclient libraries, and refactoring Metacat code references to the d1 schema changed types.

In order to sync up with DataONE 0.6.1 changes, I'm backing out ObjectFormatService changes temporarily in Metacat. Most functionality will be rolled back in using the DataONE 0.6.2 tag, but some methods in ObjectFormatService (such as getListFromDisk()) will be moved into d1_libclient_java.

Added in the 0.6.0 version of the d1_common_java library that has object format changes.

Changes in the DataONE ObjectFormat class deprecate the convert() method, and we're now using Metacat's ObjectFormatService to look up object format attributes. The following changes replace ObjectFormat.convert() with ObjectFormatService.getFormat() in several classes....

Include the DataONE 0.6.0 type schema in the SQL schema and DTD loader script.

Updating the cached object format list to the new DataONE namespace including the 'ns' domain component.

add additionalMetadata/metadata/spatialResolution/value and additionalMetadata/metadata/spatialResolution/units for indexing. Also add missing comma behind additionalMetadata/moderatorComment

use update method to update the mapping between local and guid (d1) when we get a force replication request that is an "update

remove entity encoded characters that were garbled in browser (sanparks patch)

updating CrudServiceTest with better exception handling (more specific) to match refactored CrudService.java class

generateMissingSystemMetadata was swallowing Exceptions instead of throwing. Refactored so that specific exceptions are thrown, affecting [create/update]SystemMetadata methods, too.

committing changes related to the new restservice update specification (newPid vs. obsoletedGuid)

remove entity encoded characters that were garbled in browser (sanparks patch)

replace whitespace in generated docid scope (sanparks patch from 1.9.4 branch)

use outputstream as an object, not a string. relax the Map typing to allow for mixed values. (sanparks patch)

use "object_format" element consistently so that it is replicated across instances
https://redmine.dataone.org/issues/1514

Set svn keywords on the object format list file.

The initial checkin of an object format list for Metacat, which will be used by the ObjectFormatService. The XML file will be used only if the service can't get the authoritative list from a D1 coordinating node or from within it's local Metacat database.

remove very old "metacat webservice" code - as far as i can tell it is never referenced or used. plus we have eocgrid and the new D1 rest services covering this territory now

remove very old "metacat webservice" code - as far as i can tell it is never referenced or used. plus we have eocgrid and the new D1 rest services covering this territory now

removed newline addition to test doc now that the newline problem is fixed in utilities project. Small adjustments to comments and debug statements to aid in debugging. Reordered tests to remove possible insertion between read and getLastDocid test.

zero padded date string in DocumentUtil.generateDocumentId() for readability

Use SystemUtil.getContextURL() in ResourceHandler to construct the DataONE service URL (rather than direct calls to PropertyService). This handles http and https URLs, and strips the :80 or :443 for the well known ports.

Make this class be the subclass of the MCTestCase. The super class will initialize the property service for it.

Minor changes to MetacatHandler:
- Improved logging where MetaCatServlet.class was used in getLogger() rather than MetacatHandler.class (holdover from the refactor)
- Minor formatting changes, and replacement of 'MetaCatServlet' with 'MetacatHandler' in the logging output as needed.

commenting out the pisco user tests, since they only work in production.

put in more explanatory exception methods in the private helper functions that throw exceptions, and some debug statements in the onlineData201CasesTest_1 test.

improved multipart handling (improved logging messages, code, and error checking). Added exception classname to error output when the generic Exception is thrown. Added error check for cases of null value for file parts 'sysmeta' and 'object.'