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metacat @ 6196

  • svn:ignore: build
  • svn:mergeinfo: /branches/D1_0_6_2_BRANCH:6107-6121
# Date Author Comment
6196 06/23/2011 05:10 PM ben leinfelder

allow reading from xml_revision table when we are the doc owner

6195 06/23/2011 04:10 PM ben leinfelder

CNCoreImpl is replaced by CNodeService

6194 06/23/2011 03:58 PM ben leinfelder

implement CNAuthorization

6189 06/23/2011 02:26 PM ben leinfelder

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

6188 06/23/2011 02:20 PM ben leinfelder

implement registerSystemMetadata

6187 06/23/2011 02:19 PM ben leinfelder

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

6186 06/23/2011 02:17 PM ben leinfelder

implement getLogRecords

6185 06/23/2011 01:54 PM ben leinfelder

include latest D1 common/lib changes

6184 06/22/2011 05:21 PM Jing Tao

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

6182 06/22/2011 05:01 PM ben leinfelder

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

6179 06/22/2011 11:03 AM Chris Jones

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.

6178 06/22/2011 08:13 AM Chris Jones

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

6177 06/22/2011 08:06 AM Chris Jones

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.

6176 06/22/2011 07:50 AM Chris Jones

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

6175 06/22/2011 06:12 AM Chris Jones

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

6174 06/21/2011 03:42 PM Chris Jones

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...

6156 06/17/2011 01:52 PM Jing Tao

Get username and password from a property file.

6152 06/17/2011 09:41 AM ben leinfelder

placeholder for setting up certificate manager

6151 06/17/2011 09:17 AM ben leinfelder

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

6149 06/16/2011 10:33 AM ben leinfelder

take getLogRecords impl form CrudService and use in CNCoreImpl

6148 06/16/2011 12:49 AM Matt Jones

Added NCEAS logo to header.

6147 06/16/2011 12:09 AM Matt Jones

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

6146 06/15/2011 10:44 PM ben leinfelder

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

6144 06/15/2011 09:03 AM Chris Jones

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

6143 06/15/2011 08:59 AM Chris Jones

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

6142 06/15/2011 08:56 AM Chris Jones

Removed ObjectFormatService in favor of CNCoreImpl

6141 06/15/2011 08:53 AM Chris Jones

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

6140 06/15/2011 08:50 AM Chris Jones

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

6139 06/15/2011 08:48 AM Chris Jones

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.

6138 06/15/2011 08:41 AM Chris Jones

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

6137 06/14/2011 12:03 AM Matt Jones

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

6136 06/08/2011 05:08 PM ben leinfelder

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

6135 06/08/2011 05:08 PM ben leinfelder

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

6134 06/08/2011 02:35 PM ben leinfelder

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

6133 06/08/2011 06:25 AM Chris Jones

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

6132 06/08/2011 06:24 AM Chris Jones

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

6131 06/08/2011 06:22 AM Chris Jones

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

6130 06/07/2011 02:56 PM ben leinfelder

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

6129 06/07/2011 12:08 PM ben leinfelder

include create() and reserveIdentifier() methods

6128 06/07/2011 11:14 AM ben leinfelder

include override annotation for register method

6127 06/07/2011 11:09 AM ben leinfelder

use Date not joda's DateTime

6126 06/07/2011 10:28 AM ben leinfelder

expose spatial cache regeneration option in the admin interface

6125 06/07/2011 10:27 AM ben leinfelder

force replication for newly-registered system metadata

6124 06/07/2011 09:53 AM Chris Jones

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

6123 06/06/2011 03:56 PM ben leinfelder

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

6122 06/06/2011 03:28 PM ben leinfelder

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

6121 06/06/2011 12:08 PM ben leinfelder

implement the old interface for now (until 0.6.2)

6120 06/03/2011 12:51 PM ben leinfelder

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

6119 06/02/2011 04:40 PM ben leinfelder

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

6118 06/01/2011 01:45 PM ben leinfelder

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

6108 05/27/2011 11:55 AM ben leinfelder

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?

6107 05/27/2011 09:45 AM ben leinfelder

persist system metadata replication policy and status using db tables

6105 05/26/2011 11:51 AM ben leinfelder

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

6104 05/26/2011 10:25 AM ben leinfelder

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

6103 05/25/2011 03:54 PM ben leinfelder

use 1.9.4 version

6102 05/25/2011 03:53 PM ben leinfelder

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

6100 05/25/2011 12:05 PM ben leinfelder

remove docid and rev from systemMetadata table

6099 05/25/2011 11:59 AM ben leinfelder

-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

6098 05/24/2011 04:26 PM ben leinfelder

add systemMetadataProvenance table for tracking those relationships

6097 05/24/2011 04:18 PM ben leinfelder

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

6096 05/20/2011 10:23 AM Matt Jones

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.

6095 05/19/2011 07:31 PM Matt Jones

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.

6094 05/19/2011 07:06 PM Matt Jones

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

6093 05/19/2011 05:05 PM Matt Jones

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

6092 05/19/2011 01:52 PM Matt Jones

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.

6091 05/18/2011 04:32 PM Chris Jones

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.

6089 05/18/2011 04:51 AM Chris Jones

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

6088 05/17/2011 08:02 PM Chris Jones

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....

6087 05/17/2011 07:43 PM Chris Jones

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

6086 05/17/2011 07:41 PM Chris Jones

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

6080 05/09/2011 11:25 AM barseghian

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

6079 05/05/2011 03:14 PM ben leinfelder

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

6071 05/05/2011 12:14 PM ben leinfelder

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

6069 05/05/2011 10:50 AM rnahf

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

6068 05/05/2011 10:45 AM rnahf

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

6067 05/05/2011 10:19 AM rnahf

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

6066 05/05/2011 10:10 AM ben leinfelder

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

6064 05/05/2011 10:00 AM ben leinfelder

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

6059 05/04/2011 12:39 PM ben leinfelder

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

6057 05/03/2011 04:04 PM ben leinfelder

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

6056 04/29/2011 02:17 PM Chris Jones

Set svn keywords on the object format list file.

6055 04/29/2011 02:16 PM Chris Jones

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.

6054 04/28/2011 03:08 PM ben leinfelder

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

6053 04/28/2011 02:31 PM ben leinfelder

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

6052 04/28/2011 01:53 PM rnahf

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.

6051 04/28/2011 01:05 PM rnahf

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

6050 04/26/2011 08:22 AM Chris Jones

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.

6049 04/25/2011 04:16 PM Jing Tao

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

6048 04/25/2011 03:25 PM Chris Jones

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.

6047 04/25/2011 02:28 PM rnahf

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

6046 04/25/2011 02:24 PM rnahf

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

6045 04/25/2011 11:08 AM rnahf

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.'

6044 04/25/2011 10:58 AM rnahf

added a few debugging lines in createSystemMetadata() related to contents of identifier strings

6043 04/24/2011 07:00 PM Chris Jones

Due to changes in MetacatHandler that creates system metadata from uploaded EML documents, OnlineDataAccessTest was failing certain tests because of errors in how the test documents were originally uploaded. MetacatHandler.createSystemMetadata() was throwing exceptions because of these errors, specifically when a data document is uploaded with a docid that is difeerent than the docid statement in the EML distribution URL. Most errors involved stated docids with .2 versions, and the metadata had .1 versions....

6042 04/24/2011 05:42 PM Chris Jones

Modified IdentifierManager.getDocumentInfo() to include the docid in the returned hash map, since it is useful to be able to obtain the docid and rev separately from a given fullDocidWithRev (e.g. test.1.1).

6041 04/22/2011 01:44 PM rnahf

fixing annoying error message inaccuracy

6040 04/14/2011 05:13 PM Matt Jones

Cleaned up imports.

6039 04/14/2011 05:10 PM Matt Jones

Updated D1 libraries to head to eliminate problems with date parsing -- added
Joda jar to support date parsing. Removed hardcoded DN from test file. Now
CrudServiceTest is passing again.

6038 04/14/2011 03:41 AM Matt Jones

Remove hardcoded LDAP usernames from testing so that MetaCatServletNetTest will work even using alternate
LDAP servers.

6037 04/14/2011 03:07 AM Matt Jones

Changed AuthLDAP to deal with cases where getAttributes encounters non-string
attributes (which used to cause a ClassCastException). Now, if an attribute
value can not be cast to string, we catch the class cast exception and just
skip this value. This only typically occurs when an LDAP server is set to send...