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# Date Author Comment
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...

6036 04/13/2011 08:03 PM Matt Jones

MOdified MetacatHandler to catch cases where ObjectFormat is not being set properly on data files when
generating SystemMetadata. When the EML document contains a format for an entity that maps to a null
type in ObjectFormat.convert(), then the type ends up being null and an error is generated on insertion...

6035 04/11/2011 05:46 PM ben leinfelder

allow "docid override" queries to include the results of a "normal" query - if the operator is left null, it acts as the usual override, otherwise UNION and INTERSECT modes can be used to either augment or refine the results.
this is for incorporating semantic+spatial+keyword queries into one query operation/result

6034 04/08/2011 10:22 AM ben leinfelder

remove System.out statements in favor of logging

6033 04/08/2011 08:56 AM Chris Jones

Removed hardcoded D1 node type in ResourceHandler and added in a new 'dataone.nodeType' property. Also added 'dataone.coordinatingNodeBaseURL' property which points to the CN that stores the authoritative object format list. If this instance of Metacat is a CN, it may point to itself.

6032 04/08/2011 08:28 AM Chris Jones

ResourceHandler in Metacat was set to return the KNB site URL as the MN base URL rather than the node Id. Fixed. https://redmine.dataone.org/issues/1390

6031 04/07/2011 03:17 PM ben leinfelder

initialize the HandlerPluginManager

6030 04/07/2011 03:16 PM ben leinfelder

allow the addition of properties via code

6029 04/01/2011 05:00 PM ben leinfelder

add event notification for insert/update/delete on documents (for semtools plugin)

6028 04/01/2011 10:32 AM ben leinfelder

move semtools skin to the semtools project - build into the war when adding the semtools plugin to metacat

6027 03/31/2011 05:12 PM ben leinfelder

do not attempt to check permissions when reading documents for systemMetadata generation (unless I completely do not understand this feature - please verify!).

6026 03/29/2011 01:18 PM ben leinfelder

new EML style tag

6025 03/29/2011 11:23 AM ben leinfelder

do each table separately with it's own connection - running into memory issues on dev.nceas running this.

6024 03/28/2011 02:44 PM ben leinfelder

do not drop nonexistent table (identifier is not in 1.9.3)

6023 03/28/2011 08:51 AM Chris Jones

This is the start of the ObjectFormatService, which manages the list of object formats registered within Metacat. This includes schema types, mime types, and other information related to a particular format. The service provides functionality for the DataONE MemberNode and CoordinatingNode components, with CoordinatingNodes providing the authoritative list of object formats. See https://redmine.dataone.org/issues/1378....

6022 03/25/2011 03:04 PM Duane Costa

Bug 3835 - design and implement OAI-PMH compliant harvest subsystem
Minor bug fix to handle irregular Metacat docids containing two or more dot ('.') characters. In the LTER Metacat, the following docids (scope and identifier, excluding the revision value) have that characteristic:...

6021 03/25/2011 10:43 AM Duane Costa

Bug 3835 - design and implement OAI-PMH compliant harvest subsystem
Return a 'badVerb' response when the 'verb' request parameter is missing from the request. Previously this generated a NullPointerException.

6020 03/24/2011 03:10 PM ben leinfelder

use the jaxb date parser for ISO 8601 formats. the numeric and date node values are now calculated after the document has been successfully inserted in the db so any sql exceptions do not prevent the raw node data from being saved.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2084

6019 03/23/2011 03:39 PM ben leinfelder

rollback the accessDAO changes - leaving well enough alone.

6018 03/23/2011 02:14 PM ben leinfelder

only include accessfileid when it is not toplevel

6017 03/23/2011 01:31 PM ben leinfelder

include accessfileid and subtreeid when inserting xml_access values

6016 03/23/2011 12:51 PM ben leinfelder

use access control dao for setting access in EML parser. send additional xml_access info in replication request

6015 03/22/2011 05:19 PM ben leinfelder

insert/update documents with null user and null group to circumvent access control restrictions then update the user_owner and user_updated values to reflect what exists on the originating server (pisco)

6014 03/22/2011 01:24 PM ben leinfelder

use 'user_updated' field when writing the replicated document - allows most recent ownership/permissions to be used (in case LDAP groups have shifted) and is more accurate for both updates and initial inserts (hopefully addresses the replication issue we are having with pisco)

6013 03/17/2011 09:02 AM ben leinfelder

use newer ecogrid tag to allow omission of the ecogrid query title (as is allowed in the query.xsd schema)

6012 03/16/2011 10:56 PM ben leinfelder

add support for temporal element query in pathquery
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2084

6011 03/12/2011 07:21 AM ben leinfelder

add otherEntity physical elements to indexPaths (ndp)

6010 03/04/2011 03:23 PM ben leinfelder

replace derik's settings with previous version

6009 03/04/2011 03:14 PM barseghian

add paths to indexPaths, and kar namespaces to indexNamespaces for Kepler Workflow Run Manager run-kar queries

6008 03/04/2011 02:52 PM ben leinfelder

include simple union data for search results if they are present in the resultset document

6007 03/04/2011 09:56 AM ben leinfelder

include temporal coverage dates in the path index - (for opendap metadata queries)

6006 03/03/2011 08:15 AM Chris Jones

Fixed the testNCEASLogin() password that I mistakenly changed.

6005 03/03/2011 07:47 AM Chris Jones

Now that MetacatHandler creates GUID identifier mappings and system metadata, many of the tests in IdentifierManagerTest were failing that were manually creating id mappings and system metadata.
Modified testCreateMapping() and testCreateSystemMetadataMapping() to use docids that haven't been inserted to just exercise the methods....

6004 03/02/2011 04:44 PM Chris Jones

Added a new test method testDeleteDocumentByGUID() to ensure MetacatHandler can delete based on GUID, but fall back to docid if the GUID isn't present. Modified CrudServiceTest and made some private methods public to leverage the D1 REST calls in that library (i.e. create() a doc with a GUID).

6003 03/02/2011 02:47 PM Chris Jones

The DataONE service API jar has been renamed to d1_common_java-0.5.0.jar, updated the build file accordingly. Added debug echo of the test classpath.

6002 03/02/2011 02:14 PM ben leinfelder

hide the data section unless there is actually data to display

6001 03/02/2011 02:12 PM Chris Jones

DocumentImpl.delete() now throws finer grained exceptions (not a general exception). Consequently, the classes that call it have been updated to handle the thrown exceptions, including CrudService, ReplicationHandler, and ReplicationService.

6000 03/02/2011 10:39 AM ben leinfelder

refactor the names of these Data Manager implementation classes so that it's easier to use them with the default/local versions of similar. These classes utilize Metacat-specific configuration values rather than relying soley on the bundles that are used in the stand-alone DM lib.

5999 03/01/2011 02:00 PM ben leinfelder

render the <data/> CDATA section in

 - it's a csv string

5998 03/01/2011 09:13 AM Chris Jones

To support GUIDs in MetacatHandler.handleDeleteAction(), I've added in a new method:
deleteFromMetacat() - deletes a document based on the docid
This factors the deletion code out of handleDeleteAction(). handleDeleteAction() now does a docid lookup based on GUID, and if it is not found, reverts to the deletion based on docid instead.

5997 02/28/2011 02:42 PM ben leinfelder

only include data value/operator when present in the form

5996 02/28/2011 02:42 PM ben leinfelder

refresh search when the data operator changes (changing the value is less clear...keyup event seems too eager)

5995 02/28/2011 11:57 AM ben leinfelder

use correct operators

5993 02/25/2011 12:01 PM ben leinfelder

include data search - new form fields and semQuery schema to allow searching for Characteristics data

5992 02/18/2011 12:28 PM ben leinfelder

turn off the databounds layer by default

5991 02/18/2011 12:09 PM ben leinfelder

new lines were showing up in the html source becuase of whitespace in this - removed the white space and the new lines are gone...

5990 02/18/2011 11:54 AM ben leinfelder

restyle the eml display and resultset after applying new eml css to the KNB L+F

5989 02/18/2011 11:16 AM berkley

new jar files from common and client

5988 02/18/2011 10:59 AM berkley

fixed width issue with default header

5987 02/18/2011 10:59 AM berkley

new files for mets style

5986 02/18/2011 10:10 AM ben leinfelder

[untested] loop through each origin[ator] to make a row for them

5985 02/17/2011 05:16 PM ben leinfelder

restyle the resultset after applying new eml css
use more robust form-submission js for the datapackage links

5984 02/17/2011 04:30 PM ben leinfelder

check for 'null' as well as 'public' user when rendering the header Login/Logout option

5983 02/17/2011 03:44 PM ben leinfelder

restyle default eml rendering using ESA look + feel

5982 02/17/2011 12:11 PM ben leinfelder

include eml css and then adjust lter skin to accommodate the new xsls

5981 02/17/2011 11:50 AM ben leinfelder

adjust stylesheets to accommodate new default eml rendering

5980 02/17/2011 11:28 AM ben leinfelder

use latest eml style tag

5979 02/17/2011 11:24 AM ben leinfelder

adjust stylesheets to accommodate new default eml rendering

5978 02/17/2011 09:45 AM ben leinfelder

use square edges for the borders around table groups and subgroups

5977 02/17/2011 02:57 AM Chris Jones

These are fairly significant changes to MetacatHandler.handleInsertOrUpdateAction() that add in support for creation or update of GUIDs and SystemMetadata. Upon insertion or update of DataPackages from non-DataONE aware clients (such as Morpho), the identifier table is updated by creating a GUID, and the systemmetadata table is updated with fields after the EML document is parsed for distribution information and entity typing. System Metadata documents are also generated and inserted into Metacat. The list of data entities is iterated over and System Metadata is generated for each data file as well.

5976 02/17/2011 02:39 AM Chris Jones

In MetacatHandler I've removed updateSystemMetadata() in favor of additions to insertOrUpdateSystemMetadata(). Modified createSystemMetadata() to reflect the changes as well.

5975 02/16/2011 06:23 PM Chris Jones

Modified MetacatHandler.createSystemMetadata() to take a localId, not a guid as an argument since there are times when the guid has yet to have been created, and it is created in this method if so.
Also, put the read() call to get the InputStream of the data/metadata document into it's own try/catch statement.

5974 02/16/2011 04:36 PM ben leinfelder

adjust to fit new EML look and feel

5973 02/16/2011 03:58 PM ben leinfelder

additional overrides for color

5972 02/16/2011 03:58 PM berkley

added mets to default skin

5971 02/16/2011 03:25 PM ben leinfelder

use white links override only in header menu

5970 02/16/2011 03:11 PM ben leinfelder

force the leftnav section to wrap their links

5969 02/16/2011 02:40 PM ben leinfelder

override problematic CSS properties that were introduced as part of the new look and feel for default EML display

5968 02/16/2011 01:56 PM Chris Jones

Somehow missed adding in javadoc for read(). Here it is.

5967 02/16/2011 01:52 PM Chris Jones

For now, getSystemMetadata() will be private like the other *SystemMetadata() methods.

5966 02/16/2011 01:47 PM Chris Jones

Modified MetacatHandler, updated the getSystemMetadata() method to now use read() and deserializeSystemMetadata() to produce the SystemMetadata object. Exceptions are pushed up the stack, and so accordingly, modified createSystemMetadata() to reflect the changes.

5965 02/16/2011 01:44 PM berkley

stylesheet/skins for mets data

5964 02/16/2011 11:38 AM ben leinfelder

use newer EML stylesheet tag

5963 02/16/2011 11:18 AM ben leinfelder

correctly include table cells for xsl

5962 02/16/2011 09:25 AM Chris Jones

Modified MetacatHandler, added createSystemMetadata() - generates SystemMetadata objects for newly inserted data or documents. This is intended to be used from handleInsertOrUpdateAction(), and only for documents being inserted from clients that don't support the DataONE interface. The method parses EML documents to discover data entities, and updates the system metadata for those entries, with support for describes and describedBy metadata. Currently doesn't handle FGDC, etc. documents....

5961 02/16/2011 09:14 AM Chris Jones

Modified MetacatHandler, added three methods:
getSystemMetadata() - returns a SystemMetadata object from the systemmetadata table using the given GUID. Stub only.
updateSystemMetadata() - updates the systemmetadata table using the given SystemMetadata object....

5960 02/16/2011 09:10 AM Chris Jones

Modified MetacatHandler and added two methods:
serializeSystemMetadata() - Serialize a SystemMetadata object to XML string
deserializeSystemMetadata() - Deserialize a SystemMetadata object from an XML string

5959 02/16/2011 09:07 AM Chris Jones

Modified MetacatHandler, added read() - Read a document from metacat and return an InputStream. The XML or data document should be on disk, but if not, read from the metacat database. This method should be optimized, along with others, to not write stream data to disk for performance reasons.

5958 02/16/2011 09:06 AM Chris Jones

To support generation of SystemMetadata and GUIDs, added a number of methods to MetacatHandler that are also in CrudService(). CrudService should eventually be refactored to use the handler methods. Added:
readFromFilesystem() - Read a file from Metacat's configured file system data directory, and return a FileInputStream. This code has been factored out of handleInsertOrUpdateAction()....

5957 02/15/2011 02:08 PM berkley

fixed bug where the wrong checksum alg got written to the db

5956 02/14/2011 02:03 PM Matt Jones

Updated DROP script that was missing tables and sequences.

5955 02/14/2011 11:45 AM berkley

added file extension for txt or csv files

5954 02/14/2011 11:39 AM ben leinfelder

correctly pass the search class and value when perfroming Protocol-based and Measurement-based queries (copy and paste oversight).

5953 02/13/2011 11:20 AM Chris Jones

To support the generatemissingsystemmetadata REST call, modified CrudService.createSystemMetadata() to use DataoneEMLParser and further determine object formats from EML metadata. Formats currently supported are text/plain, text/csv, image/[jpg|jp2|bmp|tiff|png], and only for EML documents with 'ecogrid://' defined entity urls....

5952 02/11/2011 02:56 PM ben leinfelder

make Data Object link more subtle since it now appears for each attribute

5951 02/11/2011 01:57 PM ben leinfelder

update skin to use new annotation schema - http://ecoinformatics.org/sms/annotation.1.0beta1

5950 02/11/2011 01:48 PM berkley

adding more debuggin and fixing bug with systemmetadata

5949 02/11/2011 11:42 AM berkley

new d1_common jar

5948 02/10/2011 06:09 PM Jing Tao

Make the schema with included schemas valid.

5947 02/10/2011 06:08 PM Jing Tao

Add a xml file for inserting during test.

5946 02/10/2011 06:07 PM Jing Tao

Add a method to test download a schema with included schemas.

5945 02/10/2011 06:06 PM Jing Tao

Add code to download the included schema.

5944 02/10/2011 04:17 PM berkley

fixed replication bug where systemmetadata was not getting procssed correctly