Metacat

default replicaStatus (aka "show replicas in results") to true rather than false

add debug statements for listObject slice debugging

Add the non-snapshot jars for the D1 libraries.

use utilities and eml RC tags for building Metacat.

include dataone.contactSubject in backup properties so it will be "remembered" during upgrades.

update release date to December

additional db indexes for pathquery performance
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

Do not set headers until response is ready to send (5756)

use jar generated from the git repo source (just in case it was different from svn). http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5755

use dual query for query slicing - one for count, another for the actual records when requested.
https://redmine.dataone.org/issues/3065

get total (or subtotal when non-slicing params are present) count as a separate query from the field selection query.

include Skye's suggestions about correctly limiting by D1 Event types

use test doi shoulder as the default for local server, at least during testing phase. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5755

first pass at DOI minting using the EZID service in mn.generateIdentifier()
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5755

Fix a minor bug in listObjects() where total was set incorrectly when total was set incorrectly when count=0. The definition of total in the D1 architecture docs says 'The total number of entries in the source list from which the slice was extracted.' With count=0, we assume the total is the total count from the entire object store. Needs testing.

remove empty package

rollback the delete() when there is an error performing part of it -- don't want to end up with partial delete.

use Identifier object not String when retrieving SM from the HZ map to set archived during delete()

for MN.update() we needed to pass the original pid, not the new pid

do not reject any schemes -- all handled the same at the moment.

simple autogen-based implementation of MN.generateIdentifier(). does not support DOIs, ARKs, etc. It does support including a fragment, returning an identifier like "<fragment>.2012113010215298206"

add link for reference on how to do record limits in oracle

limit /log and /object calls to configurable maximum count for paging. defaults to existing Metacat value of 7000

use RDBMS-specific features to limit the resultset for paging the object list -- postgres and oracle have implementations. we don''t really support mssql so I skipped that one.

use RDBMS-specific features to limit the resultset for paging -- postgres and oracle have implementations. we don''t really support mssql so I skipped that one.

Add the latest SNAPSHOT build of the hazelcast jars built by robert at:

http://dev-testing.dataone.org/maven/com/hazelcast/hazelcast/2.4.1-SNAPSHOT/hazelcast-2.4.1-SNAPSHOT.jar
http://dev-testing.dataone.org/maven/com/hazelcast/hazelcast-client/2.4.1-SNAPSHOT/hazelcast-client-2.4.1-SNAPSHOT.jar...

Update the hazelcast libraries based on the most recent build from the hazelcast trunk using patches that robert submitted via git pull requests.

include debug msg about removing docid from index queue. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5750

remove document from the indexing queue when delete is called. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5750

clean up index queue code before tackling index/delete race condition. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5750

additional release notes about archive/delete behavior and HZ upgrade

no need to mark SM as archived now that DocumentImpl.delete() does it.
https://redmine.dataone.org/issues/3406

mark documents as archived=true when they are deleted using the Metacat API.
https://redmine.dataone.org/issues/3406

look up the archived value when retrieving SystemMetadata record.
https://redmine.dataone.org/issues/3405

surround returned query in CDATA to prevent parsing of xml within xml

Update the two hazelcast jars to 2.4.1-SNAPSHOT versions that Robert generated after fixing certain hazelcast build problems.

correct the metacat.properties help anchors.

use sleeker "?" icon for the admin help links

correct the "?" links in the admin pages to the docs pages that are deployed as part of metacat.

In migrating to Hazelcast 2.4.x, replace deprecated methods.

In migrating to Hazelcast 2.4.x, replace deprecated methods. Use Hazelcast.newHazelcastInstance() rather than Hazelcast.init(). For other deprecated static methods, use the HazelcastInstance equivalent calls.

In CNodeService.updateReplicationMetadata(), we are setting the replicaVerifiedDate() when we update or wholesale add a new replica. However, in setReplicationStatus(), we only do so when there's a new entry. Change setReplicationStatus() to also update the replicaVerifiedDate on updates of existing entries to be more consistent with other changes. This affects node prioritization based on this date timestamp. Thanks to Skye for pointing this out.

To attempt to address performance and stability WRT Hazelcast communication, we're upgrading to the 2.x series of Hazelcast. remove the 1.9.x jar files, and add the 2.4.1-SNAPSHOT jars. Modify HazelcastService to handle the minor change in the ItemListener interface (now passes ItemEvent<Identifier> as an argument)....

implement query description for pathquery -- only tells callers about the pre-indexed paths we have in Metacat since there are an infinite number of "fields" when storing arbitrary XML, but we really don't want people using non-indexed paths for performance reasons anyway. I've typed all the fields as String, even though some are not just strings and can be used for numeric or data comparisons.

Implement MNQuery for "pathquery" engine. Optionally include guid in the pathquery results (https://redmine.dataone.org/issues/3083)

update pub_date when the length of that field is != 4 (use date_created in this scenario). There were 2 entries that had "193" as the pub_date.

replace new lines in creator with spaces. set blank " " titles and creators to "unknown". use "Baltimore Ecosystem Study LTER" for publisher on all BES objects.

include John Kunze's latest suggestions for improved metadata -- a lot of clean-up, especially on characters in the file. Note UTF-8 encoding of the script.

include note about pathquery performance fix (when using indexed fields)

use ObjectFormatInfo libclient utility to look up mimeType and filename extension during get() calls. Configurable mapping file is deployed by default to /var/metacat/dataone where it can then be augmented as needed. This location is controlled in the metacat.properties file (which is injected into the DataONE Settings values during weapp intitialization)....

add count for the total processed pids (from ISet iterator)

handle /object?count=0 queries using simpler (quicker) sql
https://redmine.dataone.org/issues/3065

allow getlog action to use docid parameters that do not include revision. In these cases, the latest revision will be used.

handle case where we do not have a pathexpr to check
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

simplify the xml_access query, and instead use guid to check for permission. Now the docid/rev join (to get most recent version for search results) happens "higher up" in the query.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

include log stats for total 'read' events when rendering a package.

rework simple log stats so that there is no saxon requirement (xslt 2)

pass parameters to the getLog action for rendering in xslt

remove morpho.jar -- moved needed classes into shared utilities project. (currently building form utilities trunk -- be sure to 'ant fullclean' to get the latest utilities.jar built)

remove use of HttpMessage (in morpho.jar) in favor of standard httpclient methods for calling the servlet in tests

Update d1_common_java and d1_libclient_java to the newest jar files. Add methods to CNodeService to throw NotImplemented exceptions for query(), listQueryEngines(), and getQueryEngineDescription() since these API calls are handled outside of metacat.

do not allow updates to orphan another branch of revision history. https://redmine.dataone.org/issues/3338

Change the set and get methods for the replication verified date to use java.sql.Timestamp rather than java.util.Date via setTimestamp(), not setDate(). The hh:mm:ss.sss was previously getting truncated.

include the subjects we are testing for authentication.
https://redmine.dataone.org/issues/2778

remove the max(rev) clause in favor of a more straight-forward join to xml_documents (that will have the max rev). http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

add note about sanparks/saeon spatial file download: http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5718

include inverted sendParameters() method that uses the keys as values, and the values as keys so that multiple docid parameters can be specified for the zip download. This was a regression when moving to standard httpclient rather than the roll-your-own version we had been using. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5718

integrate ecoinformatics login with the CIlogon identity mapping flow so that a user is directed through the process with no manual navigation needed (at least in the url bar). https://redmine.dataone.org/issues/1480

use version 2.0.5

shorten the systemmetadata* table names for Oracle's 30 character limit. move version to 2.0.5. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5717

ajax-ify the call to perform identity mapping (including errors)

look up CN url for portal servlet instead of hardcoding it.

look up CN url for portal servlet instead of hardcoding it.

use alternative syntax for xml_access table update since oracle does not use joins in a update statement that same way as postgres. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5717

correct Oracle syntax
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5717

use correct column (guid) for temporary index

use correct release date (September 2012)

use correct docid format when checking for existing mappings.

include sessionid when constructing the EML download link. pull from RELEASE_EML_UTILS_1_0_5 eml tag.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5709

use CDATA for docname field in docInfo so that XML parser ignores the content that can contain characters like "&

include sessionid when constructing the EML download link. pull from RELEASE_EML_UTILS_1_0_5_RC1 eml tag.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5709

use RELEASE_EML_UTILS_1_0_4 for EML stylesheets

use RELEASE_EML_UTILS_1_0_4_RC1 for EML stylesheets

include qformat parameter in docs for squery
remove mention of 'username' for getLastDocid -- should only use scope param

include missing identifier mappings during 2.0.4 upgrade (mappings may be missing due to previous replication between servers that do not house SystemMetadata)

use SchemaLocationResolver to fetch remote entries for the xml_catalog -- we want to be able to fetch included xsd files as well as use any error handling it provides for checking the schemas.

prep for 2.0.4 release

when performing query, make sure we are using the access rules of the latest revision of a given docid, otherwise we may include documents that used to be public but have been made private in subsequent revisions.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

correct the number of prepared statement parameters when inserting to xml_revisions table.
Errors like the following were showing in the replication log file:
knb 20120831-19:42:38: [ERROR]: DocumentImpl.writeReplication - Failed to create access rule for package: john.15950.1 because The column index is out of range: 12, number of columns: 11. [ReplicationLogging]

include WHERE in the sql where clause - encountered by SAEON's node admin, Alex Niehaus.

use resourceMapLocation (resolve url for the ore map) as the datacite_relatedIdentifier_isPartOf property

use lowercase 'metadata' and 'data' for the resourceType

set publisher to the source system when publisher == creator (we want them to be different, even if just for appearances)

only include public (readable) DOIs in the final output

use "lastname, firstname" convention throughout

include more descriptive data file name for title of data records

include publisher given name correctly

create docid-guid mapping during replication if it does not exist. we were [incorrectly] assuming that there would be SM coming with the document info that would fill this information in, but for traditional non-MN Metacat deployments there is no SM to provide a mapping. In this case we use the docid as the guid.

include certificate export SSL options as an example (used heavily for DataONE and Metacat Replication)

stream the replication "update" response rather than building up a complete list in a stringbuffer. prompted by findings on t he CN: https://redmine.dataone.org/issues/3141