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metacat / src / edu / ucsb / nceas / metacat @ 7765

# Date Author Comment
7765 05/23/2013 12:55 PM Matt Jones

Remove unused import.

7764 05/23/2013 12:52 PM Matt Jones

Mofdified Sitemap class to also generate the sitemap index file that is needed when more than one sitemap file is provided.

7757 05/23/2013 10:20 AM ben leinfelder

use ContentTypeInputStream interface (and ByteArray implementation) to specify the desired content-type of the InputStream returned by MN.query().

7755 05/22/2013 04:44 PM ben leinfelder

load the evicted SM back into the map on a "Refresh" so that listeners hear the update. (metacat-index, for example)

7752 05/22/2013 03:49 PM ben leinfelder

switch back to log4j statements now that I am sure certificate delegation is working.

7749 05/22/2013 03:02 PM ben leinfelder

use System.out.println until the oa4mp logging issue is resolved.

7745 05/22/2013 10:34 AM ben leinfelder

add logging for portal certificate look up process.

7743 05/22/2013 09:34 AM ben leinfelder

use relative path for oa4mp_client.xml (within servlet context). https://projects.ecoinformatics.org/ecoinfo/issues/5936

7737 05/21/2013 11:05 PM ben leinfelder

first pass at integrating CILogon/MyProxy certificates in Metacat. Configuration is specific to mn-demo-4.test.dataone.org for the time being (this will cause localhost deployments to fail webapp deployment). https://projects.ecoinformatics.org/ecoinfo/issues/5936

7735 05/21/2013 07:32 PM Matt Jones

Updated Sitemap generation to use latest version of the sitemap protocol schemas.

7730 05/20/2013 10:20 PM Jing Tao

Use the SolrQueryServiceController to get the spec version and index schema information.

7725 05/18/2013 11:46 PM Jing Tao

Change the package of SolrQueryReponseWriterFactory and SolrQueryResponseTransformer.

7720 05/18/2013 11:24 PM Jing Tao

Use the new query(SolrParams param) method of the SolrQueryServiceController.

7718 05/18/2013 05:19 PM Jing Tao

Use the SolrQueryServiceController class to handle the query.

7709 05/17/2013 02:22 PM Jing Tao

Move the cod which transformed the query response to the inputstream to the metacat-common module.
Remove some obsoleted imports.

7707 05/17/2013 12:57 PM Jing Tao

Move the code to generate the QueryResponseWriter to the metacat-common module. So it can be shared with the metacat-index module.

7703 05/17/2013 10:27 AM ben leinfelder

organize imports

7699 05/16/2013 03:21 PM ben leinfelder

remove extra lines from returned <docid/> block. https://projects.ecoinformatics.org/ecoinfo/issues/5932

7695 05/15/2013 05:16 PM ben leinfelder

Allow use of PID instead of docid in the Perl registry. At least for reading/editing and deleting existing content. Does not create content using a pid. https://projects.ecoinformatics.org/ecoinfo/issues/5932

7694 05/15/2013 03:53 PM ben leinfelder

initialize the SOLR home directory if it does not already exist.

7685 05/10/2013 02:59 PM Jing Tao

Only after reloading the core, the query result can reflect the change made in metacat-index module.

7681 05/09/2013 12:10 PM Jing Tao

Fixed a bug to put "OR" correctly in the query.
And remove the user "authorized_user" from the rightsholder clause in the query.

7680 05/09/2013 10:04 AM Jing Tao

Use the set of subjects to replace the user and groups for the solr query.

7677 05/08/2013 05:21 PM ben leinfelder

escape special XML characters when constructing a pathquery from user input (&). https://projects.ecoinformatics.org/ecoinfo/issues/3017

7671 05/08/2013 02:58 PM ben leinfelder

adjust action=zip behavior to use full docids and entity names (data files) for the zip entry. Also uses the given qformat to render the metadata. https://projects.ecoinformatics.org/ecoinfo/issues/3816

7669 05/08/2013 10:41 AM Jing Tao

Add the rightsHolder in the access filter.

7665 05/07/2013 04:54 PM ben leinfelder

adjust action=zip behavior to use full docids when checking for permissions/existence. https://projects.ecoinformatics.org/ecoinfo/issues/3816

7664 05/02/2013 05:30 PM Jing Tao

Add code to handle query for the http solr server.

7662 05/02/2013 12:47 PM Jing Tao

Use a new class to handle the solr query engine description request.

7652 05/01/2013 04:57 PM Jing Tao

Add double quotes to surrend the user or group names in the access fq. This will fix the issue if the names have white spaces.

7648 05/01/2013 02:38 PM Jing Tao

Add the access query filter.

7647 05/01/2013 01:53 PM ben leinfelder

Allow use of server-side XSLT for SOLR queries that include "wt=<qformat>". https://projects.ecoinformatics.org/ecoinfo/issues/5812

7639 04/30/2013 09:35 PM ben leinfelder

Allow null SM.submitter (per schema). There were null values in cn-dev (and probably elsewhere since it is technically allowed in the schema. But with a null value, we need to have a null Subject for the SM.submitter field, not a Subject with a null getValue() return. Encountered this when testing for: https://projects.ecoinformatics.org/ecoinfo/issues/5929.

7638 04/30/2013 04:47 PM ben leinfelder

add space to prevent syntax error when additional clause is appended. https://projects.ecoinformatics.org/ecoinfo/issues/5929.

7636 04/30/2013 02:50 PM Matt Jones

CHange replication 'update' query to use a LEFT JOIN so that the performance of the replication update action is improved, which had been causing an HTTP timeout for large metacat installations. See https://projects.ecoinformatics.org/ecoinfo/issues/5929.

7635 04/30/2013 02:46 PM Jing Tao

Add the code to read the index field information from the schema.xml.

7634 04/29/2013 04:59 PM Jing Tao

Add code to handle the solr index information. we still need to figure out how to get the information.

7625 04/25/2013 05:09 PM Jing Tao

Add the solr engine to the engine list.

7622 04/24/2013 07:34 PM ben leinfelder

use maven to manage most jar dependencies in Metacat.
Exceptions include: LSID, Datamamager (EML),

7620 04/24/2013 05:00 PM Jing Tao

Add code to handle solr query.

7609 04/23/2013 05:56 PM Jing Tao

Add a class to handle solr query.

7608 04/23/2013 04:26 PM Jing Tao

Remove those obsolete index classes.

7600 04/20/2013 06:19 PM Chris Jones

Merging the METACAT_2_0_6_BRANCH changes for [M|C]NodeService into the trunk.

7534 04/05/2013 12:38 PM ben leinfelder

allow verification date to be updated for replicas (patch from Skye). https://redmine.dataone.org/issues/3699

7520 03/22/2013 12:43 PM ben leinfelder

select only distinct guids (synch may have failed more than once for any given guid)
https://redmine.dataone.org/issues/3539

7519 03/22/2013 12:29 PM ben leinfelder

include xml_revisions.
do not allow removal of server_location = 1 documents (these are not replicas).
https://redmine.dataone.org/issues/3539

7517 03/14/2013 09:56 AM ben leinfelder

include size and format datcite elements (optional) and use more general resourceType without formatId in them (Dataset/metadata and Dataset/data). http://schema.datacite.org/meta/kernel-2.2/doc/DataCite-MetadataKernel_v2.2.pdf

7516 03/13/2013 05:11 PM ben leinfelder

lookup the title for EML files when registering DOIs.
lookup the creator from DataONE CN (if available).
add EML-based test. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

7515 03/13/2013 03:13 PM Chris Jones

Set the session to null so that the call uses the CN certificate when calling MN.systemMetadataChanged();

7514 03/13/2013 07:26 AM Chris Jones

To keep all nodes up to date with regard to system metadata changes, add the broadcastSystemMetadataChange() method that finds replica MNs in the node list and calls systemMetadataChanged(). Modify setReplicationStatus() and updateReplicationMetadata() to fire this off when a replica status changes to completed. We may decide to inform MNs at other times too, but this is a conservative amount of calls going to the MNs for now.

7512 03/12/2013 04:44 PM ben leinfelder

refactor DOI registration into separate class. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

7511 03/12/2013 04:26 PM ben leinfelder

refactor using ezid-client changes that split field names and values into separate enums. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

7510 03/12/2013 03:20 PM ben leinfelder

Correctly mint and register DOIs in teh MN API implementation. Add tests to exercise minting and creating. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

7507 03/11/2013 04:48 PM ben leinfelder

register DOIs with minimal DataCite metadata. still need to determine which details to include and when, but the plumbing is in place as we refine those rules. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

7506 03/08/2013 03:49 PM ben leinfelder

class for removing failed/invalid replicas from target nodes that previously held replicated content (KNB/LTER/PISCO/etc). https://redmine.dataone.org/issues/3539

7503 02/26/2013 10:27 AM ben leinfelder

disable EZID/DOI minting by default since we do not yet have a means of tracking minted DOIs and augmenting metadata for them when we actually receive the object in a subsequent create() or update() call. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5753

7498 02/22/2013 01:06 PM Brendan Hahn

tweak to pathquery/generic xpath handling

7495 02/22/2013 11:07 AM ben leinfelder

group user_owner clause as "AND (... OR .... OR ....)" to handle multiple pathquery <owner> elements. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5880

7494 02/21/2013 05:15 PM Brendan Hahn

accidentally added

7493 02/21/2013 05:13 PM Brendan Hahn

typo

7491 02/21/2013 12:43 PM Brendan Hahn

Search and indexing with Lucene/SOLR
Requires a manually configured SOLR installation
Not currently used by the rest of metacat

7489 01/31/2013 04:02 PM ben leinfelder

generate ID from UUID. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5840

7486 01/18/2013 02:12 PM ben leinfelder

make sure serial version is included or set on MN.update().
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5793

7480 01/07/2013 04:23 PM Brendan Hahn

Quick fix for bad handling of non-default data/backup directories.

7477 12/18/2012 05:33 PM ben leinfelder

remove indexing task from the queue when we are updating the document

7475 12/12/2012 02:38 PM ben leinfelder

move DocInfo parsing into utilities project so that it can be used by Morpho as well as Metacat.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5737

7471 12/10/2012 09:07 AM ben leinfelder

use default count = 1000 for CN.listObjects rather than -1 (because now -1 will cause an SQL error)

7469 12/08/2012 06:41 PM ben leinfelder

default replicaStatus to true for the CN.listObject call

7467 12/07/2012 10:39 AM ben leinfelder

make sure to call lock() on the SM when updating rightsholder (like every other method that gets a lock object from HZ).

7464 12/07/2012 10:25 AM ben leinfelder

CN.search() id not implemented by metacat -- making that explicit and also testing for it.

7462 12/05/2012 11:04 AM ben leinfelder

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

7461 12/05/2012 10:29 AM ben leinfelder

add debug statements for listObject slice debugging

7454 12/03/2012 02:25 PM Brendan Hahn

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

7452 12/03/2012 12:30 PM ben leinfelder

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

7451 12/03/2012 11:32 AM ben leinfelder

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

7450 12/03/2012 10:16 AM ben leinfelder

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

7448 12/02/2012 08:58 AM ben leinfelder

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

7447 11/30/2012 05:19 PM Chris Jones

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.

7446 11/30/2012 03:23 PM ben leinfelder

remove empty package

7445 11/30/2012 02:53 PM ben leinfelder

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

7444 11/30/2012 02:27 PM ben leinfelder

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

7443 11/30/2012 12:17 PM ben leinfelder

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

7442 11/30/2012 10:49 AM ben leinfelder

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

7441 11/30/2012 10:23 AM ben leinfelder

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"

7439 11/29/2012 04:52 PM ben leinfelder

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

7438 11/29/2012 04:33 PM ben leinfelder

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.

7437 11/29/2012 04:12 PM ben leinfelder

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.

7434 11/26/2012 02:28 PM ben leinfelder

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

7433 11/26/2012 02:25 PM ben leinfelder

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

7432 11/26/2012 01:50 PM ben leinfelder

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

7430 11/23/2012 10:02 AM ben leinfelder

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

7429 11/23/2012 10:00 AM ben leinfelder

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

7428 11/21/2012 04:35 PM ben leinfelder

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

7427 11/19/2012 04:03 PM ben leinfelder

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

7421 11/10/2012 03:34 PM Chris Jones

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.

7420 11/09/2012 10:57 AM Chris Jones

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.

7419 11/09/2012 08:56 AM Chris Jones

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)....

7418 11/07/2012 04:27 PM ben leinfelder

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.

7417 11/07/2012 02:53 PM ben leinfelder

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

7412 10/26/2012 09:11 AM ben leinfelder

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)....