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metacat / src / edu / ucsb / nceas @ 8210

# Date Author Comment
8210 09/16/2013 04:33 PM ben leinfelder

require authenticated session when minting a DOI/other identifier. https://projects.ecoinformatics.org/ecoinfo/issues/6086

8208 09/16/2013 03:47 PM ben leinfelder

include the dataone.subject (node admin) in the list of administrators. This allows full administrative access to objects when using certificates+d1 api. https://projects.ecoinformatics.org/ecoinfo/issues/6086

8202 09/16/2013 12:00 PM ben leinfelder

use optional template for registering DOIs at a given target. https://projects.ecoinformatics.org/ecoinfo/issues/6092

8200 09/13/2013 03:53 PM ben leinfelder

only attempt to generate OREs for objects that we know not to have them already. https://projects.ecoinformatics.org/ecoinfo/issues/6061

8193 09/13/2013 11:12 AM ben leinfelder

Generate an ORE when sci metadata is added via the Metacat API.
https://projects.ecoinformatics.org/ecoinfo/issues/6061

8190 09/12/2013 04:50 PM ben leinfelder

better checking for ORE maps when publishing DOIs (need to update the packages that contain sci meta). https://projects.ecoinformatics.org/ecoinfo/issues/6061

8189 09/12/2013 01:45 PM ben leinfelder

implement ORE check method to actually query the MN for OREs that reference the given pid.
https://projects.ecoinformatics.org/ecoinfo/issues/6061

8184 09/11/2013 10:59 AM ben leinfelder

change hazelcast group name to match the current context. https://projects.ecoinformatics.org/ecoinfo/issues/5624

8178 09/10/2013 03:17 PM ben leinfelder

check both previous and current data revisions when updating packages. https://projects.ecoinformatics.org/ecoinfo/issues/5647

8173 09/06/2013 02:22 PM ben leinfelder

avoid SQL errors when processing very old objects of type: "-//ecoinformatics.org//eml-access-2.0.0beta6//EN"

8164 08/26/2013 04:30 PM Jing Tao

If the pathquery engine is disabled, the xml path index queue will be disabled as well.

8163 08/26/2013 11:50 AM Jing Tao

If the xpath query is disabled, the query, squery and spatial_query action will be disabled as well.

8162 08/23/2013 04:01 PM Jing Tao

Add code to throw an exception if the pathquery is not enabled.
We also need to disable building index if the pathquery is disabled.

8160 08/22/2013 04:04 PM ben leinfelder

use consistent file names and zip content names. Opted for "-" separator so that the zip writer does not remove the unique part of the filename. https://projects.ecoinformatics.org/ecoinfo/issues/6054

8141 08/13/2013 12:57 PM ben leinfelder

copy the original systemMetadata when publishing a revision in order to avoid overwriting the original values - the shared map is listening! https://projects.ecoinformatics.org/ecoinfo/issues/6014

8075 07/25/2013 01:16 PM ben leinfelder

include user's fullName when validating a session. also, allow cookie session to be used if not passed in directly as a parameter

8074 07/24/2013 06:12 PM Jing Tao

Add code to modify the web.xml in metacat-index context if the metacat's name is not knb.

8034 07/18/2013 02:49 PM ben leinfelder

include filename in the package download, though we can;t really use the PID because of all the potential characters in it that are not valid for filesystems.

8028 07/18/2013 10:53 AM ben leinfelder

type the doctype="metadata" objects as "FGDC-STD-001-1998" formatId for rendering XSLT and for DataONE SystemMetadata.

8026 07/18/2013 08:13 AM ben leinfelder

use custom FileInputStream subclass to delete the temporary bagit zip when the inputstream is closed (after someone has downloaded the zip).

8025 07/18/2013 08:02 AM ben leinfelder

use ObjectFormatCache instead of ObjectFormatService because we are not calling it as a CN.

8018 07/17/2013 11:35 AM ben leinfelder

allow running the Harvester client without a source code checkout. (D. Blankman comments)

8014 07/16/2013 04:21 PM ben leinfelder

include the localid when rendering the view (used in stylesheets)

8013 07/16/2013 04:05 PM ben leinfelder

use ObjectFormatCache.getInstance().getFormat() instead of the CN service (the MN does not typically act as a CN!)

7984 07/15/2013 10:56 AM ben leinfelder

add slash for harvesterRegistration redirect.

7864 07/09/2013 10:40 AM ben leinfelder

include mn.publish() REST endpoint handling. https://projects.ecoinformatics.org/ecoinfo/issues/6024

7862 07/08/2013 06:19 PM ben leinfelder

comment out the index queue call when archive() is called - I think it is causing the duplicate events for the listener. https://projects.ecoinformatics.org/ecoinfo/issues/6030

7861 07/08/2013 06:10 PM ben leinfelder

implement the view service (uses existing skin-based dbtransform) - and include the REST endpoint. https://projects.ecoinformatics.org/ecoinfo/issues/6028

7860 07/08/2013 05:51 PM ben leinfelder

use StreamSource instead of StringReader for method signature -- can be used with different sources this way. https://projects.ecoinformatics.org/ecoinfo/issues/6019

7859 07/08/2013 05:10 PM ben leinfelder

clean up DBTransform in preparation for "view" service. https://projects.ecoinformatics.org/ecoinfo/issues/6019

7855 07/08/2013 12:14 PM ben leinfelder

include GET /package/{pid} endpoint in MN service. https://projects.ecoinformatics.org/ecoinfo/issues/6027

7853 07/05/2013 06:33 PM ben leinfelder

MN.getPackage() - test with ORE that includes 2 data files and a "metadata" file (still should be using EML for that test). https://projects.ecoinformatics.org/ecoinfo/issues/6026

7850 07/04/2013 12:33 PM ben leinfelder

First pass at MN.getPackage() implementation using Bagit library from LOC. https://projects.ecoinformatics.org/ecoinfo/issues/6026

7849 07/03/2013 09:58 PM ben leinfelder

add method for publishing existing object (usually assumed to be scimeta) with a DOI. https://projects.ecoinformatics.org/ecoinfo/issues/6014

7843 07/03/2013 10:13 AM ben leinfelder

add Metacat servlet action to force the reindexing of one or more or all pids in the system. https://projects.ecoinformatics.org/ecoinfo/issues/5945

7842 07/03/2013 12:28 AM ben leinfelder

only use MapStore/MapLoader for saving/loading IndexEvent objects. No need to use a listener since there is only the single node -- all entries are persisted to DB using the hazelcast.xml config we have for the map. https://projects.ecoinformatics.org/ecoinfo/issues/5944

7841 07/03/2013 12:03 AM ben leinfelder

add MapStore/Loader test for the IndexEvents -- adding and removing events in the DB table through hazelcast. https://projects.ecoinformatics.org/ecoinfo/issues/5944

7840 07/02/2013 04:47 PM ben leinfelder

support a "force replication delete all action" during replication. This is used when we want Metacat to remove the content from the other target replicas because the DataONE delete() action was called (more powerful than just "archive").

7839 07/02/2013 04:41 PM ben leinfelder

add simple test for the IndexEventDAO class -- adding, removing, listing events in the DB table. https://projects.ecoinformatics.org/ecoinfo/issues/5944

7830 06/25/2013 04:42 PM ben leinfelder

upgrade to Metacat 2.1.0 on the trunk. This includes a new index_event table for storing indexing events that need to be reprocessed. https://projects.ecoinformatics.org/ecoinfo/issues/5944

7829 06/25/2013 01:23 PM ben leinfelder

stub for storing IndexEvent objects in Metacat (from metacat-index processing). https://projects.ecoinformatics.org/ecoinfo/issues/5944

7827 06/25/2013 01:17 PM ben leinfelder

do not force a get() during refresh (causing EML-defined data access rules to be lost when inserting EML docs about data files). note that this reverses a change that was meant to trigger indexing, but now we are using a new queue to share index events with metacat-index and so should not be necessary.

7824 06/24/2013 12:05 PM ben leinfelder

do not use tmp file to return an inputstream on read() operations - just read from the file we already have. https://projects.ecoinformatics.org/ecoinfo/issues/6009

7823 06/21/2013 09:44 PM ben leinfelder

use standard File.createTempFile() method for uploaded data files and delete them when we are done with them. https://projects.ecoinformatics.org/ecoinfo/issues/6008

7816 06/21/2013 11:11 AM ben leinfelder

correct regex for whitespace in D1 identifier.

7812 06/20/2013 04:49 PM ben leinfelder

use an independent ISet<SystemMetadata> structure to communicate objects that should be indexed by metacat-index. https://projects.ecoinformatics.org/ecoinfo/issues/5943

7809 06/18/2013 02:59 PM ben leinfelder

do not create solr-home if there is no template to compy into that directory (need to be able to create it later if/when someone decides to use and deploy metacat-index). https://projects.ecoinformatics.org/ecoinfo/issues/6006

7808 06/18/2013 01:54 PM ben leinfelder

do not attempt to copy solr-home template from metacat-index webapp if it does not exist. This would be in cases where metacat-index is not deployed. https://projects.ecoinformatics.org/ecoinfo/issues/6006

7781 05/28/2013 01:20 PM Jing Tao

Solr will be enabled if it is in the db.enabledEngines.

7778 05/24/2013 10:20 AM ben leinfelder

do not require PortalCertificateManager be configured. Fix NPE because session was not created when using old sessionid-based authentication. https://projects.ecoinformatics.org/ecoinfo/issues/5942

7773 05/23/2013 09:45 PM ben leinfelder

handle client certificates, portal certificates and jsessionid as three ways to prove you are an uthenticated user. https://projects.ecoinformatics.org/ecoinfo/issues/5942

7772 05/23/2013 06:39 PM Jing Tao

Use some contants from the EnabledQueryEngines.

7766 05/23/2013 01:26 PM Matt Jones

Updated documentation, and added modification date to the sitemap index file entries.

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