Activity
From 04/29/2012 to 05/28/2012
05/28/2012
- 01:25 PM Revision 7194 (metacat): include eml2.0.0beta4 DTD during Metacat build so that we can continue to accept (and validate) beta4 documents.
- This arose when testing Metacat as DataONE Coordinating Node where legacy documents are being housed in the CN.
05/27/2012
05/25/2012
- 06:20 PM Revision 7192 (metacat): Don't set the replication status to failed for an object when it is called by a public user. Just throw the NotAuthorized exception. This prevents this node from being de-prioritized because of public calls to the method.
- 04:23 PM Revision 7191 (metacat): include revisions table in the initial temp table population.
- use the "first" creator listed in the EML (either org or person).
use other reasonable default values as needed to fu... - 02:30 PM Revision 7190 (metacat): add columns: publisher and pub_date. include default values for all columns - even data files should have title.
- still a few todos but closer.
https://redmine.dataone.org/issues/2815 - 12:07 PM Revision 7189 (metacat): script to generate DOI registration spreadsheet
- https://redmine.dataone.org/issues/2815
05/23/2012
- 04:41 PM Revision 7188 (metacat): share the same dbConnection when inserting and then updating SystemMetadata objects in the backing store.
- any errors encountered during the update will rollback the entire transaction and the SM record will not exist, even ...
- 03:28 PM Revision 7187 (metacat): Do not loadAllKeys() for SystemMetadataMap when Metacat first starts up. hzIdentifiers will be populated with a simple SQL statement rather than the serial loading of every single SystemMetadata object. It will remain in synch using the usual entryXXX() methods as before.
- This should save us resources where we were previously attempting to load ALL SystemMetadata into memory on startup.
- 02:22 PM Revision 7186 (metacat): use LRU eviction policy and a small (1000) map size limit to avoid running out of memory because of a large number of system metadata objects
- 02:17 PM Revision 7185 (metacat): Set the default maximum number of database connections back to 200. After discussion, we've decided it will be better to increase the PostgreSQL limit to 300 and keep Metacat's pool size pretty big.
- 09:57 AM Revision 7184 (metacat): include pidFilter handling - only matches the complete pid. Issues a warning in the Metacat logs when pidFilter cannot be applied but allows the call to getLogs() to return as though there was no pidFilter given.
- https://redmine.dataone.org/issues/2798
- 09:33 AM Revision 7183 (metacat): use at least one thread on single-processor machines.
- https://redmine.dataone.org/issues/2800
05/22/2012
- 05:46 PM Revision 7182 (metacat): Change the database.maximumConnections property to 100. PostgreSQL's docs says it can handle "a few hundred", and would need to be increased from the default 100 max_connections. For DataONE optimization, we increase max_connections, however there are more processes making connections other than metacat, so I'll reduce metacat's default share.
- 04:52 PM Bug #5608: Enable all FK constraints in Metacat production [copies]
- I've drafted a script that corrects FK violations and re-applies the original constraints. The xml_index table takes ...
- 04:47 PM Revision 7181 (metacat): script for re-applying missing FK constraints on KNB production DB.
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5608
05/21/2012
- 03:04 PM Revision 7180 (metacat): include TRACE level debugging for specific classes we want to have performance metrics for.
- 02:31 PM Revision 7179 (metacat): Add a few logging statemnts for round trip replication metrics.
- 02:12 PM Revision 7178 (metacat): add trace statements for measuring time to complete SM generation.
- 11:25 AM Revision 7177 (metacat): new D1 jars:
- prevent NPEs from the object format cache when formatId.value is null. This came up during PISCO testing
05/18/2012
- 03:05 PM Revision 7176 (metacat): default replication policy set to 0.
- 12:09 PM Revision 7175 (metacat): instead of generating SM and ORE maps during dataone configuration/MN registration, moved this all to the replication admin screen where we can target generation for specific nodes. That way it's more controlled as to when and where we generate DataONE required content.
- https://redmine.dataone.org/issues/2740
- 12:00 PM Revision 7174 (metacat): include all EML versions (had been only eml 2.1 for testing)
- 11:59 AM Revision 7173 (metacat): new d1 jars for: remove exception from method decl - was not matching the interface def and not compiling.
05/17/2012
- 05:43 PM Revision 7172 (metacat): Append more information such as user name and group to the validating session response.
- 12:46 PM Revision 7171 (metacat): remove exception from method decl - was not matching the interface def and not compiling.
05/14/2012
- 05:17 PM Bug #5608: Enable all FK constraints in Metacat production [copies]
- The server_location = -2 docs are a mismash:
docid | rev
------------------------------... - 05:16 PM Bug #5608: Enable all FK constraints in Metacat production [copies]
- the server_location=5 docs are 'seabloom' and 'borer' prefixes:
borer.13.2
borer.14.2
seabloom.10.1
seabloom.6.2
... - 05:14 PM Bug #5608: Enable all FK constraints in Metacat production [copies]
- catalog_id = 27 is a "-//ecoinformatics.org//eml-software-2.0.0beta5//EN" doctype with docid=jdoe.23.1
We have that ... - 05:10 PM Bug #5608: Enable all FK constraints in Metacat production [copies]
- For the index errors we can safely delete the index records in violation of the constraint and apply it.
For the ser... - 05:08 PM Bug #5608: Enable all FK constraints in Metacat production [copies]
- The errors encountered were....
ALTER TABLE xml_documents ADD
CONSTRAINT xml_documents_rep_fk
FOREIGN KEY (server_lo... - 12:27 PM Bug #5608: Enable all FK constraints in Metacat production [copies]
- 14.4.9. Some Notes About pg_dump:
http://www.postgresql.org/docs/8.3/interactive/populate.html - 12:14 PM Bug #5608 (New): Enable all FK constraints in Metacat production [copies]
- Looks like the FK constraints have been removed from the production knb database.
> select conname, contype, conkey,... - 02:36 PM Revision 7170 (metacat): add "Generate System Metadata" button to the replication server list display. When clicked, we generate SM for records belonging to that source server. This is only enabled when DataONE has been configured.
- https://redmine.dataone.org/issues/2762
05/09/2012
- 03:45 PM Revision 7169 (metacat): expose serverLocation parameter to run GenerateSystemMetadata for different replication parters as needed.
- https://redmine.dataone.org/issues/2740
- 11:08 AM Bug #5604: Question how to add EPSG 900913 for Google layers and how list results within a bounding-box
- Hi Eva-Maria,
With Metacat 2.0.0 (which is still in a pre-release state) you'll be able to use the OpenLayers client ... - 01:08 AM Bug #5604 (Resolved): Question how to add EPSG 900913 for Google layers and how list results within a bounding-box
- Dear Metacat developer team,
I would like to ask you 2 questions:
1.)
I am trying to use Google maps as backgr...
05/08/2012
- 05:14 PM Bug #5599: absence of line feeds in eml causes pathQuery to not find some elements
- While this is indeed odd, my hunch is that we get a placeholder leaf node for the line feed that separates <attribute...
- 12:33 PM Bug #5599: absence of line feeds in eml causes pathQuery to not find some elements
- to clarify, these pathQueries were for
<queryterm casesensitive="false" searchmode="starts-with">
<value>... - 12:32 PM Bug #5599: absence of line feeds in eml causes pathQuery to not find some elements
- To diagnose this further:
(1)
I ran pathQuery for returnfield dataset/dataTable/attributeList/, that is, the whole x... - 04:30 PM Revision 7168 (metacat): only generate system metadata for original objects.
- https://redmine.dataone.org/issues/2721
05/07/2012
- 03:54 PM Bug #5599 (New): absence of line feeds in eml causes pathQuery to not find some elements
- Presence of line feeds seems to be needed for an eml doc to get loaded properly so pathQuery can find attributeList o...
- 08:08 AM Bug #5597: eml xsl templates incomplete
- changing version to 2.0.0, though this will require modifications to the EML project if we alter the default XSLTs
05/05/2012
- 06:32 PM Bug #5597 (Resolved): eml xsl templates incomplete
- Some xslt templates for eml transform to html are incomplete in metacat 2.0.0 (on lava).
Attached are two screensh...
05/04/2012
- 04:29 PM Bug #5518: Track down the performance issue of metacat query.
- Yeah. Kepler issues a query for different metadata type because the ecogrid could handle only one return doctype. I b...
- 03:26 PM Bug #5518: Track down the performance issue of metacat query.
- Running the same query (well, with "Insect" (not plural) so the results were not cached) with 50 threads makes this p...
- 02:43 PM Bug #5518: Track down the performance issue of metacat query.
- I wrote a small test that issues the same Metacat query to a given server with parallel threads (25 for this example)...
- 02:50 PM Revision 7167 (metacat): test for running concurrent Metacat queries to mimic Kepler data search.
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5518
05/02/2012
- 04:21 PM Revision 7166 (metacat): check if person's equivalentIdentity list is null before processing recursively
- https://redmine.dataone.org/issues/2689
- 03:59 PM Revision 7165 (metacat): D1 common lib AuthUtils update
- 03:47 PM Bug #5518: Track down the performance issue of metacat query.
- There seems to be renewed concern that this is not resolved.
During the Kepler/sensor workshop Matt reported query pe... - 09:11 AM Revision 7164 (metacat): include testSynchronizationFailed() and call as the CN subject so that it is authorized.
- 09:06 AM Revision 7163 (metacat): use MN (self) as the Session.subject so that the MN.delete() call is successful.
- 08:58 AM Revision 7162 (metacat): handle authorization for delete() differently for CN vs MN.
- On the CN, only the CN (or tbd admin user) can call it.
On the MN, both the CN (or admin user) and the _same_ MN can ...
05/01/2012
- 02:55 PM Revision 7161 (metacat): comment out testDelete because it requires acting as the MN
- comment out testSynchronizationFailed because it requires acting as the CN
- 02:49 PM Revision 7160 (metacat): uncomment the MN tests (I bet this was an oversight during local testing)
- 02:48 PM Revision 7159 (metacat): add Session-less archive() method
- 11:59 AM Revision 7158 (metacat): jars with CN/MN.archive() libclient implementations
- 11:14 AM Revision 7157 (metacat): only admin users can call MN/CN.delete(). This is limited to any CN and only the MN that is calling itself
- 10:47 AM Revision 7156 (metacat): update the sysmeta data modified when setting archived=true
- https://redmine.dataone.org/issues/882
- 10:26 AM Revision 7155 (metacat): handle CN.archive() rest call: PUT /archive/{pid}
- https://redmine.dataone.org/issues/2678
- 10:25 AM Revision 7154 (metacat): correct log about 'archive' being called
- 10:15 AM Revision 7153 (metacat): handle 'archive' rest calls
- https://redmine.dataone.org/issues/2678
- 10:15 AM Revision 7152 (metacat): updated d1 jars
- 09:18 AM Revision 7151 (metacat): [optionally] do not archive the xml_documents and xml_nodes to *_revisions when 'deleting' a document. This will effectively guarantee that the document/data cannot be retrieved after delete.
- NOTE: D1 system metadata will persist (for now) so that the ID cannot be reused with the DataONE API but Metacat call...
04/30/2012
- 04:03 PM Revision 7150 (metacat): optionally remove the document/data file from the filesystem completely when 'deleting' it.
- https://redmine.dataone.org/issues/2677
- 03:42 PM Revision 7149 (metacat): newer d1 jars that include shared AuthUtilsmethod for isAuthorized() consistency
- https://redmine.dataone.org/issues/2661
- 03:35 PM Revision 7148 (metacat): implement MN and CN.archive() method -- really just the existing delete() methods.
- https://redmine.dataone.org/issues/2674
https://redmine.dataone.org/issues/2675 - 03:05 PM Revision 7147 (metacat): call MN.delete() for each replica when CN.delete() is called
- https://redmine.dataone.org/issues/2676
- 02:20 PM Revision 7146 (metacat): defer to AuthUtils for flattening out the equivIdent subject list.
- https://redmine.dataone.org/issues/2661
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