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From 04/23/2012 to 05/22/2012

05/23/2012

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.
Chris Jones

05/22/2012

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 ... ben leinfelder
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 ben leinfelder

05/21/2012

03:04 PM Revision 7180 (metacat): include TRACE level debugging for specific classes we want to have performance metrics for.
ben leinfelder
02:31 PM Revision 7179 (metacat): Add a few logging statemnts for round trip replication metrics.
Chris Jones
02:12 PM Revision 7178 (metacat): add trace statements for measuring time to complete SM generation.
ben leinfelder
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 ben leinfelder

05/18/2012

03:05 PM Revision 7176 (metacat): default replication policy set to 0.
ben leinfelder
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 ben leinfelder
12:00 PM Revision 7174 (metacat): include all EML versions (had been only eml 2.1 for testing)
ben leinfelder
11:59 AM Revision 7173 (metacat): new d1 jars for: remove exception from method decl - was not matching the interface def and not compiling.
ben leinfelder
05:43 PM Revision 7172 (metacat): Append more information such as user name and group to the validating session response.
Jing Tao

05/17/2012

12:46 PM Revision 7171 (metacat): remove exception from method decl - was not matching the interface def and not compiling.
ben leinfelder

05/15/2012

05:17 PM Bug #5608: Enable all FK constraints in Metacat production [copies]
The server_location = -2 docs are a mismash:
docid | rev
------------------------------...
ben leinfelder
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
...
ben leinfelder
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 ...
ben leinfelder
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...
ben leinfelder
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...
ben leinfelder

05/14/2012

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 ben leinfelder
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
ben leinfelder
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,...
ben leinfelder

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 ben leinfelder
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 ...
ben leinfelder
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...
unknown unknown
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... ben leinfelder

05/08/2012

04:30 PM Revision 7168 (metacat): only generate system metadata for original objects.
https://redmine.dataone.org/issues/2721 ben leinfelder
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>...
gastil gastil
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...
gastil gastil

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... gastil gastil
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 ben leinfelder

05/06/2012

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...
gastil gastil

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... Jing Tao
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... ben leinfelder
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)... ben leinfelder
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 ben leinfelder

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 ben leinfelder
03:59 PM Revision 7165 (metacat): D1 common lib AuthUtils update
ben leinfelder
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...
ben leinfelder
09:11 AM Revision 7164 (metacat): include testSynchronizationFailed() and call as the CN subject so that it is authorized.
ben leinfelder
09:06 AM Revision 7163 (metacat): use MN (self) as the Session.subject so that the MN.delete() call is successful.
ben leinfelder
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 ...
ben leinfelder

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 ben leinfelder
02:49 PM Revision 7160 (metacat): uncomment the MN tests (I bet this was an oversight during local testing)
ben leinfelder
02:48 PM Revision 7159 (metacat): add Session-less archive() method
ben leinfelder
11:59 AM Revision 7158 (metacat): jars with CN/MN.archive() libclient implementations
ben leinfelder
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
ben leinfelder
10:47 AM Revision 7156 (metacat): update the sysmeta data modified when setting archived=true
https://redmine.dataone.org/issues/882 ben leinfelder
10:26 AM Revision 7155 (metacat): handle CN.archive() rest call: PUT /archive/{pid}
https://redmine.dataone.org/issues/2678 ben leinfelder
10:25 AM Revision 7154 (metacat): correct log about 'archive' being called
ben leinfelder
10:15 AM Revision 7153 (metacat): handle 'archive' rest calls
https://redmine.dataone.org/issues/2678 ben leinfelder
10:15 AM Revision 7152 (metacat): updated d1 jars
ben leinfelder
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... ben leinfelder

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 ben leinfelder
03:42 PM Revision 7149 (metacat): newer d1 jars that include shared AuthUtilsmethod for isAuthorized() consistency
https://redmine.dataone.org/issues/2661 ben leinfelder
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
ben leinfelder
03:05 PM Revision 7147 (metacat): call MN.delete() for each replica when CN.delete() is called
https://redmine.dataone.org/issues/2676 ben leinfelder
02:20 PM Revision 7146 (metacat): defer to AuthUtils for flattening out the equivIdent subject list.
https://redmine.dataone.org/issues/2661 ben leinfelder

04/27/2012

10:24 AM Revision 7145 (metacat): check normal access control rules for getSystemMetadata before deferring to MN replica information that may grant MNs additional access to the SM.
https://redmine.dataone.org/issues/2656 ben leinfelder

04/25/2012

03:33 PM Revision 7144 (metacat): include Session-less interface methods and updated jars that define them.
ben leinfelder

04/24/2012

10:42 AM Revision 7143 (metacat): use a shared ExecutorService for replicate() calls.
https://redmine.dataone.org/issues/2623 ben leinfelder
 

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