remove the non-doi identifiers before updating the LTER - should save time on the update.https://redmine.dataone.org/issues/2858
use eml stylesheet tag (1.0.3)
use 1.0.2 d1_libclient jar (built by hudson)
set archived flag (true) when we set the obsoletedBy value in the ORE system metadata
update for 2.0.1 upgrade -- scripts, docs, readme
remove saxon jar (XSLT 2.0 support) with plans to re-add when we understand how to make it more lenient WRT to invalid character content in source XML
move to 1.0.2 d1_libclient jar for ORE generation change (URI for aggregation)
use the localId for obsoletes/obsoletedBy ORE system metadata (https://redmine.dataone.org/issues/2964)
use correct esa email list
include xml-apis*.jar when building the LSID authority.war -- without this file the authority webapp has a fatal error (no class def found) on init.
correct block formatting for tomcat config changes
add tomcat config options for DataONE identifiers with slashes
excluded the HzObjectPathMapTest$1 and HzObjectPathMapTest$2 classes which are not test classes in the test taraget.
Print the stack trace when the MMP cannot be resolved.
Use a final static string to replace the hard code.Search document title rather than id in testReplicateEML_AtoB method.
use 1.0.2 tag for EML stylesheets
update MN registration screen shot and amend instructions that say a nodeId will be assigned during registration.add section about generating SM for a new Member Node that has existing Metacat data.
use CN session when testing getLogRecords() and getOperationStatistics() becuase they are now protecting "sensitive" information
use RC for EML stylesheets before going to yet another minor revision number.
report errors during XML->HTML transformhttp://bugzilla.ecoinformatics.org/show_bug.cgi?id=5618
add 'fulldist' target to combine building of src and bin distributions
include gastil's changes re: pathquery and 'delete'http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516
Add details for configuring Apache to use client certificate authentication.
use production CN url as the default (instead of cn-dev)
Oops, previous commit suffered from a happy trigger finger. During deleteReplicationMetadata(), don't delete the replica on the replica Member Node. Call CN.delete() for that functionality. This call just updates sytem metadata (according to the API description).
remove distribution tar.gz and zip files on fullclean.
use iframe id for the login anchor since the anchor inside the iframe does not work.http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5619
get utilities source from the correct checkout location
clarify release notes for 2.0.0 (minor)
correct Javadoc link http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516
Minor logging change.
Add debug logging to delete() to understand why we're getting InsufficientKarmaException.
apply Gastil's edits. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516
add section about configuring the metacat.properties with the paths to the server certificate and key
remove unused replication properties (all certificate file based now)
use 1.0.1 DataONE jars
use KNB identifier table (post DOI generation) to update LTER identifier table.https://redmine.dataone.org/issues/2857
exclude the MockObjectPathMap class from the test target since it is not a junit test.
exclude QueryRunner in test target. This is not a junit test file.
Since we already have determined access via isAuthorized() and isAdminAuthorized(), act as the Metacat administrator during calls to DocumentImpl.delete() in archive(), passing in null username and group.
restrict getLogRecrods (both MN and CN) to be called only by admin users (the CN)https://redmine.dataone.org/issues/2855
use updated tag for EML stylesheet-only changeshttp://bugzilla.ecoinformatics.org/show_bug.cgi?id=5597
In setReplicationStatus() and UpdateReplicationMetadata(), don't allow a status state change from COMPLETED to anything other than INVALIDATED. This prevents the completed status from being overwritten due to race conditions.
do not include releaseCandidate property - does not seem to be used except for debian? packaging which was never fully implemented.
use non-snapshot D1 jars in prep for tagging/release. Still RCs
script to aid in converting denyFirst rules to allowFirsthttps://redmine.dataone.org/issues/2613
use kepler account as default
use current default tomcat6 deploy directory
include test shoulder defaults for KNB, PISCO and LTER
Fixed formatting problem in a documentation file.
use metacat.properties to specify the default checksum algorithm to use -- this way it will be easy for us to switch to whatever DataONE decrees. https://redmine.dataone.org/issues/2834
put(sm) for every pid we have a SM value for so that all members receive the entry event and can save locally.
add section about importing self-signed certificates into the Java keystore (now that we use strict verification on the java client side when calling replication endpoints).
a few additional notes about Metacat replication configuration.
Throw an exception when NOT allowed, not when allowed =).
ignore partition owner -- always attempt to look up form local store if we were unable to get the SM from the shared map.
do not check if this CN has a "perfect" copy of the SM identifiers -- we need any CN coming online to contribute the records that they have locally so that in the event that all three CNs have a partial view of things they all eventually share each others' SM entries.
Also get the list size, which may throw an NPE.
Only add an AccessPolicy to SystemMetadata during generation when the AccessPolicy is not empty. We've had some scenarios where IdentifierManager.getaccessPolicy() is returning an empty policy because of an empty permission list coming from the db. This was causing InvalidSystemMetadata exceptions during MN to MN replication.
push SystemMetadata entries from the CN that has them all to the shared map where other nodes may not have all entries. The CN with the complete copy only pushes SM entries that it does not own and that return as null because those are the ones that are missing on the other, non-complete CNs....
trace level log for looping over EVERY pid in the system.
meant to log the guids (source) not the pids (target)
logging for each step of shared identifiers loading.
remove pause/resume - seemed to make metacat just hang on SM retrieval. Add more logging when returned SM is null -- want to make sure it is becuase the local node "owns" the pid key even though there is no value for it.
due to hudson build issue, did not actually end up testing pause/resume -- trying that again
pause/resume was not enough. trying shutdown/restart
experiment with lifecycle pause/resume. hopefully it prevents our node from taking ownership of any keys before we are sure we have them all.
increase logging and add back in the call to saveLocally() in case the SM object has already been loaded into the shared map but before this node came back online.
no need to call saveLocally explicitly since loading from the shared store triggers that behavior locally because of the configured listeners.use an iterator over the shared identifiers in case this set is constantly changing.
make only one DB call to look up local pids - no need to do a pstmt for every single shared pid.
on init (start up) launch a synchronization thread that ensures all shared identifier entries have a corresponding local System Metadata entry.
use 'allowFirst' for access rules. We have deprecated 'denyFirst' and deny rules in Metacat as of 2.0.0
handle https-only server configuration -- must pull resources from https not http for the skins etc.
fix NPE (logMetacat object was not initialized) that was occurring during store()
stack trace the HZ put exception during CN-CN replication
additional debugging statements for CONCURRENT_MAP_PUT error during CN-CN replication.
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.
encode '/' and ':' in the DOI used for the resolve URL
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.
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 fully populate the spreadsheet columnshttps://redmine.dataone.org/issues/2815
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
script to generate DOI registration spreadsheethttps://redmine.dataone.org/issues/2815
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 in part.
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....
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
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.
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
use at least one thread on single-processor machines.https://redmine.dataone.org/issues/2800
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.
script for re-applying missing FK constraints on KNB production DB.http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5608
include TRACE level debugging for specific classes we want to have performance metrics for.
Add a few logging statemnts for round trip replication metrics.
add trace statements for measuring time to complete SM generation.
new D1 jars:prevent NPEs from the object format cache when formatId.value is null. This came up during PISCO testing
default replication policy set to 0.
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....