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# Date Author Comment
9783 05/18/2016 01:56 PM ben leinfelder

correct two minor differences from 2.6 merge: formatId parameter for MetacatHandler and using AuthUtils for gathering group membership information.

9781 05/18/2016 09:23 AM Chris Jones

Merge in changes from the 2.6.0 release.

9780 05/18/2016 09:01 AM Chris Jones

Merge changes from the 2.6.0 release.

9779 05/17/2016 11:11 AM ben leinfelder

merge from 2.6 branch: add support for EML 2.1.1 to DC crosswalking for OAI provider. https://projects.ecoinformatics.org/ecoinfo/issues/7030

9729 05/11/2016 10:47 AM ben leinfelder

use correct Metacat API action for retrieving access control block

9721 05/06/2016 09:52 PM Jing Tao

If the client certificate is null, Metacat will throw an exception.

9712 05/03/2016 02:51 PM ben leinfelder

merge from 2.6 branch: changes to include expect header and validatesession method

9709 05/02/2016 11:35 AM ben leinfelder

merge from 2.6 branch: use AuthUtils to gather user group subjects

9706 05/02/2016 09:51 AM ben leinfelder

merge to trunk from 2.6 branch: action=validatesession can handle Authorization token

9705 05/02/2016 09:50 AM ben leinfelder

merge to trunk: debugging statements that were added in 2.6 branch

9700 04/30/2016 12:53 PM Chris Jones

Merge changes from the 2.6.0 branch in MNodeService.allowUpdating() so it honors the localhost MN certificate.

refs https://projects.ecoinformatics.org/ecoinfo/issues/7018

9690 04/27/2016 12:14 PM ben leinfelder

merge from 2.6 branch: use AuthUtils to get group and equivalent identities rather than manually try to extract groups from subject info (can include incorrect groups for given primary subject). https://github.nceas.ucsb.edu/KNB/arctic-data/issues/163

9688 04/27/2016 11:56 AM ben leinfelder

merge from 2.6 branch: use group subject (not name) when translating Session.subjectInfo into group list for Metacat's DocumentImpl. https://github.nceas.ucsb.edu/KNB/arctic-data/issues/163

9683 04/22/2016 02:25 PM Jing Tao

Add more information on the error message if the client's certificate is not trusted.

9673 04/21/2016 08:21 AM Chris Jones

Merge the changes from the 2.6 branch into the trunk, fixing filename construction.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/151

9654 04/12/2016 08:07 AM ben leinfelder

merge from 2.6 branch: add support for EML 2.1.1 in OAI-PMH provider. https://projects.ecoinformatics.org/ecoinfo/issues/7009

9645 04/07/2016 02:23 PM ben leinfelder

merge from 2.6 branch: add method for retrieving access control block from metacat api

9638 04/04/2016 03:55 PM Jing Tao

Fixed a bug to use an identifier object to get a value in a vector.

9637 04/04/2016 01:55 PM Jing Tao

Check the chain end if obsoleted by another object.
See ticket https://redmine.dataone.org/issues/7624

9634 04/01/2016 03:50 PM Jing Tao

Use sql command to get some information rather than hazelcast.

9633 04/01/2016 03:49 PM ben leinfelder

merge changes to accommodate multiple alternative identifiers into trunk from 2.6 branch.

9629 04/01/2016 02:51 PM Jing Tao

Use a hashmap to replace a sql query to improve performance in the getHeadPID method.

9628 04/01/2016 01:37 PM Jing Tao

In the getHeadPID method, we got the field obsoletedBy from the systemmetadata table rather than the hazelcast service.

9601 03/30/2016 09:32 AM Jing Tao

Reformat the create and update method.

9600 03/30/2016 09:19 AM Jing Tao

Close the input stream on the create/update method when the code aborts.

9599 03/29/2016 02:01 PM Jing Tao

Close the the input stream from the method parameter in the create method.

9598 03/29/2016 07:42 AM Chris Jones

Merge registry changes into the trunk.

9596 03/28/2016 04:46 PM Jing Tao

Made the ssl http client not moinitor the stale connections.

9594 03/28/2016 02:53 PM Jing Tao

Use the new AutoCloseInputStream wrapper for replication. It will close but http client and input stream when the inputStream.close method is called.

9587 03/24/2016 04:16 PM Chris Jones

Merge minor registry changes from the 2.6 branch back to the trunk.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/107

9583 03/23/2016 03:57 PM Jing Tao

If a format id in the system metadata is registered in the xml_catalog table, we will use the schema location for the format id to validate the xml instance;
otherwise, we will use our previous way.

9577 03/21/2016 02:13 PM Jing Tao

Add noaa schema items on the xml_catalog table and set the version to 2.7.0

9576 03/21/2016 02:12 PM Jing Tao

Add the format_id column on the xml_catalog table.

9575 03/21/2016 02:11 PM Jing Tao

Add the upgrade script which add a new column format_id on the xml_catalog table.
It also adds the items for the noaa schema on the xml_catalog table.

9557 03/15/2016 08:12 AM Chris Jones

Add a fundingElement() method to insert the funding element into the generted EML. Ensure it is added to the template variables hash for maintaining state across stages.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/42

9554 03/10/2016 03:54 PM Chris Jones

Fix a bug in testing the validity of the CGI Session. It can't be empty or expired.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/42

9553 03/09/2016 05:41 PM Jing Tao

Change the version to 2.6.0

9552 03/09/2016 05:39 PM Jing Tao

Change the version to 2.6.0

9551 03/09/2016 12:10 PM Chris Jones

Validate the session during the modification stage, rather than just assuming a CGI session (support tokens too).

Also, fix the XML document validation issue where an <additionalParty> element is added prior to the <metadataProvider> element. This seems to be an intermittent issue, and may be due to more recent versions of perl returning hash contents more randomly than previous versions. The %orig hash passed in to personnelList() is assumed to be random now, and I just ensured the metadataProvider is first in the produced string....

9545 03/07/2016 04:15 PM Chris Jones

Modify getCredentials() to support token-based credentials.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/42

9544 03/07/2016 01:32 PM Jing Tao

Close the input stream object on the MN.replicate method.

9542 03/04/2016 11:06 AM ben leinfelder

use SM.fileName if we have it. https://projects.ecoinformatics.org/ecoinfo/issues/6970

9541 03/04/2016 10:31 AM ben leinfelder

ensure there is a file extension included for the data files in a package download. https://projects.ecoinformatics.org/ecoinfo/issues/6970

9539 03/02/2016 09:58 AM Chris Jones

We ended up not being able to use IO::Socket::SSL, so I removed the import statement. Also, add the new Perl module dependencies to the installation documentation.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/42

9538 02/29/2016 10:54 AM Jing Tao

Add code to print the the stack trace on the getPackage method in order to help us to identity some tmp file issues.

9536 02/26/2016 08:42 AM Chris Jones

Change getUsername() to also support adding usernames into an EML access element from the authentication token's 'sub' claim.
Also, add a bit of debugging output for tracing the flow of the XML generation.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/42

9535 02/26/2016 08:34 AM Chris Jones

Modify the Metacat.pm upload() method to use the correct Content-Type for the form. RFC 2388 specifies that the Content-Type should be "multipart/form-data", and that the Content-Disposition should be "form-data", along with the "name" parameter.

9534 02/25/2016 04:29 PM Chris Jones

Also handle authentication tokens when uploading data (action=upload) by using Ben's RequestUtil.getSessionData() changes.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/43

9533 02/25/2016 08:33 AM Chris Jones

dd the hasValidAuthToken() method to determine if the current token (if any) is valid. Use this and validateSession() within the script to determine if we need to call Metacat->login() or not. Add some minor debugging to work through the code stages using auth tokens....

9532 02/23/2016 11:39 AM Chris Jones

Fix a couple of syntax issues.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/42

9531 02/23/2016 11:13 AM Chris Jones

Don't forget to set the token variable from the HTTP_AUTHORIZATION environment variable.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/42

9530 02/23/2016 10:19 AM Chris Jones

Add a setAuthToken() method. when the HTTP_AUTHORIZATION environment variable is set, set the value as the `auth_token_header` instance variable in the Metacat instance passed in. This requires that the Apache installation includes an HTTP rewrite rule to pass the header on to an CGI processing the request. Call this method whenever we instantiate a Metacat object....

9529 02/23/2016 10:07 AM Chris Jones

Modify the Metacat.pm sendData() method to include the Authorization HTTP header when it's available as an instance variable.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/41

9523 02/19/2016 12:32 PM Jing Tao

In the isScienceMetacata method, the ServiceFailure exception shouldn't be caught anymore, since the code doesn't throw it.

9521 02/16/2016 08:41 AM Chris Jones

In order to access the JWT authentication token, we need to configure the Apache installation to pass the Authorization header on to CGI scripts. Do this with mod_rewrite.

refs https://github.nceas.ucsb.edu/KNB/arctic-data/issues/42

9520 02/09/2016 05:14 PM ben leinfelder

allow Metacat API calls to be made by clients providing their identity with a DataONE auth token. https://github.nceas.ucsb.edu/KNB/arctic-data/issues/43

9514 02/03/2016 09:55 AM Jing Tao

If the user doesn's specify the ldap ca file path on the metacat.properties, it will use the default one.

9500 01/22/2016 03:46 PM Jing Tao

Add the java code to handle the ezid configuration.

9494 01/20/2016 11:17 AM Jing Tao

Put a detal code on the InvalidRequest exception in the getPackage method.

9493 01/20/2016 09:59 AM Jing Tao

If the pid it is a package id in the getPackage method, the method will throw an InvalidRequest exception.

9492 01/15/2016 05:17 PM Jing Tao

Make sure to close the prepared statement on the final statement.

9491 01/15/2016 11:57 AM Jing Tao

Close the result and connection in the finally clause to make sure they being closed.

9490 01/14/2016 01:28 PM ben leinfelder

add warning when exception encountered loading SM into map.

9489 01/13/2016 01:05 PM Jing Tao

Add the dataone create event mapping to the select clause.

9488 01/12/2016 03:48 PM Jing Tao

map the metacat log event INSERT, upload and UPLOAD to the dataone log event "create"

9486 01/12/2016 10:22 AM ben leinfelder

set authoritative MN to origin MN if the client did not set it on mn.create. https://projects.ecoinformatics.org/ecoinfo/issues/6938

9484 01/11/2016 10:03 AM ben leinfelder

include metacat context in the redirect after successful harvester registration login. https://projects.ecoinformatics.org/ecoinfo/issues/6936

9483 01/06/2016 05:32 PM Jing Tao

Add a policy_id in the smReplicationPolicy table to help preserver the order of the nodes list.

9482 01/06/2016 05:28 PM Jing Tao

Use the "order by" to preserve the nodes order in the replication policy.

9481 01/05/2016 02:06 PM Jing Tao

Use the ServiceFailure to replace the InvalidRequest when it is the read-only mode (CN throws the exception).

9480 01/05/2016 09:42 AM Jing Tao

In the replicate method, the checking of the read-only mode was moved from MNodeService class to the MNResourceHandler class since it is asynchronized.

9479 01/04/2016 05:23 PM Jing Tao

The systemmetadataChanged method is asynchronized, so we put the read-only checking on the ResourceHandler class.

9478 01/04/2016 03:09 PM Jing Tao

Add the code to check if the mn is on the read-only mode.

9477 12/29/2015 12:58 PM Jing Tao

Add the code to check if the metacat is in the read-only mode.

9475 12/28/2015 03:19 PM Jing Tao

Add the code to handle the read-only mode.

9473 12/23/2015 01:33 PM Jing Tao

Add a class to determine if the metacat is in the readonly mode.

9470 12/22/2015 05:02 PM Jing Tao

Add the check that only the administrator can shrink the connection pool.

9465 12/18/2015 03:40 PM Jing Tao

Close the sql statements on the four methods - getGUID, getHeadPID, systemMetadataSIDExist and systemMetadataPIDExist.

9463 12/18/2015 03:14 PM Jing Tao

Close some prepared sql statement in the summarize method.

9455 12/16/2015 02:58 PM ben leinfelder

merge from branch: only check for d1 rightsholder when checking permissions in original metacat code base, otherwise legacy access control tests in metcat begin to fail. https://redmine.dataone.org/issues/7560

9452 12/16/2015 09:58 AM ben leinfelder

include check for d1 rightsholder when checking permissions in original metacat code base. https://redmine.dataone.org/issues/7560

9449 12/11/2015 11:50 AM Jing Tao

Add the sql file for the upgrading.

9443 12/09/2015 07:59 AM ben leinfelder

merge from 2.5.x branch: neglected to replace solr schema during 2.5.0 upgrade - this will do it for 2.5.1.

9441 12/08/2015 04:49 PM Jing Tao

Escape the user names, group name and other information in the xml format.

9437 12/07/2015 02:06 PM Jing Tao

Add the keyword "select" into the list.

9435 12/02/2015 04:31 PM Jing Tao

Reset the xml_catalog_id sequence value to the max value of the table.

9422 11/18/2015 09:56 PM ben leinfelder

remove "al" prefix from subquery since we are only querying one table and do not need to use a prefix.

9410 11/17/2015 03:41 PM ben leinfelder

merge from 2.5 branch: use subquery to do paging before joining to identifier table. https://redmine.dataone.org/issues/7491

9408 11/16/2015 04:51 PM Jing Tao

Add more statement to debug the query performance.

9391 11/03/2015 02:36 PM ben leinfelder

Use conditional method for retrieving server URL (http vs https). When metacat is configured to force SSL communication we get the https url, otherwise we get http. this allows us to use the DBTransform on localhosts that are not using SSL.

9389 11/03/2015 11:27 AM Jing Tao

Fixed a bug that the publish method should throw an io exception.

9387 11/02/2015 04:44 PM Lauren Walker

Move the editScienceMetadata method to the MNodeService class - only update packageId in EML on publish()

9386 11/02/2015 02:34 PM ben leinfelder

update documentation to reference Tomcat 7, Java 7 and newer apache config file name conventions. https://projects.ecoinformatics.org/ecoinfo/issues/6855

9385 10/29/2015 06:59 PM Jing Tao

Fixed a bug in the condition check for the archive field in the updateSystemMetadata method.

9384 10/29/2015 04:00 PM Jing Tao

The archived field can't be reset to false if it is true in the systemMetadataChanged method.

9383 10/29/2015 03:56 PM Jing Tao

Doesn't allow to reset the archived field to be false if the field is true in the updateSystemMetadata method.

9382 10/28/2015 11:14 AM Jing Tao

In the systemMetadataChanged method, we will update system metadata when the local serial version is less than or equals the comming one.

9380 10/27/2015 03:42 PM rnahf

refs #7453: modified the metacatLog message from mn.synchronizationFailed to include the syncFailed.message field. Also increased the log level to WARN.

9376 10/22/2015 12:15 PM Jing Tao

Remove the method editScienceMetadata from the update method. This method will add a packageId attribute into the eml document. Lauren will add the method to the publish method.

9375 10/21/2015 04:52 PM Jing Tao

In the systemMetadataChanged method, the object will be archived if the new archive value is true and old value is false.
The log event is recorded in the systemMetadataChanged method as well.