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  • svn:mergeinfo: /branches/D1_0_6_2_BRANCH:6107-6121

# Date Author Comment
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....

9550 03/08/2016 04:30 PM Jing Tao

Change the version of d1_common_java to 2.2.

9549 03/08/2016 04:29 PM Jing Tao

Change the version of d1_cn_index_processor to 2.2

9548 03/08/2016 04:29 PM Jing Tao

Change the version of d1_portal to 2.2

9547 03/08/2016 02:35 PM Jing Tao

Changed the d1_libclient_java from 2.1 to 2.2

9546 03/07/2016 04:29 PM Jing Tao

Change the number of fields in the test

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

9540 03/02/2016 10:04 AM Chris Jones

And don't forget the alternate Redhat instructions.

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

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.

9537 02/26/2016 03:47 PM Jing Tao

1. Set knb to version 2.
2. Centralize the lter tests into one class.

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

9528 02/19/2016 05:25 PM Jing Tao

Add a new chechsum for the new solr schema.

9527 02/19/2016 03:41 PM Jing Tao

Add beans for the iso index.

9526 02/19/2016 03:40 PM Jing Tao

Add a bean file for the iso index.

9525 02/19/2016 03:39 PM Jing Tao

Add a bean file for the iso index.

9524 02/19/2016 03:34 PM Jing Tao

Add more fields for the iso index.

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.

9522 02/19/2016 12:04 PM Jing Tao

Change its mime type from binary to text.

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

9518 02/05/2016 11:54 AM ben leinfelder

comment out (duplicate) EML download link since it does not apply in the CN context and the same functionality exists elsewhere in the MetacatUI rendering. https://redmine.dataone.org/issues/7639

9515 02/03/2016 02:04 PM Jing Tao

Removed the sepcified path for the ldap ca file.

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.

9513 01/28/2016 05:14 PM Jing Tao

Remove the bypass button.

9512 01/28/2016 05:13 PM Jing Tao

Update the ezid configuration screenshot.

9510 01/28/2016 03:39 PM Jing Tao

Add the help icons on the page.

9509 01/28/2016 03:37 PM Jing Tao

Use a new screenshot with the help icon.

9507 01/28/2016 11:38 AM Jing Tao

Fixed a typo.

9506 01/28/2016 11:31 AM Jing Tao

Add the ezid section.

9505 01/28/2016 11:28 AM Jing Tao

Add the section for ezid.

9504 01/27/2016 04:24 PM Jing Tao

Updated the screenshot for the configuration pages.

9503 01/25/2016 03:06 PM Jing Tao

Add the items for the ezid backup.

9502 01/25/2016 03:05 PM Jing Tao

Change the label.

9501 01/22/2016 04:44 PM Jing Tao

fixed a label issue.

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

Add the java code to handle the ezid configuration.

9499 01/22/2016 03:45 PM Jing Tao

Add a new property to show the status of configuration of the ezid service.

9498 01/22/2016 03:44 PM Jing Tao

Add a page for configuring the ezid.

9496 01/21/2016 02:20 PM Jing Tao

remove the password of the doi user.

9495 01/20/2016 11:30 AM Jing Tao

The getPackage method should throw an exception since the id is a data object.

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"

9487 01/12/2016 02:19 PM ben leinfelder

comment out the party annotation-target - don't think we'll be using this anytime soon (had been for annotating with orcids)

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

9485 01/11/2016 10:07 AM ben leinfelder

remove ant commands in harvester configuration instructions. https://projects.ecoinformatics.org/ecoinfo/issues/6937

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.

9476 12/28/2015 04:09 PM Jing Tao

In the clean method, the metacatui build directory will be deleted as well.

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

Add the code to handle the read-only mode.

9474 12/23/2015 01:33 PM Jing Tao

Add a junit test.

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

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

9472 12/23/2015 01:31 PM Jing Tao

Add a new property named application.readOnlyMode.

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

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

9469 12/21/2015 03:49 PM Jing Tao

'Change the verion of the production CN from the v1 to the v2.

9467 12/18/2015 04:30 PM Jing Tao

Add two new test methods to test systemMetadataPIDExists and systemMetadataSIDExists.

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.

9461 12/18/2015 11:28 AM ben leinfelder

include expiration configuration option for NCEAS accounts to prevent errors during account registration. https://projects.ecoinformatics.org/ecoinfo/issues/6917

9459 12/16/2015 04:41 PM ben leinfelder

merge from 2.0 branch: use updated node list information from cn-dev so that test will match current state of env. https://redmine.dataone.org/issues/7534

9457 12/16/2015 04:37 PM ben leinfelder

merge from 2.0 branch: initialize mock cn for test to run successfully.

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

9451 12/11/2015 11:56 AM Jing Tao

Change the version to 2.6.0

9450 12/11/2015 11:53 AM Jing Tao

Set the metacat to 2.6.0 and add the db upgrade scripts.

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

Add the sql file for the upgrading.

9448 12/11/2015 11:45 AM ben leinfelder

merge jing's commit from the 2.5 branch to include the 2.5.1 upgrade utility in properties file.

9446 12/09/2015 03:48 PM Jing Tao

Removed the jar file since it is replaced by the jar file from the maven.

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.

9439 12/08/2015 04:18 PM Jing Tao

Change the metacatui to 1.8.1

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.

9427 11/24/2015 01:51 PM ben leinfelder

merge from branch: use hash for latest solr schema

9425 11/19/2015 11:44 AM ben leinfelder

add checks on archived flag to avoid NPE.

9424 11/19/2015 08:44 AM ben leinfelder

only consult fields to merge if there was an existing referenced doc

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.

9421 11/18/2015 09:12 PM ben leinfelder

added 4 new schema fields so need to account for them in the test case.

9420 11/18/2015 04:41 PM ben leinfelder

subclass AnnotatorSubprocessor for use in metacat-index (uses embedded solr server and solrj for retrieving/merging existing documents).

9419 11/18/2015 04:03 PM ben leinfelder

bump trunk to 2.6.0-SNAPSHOT and pull in d1 dependencies at 2.1.0-SNAPSHOT to continue trunk development.