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# Date Author Comment
8921 10/21/2014 06:32 PM Jing Tao

Add a script to move the db from 8.3 to 9.1 base on a dumped file.

8920 10/21/2014 10:58 AM Jing Tao

Use the pg_dumpall command to back up all information of the database.

8919 10/20/2014 07:35 PM Jing Tao

Add the code to backup the cerificate/key of the apache server.

8918 10/20/2014 04:46 PM Jing Tao

Removed the code to write the backup file to a dvd drive.

8917 10/20/2014 02:56 PM Jing Tao

Added the code to copy Metacat and other web applications from the webapps directory in tomcat6 to tomcat7.
It also update the value of deploy.applicationDir in the metacat.properties file as well.

8916 10/20/2014 01:10 PM Jing Tao

Only insert new configuration lines once to the /etc/tomcat7/catalina.properties.

8915 10/20/2014 11:34 AM Jing Tao

Used variables to replace hard code in sed command. Also we have to escape the variables.

8913 10/20/2014 09:42 AM Jing Tao

Used variables to replace the hard code.

8912 10/17/2014 06:15 PM Jing Tao

Add the code to modify the workers.properties file.

8911 10/17/2014 05:13 PM Jing Tao

Fixed typo.

8910 10/17/2014 05:02 PM ben leinfelder

use http://tools.ietf.org/rfc/rfc3023 spec for conformsTo property. use the full xpath for EML dataTable and attribute selectors

8909 10/17/2014 04:49 PM Jing Tao

Add a script to install openjdk 7 and tomcat 7.
It also configures java, javac,keytools and tomcat7.

8903 10/15/2014 04:34 PM Jing Tao

Added the code to inform users the pid was deleted in the NotFound exception.

8901 10/14/2014 06:11 PM Jing Tao

Added the code to check if a not-found object was deleted in the isAuthorized method.

8899 10/14/2014 06:01 PM Jing Tao

Move the code to get the object in front of the method to get the system metadata.

8896 10/14/2014 01:44 PM Jing Tao

Add a utility method for determine if there is a delete event for a given id.

8889 10/10/2014 02:16 PM Jing Tao

Removed the method which had the byte array attribute.

8887 10/10/2014 02:10 PM Jing Tao

Remove the system metadata for data objects.

8884 10/10/2014 02:01 PM Jing Tao

change the way to delete the solr index of a resource map.

8883 10/10/2014 01:23 PM Jing Tao

Backup the /etc/apache2/site-enabled directory.

8882 10/09/2014 04:40 PM Jing Tao

Remove the code to stop/start ldap server.
Change the script name to stop/start tomcat.
Also backup metacat.properties.

8880 10/06/2014 10:32 PM Jing Tao

Replace the operator "=~' by "eq" in comparing the two password fields.

8877 10/06/2014 05:42 PM Jing Tao

dd a new routine to check if the uid has been taken already in the production space during the creation process.

8874 09/23/2014 06:27 PM ben leinfelder

add /token endpoint for annotatorJS/annotateIt.org integration. https://github.com/DataONEorg/sem-prov-design/issues/18

8869 09/18/2014 03:12 PM Jing Tao

Persitence the system metadata object in the memory before deleting it from hazelcast.

8866 09/16/2014 05:18 PM Jing Tao

Add the code to handle the delete of the resource map.

8854 09/12/2014 04:17 PM Jing Tao

Make the delete method work.

8852 09/12/2014 04:03 PM Jing Tao

Make the deleteSystemmetadata method really roll-backable.

8850 09/12/2014 03:56 PM Jing Tao

Add the code to delete systemmetadata.

8846 09/04/2014 03:24 PM Jing Tao

Add the code to delete the records in the xml_accesssubtree table.

8844 09/02/2014 02:07 PM ben leinfelder

use configured auth.base rather than hard-coded dc=ecoinformatics,dc=org. https://projects.ecoinformatics.org/ecoinfo/issues/6592

8842 08/22/2014 05:50 PM Jing Tao

Add a code to check if the pathquery engine is enabled in the checkIndexPaths method.

8829 08/06/2014 01:48 PM ben leinfelder

convert v2 SM to v1 SM for the v1 service call response

8826 08/06/2014 01:09 PM ben leinfelder

update to use v2 types for indexing

8821 08/04/2014 04:08 PM Jing Tao

For the existing uidnumber, we decrease the size of vector for sorting.

8820 08/04/2014 10:04 AM Lauren Walker

Login automatically via curl rather than manually entering the cookie info for the registry test script

8819 08/01/2014 09:20 AM Jing Tao

Add the code to check if the existing highest uidNumber really exists.

8818 07/31/2014 06:10 PM Jing Tao

In the getNextUidNumber method, a mechanism to look up the highest existing udiNumber was added.

8816 07/29/2014 05:33 PM Lauren Walker

Create a lock file for the registry
if one doesn't exist

8815 07/29/2014 04:35 PM Lauren Walker

Allow the registry form to specify a docid scope

8814 07/29/2014 03:53 PM Lauren Walker

Only lock the local docid file when creating a new docid, not when inserting, for faster upload times. Remove extra debug messages from testing.

8813 07/28/2014 05:22 PM Lauren Walker

Fix bug in the online registry where data files were not using the new docid creation process

8812 07/28/2014 03:57 PM Lauren Walker

Lock a local file while docids are being created so multiple docs can be uploaded at once

8811 07/24/2014 10:25 AM ben leinfelder

remove CN.systemMetadataChanged in favor of the CN.updateSystemMetadata method. Otherwise there's no good way to know where to fetch the auth copy from since the SM change might be to switch the authMN!

8810 07/23/2014 04:19 PM ben leinfelder

add support for v2 DataONE API.

8802 05/29/2014 02:53 PM ben leinfelder

remove dependency on HttpMessage that was in the utilities project but is now removed in favor of newer (standard) http client library code.

8800 05/28/2014 11:49 AM ben leinfelder

Include PDF version of the metadata in the package download. https://projects.ecoinformatics.org/ecoinfo/issues/6053

8795 05/22/2014 01:59 PM ben leinfelder

take advantage of the ezidclient for multi-threaded/asynchronous DOI registration. This will be most useful for doing large batch updates and not so much for the one-at-a-time publish actions but works in either context. https://projects.ecoinformatics.org/ecoinfo/issues/6440

8794 05/21/2014 06:24 PM ben leinfelder

use a member instance of ezid service that only logs in every 24 hours (or other time TBD) instead of every time there is an interaction with the service. Saves us many calls when doing batch updates to ezid but keeps us from trying to use expired sessions. Motivated by https://projects.ecoinformatics.org/ecoinfo/issues/6440

8792 05/20/2014 04:11 PM ben leinfelder

prevent js scriptlets from running when we return error messages to the client by escaping any potentially harmful xml blocks. https://projects.ecoinformatics.org/ecoinfo/issues/6224

8791 05/20/2014 04:09 PM ben leinfelder

allow updates to all doi: prefixes - realized we are already restricting to specific replica servers when updating these. worst case is we try to update a registration for which we are not the owner. https://projects.ecoinformatics.org/ecoinfo/issues/6440

8790 05/20/2014 04:08 PM ben leinfelder

show the SM and ORE generation buttons even if they have not registered/configured dataone. many potential MNs want to see their generated SM before registering (and we want them to too!).

8789 05/20/2014 10:40 AM ben leinfelder

restrict DOI updates to DOIs that match our server shoulder -- may consider opening this up to any "doi:" prefix if this is too restrictive. https://projects.ecoinformatics.org/ecoinfo/issues/6440

8788 05/19/2014 02:21 PM ben leinfelder

use separate surName and givenNames to lookup ORCIDs.

8784 05/15/2014 03:17 PM ben leinfelder

all full-text queries for ORCID, but it isn't that great because we might have a"PISCO" creator that shows us in may different orcid profiles...false matches.

8777 05/14/2014 12:04 PM ben leinfelder

use HttpClient to query orcid so I can easily set headers and such -- getting 503s from their production server when I test on dev.nceas...odd

8776 05/14/2014 11:43 AM ben leinfelder

adjust tests for production service -- more "real" information shows additional return values from the query.

8775 05/14/2014 09:18 AM ben leinfelder

switch to the production ORCID server for looking up orcid matches for our creators.
add test to summarize how many creator matches we can actually find. https://projects.ecoinformatics.org/ecoinfo/issues/6423

8771 05/13/2014 03:31 PM ben leinfelder

change the hazelcast group name to be the default "metacat" instance so that the metacat-index tests pass without additional local configuration, at least when running a default metacat deployment.

8770 05/12/2014 11:31 AM ben leinfelder

do not set archived=false for all CN.create calls. The CN will use create() even harvesting content that is new to it and needs to handle already-archived content. https://projects.ecoinformatics.org/ecoinfo/issues/6475

8769 05/09/2014 01:48 PM ben leinfelder

cache the imported models to avoid timeouts from remote hosts (or being locked out for too many requests in a given time period).

8768 05/08/2014 04:25 PM ben leinfelder

process all the returned annotation suggestions until we find one that is appropriately located in the subclass hierarchy for the given superclass.

8767 05/08/2014 04:23 PM ben leinfelder

use in-memory TDB dataset for querying annotations for indexing -- this comes with the same reasoning capabilities as the directory-based one, but has the benefit of not filling the directory with triples that will not be used again. prepping for d1 AHM

8765 05/07/2014 11:12 PM ben leinfelder

when indexing annotations directly, just use an in-memory triple store rather than TDB since we remove each graph as it is processed (and my TDB instance would get into the multi-GB range with a few runs, even if I removed the old models)

8764 05/05/2014 05:17 PM ben leinfelder

redirect "short form" metacat read URIs to the the new Metacat UI using the configured UI context. This translates the docid -> pid to use the correct identifier for the correct service. https://projects.ecoinformatics.org/ecoinfo/issues/6546

8763 05/02/2014 04:39 PM ben leinfelder

simplify lookup for classes and orcid. remove the "random" annotation code branches -- just too confusing to look at those bogus classes especially now that we have "real" generated annotations.

8760 04/30/2014 01:02 PM Lauren Walker

Add admin service to update DOI registrations by specifying a list of formatIds or DOIs, or update all.

8759 04/29/2014 05:21 PM ben leinfelder

use new method to override the CN URL when constructing a CNode instance. see https://redmine.dataone.org/issues/5142

8757 04/29/2014 04:54 PM ben leinfelder

first pass at direct EML->semantic index method. Still produces an RDF model, but does not persist it in Metacat, only in the triplestore. Allows us to re-run without adding stale RDF to the MN store.

8749 04/28/2014 03:30 PM Jing Tao

Store the cn url in the backup.

8748 04/24/2014 01:28 PM ben leinfelder

switch to use FIleUpload instead of O'Reilly COS library for handling chunked file uploads. https://projects.ecoinformatics.org/ecoinfo/issues/6517

8747 04/24/2014 01:26 PM ben leinfelder

forgot to check in the actual class: first pass at allowing admins to update DOI registration. This only acts on EML objects at the moment and is meant to illustrate one mechanism for updating the DOIs. https://projects.ecoinformatics.org/ecoinfo/issues/6530

8746 04/23/2014 12:35 PM ben leinfelder

first pass at allowing admins to update DOI registration. This only acts on EML objects at the moment and is meant to illustrate one mechanism for updating the DOIs. https://projects.ecoinformatics.org/ecoinfo/issues/6530

8745 04/23/2014 10:19 AM ben leinfelder

correct the ORE lookup query syntax and add junit assertion to check that it continues to function as expected. https://projects.ecoinformatics.org/ecoinfo/issues/6529

8744 04/22/2014 03:38 PM ben leinfelder

index the ORE after we submit the metadata for indexing. https://projects.ecoinformatics.org/ecoinfo/issues/6520

8743 04/22/2014 11:43 AM ben leinfelder

include BioPortal lookup for Entity matches using the data table description. TODO: only associate measurements to the entity observation if they apply.

8739 04/17/2014 02:19 PM Jing Tao

Index the document after it has been inserted.

8738 04/17/2014 02:18 PM Jing Tao

Index the document after document is written to the db.

8724 04/02/2014 03:36 PM ben leinfelder

check for null entities and/or attributes (typically when otherEntity is being used in EML).

8723 04/02/2014 03:35 PM ben leinfelder

remove extra space in log message

8718 03/31/2014 11:11 AM ben leinfelder

attribute the datapackage to the creator (using orcid if we can find it). https://projects.ecoinformatics.org/ecoinfo/issues/6267
https://projects.ecoinformatics.org/ecoinfo/issues/6423

8717 03/31/2014 10:31 AM ben leinfelder

add test for BioPortal annotator service.

8716 03/28/2014 03:51 PM ben leinfelder

refactor web service calls to bioportal and orcid outside of the annotator class. test with orcid sandbox server. include orcid uri for the annotations being generated (we can index these and drive our searches on these values down the road). related to this: https://projects.ecoinformatics.org/ecoinfo/issues/6423 and also some semtools tasks.

8715 03/27/2014 04:54 PM ben leinfelder

remove leading '?' in the query parameter for MN.query() implementation. We want it to match CN behavior/expectations and comply with the DataONE specification for the interface. https://projects.ecoinformatics.org/ecoinfo/issues/6488

8714 03/26/2014 04:05 PM ben leinfelder

Use OBOE-SBC ontology for looking up concepts (it contains subclasses of our OBOE Characteristic and Standard superclasses). Restrict annotations to only subclasses that fit the OBOE model. Correct the xpointer and individual naming conventions so they are unique, but express the exact entity/attribute being annotated.

8713 03/26/2014 03:10 PM ben leinfelder

remove my api key. oops

8712 03/26/2014 03:02 PM ben leinfelder

add comment/pointer to BioPortal annotation service.

8711 03/26/2014 03:00 PM ben leinfelder

Include method to look up annotation classes from BioPortal. We still have OBOE-SBC in there, and theyhave the SWEET ontology. The suggestions returned are not perfect, but they can be better than nothing. Ideally, we'd only query a few ontologies so we don't end up using terms from medical ontologies that aren't really appropriate for our domain. https://projects.ecoinformatics.org/ecoinfo/issues/6256

8710 03/24/2014 04:17 PM ben leinfelder

Add xpointer FragmentSelectors to each annotation.
Split attribute label into tokens to attempt matching to OBOE concepts.

8709 03/23/2014 12:11 AM ben leinfelder

include code to generate random annotations for UI testing. Effective, but can be confusing to see so many unrelated concepts on duplicate EML packages.

8707 03/21/2014 01:21 PM ben leinfelder

include SSLVerify* directives for client certificates and a pointer for getting the DataONE chain files.

8704 03/14/2014 03:33 PM Jing Tao

Remove the code to lookup alias dn in the getGroups method.

8703 03/14/2014 01:16 PM Jing Tao

Rather than directly to modify the env, we use context.addToEnv.
This fixed a bug in non-tls env, the alias log-in doesn't work.

8702 03/14/2014 10:59 AM ben leinfelder

first pass at generating annotations from EML attribute information. uses the OpenAnnotation model that the metacat-index tests assume which allows us to populate dynamic index fields for the annotation class[es]. There is still much to be done with finding appropriate concepts for each attribute. https://projects.ecoinformatics.org/ecoinfo/issues/6256

8700 03/06/2014 03:28 PM Lauren Walker

Edited the replicaPolicies script to print out a list of IDs that have a different authoritative member node, the number of successes, and failures at the end.

8699 03/05/2014 11:46 AM Lauren Walker

Add comments to bash script to explain its function and dependencies

8698 03/05/2014 11:30 AM Lauren Walker

Added a bash script to call /replicaPolicies/{pid} via the DataONE API for all objects in a MN or a list of ids.

8689 03/03/2014 03:41 PM ben leinfelder

support content from all serverLocations when summarizing entity info (semtools)

8678 02/28/2014 04:06 PM ben leinfelder

allow "+" in solr query syntax. https://projects.ecoinformatics.org/ecoinfo/issues/6435

8670 02/26/2014 10:49 PM ben leinfelder

include read events when re-indexing obsoleted objects. https://projects.ecoinformatics.org/ecoinfo/issues/6424