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metacat @ 6016

# Date Author Comment
6016 03/23/2011 12:51 PM ben leinfelder

use access control dao for setting access in EML parser. send additional xml_access info in replication request

6015 03/22/2011 05:19 PM ben leinfelder

insert/update documents with null user and null group to circumvent access control restrictions then update the user_owner and user_updated values to reflect what exists on the originating server (pisco)

6014 03/22/2011 01:24 PM ben leinfelder

use 'user_updated' field when writing the replicated document - allows most recent ownership/permissions to be used (in case LDAP groups have shifted) and is more accurate for both updates and initial inserts (hopefully addresses the replication issue we are having with pisco)

6013 03/17/2011 09:02 AM ben leinfelder

use newer ecogrid tag to allow omission of the ecogrid query title (as is allowed in the query.xsd schema)

6012 03/16/2011 10:56 PM ben leinfelder

add support for temporal element query in pathquery
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2084

6011 03/12/2011 07:21 AM ben leinfelder

add otherEntity physical elements to indexPaths (ndp)

6010 03/04/2011 03:23 PM ben leinfelder

replace derik's settings with previous version

6009 03/04/2011 03:14 PM barseghian

add paths to indexPaths, and kar namespaces to indexNamespaces for Kepler Workflow Run Manager run-kar queries

6008 03/04/2011 02:52 PM ben leinfelder

include simple union data for search results if they are present in the resultset document

6007 03/04/2011 09:56 AM ben leinfelder

include temporal coverage dates in the path index - (for opendap metadata queries)

6006 03/03/2011 08:15 AM Chris Jones

Fixed the testNCEASLogin() password that I mistakenly changed.

6005 03/03/2011 07:47 AM Chris Jones

Now that MetacatHandler creates GUID identifier mappings and system metadata, many of the tests in IdentifierManagerTest were failing that were manually creating id mappings and system metadata.
Modified testCreateMapping() and testCreateSystemMetadataMapping() to use docids that haven't been inserted to just exercise the methods....

6004 03/02/2011 04:44 PM Chris Jones

Added a new test method testDeleteDocumentByGUID() to ensure MetacatHandler can delete based on GUID, but fall back to docid if the GUID isn't present. Modified CrudServiceTest and made some private methods public to leverage the D1 REST calls in that library (i.e. create() a doc with a GUID).

6003 03/02/2011 02:47 PM Chris Jones

The DataONE service API jar has been renamed to d1_common_java-0.5.0.jar, updated the build file accordingly. Added debug echo of the test classpath.

6002 03/02/2011 02:14 PM ben leinfelder

hide the data section unless there is actually data to display

6001 03/02/2011 02:12 PM Chris Jones

DocumentImpl.delete() now throws finer grained exceptions (not a general exception). Consequently, the classes that call it have been updated to handle the thrown exceptions, including CrudService, ReplicationHandler, and ReplicationService.

6000 03/02/2011 10:39 AM ben leinfelder

refactor the names of these Data Manager implementation classes so that it's easier to use them with the default/local versions of similar. These classes utilize Metacat-specific configuration values rather than relying soley on the bundles that are used in the stand-alone DM lib.

5999 03/01/2011 02:00 PM ben leinfelder

render the <data/> CDATA section in

 - it's a csv string

5998 03/01/2011 09:13 AM Chris Jones

To support GUIDs in MetacatHandler.handleDeleteAction(), I've added in a new method:
deleteFromMetacat() - deletes a document based on the docid
This factors the deletion code out of handleDeleteAction(). handleDeleteAction() now does a docid lookup based on GUID, and if it is not found, reverts to the deletion based on docid instead.

5997 02/28/2011 02:42 PM ben leinfelder

only include data value/operator when present in the form

5996 02/28/2011 02:42 PM ben leinfelder

refresh search when the data operator changes (changing the value is less clear...keyup event seems too eager)

5995 02/28/2011 11:57 AM ben leinfelder

use correct operators

5993 02/25/2011 12:01 PM ben leinfelder

include data search - new form fields and semQuery schema to allow searching for Characteristics data

5992 02/18/2011 12:28 PM ben leinfelder

turn off the databounds layer by default

5991 02/18/2011 12:09 PM ben leinfelder

new lines were showing up in the html source becuase of whitespace in this - removed the white space and the new lines are gone...

5990 02/18/2011 11:54 AM ben leinfelder

restyle the eml display and resultset after applying new eml css to the KNB L+F

5989 02/18/2011 11:16 AM berkley

new jar files from common and client

5988 02/18/2011 10:59 AM berkley

fixed width issue with default header

5987 02/18/2011 10:59 AM berkley

new files for mets style

5986 02/18/2011 10:10 AM ben leinfelder

[untested] loop through each origin[ator] to make a row for them

5985 02/17/2011 05:16 PM ben leinfelder

restyle the resultset after applying new eml css
use more robust form-submission js for the datapackage links

5984 02/17/2011 04:30 PM ben leinfelder

check for 'null' as well as 'public' user when rendering the header Login/Logout option

5983 02/17/2011 03:44 PM ben leinfelder

restyle default eml rendering using ESA look + feel

5982 02/17/2011 12:11 PM ben leinfelder

include eml css and then adjust lter skin to accommodate the new xsls

5981 02/17/2011 11:50 AM ben leinfelder

adjust stylesheets to accommodate new default eml rendering

5980 02/17/2011 11:28 AM ben leinfelder

use latest eml style tag

5979 02/17/2011 11:24 AM ben leinfelder

adjust stylesheets to accommodate new default eml rendering

5978 02/17/2011 09:45 AM ben leinfelder

use square edges for the borders around table groups and subgroups

5977 02/17/2011 02:57 AM Chris Jones

These are fairly significant changes to MetacatHandler.handleInsertOrUpdateAction() that add in support for creation or update of GUIDs and SystemMetadata. Upon insertion or update of DataPackages from non-DataONE aware clients (such as Morpho), the identifier table is updated by creating a GUID, and the systemmetadata table is updated with fields after the EML document is parsed for distribution information and entity typing. System Metadata documents are also generated and inserted into Metacat. The list of data entities is iterated over and System Metadata is generated for each data file as well.

5976 02/17/2011 02:39 AM Chris Jones

In MetacatHandler I've removed updateSystemMetadata() in favor of additions to insertOrUpdateSystemMetadata(). Modified createSystemMetadata() to reflect the changes as well.

5975 02/16/2011 06:23 PM Chris Jones

Modified MetacatHandler.createSystemMetadata() to take a localId, not a guid as an argument since there are times when the guid has yet to have been created, and it is created in this method if so.
Also, put the read() call to get the InputStream of the data/metadata document into it's own try/catch statement.

5974 02/16/2011 04:36 PM ben leinfelder

adjust to fit new EML look and feel

5973 02/16/2011 03:58 PM ben leinfelder

additional overrides for color

5972 02/16/2011 03:58 PM berkley

added mets to default skin

5971 02/16/2011 03:25 PM ben leinfelder

use white links override only in header menu

5970 02/16/2011 03:11 PM ben leinfelder

force the leftnav section to wrap their links

5969 02/16/2011 02:40 PM ben leinfelder

override problematic CSS properties that were introduced as part of the new look and feel for default EML display

5968 02/16/2011 01:56 PM Chris Jones

Somehow missed adding in javadoc for read(). Here it is.

5967 02/16/2011 01:52 PM Chris Jones

For now, getSystemMetadata() will be private like the other *SystemMetadata() methods.

5966 02/16/2011 01:47 PM Chris Jones

Modified MetacatHandler, updated the getSystemMetadata() method to now use read() and deserializeSystemMetadata() to produce the SystemMetadata object. Exceptions are pushed up the stack, and so accordingly, modified createSystemMetadata() to reflect the changes.

5965 02/16/2011 01:44 PM berkley

stylesheet/skins for mets data

5964 02/16/2011 11:38 AM ben leinfelder

use newer EML stylesheet tag

5963 02/16/2011 11:18 AM ben leinfelder

correctly include table cells for xsl

5962 02/16/2011 09:25 AM Chris Jones

Modified MetacatHandler, added createSystemMetadata() - generates SystemMetadata objects for newly inserted data or documents. This is intended to be used from handleInsertOrUpdateAction(), and only for documents being inserted from clients that don't support the DataONE interface. The method parses EML documents to discover data entities, and updates the system metadata for those entries, with support for describes and describedBy metadata. Currently doesn't handle FGDC, etc. documents....

5961 02/16/2011 09:14 AM Chris Jones

Modified MetacatHandler, added three methods:
getSystemMetadata() - returns a SystemMetadata object from the systemmetadata table using the given GUID. Stub only.
updateSystemMetadata() - updates the systemmetadata table using the given SystemMetadata object....

5960 02/16/2011 09:10 AM Chris Jones

Modified MetacatHandler and added two methods:
serializeSystemMetadata() - Serialize a SystemMetadata object to XML string
deserializeSystemMetadata() - Deserialize a SystemMetadata object from an XML string

5959 02/16/2011 09:07 AM Chris Jones

Modified MetacatHandler, added read() - Read a document from metacat and return an InputStream. The XML or data document should be on disk, but if not, read from the metacat database. This method should be optimized, along with others, to not write stream data to disk for performance reasons.

5958 02/16/2011 09:06 AM Chris Jones

To support generation of SystemMetadata and GUIDs, added a number of methods to MetacatHandler that are also in CrudService(). CrudService should eventually be refactored to use the handler methods. Added:
readFromFilesystem() - Read a file from Metacat's configured file system data directory, and return a FileInputStream. This code has been factored out of handleInsertOrUpdateAction()....

5957 02/15/2011 02:08 PM berkley

fixed bug where the wrong checksum alg got written to the db

5956 02/14/2011 02:03 PM Matt Jones

Updated DROP script that was missing tables and sequences.

5955 02/14/2011 11:45 AM berkley

added file extension for txt or csv files

5954 02/14/2011 11:39 AM ben leinfelder

correctly pass the search class and value when perfroming Protocol-based and Measurement-based queries (copy and paste oversight).

5953 02/13/2011 11:20 AM Chris Jones

To support the generatemissingsystemmetadata REST call, modified CrudService.createSystemMetadata() to use DataoneEMLParser and further determine object formats from EML metadata. Formats currently supported are text/plain, text/csv, image/[jpg|jp2|bmp|tiff|png], and only for EML documents with 'ecogrid://' defined entity urls....

5952 02/11/2011 02:56 PM ben leinfelder

make Data Object link more subtle since it now appears for each attribute

5951 02/11/2011 01:57 PM ben leinfelder

update skin to use new annotation schema - http://ecoinformatics.org/sms/annotation.1.0beta1

5950 02/11/2011 01:48 PM berkley

adding more debuggin and fixing bug with systemmetadata

5949 02/11/2011 11:42 AM berkley

new d1_common jar

5948 02/10/2011 06:09 PM Jing Tao

Make the schema with included schemas valid.

5947 02/10/2011 06:08 PM Jing Tao

Add a xml file for inserting during test.

5946 02/10/2011 06:07 PM Jing Tao

Add a method to test download a schema with included schemas.

5945 02/10/2011 06:06 PM Jing Tao

Add code to download the included schema.

5944 02/10/2011 04:17 PM berkley

fixed replication bug where systemmetadata was not getting procssed correctly

5943 02/10/2011 10:56 AM berkley

think I fixed the connection problem. one connection in IdentifierManager was being leaked. added more debug info in case it happens again

5942 02/10/2011 10:27 AM Jing Tao

Add a test file for XMLSchemaServcieTest.

5941 02/10/2011 10:27 AM Jing Tao

Add a static method to get base url base on a schema url.

5940 02/09/2011 05:03 PM Jing Tao

Add a junit test file for testing the XMLSchemaParser class.

5939 02/09/2011 05:02 PM Jing Tao

Add test schema for downloading included xsd file.

5938 02/09/2011 05:00 PM Jing Tao

A sax handler class can get included schema path.

5937 02/09/2011 11:36 AM ben leinfelder

remove old spatial templates
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2188

5936 02/09/2011 11:34 AM ben leinfelder

remove JPL NASA layer - no longer operational

5935 02/09/2011 10:02 AM ben leinfelder

photoshop file for creating the on/off query widget for openlayers

5934 02/09/2011 09:55 AM ben leinfelder

remove sanparks boundaries from the default map, but allow them to be added as an additional layer from the saeon/sanparks skin.
use css to style the spatial query search widget control
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2188

5933 02/08/2011 02:08 PM berkley

added some debug info to DBConnectionPool

5932 02/08/2011 02:06 PM ben leinfelder

include title for the spatial query control widget (on hover)

5931 02/08/2011 12:06 PM berkley

removed comments from crudservicetest

5930 02/08/2011 12:05 PM berkley

fixed typo that prevented replication

5929 02/08/2011 11:46 AM berkley

fixed node response bug

5928 02/08/2011 11:30 AM ben leinfelder

add custom Pan/Zoom/Query control. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2188

5927 02/07/2011 03:41 PM berkley

fixed update problem

5926 02/07/2011 02:49 PM berkley

put the pid in the info section of the url

5925 02/07/2011 11:31 AM Jing Tao

Add a comment to the new target install-configured-metacat.

5924 02/07/2011 11:20 AM Jing Tao

Using echo to replace propertyfile in order to avoiding character escape.

5923 02/07/2011 10:50 AM berkley

fixed content type problem where csv files were set as text/xml

5922 02/04/2011 06:34 PM berkley

fixed problem with count in listObjects()

5921 02/04/2011 06:14 PM Matt Jones

Cleaned up warnings, removed dead code.

5920 02/04/2011 05:53 PM Matt Jones

Updated to most recent DataONE libraries. Updated CrudService to set the correct origin MN and auth MN in system metadata. Refactored exception passing. More work to come in generating SystemMetadata.

5919 02/04/2011 04:45 PM Jing Tao

Add a target to change the configuration value to be true.

5918 02/04/2011 01:05 PM berkley

removed debug statements

5917 02/04/2011 12:39 PM berkley

fixed bugs in listObjects

5916 02/04/2011 11:30 AM Matt Jones

Add in correct node references in system metadata.