Metacat

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

restyle default eml rendering using ESA look + feel

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

adjust stylesheets to accommodate new default eml rendering

use latest eml style tag

adjust stylesheets to accommodate new default eml rendering

use square edges for the borders around table groups and subgroups

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.

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

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.

adjust to fit new EML look and feel

additional overrides for color

added mets to default skin

use white links override only in header menu

force the leftnav section to wrap their links

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

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

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

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.

stylesheet/skins for mets data

use newer EML stylesheet tag

correctly include table cells for xsl

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....

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....

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

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.

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()....

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

Updated DROP script that was missing tables and sequences.

added file extension for txt or csv files

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

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....

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

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

adding more debuggin and fixing bug with systemmetadata

new d1_common jar

Make the schema with included schemas valid.

Add a xml file for inserting during test.

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

Add code to download the included schema.

fixed replication bug where systemmetadata was not getting procssed correctly

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

Add a test file for XMLSchemaServcieTest.

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

Add a junit test file for testing the XMLSchemaParser class.

Add test schema for downloading included xsd file.

A sax handler class can get included schema path.

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

remove JPL NASA layer - no longer operational

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

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

added some debug info to DBConnectionPool

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

removed comments from crudservicetest

fixed typo that prevented replication

fixed node response bug

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

fixed update problem

put the pid in the info section of the url

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

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

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

fixed problem with count in listObjects()

Cleaned up warnings, removed dead code.

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.

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

removed debug statements

fixed bugs in listObjects

Add in correct node references in system metadata.

Cleanup harvester exceptions and generics.

remove httpclient 3.1 and custom-built httpclient.jar
rework MetacatClient (and other classes) to use httpclient 4
updated build to not create httpclient.jar
encoding tests now pass.

blank configuration value should be treated the same as null

Fix the MetadataTypeRegisterTest because it had the wrong URI for METS.

Added download links.

the new name of the jar file.

rename this jar file to xercesImpl-2.11.0.jar

Additional layout and styles for metacat documentation.

UPdated documentation for the web.

few bug fixes for listObjects

Add new version of jar file from xerces 2.11.0.

Add a new version of aml-apis jar file from xerces 2.11.0.

Add new version of xerces jar file.

Add jar file from xerces 2.11.0.

remove old version of xerces jar file.

Remove redundant jar file.

remove redundant jar file.

remove redundant jar file.

remove redundant jar file.

Remove redundant jar file.

added code to do database query for listObjects

new properties for d1 MN

Cleaned up unused imports.

update to ECOGRID_1_2_2RC2 tag

remove the empty dir.

This is redundant to the WorkflowSchedulerCleintTest in wsfscheduler svn module.

use more unique scope (document id prefix) so that getlastdocid runs successfully. use superclass generateDocumentId() method

pass the root exception message up the call chain so that it can effectively be reported as a helpful error message. also, the JUnit test expects the specific error message (SchemaRegistryTest)

adding fields for additional system metadata info

use the read() method instead of manually calling with parameters

new paths for metacat populator