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From 02/05/2011 to 03/06/2011

03/04/2011

03:23 PM Revision 6010 (metacat): replace derik's settings with previous version
ben leinfelder
03:14 PM Revision 6009 (metacat): add paths to indexPaths, and kar namespaces to indexNamespaces for Kepler Workflow Run Manager run-kar queries
barseghian
02:52 PM Revision 6008 (metacat): include simple union data for search results if they are present in the resultset document
ben leinfelder
09:56 AM Revision 6007 (metacat): include temporal coverage dates in the path index - (for opendap metadata queries)
ben leinfelder

03/03/2011

08:15 AM Revision 6006 (metacat): Fixed the testNCEASLogin() password that I mistakenly changed.
Chris Jones
07:47 AM Revision 6005 (metacat): 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 e... Chris Jones
04:44 PM Revision 6004 (metacat): 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).
Chris Jones

03/02/2011

02:47 PM Revision 6003 (metacat): 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.
Chris Jones
02:14 PM Revision 6002 (metacat): hide the data section unless there is actually data to display
ben leinfelder
02:12 PM Revision 6001 (metacat): 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.
Chris Jones
10:39 AM Revision 6000 (metacat): 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.
ben leinfelder

03/01/2011

02:00 PM Revision 5999 (metacat): render the <data/> CDATA section in <pre/> - it's a csv string
ben leinfelder
09:13 AM Revision 5998 (metacat): 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(...
Chris Jones

02/28/2011

02:42 PM Revision 5997 (metacat): only include data value/operator when present in the form
ben leinfelder
02:42 PM Revision 5996 (metacat): refresh search when the data operator changes (changing the value is less clear...keyup event seems too eager)
ben leinfelder
11:57 AM Revision 5995 (metacat): use correct operators
ben leinfelder

02/25/2011

12:01 PM Revision 5993 (metacat): include data search - new form fields and semQuery schema to allow searching for Characteristics data
ben leinfelder

02/22/2011

09:46 AM Bug #5316: Interactive map doesn't work with firefox
This is a known issue with the old MapBuilder interface used to render the spatial layers in Metacat 1.9.x.
The forth...
ben leinfelder

02/19/2011

06:57 AM Bug #5316 (Resolved): Interactive map doesn't work with firefox
The interactive map, for example
http://knb.ecoinformatics.org/knb/style/skins/nceas/map.jsp
doesn't work with ...
Eva-Maria Gerstner

02/18/2011

12:28 PM Revision 5992 (metacat): turn off the databounds layer by default
ben leinfelder
12:09 PM Revision 5991 (metacat): new lines were showing up in the html source becuase of whitespace in this - removed the white space and the new lines are gone...
ben leinfelder
11:54 AM Revision 5990 (metacat): restyle the eml display and resultset after applying new eml css to the KNB L+F
ben leinfelder
11:16 AM Revision 5989 (metacat): new jar files from common and client
berkley
10:59 AM Revision 5988 (metacat): fixed width issue with default header
berkley
10:59 AM Revision 5987 (metacat): new files for mets style
berkley
10:10 AM Revision 5986 (metacat): [untested] loop through each origin[ator] to make a row for them
ben leinfelder
05:16 PM Revision 5985 (metacat): restyle the resultset after applying new eml css
use more robust form-submission js for the datapackage links ben leinfelder
04:30 PM Revision 5984 (metacat): check for 'null' as well as 'public' user when rendering the header Login/Logout option
ben leinfelder

02/17/2011

03:44 PM Revision 5983 (metacat): restyle default eml rendering using ESA look + feel
ben leinfelder
12:11 PM Revision 5982 (metacat): include eml css and then adjust lter skin to accommodate the new xsls
ben leinfelder
11:50 AM Revision 5981 (metacat): adjust stylesheets to accommodate new default eml rendering
ben leinfelder
11:28 AM Revision 5980 (metacat): use latest eml style tag
ben leinfelder
11:24 AM Revision 5979 (metacat): adjust stylesheets to accommodate new default eml rendering
ben leinfelder
09:45 AM Revision 5978 (metacat): use square edges for the borders around table groups and subgroups
ben leinfelder
02:57 AM Revision 5977 (metacat): 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.
Chris Jones
02:39 AM Revision 5976 (metacat): In MetacatHandler I've removed updateSystemMetadata() in favor of additions to insertOrUpdateSystemMetadata(). Modified createSystemMetadata() to reflect the changes as well.
Chris Jones
06:23 PM Revision 5975 (metacat): 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. Chris Jones
04:36 PM Revision 5974 (metacat): adjust to fit new EML look and feel
ben leinfelder

02/16/2011

03:58 PM Revision 5973 (metacat): additional overrides for color
ben leinfelder
03:58 PM Revision 5972 (metacat): added mets to default skin
berkley
03:25 PM Revision 5971 (metacat): use white links override only in header menu
ben leinfelder
03:11 PM Revision 5970 (metacat): force the leftnav section to wrap their links
ben leinfelder
02:40 PM Revision 5969 (metacat): override problematic CSS properties that were introduced as part of the new look and feel for default EML display
ben leinfelder
01:56 PM Revision 5968 (metacat): Somehow missed adding in javadoc for read(). Here it is.
Chris Jones
01:52 PM Revision 5967 (metacat): For now, getSystemMetadata() will be private like the other *SystemMetadata() methods.
Chris Jones
01:47 PM Revision 5966 (metacat): 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.
Chris Jones
01:44 PM Revision 5965 (metacat): stylesheet/skins for mets data
berkley
11:38 AM Revision 5964 (metacat): use newer EML stylesheet tag
ben leinfelder
11:18 AM Revision 5963 (metacat): correctly include table cells for xsl
ben leinfelder
09:25 AM Revision 5962 (metacat): 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.
Added sizeOfStream() - Find the size (in bytes) of a stream. Note: This needs to refactored out of MetacatHandler and... Chris Jones
09:14 AM Revision 5961 (metacat): Modified MetacatHandler, added three methods:
getSystemMetadata() - returns a SystemMetadata object from the systemmetadata table using the given GUID. Stub only.
...
Chris Jones
09:10 AM Revision 5960 (metacat): Modified MetacatHandler and added two methods:
serializeSystemMetadata() - Serialize a SystemMetadata object to XML string
deserializeSystemMetadata() - Deserialize...
Chris Jones
09:07 AM Revision 5959 (metacat): 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.
Chris Jones
09:06 AM Revision 5958 (metacat): 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... Chris Jones

02/15/2011

02:08 PM Revision 5957 (metacat): fixed bug where the wrong checksum alg got written to the db
berkley

02/14/2011

02:48 PM Bug #5262: EML document owner can't read the document
Hrrm, it seems our code doesn't trim the username.
In AuthLdap.authenticateTLS:
I added a information line to displ...
Jing Tao
01:47 PM Bug #5262: EML document owner can't read the document
Hi, Matt:
Yes, the user name with extra space can login. The username field in EcogridWriter is used for login. The ...
Jing Tao
11:54 AM Bug #5262: EML document owner can't read the document
Trimming strings on input like this is always dangerous. My guess is that the bug arises because someone through a '... Matt Jones
11:42 AM Bug #5262: EML document owner can't read the document
Somehow, in EcogridWriter actor, author put an extra space after uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org.
...
Jing Tao
02:03 PM Revision 5956 (metacat): Updated DROP script that was missing tables and sequences.
Matt Jones
11:45 AM Revision 5955 (metacat): added file extension for txt or csv files
berkley
11:39 AM Revision 5954 (metacat): correctly pass the search class and value when perfroming Protocol-based and Measurement-based queries (copy and paste oversight).
ben leinfelder

02/13/2011

11:20 AM Revision 5953 (metacat): 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.
Todo: transition to using the EML Data Manager library's DataPackage parsers to handle a broader set of metadata type... Chris Jones

02/11/2011

02:56 PM Revision 5952 (metacat): make Data Object link more subtle since it now appears for each attribute
ben leinfelder
01:57 PM Revision 5951 (metacat): update skin to use new annotation schema - http://ecoinformatics.org/sms/annotation.1.0beta1
ben leinfelder
01:48 PM Revision 5950 (metacat): adding more debuggin and fixing bug with systemmetadata
berkley
11:42 AM Revision 5949 (metacat): new d1_common jar
berkley
10:46 AM Bug #5300: SchemaLocationResolver fails to download included xsd files
Add a new class XMLSchemaPaser which can extract the included schema information.
In XMLSchemaService class, add a ne...
Jing Tao
06:09 PM Revision 5948 (metacat): Make the schema with included schemas valid.
Jing Tao
06:08 PM Revision 5947 (metacat): Add a xml file for inserting during test.
Jing Tao
06:07 PM Revision 5946 (metacat): Add a method to test download a schema with included schemas.
Jing Tao
06:06 PM Revision 5945 (metacat): Add code to download the included schema.
Jing Tao
04:17 PM Revision 5944 (metacat): fixed replication bug where systemmetadata was not getting procssed correctly
berkley

02/10/2011

10:56 AM Revision 5943 (metacat): think I fixed the connection problem. one connection in IdentifierManager was being leaked. added more debug info in case it happens again
berkley
10:27 AM Revision 5942 (metacat): Add a test file for XMLSchemaServcieTest.
Jing Tao
10:27 AM Revision 5941 (metacat): Add a static method to get base url base on a schema url.
Jing Tao
05:03 PM Revision 5940 (metacat): Add a junit test file for testing the XMLSchemaParser class.
Jing Tao
05:02 PM Revision 5939 (metacat): Add test schema for downloading included xsd file.
Jing Tao
05:00 PM Revision 5938 (metacat): A sax handler class can get included schema path.
Jing Tao

02/09/2011

02:37 PM Bug #5300: SchemaLocationResolver fails to download included xsd files
Here is a way probably resolve this issue:
In edu.ucsb.nceas.metacat.service.XMLSchemaService lcass, we will add two...
Jing Tao
01:40 PM Bug #5300 (Resolved): SchemaLocationResolver fails to download included xsd files
I am trying to insert an eml document with embedded sensorML into metacat.
But i get the error:
knb 20110209-11:20:...
Jing Tao
11:41 AM Bug #4307: Upgrade Geoserver to prevent Metacat crashes
Shape files were corrupted by the ant build (filtered copy treated them as text).
Configuration allows for bypass and...
ben leinfelder
11:37 AM Bug #2188: replace web client with OpenLayers
New OpenLayers implementation is now in trunk - old MapBuilder has been removed. ben leinfelder
11:36 AM Revision 5937 (metacat): remove old spatial templates
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2188 ben leinfelder
11:34 AM Revision 5936 (metacat): remove JPL NASA layer - no longer operational
ben leinfelder
10:02 AM Revision 5935 (metacat): photoshop file for creating the on/off query widget for openlayers
ben leinfelder
09:55 AM Revision 5934 (metacat): 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
ben leinfelder

02/08/2011

02:08 PM Revision 5933 (metacat): added some debug info to DBConnectionPool
berkley
02:06 PM Revision 5932 (metacat): include title for the spatial query control widget (on hover)
ben leinfelder
12:06 PM Revision 5931 (metacat): removed comments from crudservicetest
berkley
12:05 PM Revision 5930 (metacat): fixed typo that prevented replication
berkley
11:46 AM Revision 5929 (metacat): fixed node response bug
berkley
11:30 AM Revision 5928 (metacat): add custom Pan/Zoom/Query control. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2188
ben leinfelder
11:30 AM Bug #2188: replace web client with OpenLayers
added new map control for metacat spatial query. now you can Pan/Zoom/Search depending on which control is selected ben leinfelder
10:25 AM Bug #5288: Metacat got "java.lang.OutOfMemoryError: PermGen space" after new geoserver update
GeoServer recommends increasing your container's default settings:
http://docs.geoserver.org/stable/en/user/productio...
ben leinfelder

02/07/2011

03:41 PM Revision 5927 (metacat): fixed update problem
berkley
02:49 PM Revision 5926 (metacat): put the pid in the info section of the url
berkley
11:44 AM Bug #5294: Enable Junit test on http://dev-testing.dataone.org:8080/hudson/job/Metacat/
It turns out that Metacat is using a customized properties file management system.It makes the properties file more r... Jing Tao
11:31 AM Revision 5925 (metacat): Add a comment to the new target install-configured-metacat.
Jing Tao
11:20 AM Revision 5924 (metacat): Using echo to replace propertyfile in order to avoiding character escape.
Jing Tao
10:50 AM Revision 5923 (metacat): fixed content type problem where csv files were set as text/xml
berkley
 

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