Updated the build to properly locate the servlet jar depending on whichversion of tomcat is being used, tomcat5 or tomcat6.
when looking up group membership, skip referrals that have errorshttp://bugzilla.ecoinformatics.org/show_bug.cgi?id=4900
skip referrals that have errors (connection timeout, host down, etc)http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4900
Refactored putObject method to separate the create() and update() portions in order to match the method signatures needed for DataONE.
Modified ResourceHandler.deleteObject() to take a globally unique id (guid)as input rather than a metacat-conformant docid. The guid is translatedinto a metacat docid which is then used in the handleDelete() call. So nowMetacat supports use of arbitrary identifiers for delete operations, but...
Added support to ResourceHandler to allow the putObject method to usearbitrary guid strings as input. These strings are examined, and if theymatch the Metacat docid format (scope.id.rev), they are used directly. Ifthe id is a string in another format, a new localId is generated based on...
Adding a new property to be used as an identifier prefix by default.
Updated MetacatRestClientTest so that the tests are actually calling fail() when errors occur, and fixed all sixteen tests so that they run successfullyand can be run from any client (i.e., they don't depend on particulardocuments being present in Metacat). The 'restfiles' directory can probably ...
Fixed bug in getNextRevision() where "error" documents were not beingdetected properly before searching for the next identifier.
Added initial support for arbitrary string identifiers in metacat (referred to as a guid). The new identifier table is used to map arbitrary string identifiers to Metacat's current docid format (referred to as the localId). Added a new IdentifierManager class to manage this table, adding new mappings as objects are added to the system. Modified the MetacatTest service to utilize this mapping table to look up a localId from a guid. IdentiferManagerTest is working with these guids now, as is the MetacatTest service get() method, but other parts of the system are unaware of them (e.g., create, update, delete operations are unaware, and no mapping is created when new documents are created). As a consequence, the MetacatRestClientTest is not working (although it also had lots of hardcoded dependencies that need to be fixed as well).
Added copyright, license, and class documentation.
Modified table structure to change identifiers table (previously unused) to represent a mapping between arbitrary string identifiers and metacat docids.More information in https://trac.dataone.org/ticket/361. Modifications toOracle schemas were made but not tested.
Fixed typos in metacat documentation.
Removed version as not sure when this will be delivered, so be agnostic.
Adding new documentation section for Metacat design documents in Sphinx/ReStructured Text format. Build this documentation using theprovided Makefile, assuming that both Sphinx and PlantUML are installed and on the local executable path by running 'make plantuml html'....
Fix two issues: Remove State from 'Data Set Contact' section of confirmation form (part of #3922), and make sure when editing a document that email addresses are picked up appropriately (capitalization).
Modified ResourceHandler to change the GET url from /objects to /object tomatch the DataONE method name.
Update the filename reference
Merging in REST interface implementation that was created by Serhan Akin. Main change isa refactored MetaCatServlet.java class, in which all of the handle* methods were movedinto a separate MetacatHandler.java class. This allows both the standard MetaCatServlet...
Adding missing brackets in else clause. Need to verify with Daigle that this is what he meant.
Move the chunking of large test element data to centralized location in DBSAXNode.writeChildNodeToDB(). Beff up logging
Beef up log messages
add delay in insertSpatialDocs test to avoid buildIndex conflict
Add debug log statements
make sure querygroup is not null before trying to print it.
Re-add the build dir property so the lsid server can build
Populate esa home links with skin property value
Get the latest revision from metacat when a modify call docid does not have a revision number.
Send appropriate message when trying to update a docid that was previously deleted.
Reformat file. No code change.
do a quick retry if building path index fails with a SQL error
Make sure buildIndex throws an exception if it has a sqlexception. That way the indexing object will be added to the indexing queue and reprocessed.
PDF version of doc
Pass the doc xml as a string to docImpl.write and writeRepication. This is so a reader can be create for the parsing and for the write to disk. Also created a db access class for xml query result deletion.
Update java version references to java 6
Remove redundant Version information
Add 1.9.2 release notes.
Fixed typo in docs.
Updated index page to hide obsolete documentation and provide a simplerdescription of Metacati, as well as links to where Metacat is in use.
make constants final
change dropdown select event to work on IE.
Fix the bug of http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4645. handleGetRevisionAndDocTypeAction will search both xml_documents and xml_revisions table.It also changed some constrain in AccessionNumber when user update a document, of which all previous versions are in xml_revisions table.
Fix main cross browser gui compatibility issues in sanparks tpc skin.
Remove commas from the end of lists because they break IE
remove the "optional" tip since it is not currently optional
add required authentication exception class so that the scheduler can compile
add properties expected by the DB property service
use workflowscheduler DB
use @class attribute for path queries rather than @name
Add a sleep statement between getting the dtd from source and checking for it via url. Add method names to log output.
Get all eml code from svn instead of cvs
Log doc and rev query counts and times. Fix mis-spellings.
remove extra open paren
remove call to print busy db connections
add xml_revisions docid index
Add debug to show sql
Fix for Bug #4637 - Metacat Harvester fails to catch some insert and update failures. As per comments in the bug entry, the Metacat Harvester logic has been modified to examine the Metacat client return string to confirm that it contains the substring "<success>" following an insert or update operation. It no longer considers just the absence of an exception as indicative of a successful operation.
log connection warnings only when thresholds are exceeded. Add method names to log output
add method name to log statements
fix spelling of word additional
add method name to log messages and create configured thresholds for warning messages
add parc-moderators to config.username
I've added the PARC and PISCO organizations to the delete and confirm form templates for the data registry application.
Change log levels where appropriate and add class/method name to output.
Change warn messages to info
beef up error log messages
Make sure session data exists before extracting information
Separate code to do tls and non-tls authentication. Introduce AuthTLSException to make error handling easier.
Beefed up the logging
remove registry.config.username value
Start to flesh out the eclipse metacat setup document
Create some basic workflow scheduler system installation documents
When comparing lat and long ranges, make sure the values have content first. Perl values with no content = 0.
Change add sql to use a prepared statement. Only try to download a cert if a url was provided.
change unregister error message to be an info message
fix file name reference for skin configuration file
added a commented out line for auth.moderators for the parc system. This will get uncommented on the parc system and the existing auth.moderators will be commented out.
I've removed the value for the PARC registry.config.site property since it isn't appropriate to this skin, and causes the registry CGI to produce two organization creator elements with the same value.
hard code parc home url
Redirect data.palmyraresearch.org to parc skin
I've added the PARC organization to the login form template.
I've replaced hard-coded URL strings in the PARC skin files with their appropriate variables in JSP, TT2, and XSL.
This updates the Registry login form to handle PARC logins. I've changed the template to load the PARC header and footer if the cfg = parc.
added parc to list of available skins.
Fix errors in workflow scheduler unit test
Create database scripts for workflow scheduler
Do not register the session service
I'm adding two PARC-specific templates to the CGI templates directory. This is a temporary addition, since these templates should reside in the PARC skin. However, the NCEAS skin has templates in this location as well, and all four files will be relocated once bug #4573 has been resolved where the register and ldapweb CGIs change.
I'm adding the spatial support files for the PARC skin. At the moment, the spatial option in the skin is not being used, but these files have been modified slightly from the NCEAS skin version in branding only.
I've added in the XSL stylesheets for the PARC skin. The parc, parc-eml, parc-common and login stylesheets have been changed slightly for PARC branding.
I'm adding the settings and map JSPs. These are placeholder files since the map is not used in the PARC skin, and the settings file merely import common settings for the skin, but doesn't modify any of the interface settings.
These are the minimal images used in the PARC skin layout. The research banner comes from the research section of the PARC website.
I've added the PARC CSS file, which uses colors and images found at the PARC website.
These are the index files for the PARC skin. The html file provides the standard redirect to the JSP. The JSP has been PARC branded, and the layout has changed slightly to work with the http://www.palmyraresearch.org website layout (e.g. some navigation links have been removed).
I'm adding the parc.cfg configuration file, which is effectively a copy of the nceas.cfg file.
This is the PARC XML configuration file. I've removed the EML beta 4-6 doctype identifiers since this skin will only deal with EML 2.1.0 documents.