Metacat

Bug 3835 - design and implement OAI-PMH compliant harvest subsystem

Fix a bug in the EML to Dublin Core crosswalk XLSTs. First and last names were being concatenated. The fix is to place the space character inside an xsl:text element.

removing unused search pages (leftover from 'default' skin copy)

separate the class and the ontology from the the URI for easier reading. putting them in a table also helps

include links from annotation to the data package metadata

include stylesheet to display annotation document on it's own (in addition to within a resultset)

include the column name that the measurement is mapped to

list the currently registered ontologies (in case someone wants to unregister them?)

rearrange the ontology registration page - bioportal-hosted ontologies come first

include dropdown of all bioportal ontologies - you can choose to register or unregister them with metacat for annotation-based searching. perhaps not the most elegant workflow, but better than having to manually collect the URIs and URLs.

include annotation display in the search results - NOTE using XPath 2.0 function for accessing the ontology URIs that are included as namespaces in the annotation. adding Saxon jar for this.

include a page for [un]registering ontologies with the ontology manager in the semtools plugin

minor upgrade to commons-logging (1.0.3->1.0.4)

basic query can be issued and includes:
-match any/all
-from same observation
-for Entity, Characteristic, Standard, Protocol, Measurement

use same xercesImpl as geoserver (2.4)

upgrade to xalan 2.7 from 2.5.1 (geoserver was using 2.7 already)

upgrade commons-collections (3.2) and commons-lang (2.5) - avoid conflicts with semtools plugin that requires these newer jars.

upgrade the log4j jar - reduces the duplicate jars to wade though in the build process

don't include the semtools plugin in the default config

remove chad's local changes (server, db, etc) - but preserve the D1 config values that were added

new values for mets namespace

moved the dataone types to the metacat.properties file

removing old service api jar

new dataone jars

include MetacatHandlerPlugin interface so that other projects [semtools] can extend the actions handled by Metcat without editing the codebase directly. The SemtoolsPlugin is the prototype for this and can be registered using the Metacat admin interface. Note that the plugin implementation class and supporting jars must be included in the webapp in order for the request to be handled correctly (the semtools build is injecting these as part of it's build process).

include 1.9.3 upgrade script in trunk

use localhost as defaults for the properties

include bioportal widgets, at least for an example.
oboe-sbc and oboe are both registered as tests.

map the eml 2.1.0 documents to be rendered by the correct (existing) stylesheet.

Merge 1.9.3 branch to the trunk.

merge 1.9.3 change to include karxml 2.1 documents in search/rendering

remove "indus" urls

adding dataone to the login org choice for the dev skin

reverting accidental cahgnes

fixing another null auth token bug

reverting accidentally committed changes

trying another build../cicore/cn-buildout/dataone-cn-metacat/usr/share/metacat/knb.war

MetacatPopulator is now working. It allows you to do a query from one metacat instance, then insert any returned docs into another metacat instance

d1client jar

tracked down streaming bug. now need to figure out a better way to fix it.

added a DataOneLogger for event notifications on the CN. The logger is called DataOneLogger and can be managed in the log4j.properties file

finished getLogRecords. Fixed some date bugs in metacat.

changed getLogRecords to use new classes for log events

new service layer jar

starting point for semtools skin. augmenting default skin with Annotation documents.
not yet semantically enhanced search capabilities, but you can see a listing of both EML and Annotations on the server.

mostly done with generating systemmetadata from legacy knb docs. need to write a better test and enable this through the ResourceHandler then it will be done.

Commit the change for Madhusudan Gujral from java.net.URL url = new java.net.URL;
to java.net.URL url = new java.net.URL;

Fixed bug the download link didn't work.

Add a mapping between kar xml namespace and karxml.xsl.

Add a style sheet to transform kar xml document.

added the renamed Java classes for ObjectList

Change the search query according to the karxml change.

changed the detailCode for DataOne exceptions to a string

added getSystemMetadata to ResourceHandler and changed the url format to be meta/guid. added a new servlet reponse handler in the web.xml file to handle the new urls and send them to the RestServlet.

Change the return type from kar to the namespace.

adding stax jar. if this is somewhere else, i'll remove it, but i'm unable to find it anywhere in dataone

Refactored metacat to use dataone-service-api-0.3.0 jar file, with the new JIBX generated types and serialization. Included JIBX runtime jar in metacat to handle serialization and deserialization of SystemMetadata objects. Removed the old API jar file.

Modifications to support the DataONE service API version 0.1.0. For DataONE, the get() and
create() services are partially complete. Several more functions and checks need to be added to
create() before it is viable. This DataONE support is not complete, and the current support breaks the MetacatRestClientTest for the time being (this client will eventually be removed).

Merge 1.9.2 changes back into the trunk

Adding commons-io jar for the IOUtils utilities for stream manipulation.

Modified readFromMetacat() to pass most exceptions up the call stack, which
allows creation of new entry points for calling reads. Still need to
continue factoring out the HTTPServletResponse that is passed in in order to
make entrypoints that are not servlet based possible. Problem now is in...

Excluding the Maven ant tasks jar from the metacat war distribution because
it is not needed (its only used to build dataone-service at build time, and
is unused at runtime), and it conflicts with jar files checked in for Spring
as part of the geoserver install. Also updated dataone interface...

Modified the build.xml to include a new task for building the dataone
service api package, which generates a jar file that is put into lib. This
task depends on maven being installed in maven.home, and depends on the
DataONE service_api being checed out in a sibling directory to the build....

Adding a new property to be used as an identifier prefix by default.

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 to
Oracle schemas were made but not tested.

Modified ResourceHandler to change the GET url from /objects to /object to
match the DataONE method name.

Merging in REST interface implementation that was created by Serhan Akin. Main change is
a refactored MetaCatServlet.java class, in which all of the handle* methods were moved
into a separate MetacatHandler.java class. This allows both the standard MetaCatServlet...

Populate esa home links with skin property value

change dropdown select event to work on IE.

Fix main cross browser gui compatibility issues in sanparks tpc skin.

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 properties expected by the DB property service

use @class attribute for path queries rather than @name

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.

remove registry.config.username value

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.

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).

Here are the three javascript libraries associated with the PARC skin. The only real changes are in the search.js file, where metacat searches have absolute XPaths in the search criteria. The return fields remain as relative XPaths to be consistent with the rendering code for the skin.

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.

I'm adding the Metacat metadata properties file for the PARC installation.

I'm adding the properties file configured for the Palmyra Atoll Research Consortium's installation.

I'm adding in the parc directory, which will contain the skin for the Palmyra Atoll Research Consortium.

special handling for RDF namespace documents (semtools project)