updated all exception codes to match spec
new config changes
fixed task 729
fixed a bunch of small errors, did some reformatting, and fixed a bug that I thought was fixed last week
fixed redmine task 864. Metacat will now download an http:// referenced schema when a reference is put in the xml_catalog table.
allow default style to be used for the registry (added login mapping)
fixing redmine task 738
fixing trac bug 828
minor changes to crudservicetest
adding a test that I forgot to check in a while back
test for the profiler
profiler code for metacat
exception to throw when the sax parse should stop
new client jar
look up the active annotation classes
Bug 3835 - design and implement OAI-PMH compliant harvest subsystem
Improve handling of 'eml:eml/dataset/publisher' element to 'dc:publisher' element crosswalk.
browse/search/madlib hybrid sample
use newer SBC-ish style for the default skin
include css classes for skins (like default and semtools) that use the "subGroup" class
correctly set the map location based on organizationScope
correctly set the organizationScope from the request value - filters the search results by location
not sure why this did not come up earlier when I stared upgrading some of the jar dependencies, but I've been having problems deploying Metacat because of a xerces error. upgrading to 2.7.1 fixed it - thinking the xml-apis and xerces jars need to be somewhat in lockstep with each other.
added notes on packages to upload with knb-mn
use <p> consistently when providing a tooltip for the full class URI
number of changes:-list measurements across the screen under their observation-use title attributes for full ontology class URI, only show full URI for the entity class since there is horizontal room-make the annotation box more compact and intuitive for both screens (details and search results)
make DP title bold in result set
nest annotation groupings nicely for each obs/meas
include nesting borders
integrate Annotation in resultset better
place annotation information in the same cell as the data package title/id
include content in a wrapper div for margins
comment out debugging alert()
do not make hyperlinks extra bold
reduce white space
include some gray in the paragraphs
changed log labels per trac 843
use "Myriad..." fonts, then cascade down to Arial, sans... Lifted from BioPortal L+F
only show that an annotation exists in the resultset, not the full details
fixed bug 818
make the header hyperlinks bold
reduce header font sizes
wrap content in div for marginsadd bottom margin on header
include clearer font [size]add leaf at right
new jar file
use light grey for backgroundsdark grey for links
don't use green for links
include new graphic header for semtools skin.adjust css to fit better
updated the metacatpopulator to use the d1 eml parser to create system metadata in a smarter fashion.
only surround main dataset with border to avoid a weird border artifact when displaying sub-groups of the eml package
include header/footer like in the old JS-based template
do away with the "eml-common.xsl" - it's not really worth it in terms of being able to customize for each skin
use sbclter css
use shared style sheets for rendering eml. this is sbclter/pisco-like
consolidate shared stylesheets - no differences between 2.0.1 and 2.1.0 directories
better log message
remove duplicate "attributeindex" parameter
more debugging for objectInfo problem
checking for a null objectformat
backtracking
add some error output
added a check for bad data into listObjects
commented out a println
new service api jar
updated DB scripts for D1 schemas
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.
changed improper use of getFS() to a /. getFS() should never be used with a URL since it will return \ on windows which is not a valid separator in a URL.
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
added METS schemas to db scripts
added METS schema to the catalog
moved the dataone types to the metacat.properties file
updated for new dataone jars
changes to work with new dataone jars
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).