Metacat

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 margins
add bottom margin on header

include clearer font [size]
add leaf at right

new jar file

use light grey for backgrounds
dark 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

consolidate shared stylesheets - no differences between 2.0.1 and 2.1.0 directories

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

checking for a null objectformat

checking for a null objectformat

backtracking

add some error output

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

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.

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).

include 1.9.3 upgrade script in trunk

updated folder name for schemas

added explicit 200 codes to ResourceHandler

use localhost as defaults for the properties

print the workflow server name

added better logging and http code setting

changed metacat to get the new version of the d1 schemas

fixed bug where the query cache was not getting reset by a REST insert/query combo.

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

do not attempt to drop 'identifier_id_seq' - it does not seem to exist

add 1.9.3 upgrade scripts to trunk

[merged from 1.9.3 branch] security fix: never unregister the "public" user session

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

re-added some code inadvertently removed

merged with version from 1.9.3 branch to fix bug with character encodings

added a todo

new todos from code review with roger

merging changes from branch

merging test changes into the trunk

remove "indus" urls

fixed a bug where if you don't build from a directory called 'metacat' unintended files can be copied from another 'metacat' directory by the ecogrid build files

added TODOs and cleaned up the code a bit