Metacat

Did editing to support changes mentioned in bug 1295

Made changes mentioned in Bug 1295.

deletaData.tmpl added a space in the end of docid. This led to an error while deleteing. This error was pointed out by Rick in his document.

Adding in a web.xml file specific to tomcat 5. Notice servlet.jar is
now servlet-api.jar

The tomcat 5 release notes includes this:

------------------------
Enabling invoker servlet:
------------------------

Starting with Tomcat 4.1.12, the invoker servlet is no longer available by...

In order to use tomcat five, a couple of changes in web.xml need to take place.
I'm adding in web.xml.tomcat5 as a choice with the changes.

deleted versions 22 and r2a to avoid confusion and duplication.

Revisions to Harvester Class Diagram and Harvester Class Descriptions.

Resubmitted as binary. Modification of the Harvester database ER diagram. Includes foreign key added to the XML_DOCUMENTS table from the SITE_SCHEDULE table

Resubmitted as binary. Modification of the Harvester database ER diagram. Includes foreign key added to the XML_DOCUMENTS table from the SITE_SCHEDULE table

Modification of the Harvester database ER diagram. Includes foreign key added to the XML_DOCUMENTS table from the SITE_SCHEDULE table

Fixed hardcoded admin account so that it works with more than just OBFS
Registry.

New site list for NRS reserves in the confgiruation file from K Browne.

Fixed registry bug involving a string comparison (used numeric
equality instead of string equality).

Adjusted the text on the NCEAS repository page. Changed the project list
so that it now displays short title but uses the long title in the
entry. This was doen because the long titles were far too long to display
decently in the list (the box scrolled way off the right of the page).

Removed unneeded Net::LDAP dependency. Now all authentication occurs
indirectly through Metacat.

Added skin for the UCNRS data registry based on earlier work. Minor
modifications to the templates to accomodate this. Fixed a validation
bug in the register-dataset.cgi, and removed an unnecessary Net::LDAP
login as well because the authentication is handled by metacat.

Restoring AuthLdap to previous search filter. Determined that the problem was
a missing o: attribute in the UCNRS LDAP directory. Adding it in makes the old
method work. The change I had made caused some confusion about authentication
because using just uid for a filter caused too many return dn's, and it was just...

Fixed validation check for samplingDescription.

Another eml.jar version with the appropriate config.xml in place.

New eml.jar that includes the parser bug fix against eml-2.0.0 schemas.

Changed label for NCEAS project group list on the web form.

Changes to re-enable the nceas admindb access for the production install.

Removed some debugging test code that isn't needed.

Revised the registry guide to include descriptions of the new fields, and
made some minor formatting changes.

Changing version in build in preparation for a release.

Added studyExtent and samplingDescription fields to the registry to accomodate
Sandy's request for a temporalDescription field. This is a little more than
she wanted, but it was needed to satisfy EML minimum requirements.

Modified LDAP authentication to support a lookup for the NRS system. If
the auth on the provided string fails as a DN, try to look up a new
DN based on the UID. If we get a match, use that DN for auth and see
if that works. This allows us to use a referral within the...

Update result set from relation to trip.

Removed obsolete SRB support files that are no longer used.

Added taxonomic coverage and authority fields, and fixed a bug in reentry
with the methods fields. Now we are collecting information on all of the
additional fields Sandy requested except for a general temporal description,
which doesn't fit neatly in EML. Will need to consider how to accomodate...

Added the ability to describe taxonomicCoverage to the registry. This
allows an arbitrary number of species or other taxa to be listed, and the
editing form can dynamically grow through a simple javascript approach
(also used in Methods). Need to test thoroughly, and need to test on...

Added geographic description to the fields of data collected, as it is
a required field and was being improperly defaulted to an empty string in the
XML document. This is a new field for all registries.

Modifications to add "Methods" collection to the data registry, and to
make the forms HTML 4.0.1 valid (in an attempt to figure out some of
the rendering and layout oddities I'm seeing).

Changed "Document ID" to "ID" which is mroe appropriate for data packages.

New formatting and text for the NCEAS data registry.

Further changes to the registry scripts to support the NCEAS registry
with access to the project list fromthe admindb. Also, fixed a bug with
the script where creators were getting duplicated in the editing process
accidentally.

Configuration file for NCEAS registry.

Modifications that allow working group entries to be put in as creators, and
a whole bunch of re-formatting for horribly formatted code that I need to
read to finish this thing up.

Adding style files for the new NCEAS skin for metacat, which includes
files needed for the NCEAS data repository.

Updated registry further for NCEAS-specific needs. Confirm data template
now handles new wg field. Still need to write WG metadata into EML document.

Additional work on the NCEAS/AdminDB integration. Working Groups now
presented as a dropdown box for multiple selection. Need to write the
info to the XML file now and handle it in confirmation template.

Preliminary changes to support the NCEAS data registry connection to the
AdminDB to retrieve project lists.

Harvester Class Diagram

Remove corrupted version

Revisions to the Harvester ERD diagram showing how I think the design can
be simplified to eliminate duplicate information. Needs further work
before it is implementable.

Harvester Class Diagram, class descriptions, sequence of operations.

Improvements to the OBFS stylesheet, especially for EML display. Now we
import the eml_xsl.css stylesheet and override several of its templates.

Relocated to metacat/lib/harvester

Relocated to metacat/docs/dev/harvester

Relocate to metacat/docs/dev/harvester

took out h2 tags, added valign=top to TD containing logo, and added missing quotes on a link target=top

deleted harvesterConfiguration.xsd. This has been replaced by harvestDocument.xsd now found in metacat/lib/harvester and metacatHarvesterERD.vsd (/metacat/docs/dev/harvester) which models the database tables to be added to metacat.

This is the harvesterDocument.xsd. It will be used to validate harvestDocument.xml documents.

This is the metacat database schema with the additions for harvester.

moved document to metcat/test/harvest directory

This is a sample of a harvest document relocated from the metacat/lib directory

This is a sample of a harvest document.

This is an xml schema that describes the harvest document. The harvest document provides a metacat docid, a document type and a url for "get" ing the eml document.

Enabled stylesheet parameters to be passed through metacat even when the
'query' function is called. Previously, query would interpret all
parameters except a few hardcoded ones to be pathexpressions that should be
built into a squery. Now, metacat.properties contains a new configuration...

Updates that allow registry script to update the lastid field more efficiently
by calling the metacat 'getlastdocid' function for a given scope. Also some
debugging support added, and a bug where the error message was inproperly
saved across calls to metacat, resulting in spurious error messages.

Build changes that allow the registry install dependency on the beta
6 stylesheet converters to be automatically satisfied. Now, if the
webmdentry module hasn't been checked out, it is, but otherwise the
checkout is skipped. A similar technique could be used for the EML...

Added new function "getLastId" to the Metacat.pm perl Metacat client. Returns
the hisghest docid in use in a given scope.

New build system that creates a war file and deploys it to tomcat. Also
updated the web.xml files so that a better servlet path is used. Now, by
default, the servlet path will be: /knb/metacat (as opposed to the
prior servlet path which was /knb/servlet/metacat and depended on the...

Moved the metacat.properties file from the jar file to now be located in
the tomcat context directory in WEB-INF. Now the metacat configuration is
editable in place. This change depends on a new Options.java class in the
utilities module, so be sure you do a "clean" build in metacat so that you...

Add harvester targets

Improvements to Harvester single file upload servlets

Harvester forms to support single file upload to metacat.

Fixed links to ldapweb to include the cfg param for proper styling.

removed search box from header

corrected image path

missed an edit when fixing the bug whereby form names aren't allowed to contain hyphens

build props for production metacat on ecoinfo

bug fix: added code to strip brackets and hyphens from form names in results page

added conditional setting of tomcat servlet.jar path, based on tomcat version in build properties

made results page table header into <th> so we can apply a different css style to eml stylesheet subheaders. added whitespace above& below section headers

overhaul of ant build file. removed duplicate code for getting dtds and schema. Renamed these targets, pulled all code for copying xsl into a single target (still need separate targets for getting beta6 eml files nad eml2+ files, since older version uses dtds instead of schema.) In future, as eml versions are added, the geteml2+ target shoudl be updated to use the ant iterator class found in the utilities module - this would enable the cvs tags to be defined as a comma-delimited list, and then a common target can be called multile times to do the checkouts, instead of duplicating code. Also added description= attributes to all the targets that looked as if they shoudl be public. These now appear (with their descriptions) when the user types ant -projecthelp

changed getdtdschema tarhet to copy eml css to cvs source tree metacat/lib/style/common directory, same as the copy for the XSL stylesheets. Created new ant parameter to hold value of path lib/style/common.

fixed iframe tag- had multiple closings. Also added text for browsers that can't display iframes

Remove email notification from registry script.

cleaned up css greatly by importing eml css and knb css

knb.css now impots common eml css file - still need to fix layout in eml display tho' - something is being overridden and messes up alignment

changed knb skin index page to forward to knb site and include any user params in url. changed resultset.xsl so qformat is handled properly in posts. changed build file to copy default.css from eml checkout to style/common so other skin-specific css can import it if reqd

added JS to maintain ?name=value url params thru' redirect

added search gif used in default homepage

added line to installCommon target that copies the metacat-client.jar to the WEB-INF/lib directory

This is the merge from the branch WEB_UI_REDESIGN_BRANCH back into the head.
The only files that have been removed are those in lib/style/eml2; other files
that have been cvs removed (only from lib/ and lib/style) have been re-added
elsewhere (i.e. moved from one directory to another)....

Remove unneeded file Upload999.java

If the sessionid is null and user will be treated as public.

Get rid of doctype declare in transfer.

Set system id for transforming.

Modified a method and can be reused.

A proposed configuration file format for the metacat harvester. This format is a simple XML document that details the schedule for harvesting, the user under which harvested documents should be owned, and the list of documents to be harvested,

If db pool size is maxium and no connection is free. The checkout will be wait.

superseded - now these elements are pulled in from the knb website

Harvester UML activity diagram in jpeg format. This is a preliminary look at some "value added" or quality control componenets. Created initially in Oracle's JDeveloper

Harvester UML activity diagram in svg format. This is a preliminary look at some "value added" or quality control componenets. Created initially in Oracle's JDeveloper

Harvester UML activity diagram in jpeg format. Created initially in Oracle's JDeveloper

Harvester UML activity diagram in svg format. Created initially in Oracle's JDeveloper

new include files for metacat web pages - header and search box. Still need to remove hard-coded context uris

Add a checking for xml_nodes insert finished, then start build index table.