Metacat

Some refactoring of the printExtendedSQL()
methods to eliminate redundancy in the code and
to provide more readable documentation.

Moved decision about whether to use xml_index for
query to the metacat.properties as "usexmlindex". Default
is now false. Still have some refactoring to do to remove a
few more uses of the xml_index table.

Replaced properties file that I accidentally overwrote. Reverting to 1.3.

Removed unused references to abstractpath, and some unudes javascript.

Created new printExtendedSQL function that can get the extended
return fields using only xml_nodes and not xml_index. One
step closer to eliminating the dependence ofn xml_index.

Created test class QuerySpecificationTest and started process of removing the xml_index from the QuerySpecification code. Reformatted some classes for readability.

Removed the "getdataguide" action as it was always experimental and is no longer used in metacat or morpho.

removed the 3 versions of printPackageSQL which are no longer used by metacat. This eliminates some dependency on xml_index.

Harvester properties file

Login page for Harvester Registration Servlet

Implement Harvester Registration Servlet

Additional scheduling logic

Changes to Harvester properties

Changes to log entries

Changes to harvester targets

Made changes in these three files so that getPrincipal returns back more details about users and groups. Users now contain userDN, user Name and user Email. Groups now contain Group name and Group description. So some function calls which returned single string array earlier now returns multiple string arrays. AuthSession.java called one of these functions - so accordingly changes were made to fix that part of the code.

Fixed a bug which doesn't occur everytime. The bug occurs when lastid in (cfg).lastid is not unique. i.e. there is already a document in the server which has same docid. The earlier algorithm was:

while(not unique){
get accession number;
update accession number written in document; (BUG)...

Added extra parameters (cfg & docid) to be passed on to generic response screen.

Set new URL for the NCEAS registry home. I forgot to commit this earlier.

Made changes so that *.gif and *.png are copied without filtering.

Debug level was changed and a few extra lines were added in last commit.
Restored those to previous values.

Added target for installing skins. Target name is install-skin. It is dependent on init. It take skin name as input from user, creates a directory in skins directory and copies files to that directory.

removed sid's space and added a >> before titles, so datasets with no title will still have a clickable link on results listings. Sid's space was not visible unless the user did a mouse-over

added sessionid hidden fields, based on $sessid transformer parameter set by DBTransform.java

made changes so that organization name for the site or project is entered before
any other creater.

Added space at the end of title that is returned back. This is done so that documents with no title can be clicked on.

Made changes in entryForm.tmpl so that it shows site list for specnet skin.

Adding registry skin for SpecNet.

Fixed the bug for sessionid storing, revision couldn't be zero and Ldap DN is case sensitive.

In test client package, get rid of HttpClient in parameter. Because, http client has cookies and we couldn't test session id.

Replaced Hash table with Vector of Vector datastructure in getting <param> from Query. This was done so that the results are represented in same order as they appeared in the document.

fixed a bug in reloading of kewords from an eml file for edit-datapackage form.

Made changes in the formatting display of Project list.

Fixed a bug in sorting of records. Now the result sent back is title sorted.

Fixed bug that version could not be zero in replication.

Minor changes to allow the registry to work in the knb skin, mainly in
how to treat the 'site' field. Now it is a free-text organization
field in the KNB skin. Need to test, install this on ecoinfo and link it
into the KNB web pages.

Added subroutine for replacing characters that might create problem in HTML.
Specifically written for "being used in any text field. This create a
problem in confirmData template, when you specify input name value pair with value
having a " in it.

Additional Harvester development

Fixed a small bug.

Fix enter for bug 1306.

Fix for bug 1325. new javascript function added.

Made changes so that & and other characters dont mess up the url that is passed to metacat.

Additional development of Harvester implementation

Added a new OBFS site to the list of sites. Information provided by Stromberg.

Mixed a bug reported by Rick and Dan. The form inserted a organizationName tag with no value. This happened only in NCEAS as the tag was included from the drop down site list which doesnot exsist in NCEAS version. Hence, a empty tag was inserted in the eml document.

Bug 1301 - changes made for a repeatable add keyword button

Bug 1301 - changes made for a repeatable add keyword button.

Made changes to fix bug# 1300: 1,2,3,4

Made text changes mentioned in bug# 1308

Made changes to fix bug# 1326. The templateVar are now passed on to the responseTemplate also in case of error - so that it can show a link which will send all the values back to register-dataset.

Changes made to fix bug# 1326. There is a link which call register-dataset.cgi with all the inputs such as that resgiter-dataset calls reEnterDataSet

Harvester source files

Deleting .project file that was added by mistake by Eclipse (and me).

Comments and notes on registry by Rick Reeves and Andrea Chadden. I have annotated it with bug #s and comments.

Made changes to fix Bug 1311 1)

Added docid in edit form - Bug 1304

Added a view button as mentioned in bug 1304.

Made some hanges mentioned in bug 1297.

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.