Metacat

Interim checkin of EventLog reporting structure. Still basically incomplete but compiles.

Add three new Harvester tables

Omit HARVEST_OPERATION_TABLE and store harvest operations in properties file instead

Add new Harvest Operation Properties to replace the HARVEST_OPERATION_TABLE

Fixed the returndoctype bug in DBQuery as described in bug 1451. Now,
results are returned even if returndoctype is null, which is the
appropriate behavior.

Implement sending email reports to harvest administrator and site administrator

Patched to make the date-time value insertion work under oracle. Now it
tests fine under both oracle and postgres. Still need to write an
access/query function.

Updated build.xml to add targets for doing the 1.4 database sql upgrades.
Also note I made it work with both oracle and sql, and note that the MS
SQL Server sql scripts seem to be lacking -- some are missing. Need to
resolve this before release.

Added additional logging calls for read, upload, insert, update, delete, and
other commands. Now need to get a reporting function working and this
bug 101 will be largely finished.

Modified EventLog to eliminate the separate revision column and instead fold
that into the docid string. Log now includes read events, but need to update
the data sent there.

New EventLogTest modifying the log call to exclude revision.

Modified SQL scripts to add the new access_log table. I've partially tested this under postgres but have not yet tested under oracle.

Reformatted code for readability and consistency.

Added javadoc that was missing for the EventLogData class.

Added classes for basic event logging support. These classes write log entries to the database connection. Still to do: query the event log, write oracle sql code (postgres is done), possibly allow the log to be archived to a text file, and possibly do the dtabase writes asynchronously via a caching mechanism.

Made change in result tag that is returned in getprincipals action. Replaced userdn with username.

Added GPL license text to harvester source files.

Fixed a bug the text filed in path xml query maybe splited.

Fixed a bug if a document already has index, but now metacat doesn't use index. If you try to delete this one, will cause error.

Clean up some code.

Add new option for return set size.

Revise the handle query and squery method, not finished yet.

Add a new transform method.

Add a new transferm method for string reader.

Implement harvester scheduing capabilities and sending email reports to the Harvester Administrator

Validate user input data in registration servlet

Improve authorization logic for single file uload servlet

Add delete capability to single file upload servlet

Updates to static html login and upload

Add delay and smtpServer properties

Set content type properly for getversion action.

Added a simple action for finding out the current metacat version. The information is pulled from the property file, so be sure to update the version in the property file before shipping a release.

Fixed a bug in the new recursive SQL statements that prevented them from operating on oracle. Now they should work on both oracle and postgres.

Reformatted source for readability and conformance.

Excluded the update of the xml_index table in insert,update, and delete if the usexmlindex option is set to false.

Reformatted DBQuery.java for readability and consistency.

Changed printAttributeQuery() to no longer depend on the xml_index table. Now, if useXMLIndex is false, the method will use a recursive query on xml_nodes to match paths instead of using xml_index.

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.