Metacat

Added the trailing '/' that was ommitted when XPATH queries included attributes.
This is a partial bug fix for:

http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2052

Fixed bug in command-line mode which caused array index out of bounds exception.

Changed default maxHarvests value to 0. Added logic to ignore maxHarvests value when it is set to 0 or a negative number. This allows Harvester to run indefinitely without shutting down after reaching a maximum number of harvests. The previous default value of 30 would cause Harvester to terminate after 30 harvests.

Added code to check if the document is indexed yet! So entry into xml_queryresult is only made if the doc is in xml_index.

Added code such that an offset can be specified in metacat.properties for entering records into xml_queryresult table. The value of xml_returnfield.usage_count should be more than the value specified in metacat.properties for records to be entered into xml_queryresult. so if you want results for any combination of returnfields should be stored in xml_queryresult only after that combination has been requested 50 times, set this value to 50

Modify the update for xml_relation.

Made changes in the sql scripts to create new tables xml_returnfield and xml_queryresult

Changes for entering new records into xml_queryresult:

1. Added a function which checks if there is a record exsists in xml_returnfield table for a given combination of return fields. If a record is found, the id for the record is returned. otherwise a new record is created in the xml_returnfield table and the id of the new record is returned....

Added code for updating xml_queryresult for action=delete and action=update

For both actions, the entries in xml_queryresult are deleted.
This works for action=update because deletion of entry is simple and the entries will be created again when the docid is part of a search result next time.

Added a function which gives back a string which is generated by sorting the returnfields requested for given query specifications

Changes made in the css for the skins.

Fixed some bugs from previous commits. Veronique changes the text of error messages. Added a new stage to distinguish errors because of logins.

Added new actions so that error message is not shown the first time resetPassword and changePasswords are called. Also fixed a bug where $cfg was not being passed to genericHeader.tmpl

Modified the offset which is used for creating the resultset. This helps in fixing the 'more than 1000 enteries in IN query' bug on Oracle.

Changed the code which handles Associated Party, Keywords and Taxonomic Information.

Added a check for eml2.0.1 documents in ContentTypeProvider.java

Add new query to fix existed xml_relation table datapackage type bug.

Using a variable to replace the hard code for namesapce in inserting record to xml_relation table.

Fixed a bug in the format of query result.

Added sql command to delete also schema entries also. Earlier the script only deleted old dtd entries

SQL command to update system_id to points to localhost.

Formatting improvements.

Formatting improvements.

Implement a new HarvesterServlet for running Harvester as a servlet. This eliminates the need to run Harvester in a terminal window. By default, the HarvesterServlet is commented out in lib/web.xml.tomcat(3,4,5). The user documentation will be modified to instruct Harvester administrators to uncomment the HarvesterServlet entry.

Re-implement logic to prune old log entries from the HARVEST_LOG and HARVEST_DETAIL_LOG tables. The old logic caused integrity constraint violations in the database because it tried to delete parent records from HARVEST_LOG prior to deleting child records from HARVEST_DETAIL_LOG....

Formatting improvements.

nodedata added to xml_index for nodes with nodetype=ATTRIBUTE also.

Modified code to add nodedata column to xml_index and enter data into it from xml_nodes table

Modified xmltables to add nodedata as part of the xml_index tables.

Modifying code so that nodedata is stored in xml_index table next to the paths.
This helps in making the search faster.

Increase number of rows in harvest list from 300 to 1200.

Fixed a bug from previous commit

Some more modifications so that % search doesnt run a select on xml_nodes.

Modified code to fix bug # 1850

Change default document type in Harvest List Editor to eml-2.0.1.

Remove DOS end-of-line carriage returns.
Other minor formatting improvements to the code.

Modified code so that when a % search is done, a xml_nodes search is not done. This search is not required and hence saves time in doing a % search

Added code to check for NaN while converting String to double.

Added code to check for NaN valuse which converting string to double.

Fix for bug# 1344

Fixed a bug in containsKey() function.

Modified database creation sql code so that in xml_nodes, nodedatanumerical coulmn is added.

Modified 'insert xml_nodes...' so that numerical data is added into numericalnodedata also.

Modified handling of greater-than and less-than so that comparison is done against nodedatanumerical column.

Modified code to work with Postgresql also.

Adding new java code which upgrades the database for version 1.5

Fixed a bug in previous commit. Moved normalization function before the string size is counted so that size change due to normalization is taken into account.

Added code to fix bug 1323. % sign is replaced by its http equivalent now

Added code to check id document is passed as part of the params. This is done toprevent NullPointerException which results in sending null to the user.

Added code to fix bug# 1344. Response template is called when cancel delete is pressed.

Integrating ldapweb.cgi & create-ldap-account.pl into metacat CVS tree.

Made changes to fix bug# 1538. Changed the code of the normalize function in MetaCatUtil.java. Earlier code was not taking care of characters above 123.

In DBSAXHandler.java, added call to normalize function before text is written to db.

Add a new method to get newest version of a given document.

Add a new method to get newest version for a given document.

Fixed bug #1551 by adding a conditional statement.

Made changes to fix bug# 1310. Now while parsing old documents, the script checks for ACLs also.

Modify value of redirect to match the servlet-mapping URL values in web.xml. The old value used the servlet class name. This worked in Tomcat 4 but seems to break in Tomcat 5 on Windows. The new value uses the servlet-mapping URL value. This should work in both Tomcat 4 and Tomcat 5.

Minor enhancement to support multiple email addresses for harvester administrator and site contact. Each address is separated by a comma or semicolon.

Thanks Jing, Fixed those code comments.

Adde a function to the metacat client to set access on an xml document in a
metacat repository.

Modified buildIndex() to now include an '@' sign in the path for ATTRIBUTE
nodes. Removed a bunch of debugging information. Fixed the BuildIndexTest
so that it would work on any machine (removed hardcoded paths).

Added code that changes the node column size

Added in servlet action 'buildindex' for building the XML_index table entries
for either a set of documents (if one or more docid params are provided) or
for the whole set of documents in the xml_documents table. The buildindex
action is restricted to only be accessible by users who are listed in the...

Changed DBSAXHandler.run() to now use the new DocumentImpl.buildIndex() method
for populating the xml_index table. The new method uses a jdbc ResultSet
for populating the index rather than doing it with the DBSAXNode, so it is
faster and can be run at any time on any document. This will allow us to...

Compose the Metacat URL from the httpserver and the servletpath properties, replacing hard-coded references to servlet.

Send redirect to HarvesterRegistration, instead of using the full class name which works on Tomcat-only installations but not with Apache.

Change the date format to one that is standard on both Oracle and Postgres.

Whitespace changes that fix a few formatting problems after Jing's commit.

Add new feature that delete can be broadcasted by force replication.

The new buildIndex() function now can write allof the appropriate index paths to the database for any given document. Next need to create a function to rebuild on demand, and modify DBSAXHandler.run() to use the new buildIndex() function.

Added changes to buildIndex() function. Now it is finding the right set of
paths, just have to save these in a hash and then add them to the DB xml_index
table.

changed function parameters in accordance with changes in PermissionController

Modified inline data permission handling, so that access rules for old version of inline data can be checked correctly.

Added a function which returns inline data id with out the revision number.

Changed error text that is returned when an invalid eml is inserted.

Add a code to load eml201 parser to fix the bug that couldn't generate access rule for eml201 doc.

Added sql for counting packages.

Fixed a bug in creation of EML documents when coordinates from the site_list have to be used.

Added lines for updating xml_catalog in the upgrade script to point to the
new schema locations.

Fixed error in handling of multiple additional metadata tags...

New schema changes, including upgrade scripts. Includes renamed postgres
scripts.

removed errors being generated in handling of qformat when action=insert. If qformat is not specified, xml is assumed as default.

Beginning new method for building the xml_index table. This uses the
JDBC resultset directly rather than DBSaxNode, and recurses through the
records of the table. The new function 'buildIndex()' would be called, but
currently is not linked in to any code, so it shouldn't get in the way....

removed a bug which was pointed out by Bing and fixed by Jing.

Removed some unused code

Added new upload function which takes InputStream as input.

fixed some bugs in document update

Added method to metacat client for reading inline data - readInlineData()

Fixed a bug in upload function. For online data updates, access was not checked.

Modifications to the registry to support the new ESA skin. Factored out some of
the configuration-specific code into properties that are set in the various
cfg files in the skins. New properties in the cfg files are lsite, usite,
showSiteList, showWgList, showOrganization. These now need to be set in every skin...

Fixed handling of various docid formats.

Code added to handle errors resulting from following urls:
http://metacat.nceas.ucsb.edu/knb/metacat?action2 - no action specified
http://metacat.nceas.ucsb.edu/knb/metacat?action=insert - no docid specified
http://metacat.nceas.ucsb.edu/knb/metacat?action=login - no username specified...

Added check for null condition so that proper error text is returned to user.

Checked to be sure the instance has been initialized in the getDBCOnnection
static method call. Assuming it has been initialized could (and does)
lead to NullPointerExceptions when used outside of the metacat servlet
if the conneciton pool isn't initialized properly.

Reformatted code for readability. It was crazy. Still has problems, but its
better. Will be working on some new methods on monday.

Fixed a bug in access handling when no access is specified.

Added eml-2.0.1 tags for eml processing.

Also fixed a bug. The error returned in case of no revision number specified was just null. Now it says that revision number is required.

Merging in changes made in branch 'dataaccess' by Jing Tao.

Added upload functionality to metacat client for upload online data

Add warning if default harvest list file is not found on disk.

Change relative path to harvestList.xsd schema to allow harvest list editor to run standalone.