Metacat

Adding new files for upgrading version 1.5 database to version 1.6 database

Added code to create new tables xml_path_index and xml_nodes_revisions...

Changed the name of the function

Modified xmltables script so that:
1. Foreign key for rootnodeid in xml_revision points to xml_node_revision table instead of xml_nodes
2. Added a new table xml_path_index which is used to index the paths specified by user in metacat.properties
3. Addes a new table xml_nodes_revision which stores the nodes of old revisions and deleted documents

Fixed bug in previous commit

Modified postgres script so that:
1. Foreign key for rootnodeid in xml_revision points to xml_node_revision table instead of xml_nodes
2. Added a new table xml_path_index which is used to index the paths specified by user in metacat.properties
3. Addes a new table xml_nodes_revision which stores the nodes of old revisions and deleted documents...

Added a new function which can used to control the carriage return at the end of the debug message and 'Metacat' in front of the message...

Making changes in postgres db upgrade script such that instead of JDBC, SQL is used for updating the DB

Fixed a bug in printSQL function. The bug came into the picture for queries which involve multiple query groups and one of the query groups does a % search.

Adding perl script for changing ldap password for an account.

Added code to delete all entries in xml_queryresult table when buildIndex for a docid is called.

Adding the call to normalize function for now -- too many calls to normalize function are made and this needs to be looked into. Removing call to normalize function caused trouble in text like this "A&B"

Fixed a bug in last commit. Doing a search like
pathquery version="1.2">
<returndoctype>eml://ecoinformatics.org/eml-2.0.0</returndoctype><returnfield>originator/individualName/surName</returnfield><querygroup operator="INTERSECT"><queryterm casesensitive="false" searchmode="contains"><value>%</value></queryterm><queryterm casesensitive="false" searchmode="contains"><value>National Center for Ecological Analysis and Synthesis</value><pathexpr>organizationName</pathexpr></queryterm></querygroup></pathquery>...

Fixed a bug - when returnfield_id is not found in xml_returnfield, records are not added to xml_queryresults

Modified the upgrade java script to provide more effective feedback during the
nodedata copy operation so that users don't think it has failed or crashed.

Modified the code so that lastid file is created in a skin when lastid file is not found.
Commented out the code which uses AdminDB module and uncommented the test function.

1. removed the call to QuerySpecification.printAttributeSQL() from QuerySpecification.printExtendedSQL()
2. in QuerySpecification.printExtendedSQL() if ( returnFieldList.size() == 0 ) then it returns null
3. DBQuery.addReturnfield() doesnt execute the element query if printExtendedSQL returns null

A minor change from containAtrributeReturnField to
containsAttributeReturnField

I've added in a test in QuerySpecification.printExtendedSQL that checks
to see if attributes, and sometimes only attributes, are in the original
returnfield request. If so, the printAttributeQuery is called.

Changed the handleReturnField() method so that it handles path expressions with
only attributes in the path.

Added a check if printAttributeQuery() for returnPath to see that it is not null so that that this doesnt happen

xml_index.path like 'null' AND xml_nodes.nodename like 'id'

Fixed a bug in previous commit

Modified code for computing the returnfield string - earlier only elements were used to construct the string. e.g. /dataset/title
Now attributes are also added to the returnfield. e.g. title/@id

Replaced 1.4.0 with release

When a path expression includes element content and attribute content, then
the SQL generated needs to search for attribute nodetypes with parent
nodenames equal to the path expression element content. However, when
only searching for attribute content (such as just @packageId), then...

When searching for attributes in the XPATH expression, an 'index out of bounds'
exception was thrown when only an attribute was included in the path string.

This fix changes the pathexpr.indexOf comparison to 0 rather than 1, since
the index starts at 0....

dropping the sequences as well in the postgres drop list.

Added new tables from metacat 1.5 to the drop list.

Removing call to normalize from getNodeRecordList()

Changing the normalize function. Adding changes submitted by Johnoel. Removing code for converting " as " can be stored as it on Oracle. Removing code which strips out \n and \r

Removed occurence of enum which is a keyword in Java 1.5

Removed occurence of enum which is a keyword in Java 1.5

Changed the queries so that PreparedStatement.setString() and .setInt() are used instead of write the string directly into the sql statements

Removed the code which created triggers. Added this code in the build file

Removing code added for creating nodedata column in xml_index table

Fixed a bug from previous commit which removed whitespaces from documents.

Removed irrelevant code from previous commit

Removed code which entered value for nodedata in xml_index

Modified code such that nodedata column in xml_index is not created and used. So now we are using the same logic for using xml_index which was used for metacat release 1.4

Replaced Usage Constraints with Usage Rights and Data Originator with Dataset Owner.

(Commit done by Saurabh Garg for Veronique)

Added new database upgrade script for postgres.
Modified the database upgrade script for oracle
Added comment to DBquery.java
Fixed a bug in xmltables.sql

Added code so that metacat administrator can delete any document.

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.