Metacat

Minor edits to installation instructions for Metcat 1.5.0.

Adding perl script for changing ldap password for an account.

Removing the token for cvsroot for checking out webmdentry as build.xml no longer depends on webmdentry module

Removing dependency on webmdentry module

an index page for the developer tools

Increase height of .iframesearchboxclass to accomodate Internet Explorer.

Changes in tablehead and highlight styles made by Veronique Connolly

(Submitted by Saurabh Garg for Veronique Connolly)

Skin for Kruger National Park. Includes some improved text for the main
page, as well as addition of a login form for the main page.

Ne wlogin form for dev skin that does not require the full DN.

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

Fixed a bug - there is a white space at the end of data medium

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"

Adding move up, move down and delete gifs for register-dataset.cgi

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

added an upload form for binary files in the dev skin

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.

Updated properties to use release from the build.xml file.

Updated version in the metacat properties to 1.5.0rc1.

Add an "advanced search" link that points to the LTER query interface page.

Updated README with contributors.

Fixed typos in README, update version for release.

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.

Replacing token for checkout of eml-2.0.1

Fix documentation bug. The documentation said that the operator name was INTERSECTION, but the actual name is INTERSECT.

Changes made for release 1.5

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.

Adding lter skin.

Commenting out lines regarding /servlet/metacat again as we are trying to use "/context/metacat" where context is the tomcat context.

Fixed web.xml so that /servlet/metacat/* points to the metacat servlet

Added tomcat5 in build.properties
In build.xml, fixed a bug from previous commit

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

Changes in the documentation for the new release

Replaced 1.4.0 with release

Added code which checks out utilities from cvs. Modified distsrc to include utilities src also. Changed version from 1.4 to 1.5

Changing username from knb to metacat for postgres

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.

Updated install instructions with IPv6 instructions for postgres.

Changed "NCEAS Data Registry" to "NCEAS Data Repository" for sender. Veronique

(Commit done by Saurabh Garg for Veronique)

Changed "registry" to "repository" for the nceas skin. Veronique Connolly

(Commit done by Saurabh Garg for Veronique)

Commenting out link to /servlet from web.xml for tomcat5

Removed unwanted code.

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

Fixed a bug in previous commit and added a test for characters like mu.

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

• empty log message ***

Added code which creates the triggers for the new tables. This is for Oracle only.

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 typo.

Adding test for checking Metacat behaviour when characters outside A-Z,a-z,0-9 are entered.

Related bugs: 1711, 1538 (1711 has been fixed as tested by this file. Have to add code to test 1711)

Currently checking for
> when < > & is entered - test fails as expected as document is invalid...

Changes made to the css files by Veronique (tablehead class).

(Committed done by Saurabh Garg for Veronique)

Changes made by Veronique to generic guide following Mark Stromberg suggestions.

(Commit done by Saurabh Garg for Veronique)

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

Modified text, style and formating for the skins.

(Commit done by Saurabh Garg for Veronique)

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

(Commit done by Saurabh Garg for Veronique)

Modified so that database upgrade script to version 1.5 is called based on which database the user is using.

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

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.

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

Fixed a bug in last commit

Added new parameters to control the size of resultset for browsers and application like morpho. Also a parameter to specify the length of xml_queryresult.queryresult_string

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

Registry templates redesigned by Veronique Connolly and Saurabh Garg

Changes to the Data Registry Guide made by Veronique Connolly

Fixed formatting of the html page generated by using tables in all ldap files.

(Commit done by Saurabh Garg for Veronique)

Changes made by Veronique and Saurabh in the css for the skins.

Made changes in the contact information for the skins.

Modified the text in the index files.

(Commit done by Saurabh Garg for Veronique)

Modified the text in the header files.

(Commit done by Saurabh Garg for Veronique)

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.

Changes made to Data Registry Guide by Veronique Connolly

(Commit done by Saurabh Garg for Veronique)

Changes made to Data Registry Form by Veronique Connolly and Saurabh Garg

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

Changes made to Data Registry Guide by Veronique Connolly

(Commit done by Saurabh Garg for Veronique)

Modify harvestListEditorDist target to create the Harvest List Editor distribution using naming conventions that are consistent with other KNB releases.