This document is made up of three sections, describing installation , post-installation work , performance and the admin interface



  • The icat distribution: icat.ear-4.3.1-distro.zip
  • A suitable deployed container (here assumed to be glassfish though tomcat should be sufficient) to support a web application. Testing has been carried out with Glassfish 3.1.2. Glassfish installation instructions are available.
  • A database as described in Database installation instructions installed on the server
  • Deployed ICAT authenticators.
  • Python (version 2.4 to 2.7) and the python-suds package installed on the server.
  • MySQL-python must be installed if you have an MySQL 4.2.x schema you need to upgrade.
  • cx_Oracle must be installed (in addition to an Oracle client) if you have an Oracle 4.2.x schema you need to upgrade.
  • icat-setup version 1.1.x or higher must be installed if you have a 4.2.x schema you need to upgrade and you wish to preserve existing rules but is also generally a useful component to install.
  • ice , the ICAT editor will make it easier to configure your ICAT.

Summary of steps

  1. Upgrade the database schema if you already have a 4.2.x version which you wish to use with ICAT 4.3.1. If you have already upgraded to ICAT 4.3.0 then no changes to the database are required.
  2. Please follow the generic installation instructions
  3. See if it works.

Schema upgrade

This is for upgrading a 4.2.5 schema to 4.3.1. If you have already upgraded to 4.3.0 skip this step as the database structures for 4.3.0 and 4.3.1 are identical. Do not attempt to use this procedure on a 4.3.0 schema!

  1. Back up the database in case it should get into a state from which recovery is impractical.
  2. Run the get_rules program to save the rules in the format accepted by icat-setup. This must be run as somebody who has read access to the rules. For example: ./get_rules.py https://example.com:8181 db username root password password The program should report how many rules it has saved and where.
  3. Ensure that nobody tries to use ICAT while it is being upgraded - the simplest approach is to undeploy the old one which can be done from the command line or by using a web browser and connecting on the admin port (typically 4848) and undeploying from there.
  4. For MySQL edit username, password, schema and dbhost at the top of the file ./upgrade_mysql_4_2_5.py and run it or or for Oracle, edit username , password and db at the top of the file ./upgrade_oracle_4_2_5.py and run that. Note that the procedure has been tested on ICAT 4.2.5 but should work for earlier 4.2 versions. The script will first check that everything should go work. If it reports problems fix them and try again. Once it gets past the checking stage it starts the conversion which can take a long time (many hours for a production system). At the end you should have a 4.3.1 database. Any indices which had been created manually will have been removed.

The icat.setup.properties file

is the name of the jdbc driver and must match the jar file for your database that you stored in the previous step.
identifies the icat database and how to connect to it.
is the top level of the glassfish installation. It must contain "glassfish/domains", and will be referred to here as GLASSFISH_HOME as if an environment variable had been set.
is the administration port of the chosen glassfish domain which is typically 4848.

For a local oracle-xe installation the following values of driver and icatProperties should be good except for the user and password values:


Note the "'" which is needed because the url contains colons which also separate individual properties.

For MySQL:


The icat.properties and icat.log4j.properties files

If you wish to modify the provided logging levels then rename icat.log4j.properties.example to icat.log4j.properties and update the icat.properties file to reference it as explained below. The icat.properties file may need other changes:

Defines the lifetime of an ICAT sessionid. You should avoid making it have a long duration as this increases the risk if it is intercepted, lost or stolen.
Is a space separated list of user identifiers having full access to the authorization tables: Rule, Group, User and UserGroup. The format of the user identifier is determined by the chosen authentication plugin. The authn_db and authn_ldap plugins may be configured to either return the simple user name or to prepend it with a name identifying the mechanism. For example if there is a an entry "root" in the database then if the authn_db authenticator is configured without a mechanism then the user name to consider will be just "root", however if it has been configured with a mechanism of "db" then the string "db/root" must be specified.
is a space separated set of mnemonics for user to select the plugin in the login call. This must not reference plugins which are not installed as plugins are checked when ICAT performs its initialisation; if plugins are missing ICAT will not start.
is the jndi name to locate the plugin. When you installed the plugin a message would have appeared in the server.log stating the JNDI names. For example for authn_db you would expect to see java:global/authn_db.ear-1.0.0/authn_db.ejb-1.0.0/DB_Authenticator. There must be one such entry for each plugin.
is a space separated set of Entity names for which you with to generate notifications. For each one there must be another line saying under what conditions you wish to generate a notification for the entity.
notification.<entity name>
a string of letters taken from the set "C", "U" and "D" indicating for which operations (create, update and delete) you wish to be notified for that kind of operation on the entity.
is a space separated set of call logging destinations - currently valid destinations are "table" and "file". For each one there must be another line saying under what group of calls you wish to log.
a string of letters taken from the set "S", "R" and "W" indicating for which group of calls you wish to generate a log entry. "S" denotes session calls (login, refresh and logout); "R" is used for the various read calls and "W" is used for all write calls (create, update and delete).
This is optional. If present it must specify the path to a log4j.properties file. The path may be absolute or relative to the config directory.
This is optional. It is the path to a directory (whose parent must exist) in which to store the lucene index. If this is specified then lucene.commitSeconds must also be specified. If it is omitted then lucene indices will not be created and the searchText() call will return nothing.
the interval in seconds between committing lucene changes to disk and updating the index. If you set it to 300 then searchText() calls will see what was available at some time in the past (up to 5 minutes ago) and which is also currently present.
the number of changes to accumulate before committing them to disk. If the number is too high there can be memory problems. Currently this is only used by the call to lucenePopulate.

Check that ICAT works

A small test program, testicat, will have been installed for you. This is a python script which requires that the suds client is available. This connects as one of the root users you defined as 'rootUserNames' in the icat.properties file. Invoke the script specifying the url of the machine on which the ICAT service is deployed (something like https://example.com:8181), the mnemonic for the chosen authentication plugin followed by the credentials for one of the root user names supported by that plugin. These credentials should be passed in as pairs of parameters with key followed by value. For example: testicat https://example.com:8181 db username root password secret

It should report:

Logged in as ... with 119.9... minutes to go
Login, search, create, delete and logout operations were all successful.

This script can be run at any time as it is almost harmless - it simply creates a "Group" with an unlikely name and removes it again.

In case of problems, first erase the directory /tmp/suds and try the testicat again. If it still fails, look at the log files: server.log and icat.log which can both be found in the logs directory below your domain. Look also at the relevant authenticator log.

Post-installation work

Fresh Install

If this is a fresh install then you can use icat-setup to add rules to ICAT, then use ice to create a Facility and other high level entities.

If you are using Oracle the type NUMBER(38, 19) will have been used for all floating point numbers. This constrains the values that can be stored - they may be truncated or rejected. To fix this please execute the SQL statements in fix_floats_oracle.sql


If you have performed a schema upgrade then you should restore the rules using the icat-setup tool. For example:

icat-setup -f rules.authz https://example.com:8181 db username root password secret

This assumes that you are in the directory where ran get_rules.py which will created a file rules.authz. The credentials (keyword value pairs following the authenticator mnemonic) should be those of one of the users specified in the rootUserNames of the icat.properties file.

Please check the rules.authz first as it will not work if it references entities that no longer exist. For example "Group" must be replaced by "Grouping" and InputDatafile is no longer part of ICAT. Also because some problems have been found with conditions containing dots (such as "InvestigationUser [user.name='fred']") in rules these must now be re-expressed without dots.

Finally you should run the icatadmin populate command to populate lucene for all existing data as in the example below:

icatadmin https://example.com:8181 db username root password secret -- populate --timeout 3600


To improve performance:
  • Consider creating the indices defined in indices.sql. Indices can make a huge difference to the database performance but there is also a small cost for each index.
  • Make entities readable by anyone if they contain no sensitive information. This is generally the case for those entities that implement an many-to-many relationship. For example InvestigationUser relates Investigation to User but has no attributes. By making it world readable no access to Investigation or User is granted. An in memory cache of world readable entities is maintained by ICAT.
  • Add entries to PublicStep to allow the INCLUDE mechanism to be less costly. PublicStep is explained in the ICAT Java Client User Manual. Its contents are also held in an in-memory cache for performance.

The icatadmin tool

Administration operations have been added to the ICAT API and are accessible via the icatadmin tool which will have been installed by the setup.py script. It should be invoked as:

icatadmin <url> <plugin> <credentials>... -- <command> <args>...

to run a single command or

icatadmin <url> <plugin> <credentials>...

to be prompted for a series of commands as shown below. In either case if you specify '-' as the password you will be prompted for it. Note that in the single command case the "--" marker is needed to terminate the list of credentials. For example:

icatadmin https://example.com:8181 db username root password secret -- properties
. Only users mentioned in the rootUserNames of the icat.properties file are authorized to use this command.

lists the active contents of the icat.properties file. It does this by examining the properties after they have been read in so any superfluous definitions in the original properties file will not be seen.
populate [<entity name>]
re-populates lucene for the specified entity name. This is useful if the database has been modified directly rather than by using the ICAT API. Note that because of caching, ICAT should be reloaded after any direct database modifications are made. This call is asynchronous and simply places the request in a set of entity types to be populated. When the request is processed all lucene entries of the specified entity type are first cleared then the corresponding icat entries are scanned to re-populate lucene. To find what it is doing please use the "populating" operation desribed below. It may also be run without an entity name in which case it will process all entities.
returns a list of entity types to be processed for populating lucene. Normally the first item returned will be being processed currently.
instructs lucene to update indices. Normally this is not needed as it is will be done periodically according to the value of lucene.commitSeconds
clears all the lucene indices - but does not commit.
search <query> [<maxCount> [<entityName>]]
searches lucene indices and returns a list of entity_name:entity_id values. Arguments are
a lucene query which should be enclosed in quotes if it contains more than one word. Queries can contain AND and OR in upper case as well as parentheses. The default operator is OR. Wildcards of * and ? are also supported. Other features are described in the user documentation for the searchText call.
maximum number of values to return (defaults to 100)
if specified, this restrict results to entities with this name