Preparing an Instant JChem project

1. Create a new project or open an existing one in IJC. You can choose from an empty project, a project with an existing database or a project with already imported demo data.

2. Set up the desired security configuration for the project. Please note that a project with the Default (anonymous) security policy cannot be used in Plexus Suite.
   A detailed description can be found in the relevant part of the Instant JChem user documentation.

3. Create the necessary user accounts and assign the appropriate user roles to them. The details for managing user accounts can be found in the Instant JChem User Guide.

4. Add your chemical data to the project and design any database views (tables and forms) you will need for browsing the data in Plexus. Make sure that these database views are accessible for every user with the appropriate user role. A more detailed description about sharing database items is available here.

5. Connect to the schema as administrator and in the Schema Settings dialog select the Remember username and Remember password options.

6. Disconnect the schema.

7. Close the IJC project.

Configuring a database connection

A database connection is described in a schema configuration (.ijs) file. In order to connect to a database from Plexus Suite, each .ijs file has to be put

• either in its default location, in the ${HOME}/.chemaxon/plexus-suite folder in UNIX systems (or in the %USERPROFILE%\chemaxon\plexus-suite\ folder in a Windows system);

• or in a location specified in the ijc.schemas.dir property of the webapp/WEB-INF/classes/nps.properties file packed in the downloaded .war file.

Please note that before version 15.11.16, the default configuration directory was ${HOME}/.instantjchem/ijcWebServer/ (or %USERPROFILE%\.instantjchem\ijcWebServer\ on Windows). From 15.11.16, the default directory has become ${HOME}/.chemaxon/plexus-suite/. While Plexus Suite can still work with the old configuration, it is recommended that you migrate your configuration files to this new location.
If neither the old nor the new configuration folder exists, Plexus will create it at its current default location.

Even if using a Derby database, the .ijs file must contain the URL to the database. This information can be found in the Instant JChem desktop application: in the Projects window right-click on the schema's node and select Schema settings.
For a detailed description, please, check the Instant JChem user documentation.

The schema configuration file has to contain the ijc.username and ijc.password properties (as well as the database.username and database.password properties if necessary). In addition, the ijc username and password has to belong to a user account which has administrator role assigned to it in Instant JChem.

As there are differences between use cases of Plexus Suite, it is useful to apply some connection pool settings in schema configuration. These settings have to be saved for each schema in its respective .ijs file and the same properties as for Instant JChem are available. Please note that the default settings for maximum active connection is set to 6, which might become a performance limitation for organisations with high number of concurrent users who have to share the defined number of connections.

Every deployed schema should have the same security setting because the user login details are used for every schema in the Plexus directory. Since 15.12.7.0 version the server attempts to authenticate the user against the first schema and in case it fails, no other attempts are made. This behavior can be changed in the nps.properties file using the multiple.schemas.auth property. Setting this property to true leads to the user login details being used for authentication in all schemas available. The nps.properties file can be found in the WEB-INF/classes/ directory in the downloaded .war file.

You should use different user accounts for connecting to your database with the Plexus web application and with the Instant JChem desktop application. Starting the Plexus server with user "A" defined in the .ijs file and later connecting to the database with the same user from Instant JChem results in the server producing runtime errors.

Maximizing the number of simultaneous queries

Another property can be added to the schema configuration (.ijs) file to set the maximum number of queries which can run simultaneously on the server side. The default value is five simultaneous queries. You change this value by adding the following line to your .ijs file (replace the text in italics with the actual number of parallel queries enabled):

<entry key = "server.max.queries">maximum number of simultaneously running queries</entry>

When the number of parallel queries exceeds this value, the subsequent queries will be waiting in a queue on the server side.