Software

• CentOS, RedHat, Debian or Ubuntu operating system x86_64 version.

Find information for cases of other linux systems

• postgresql-94 relational database (preferred download page) for JPC versions up to 2.0

• postgresql-95 relational database for JPC versions starting from 2.1

See help to upgrade of postgreSQL 9.4 to postgreSQL 9.5

• availability of hstore extension of postgresql (e.g., contrib package)

• Java8 runtime environment

Hardware

The memory need of JChem PostgreSQL Cartridge strongly depends on the format of the chemical structures to be stored. In the next table, the approximate memory need of 10 M PubChem molecules in SD file format and in SMILES format are compared. The presented memory setup is optimized for execution speed. Lower amount of memory may be used, in this case performance drop is expected. Further details can be found in the Performance tuning of searches in big tables section.

Install PostgreSQL Cartridge

Download the latest version of PostgreSQL Cartridge from here. In order to install the latest version (as root), change the x.y (version information) in the following statement to the current one:

In CentOS:

In RedHat or Debian:

See also Getting started guide for PostgreSQL and Java8 installation.

Before the first use

1. Install your license file

   Copy a valid ChemAxon license to /etc/chemaxon/license.cxl or set its location in /etc/chemaxon/jchem-psql.conf file. Required license in the license file is 'Postgres Cartridge'.
   The jchem-psql user should have read access to the license file.

2. Initialize index directory

   sudo service jchem-psql init

   If you encounter any problem in your java installation, set your JAVA_HOME in the file /etc/default/jchem-psql.

   Initialization does not start the service, you must start it manually.

3. First start

   sudo service jchem-psql manual-start

Create extension in a database

Each chemical database should have the following extensions created separately.

1. Create a new user and database

   sudo su postgres

   createuser testuser

   createdb testdb -O testuser

2. Install the extensions (you must be postgres user or any other user who has create extension privilege)

   psql testdb

   testdb> CREATE EXTENSION chemaxon_type;

   testdb> CREATE EXTENSION hstore;

   testdb> CREATE EXTENSION chemaxon_framework;

   If you experience any error during the CREATE EXTENSION steps, please check this page which gives hints relating non-standard PostgreSQL setup.

3. Checking JChem PostgreSQL Cartridge installation

   If jchem-psql service is running, the following query can be executed without any problem:

   testdb> SELECT 'C'::Molecule('sample') |<| 'CC'::Molecule;

   This select statement executes a substructure search, with a Carbon atom as the query and ethane as the target structure. You must receive true (t) as output. See details of Molecule type below.

Service

The service can be started/stopped using:

ENABLED=1 (default) setting in /etc/default/jchem-psql file makes the service start on system boot and start manually by start.

If you want the service not to start on system boot, set ENABLED=0 in the /etc/default/jchem-psql file. In that case, manual-start must be run.

Configure JChem-psql server

The following configuration parameters are available on PostgreSQL side:

They - with the exception of shared_buffers - can be edited as an ordinary Postgres configuration parameter:

• in the postgresql.conf file (e.g., /etc/postgresql/9.4/main/postgresql.conf)

• can be overwritten in the current session:

  SET chemaxon.hit_retrieval_batch_size to 1000;

• to see the current value:

  SHOW chemaxon.hit_retrieval_batch_size;

The following configuration parameters are available on JChem-psql server side:

These parameters can be configured in the /etc/chemaxon/jchem-psql.conf file.

Changing these parameters except maxOpenSessionCount requires new initialization of jchem-psql service. Please note that this will purge all jchem-psql index data hence the indexes need to be dropped and recreated again.

Upgrade with keeping existing molecule type data

If not only JChem PostgreSQL Cartridge, but postgreSQL database upgrade is also needed ( e. g., from JPC 2.1 postgreSQL 9.5 is required), find an example of how to upgrade of postgreSQL 9.4 to postgreSQL 9.5.

1. Stop the service

   sudo service jchem-psql stop

2. Install the new version

3. Initialize the service (this step deletes the old indexes)

   sudo service jchem-psql init

   Only the index contents are deleted, the molecule records stored in the PostgreSQL database stay untouched.

4. Start the service

   sudo service jchem-psql manual-start

5. Upgrade your existing postgresql database

   1. Update the extensions

      sudo su postgres

      psql

       

      # ALTER EXTENSION chemaxon_type UPDATE;

      # ALTER EXTENSION chemaxon_framework UPDATE;

      In some cases of the upgrade process, you have to drop the indexes before altering the chemaxon_framework extension. If you receive an error message like

      "ERROR: cannot drop operator class chemindex_int_ops for access method chemindex because other objects depend on it

      DETAIL: index upg_ind depends on operator class chemindex_int_ops for access method chemindex

      HINT: Use DROP ... CASCADE to drop the dependent objects too.",

      you have to drop the index referred in the DETAIL part of the message and repeat step

      # ALTER EXTENSION chemaxon_framework UPDATE;

   2. Reindex the database

      Upgrade to 2.7 or above

      When you upgrade to JPC 2.7 or above and want to take the advantage of performance improvements implemented in 2.7, you have to update the tables storing chemical structures. The indexes should be dropped before the upgrade and recreated thereafter.

      update table_name set structure_column_name = structure_column_name::text::molecule('molecule_type_name');

      Example:

      drop index myindex;

      update mytable set mol = mol::text::molecule('sample');

      create index myindex on mytable using chemindex(mol);

      //or

      create index myindex on mytable using sortedchemindex(mol);

      If the above table update is skipped, reindex database is necessary:

      psql

      # reindex database <database name>;

      If you miss this step, all indexes of type chemindex will not function properly.

Upgrade without keeping existing molecule type data

If not only JChem PostgreSQL Cartridge, but postgreSQL database upgrade is also needed ( e. g., from JPC 2.1 postgreSQL 9.5 is required), find an example of how to upgrade of postgreSQL 9.4 to postgreSQL 9.5.

1. Before installing the new version, drop the following extensions

   DROP EXTENSION chemaxon_framework CASCADE;

   DROP EXTENSION chemaxon_type CASCADE;

   If you drop the chemaxon_type extension, it will implicitly drop all chemical columns.

2. Stop the service

   sudo service jchem-psql stop

3. Delete the content of the index directory

   sudo rm -rf /var/lib/jchem-psql/store/*

4. Install the new version