ChemInventory is a simple, fast, and flexible HTTP based chemical inventory server. It allows storing and tracking of chemicals including their structures, bottles, locations, and suppliers. It provides fast structure search by substructure-, exact match-, and similarity-search. It uses OpenChemLib (a Java based cheminformatics framework), Simple-Framework (a robust Java based HTTP(S) engine), and MySQL.
ChemInventory does not use a pre-defined entity relationship model. It rather reads table names, column names and column types from a configuration file, automatically builds a table creation script and all SQL commands needed to communicate with the database. It, however, requires two mandatory tables: one that contains bottles and another one that contains chemical structures. It also expects a 1-to-N relationship from the latter to the former. Therefore, the create_db.sql file and the supplied test data are just examples of a possible table structure.
When up and running, ChemInventory server listens on a dedicated port for HTTP based search requests. It can be used as virtual host of a web server to be accessible under a web-server subdomain (e.g. https://cheminventory.organisation.org). ChemInventory is meant to work in combination with a Web-based and/or Java-based front end application that let's end users store, edit and search bottles of chemicals. These client applications are not part of this project, yet.
ChemInventory requires JRE 8 or newer, OpenChemLib, SimpleFramework, and MySQL (or ProstgreSQL). All dependencies are included with this project in the lib folder.
git clone https://github.com/thsa/cheminventory.gitProvided, you have installed MySQL-Server, run the following command on a Linux computer to create a new inventory test database including test data.
./create_dbFor information about how to install MySQL or how to create an empty inventory database check the comments in the create_db file.
./build_alljava -jar inventoryserver.jar -c test_config.txtTo display the help page open a web browser and access the server's URL
http://localhost:8092/?what=help
An example for a little more complex query would be
http://localhost:8092/?what=query&smiles=c1ccccc1O&b.current_amount=>5&s.name=ABC
This will retrieve all bottles from supplier 'ABC' with a phenol substructure and a current amount above 5 g or ml.
For a different database structure, i.e. different tables with different columns, adapt the config_test.txt file to your needs. Then use the inventory server to create a new table creation script, e.g.:
java -jar inventoryserver.jar -tcs -c my_config.txt > createMyDB.sqlThen launch the server with your updated my_config.txt and it will work with the new entity relationship model.
ChemInventory. Copyright (C) 2024 Thomas Sander, openmolecules.org
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.