NwbQueryEngine

This is a prototype of a query engine used for NeurodataWithoutBorders format

Getting started:

Prerequisites

• For running only Installed JRE 8

• For programmers

1. Installed JDK 8
2. Installed Maven
3. Installed git-lfs
4. Installed your favorite IDE

Running

• compile with mvn clean package -Djava.library.path=src/main/resources/

• run java -Djava.library.path=src/main/resources/ -jar target/nwbqueryengine-1.0-SNAPSHOT-jar-with-dependencies.jar file query

e.g: java -Djava.library.path=src/main/resources/ -jar target/nwbqueryengine-1.0-SNAPSHOT-jar-with-dependencies.jar /home/user/file.nwb "processing=(electrode_idx>30)"

Python support:

• install py4j by pip install py4j

• run server java -Djava.library.path=PATH_TO_RESOURCES_DIR -jar target/nwbqueryengine-1.0-SNAPSHOT-jar-with-dependencies.jar pyserver

• For running on a remote host parameter -Dhost.ip=remote-host-ip must be used

• run python code such as:

 >>> from py4j.java_gateway import JavaGateway
 >>> from py4j.java_gateway import GatewayParameters
 >>> gateway = JavaGateway() # for localhost
 >>> gateway = JavaGateway(gateway_parameters=GatewayParameters(address='remote host ip')) # or for remote host
 >>> res = gateway.executeQuery("file or dir with nwb files", "query")
 >>> for x in res:
 ...     print (x)

Maven

    <dependency>
        <groupId>edu.berkeley</groupId>
        <artifactId>nwbqueryengine</artifactId>
        <version>1.0-SNAPSHOT</version>
    </dependency>
    
    <repository>
        <id>snapshots</id>
        <url>http://eeg.kiv.zcu.cz:8081/nexus/content/repositories/snapshots/</url>
    </repository>

Output

If the tool is run from a command line the output is a triple containing the NWB file name, dataset path and a value. If the tool is used as a library in a third-party program then this program is responsible for formatting the output.

Logging

logging (e. g. logging level, log file location) can be configured in src/main/resources. log4j library is used. Do not use degug level in production. It can dramatically affect performance