DockerUtil

java.lang.Object
- biolockj.util.DockerUtil

```
public class DockerUtil
extends Object
```
DockerUtil for Docker integration.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`AWS_EFS` Docker container root user EFS directory
`static String`	`AWS_EFS_DB` Docker container root user DB directory
`protected static String`	`BLJ_BASH` Docker image name for simple bash scripts (awk,gzip,pear).
`protected static String`	`COMPUTE_SCRIPT` Docker environment variable holding the name of the compute script file: "COMPUTE_SCRIPT"
`static String`	`CONTAINER_BLJ_DIR` Docker container BioLockJ installation directory: "/app/biolockj"
`static String`	`CONTAINER_BLJ_SUP_DIR` Docker container blj_support directory: "/app/blj_support"
`static String`	`CONTAINER_CONFIG_DIR` All containers mount the host `Config` directory to the container volume: "/mnt/efs/config"
`static String`	`CONTAINER_DB_DIR` Some containers mount a database to the containers "db" volume: "/mnt/efs/db"
`static String`	`CONTAINER_INPUT_DIR` All containers mount the host "input.dirPaths" to the container "input" volume: "/mnt/efs/input"
`static String`	`CONTAINER_META_DIR` Some containers mount the "metadata.filePath" to the container "meta" volume: "/mnt/efs/metadata"
`static String`	`CONTAINER_OUTPUT_DIR` All containers mount "internal.pipelineDir" to the container volume: "/mnt/efs/pipelines"
`static String`	`CONTAINER_PRIMER_DIR` Some containers mount the "trimPrimers.filePath" to the containers "primer": "/mnt/efs/primer" volume.
`protected static String`	`DEFAULT_DOCKER_HUB_USER` Name of the BioLockJ Docker account ID: "biolockj"
`protected static String`	`DOCKER_HUB_USER` `Config` name of the Docker Hub user with the BioLockJ containers: "docker.user" Docker Hub URL: https://hub.docker.com By default the "biolockj" user is used to pull the standard modules, but advanced users can deploy their own versions of these modules and add new modules in their own Docker Hub account.
`static String`	`DOCKER_ROOT_HOME` Docker container root user $HOME directory
`protected static String`	`SAVE_CONTAINER_ON_EXIT` `Config` property removed the default --rm flag on docker run command if set to TRUE: "docker.saveContainerOnExit"
`static String`	`SPAWN_DOCKER_CONTAINER` Name of the bash script function used to generate a new Docker container: "spawnDockerContainer"

Constructor Summary

Constructors
Constructor and Description

DockerUtil()

Constructors
Constructor and Description
`DockerUtil()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static List<String>`	`buildSpawnDockerContainerFunction(BioModule module)` Build the "spawnDockerContainer" method, which takes container name, in/out port, and optionally script path parameters.
`static String`	`getDockerImage(BioModule module)` Return the name of the Docker image needed for the given module.
`static String`	`getDockerUser(BioModule module)` Return the Docker Hub user ID.
`static File`	`getDockerVolumeDir(String prop, String containerPath)` Get mapped Docker system File from `Config` directory-property by replacing the host system path with the mapped container path.
`static File`	`getDockerVolumeFile(String prop, String containerPath)` Get mapped Docker system File from `Config` file-property by replacing the host system path with the mapped container path.
`static String`	`getDockerVolumePath(String path, String containerPath)` Get Docker file path through mapped volume
`static String`	`getImageName(BioModule module)` Return the Docker Image name for the given class name. Return "blj_bash" for simple bash script modules that don't rely on special software Class names contain no spaces, words are separated via CamelCaseConvension. Docker image names cannot contain upper case letters, so this method substitutes "_" before the lower-case version of each capital letter. Example: JavaModule becomes java_module
`static String`	`getImageVersion(BioModule module)` Get the Docker image version if defined in the `Config` file If not found, return the default version "latest"
`static boolean`	`hasDB(BioModule module)` Function used to determine if an alternate database has been defined (other than /db).
`static boolean`	`inAwsEnv()` Return TRUE if running in AWS (based on Config props).
`static boolean`	`inDockerEnv()` Return TRUE if running in AWS (based on Config props).
`static boolean`	`isDirectMode()` Return TRUE if runtime parameters indicate attempt to run in direct mode

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - AWS_EFS
```
public static final String AWS_EFS
```
    Docker container root user EFS directory
    
    See Also:
    
    Constant Field Values
  - AWS_EFS_DB
```
public static final String AWS_EFS_DB
```
    Docker container root user DB directory
    
    See Also:
    
    Constant Field Values
  - CONTAINER_BLJ_DIR
```
public static final String CONTAINER_BLJ_DIR
```
    Docker container BioLockJ installation directory: "/app/biolockj"
    
    See Also:
    
    Constant Field Values
  - CONTAINER_BLJ_SUP_DIR
```
public static final String CONTAINER_BLJ_SUP_DIR
```
    Docker container blj_support directory: "/app/blj_support"
    
    See Also:
    
    Constant Field Values
  - CONTAINER_CONFIG_DIR
```
public static final String CONTAINER_CONFIG_DIR
```
    All containers mount the host Config directory to the container volume: "/mnt/efs/config"
    
    See Also:
    
    Constant Field Values
  - CONTAINER_DB_DIR
```
public static final String CONTAINER_DB_DIR
```
    Some containers mount a database to the containers "db" volume: "/mnt/efs/db"
    
    See Also:
    
    Constant Field Values
  - CONTAINER_INPUT_DIR
```
public static final String CONTAINER_INPUT_DIR
```
    All containers mount the host "input.dirPaths" to the container "input" volume: "/mnt/efs/input"
    
    See Also:
    
    Constant Field Values
  - CONTAINER_META_DIR
```
public static final String CONTAINER_META_DIR
```
    Some containers mount the "metadata.filePath" to the container "meta" volume: "/mnt/efs/metadata"
    
    See Also:
    
    Constant Field Values
  - CONTAINER_OUTPUT_DIR
```
public static final String CONTAINER_OUTPUT_DIR
```
    All containers mount "internal.pipelineDir" to the container volume: "/mnt/efs/pipelines"
    
    See Also:
    
    Constant Field Values
  - CONTAINER_PRIMER_DIR
```
public static final String CONTAINER_PRIMER_DIR
```
    Some containers mount the "trimPrimers.filePath" to the containers "primer": "/mnt/efs/primer" volume.
    
    See Also:
    
    Constant Field Values
  - DOCKER_ROOT_HOME
```
public static final String DOCKER_ROOT_HOME
```
    Docker container root user $HOME directory
    
    See Also:
    
    Constant Field Values
  - SPAWN_DOCKER_CONTAINER
```
public static final String SPAWN_DOCKER_CONTAINER
```
    Name of the bash script function used to generate a new Docker container: "spawnDockerContainer"
    
    See Also:
    
    Constant Field Values
  - BLJ_BASH
```
protected static final String BLJ_BASH
```
    Docker image name for simple bash scripts (awk,gzip,pear).
    
    See Also:
    
    Constant Field Values
  - COMPUTE_SCRIPT
```
protected static final String COMPUTE_SCRIPT
```
    Docker environment variable holding the name of the compute script file: "COMPUTE_SCRIPT"
    
    See Also:
    
    Constant Field Values
  - DEFAULT_DOCKER_HUB_USER
```
protected static final String DEFAULT_DOCKER_HUB_USER
```
    Name of the BioLockJ Docker account ID: "biolockj"
    
    See Also:
    
    Constant Field Values
  - DOCKER_HUB_USER
```
protected static final String DOCKER_HUB_USER
```
    Config name of the Docker Hub user with the BioLockJ containers: "docker.user"
    Docker Hub URL: https://hub.docker.com
    By default the "biolockj" user is used to pull the standard modules, but advanced users can deploy their own versions of these modules and add new modules in their own Docker Hub account.
    
    See Also:
    
    Constant Field Values
  - SAVE_CONTAINER_ON_EXIT
```
protected static final String SAVE_CONTAINER_ON_EXIT
```
    Config property removed the default --rm flag on docker run command if set to TRUE: "docker.saveContainerOnExit"
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - DockerUtil
```
public DockerUtil()
```
- Method Detail
  - buildSpawnDockerContainerFunction
```
public static List<String> buildSpawnDockerContainerFunction(BioModule module)
                                                      throws Exception
```
    Build the "spawnDockerContainer" method, which takes container name, in/out port, and optionally script path parameters.
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    Bash function to run docker
    
    Throws:
    
    Exception - if unable to build the function
  - getDockerImage
```
public static String getDockerImage(BioModule module)
                             throws Exception
```
    Return the name of the Docker image needed for the given module.
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    Docker image name
    
    Throws:
    
    Exception - if errors occur
  - getDockerUser
```
public static String getDockerUser(BioModule module)
```
    Return the Docker Hub user ID. If none configured, return biolockj.
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    Docker Hub User ID
  - getDockerVolumeDir
```
public static File getDockerVolumeDir(String prop,
                                      String containerPath)
                               throws Exception
```
    Get mapped Docker system File from Config directory-property by replacing the host system path with the mapped container path.
    
    Parameters:
    
    prop - Config directory-property
    
    containerPath - Local container path
    
    Returns:
    
    Docker volume directory or null
    
    Throws:
    
    Exception - if path is defined but is not an existing directory or if runtime-errors occur
  - getDockerVolumeFile
```
public static File getDockerVolumeFile(String prop,
                                       String containerPath)
                                throws Exception
```
    Get mapped Docker system File from Config file-property by replacing the host system path with the mapped container path.
    
    Parameters:
    
    prop - Config file-property
    
    containerPath - Local container path
    
    Returns:
    
    Docker volume file or null
    
    Throws:
    
    Exception - if path is defined but is not an existing file or if runtime-errors occur
  - getDockerVolumePath
```
public static String getDockerVolumePath(String path,
                                         String containerPath)
```
    Get Docker file path through mapped volume
    
    Parameters:
    
    path - Config file or directory path
    
    containerPath - Local container path
    
    Returns:
    
    Docker file path
  - getImageName
```
public static String getImageName(BioModule module)
                           throws Exception
```
    Return the Docker Image name for the given class name.
    Return "blj_bash" for simple bash script modules that don't rely on special software
    Class names contain no spaces, words are separated via CamelCaseConvension.
    Docker image names cannot contain upper case letters, so this method substitutes "_" before the lower-case version of each capital letter.
    
    Example: JavaModule becomes java_module
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    Docker Image Name
    
    Throws:
    
    Exception - if errors occur
  - getImageVersion
```
public static String getImageVersion(BioModule module)
```
    Get the Docker image version if defined in the Config file
    If not found, return the default version "latest"
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    Docker image version
  - hasDB
```
public static final boolean hasDB(BioModule module)
                           throws Exception
```
    Function used to determine if an alternate database has been defined (other than /db).
    
    Parameters:
    
    module - BioModule
    
    Returns:
    
    TRUE if module has a custom DB defined
    
    Throws:
    
    Exception - if errors occur
  - inAwsEnv
```
public static boolean inAwsEnv()
                        throws Exception
```
    Return TRUE if running in AWS (based on Config props).
    
    Returns:
    
    TRUE if pipeline.env=aws
    
    Throws:
    
    Exception - if errors occur
  - inDockerEnv
```
public static boolean inDockerEnv()
```
    Return TRUE if running in AWS (based on Config props).
    
    Returns:
    
    TRUE if pipeline.env=aws
  - isDirectMode
```
public static boolean isDirectMode()
```
    Return TRUE if runtime parameters indicate attempt to run in direct mode
    
    Returns:
    
    boolean

Class DockerUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

AWS_EFS

AWS_EFS_DB

CONTAINER_BLJ_DIR

CONTAINER_BLJ_SUP_DIR

CONTAINER_CONFIG_DIR

CONTAINER_DB_DIR

CONTAINER_INPUT_DIR

CONTAINER_META_DIR

CONTAINER_OUTPUT_DIR

CONTAINER_PRIMER_DIR

DOCKER_ROOT_HOME

SPAWN_DOCKER_CONTAINER

BLJ_BASH

COMPUTE_SCRIPT

DEFAULT_DOCKER_HUB_USER

DOCKER_HUB_USER

SAVE_CONTAINER_ON_EXIT

Constructor Detail

DockerUtil

Method Detail

buildSpawnDockerContainerFunction

getDockerImage

getDockerUser

getDockerVolumeDir

getDockerVolumeFile

getDockerVolumePath

getImageName

getImageVersion

hasDB

inAwsEnv

inDockerEnv

isDirectMode