edu.illinois.ncsa.datawolf.service.utils

Class WorkflowUtil

java.lang.Object

edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil

public class WorkflowUtil
extends Object

Constructor Summary

Constructors

Constructor and Description
WorkflowUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static CommandLineImplementation	createCommandlineImplementation(String executable, String captureStdOut, String captureStdErr, boolean joinStdOutStdErr, List<CommandLineOption> commandLineOptions, Map<String,String> env) Create command line implementation based on options, standard out/error logs, environment, etc
static CommandLineOption	createCommandlineOption(CommandLineOption.Type type, String value, String flag, String optionId, CommandLineOption.InputOutput inputOutput, String filename, boolean commandline) Create command line option
static Execution	createDAPWorkflow(String fileId, String fenceURL, String token, Person creator)
static Execution	createDTSWorkflow(String fileId, String fenceURL, String token, Person creator) Creates a workflow representing the DTS extractors ran on a file
static Workflow	createWorkflow(String title, String description, Person creator) Create an empty workflow
static WorkflowStep	createWorkflowStep(String title, Person creator, WorkflowTool tool, Map<String,String> inputs, Map<String,String> outputs, Map<String,String> parameters) Create workflow step
static WorkflowTool	createWorkflowTool(String title, String description, String version, Person creator, List<WorkflowToolParameter> parameters, List<WorkflowToolData> inputs, List<WorkflowToolData> outputs, Set<FileDescriptor> blobs, String impl, String executor) Create workflow tool
static WorkflowToolData	createWorkflowToolData(String title, String description, String mimeType) Create workflow tool data
static WorkflowToolParameter	createWorkflowToolParameter(String title, String description, boolean allowNull, WorkflowToolParameter.ParameterType type, boolean hidden, String value) Create workflow tool parameter
static List<Dataset>	getDapDatasets(List<String> datasets, String fenceURL, String token, Person creator)
static String	getDAPLogFile(String fileId, String fenceURL, String token)
static String	getDAPScript() Create DataWolf tool shell script for calling SoftwareServers
static String	getDTSShellScript() Shell script to run DTS extractor
static List<String>	getDTSTools(String fileId, String fenceURL, String token) Get list of DTS tools
static com.google.gson.JsonElement	getMetadata(String fileId, String fenceURL, String token) Get metadata for file extraction from api/files/{file-id}/metadata.jsonld
static com.google.gson.JsonElement	getMetadataJsonLD(String fileId, String fenceURL, String token) Get metadata for file extraction from api/files/{file-id}/metadata.jsonld

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

WorkflowUtil

public WorkflowUtil()

Method Detail

createDAPWorkflow

public static Execution createDAPWorkflow(String fileId,
                          String fenceURL,
                          String token,
                          Person creator)
                                   throws Exception

Throws:

Exception

createDTSWorkflow

public static Execution createDTSWorkflow(String fileId,
                          String fenceURL,
                          String token,
                          Person creator)
                                   throws Exception

Creates a workflow representing the DTS extractors ran on a file

Parameters:

fileId - - id of the file to create the workflow for

dtsURL - - DTS URL to communicate with

creator - - user to create the workflow under

Returns:

workflow representing DTS extractors

Throws:

Exception

createWorkflow

public static Workflow createWorkflow(String title,
                      String description,
                      Person creator)

Create an empty workflow

Parameters:

title - Title of workflow

description - description of workflow

creator - workflow creator

Returns:

Empty workflow

createWorkflowStep

public static WorkflowStep createWorkflowStep(String title,
                              Person creator,
                              WorkflowTool tool,
                              Map<String,String> inputs,
                              Map<String,String> outputs,
                              Map<String,String> parameters)

Create workflow step

Parameters:

title - step title

creator - step creator

tool - workflow tool associated with the step

inputs - step inputs

outputs - step outputs

parameters - step parameters

Returns:

workflow step

createWorkflowTool

public static WorkflowTool createWorkflowTool(String title,
                              String description,
                              String version,
                              Person creator,
                              List<WorkflowToolParameter> parameters,
                              List<WorkflowToolData> inputs,
                              List<WorkflowToolData> outputs,
                              Set<FileDescriptor> blobs,
                              String impl,
                              String executor)

Create workflow tool

Parameters:

title - tool title

description - tool description

version - tool version

creator - tool creator

parameters - tool parameters

inputs - tool inputs

outputs - tool outputs

blobs - file blobs associated with the tool

impl - tool implementation

executor - tool executor type

Returns:

Workflow tool

createWorkflowToolParameter

public static WorkflowToolParameter createWorkflowToolParameter(String title,
                                                String description,
                                                boolean allowNull,
                                                WorkflowToolParameter.ParameterType type,
                                                boolean hidden,
                                                String value)

Create workflow tool parameter

Parameters:

title - parameter title

description - parameter description

allowNull - parameter accepts null

type - parameter type

hidden - is parameter hidden

value - initial parameter value

Returns:

Workflow tool parameter

createWorkflowToolData

public static WorkflowToolData createWorkflowToolData(String title,
                                      String description,
                                      String mimeType)

Create workflow tool data

Parameters:

title - tool data title

description - tool data description

mimeType - tool data mime type

Returns:

Workflow tool data

getDapDatasets

public static List<Dataset> getDapDatasets(List<String> datasets,
                           String fenceURL,
                           String token,
                           Person creator)

getDTSTools

public static List<String> getDTSTools(String fileId,
                       String fenceURL,
                       String token)
                                throws org.apache.http.client.ClientProtocolException,
                                       IOException

Get list of DTS tools

Parameters:

fileId - file id

fenceURL - BD-API gateway URL

token - authorization token

Returns:

List of DTS tools

Throws:

org.apache.http.client.ClientProtocolException

IOException

getMetadata

public static com.google.gson.JsonElement getMetadata(String fileId,
                                      String fenceURL,
                                      String token)
                                               throws org.apache.http.client.ClientProtocolException,
                                                      IOException

Get metadata for file extraction from api/files/{file-id}/metadata.jsonld

Parameters:

fileId - file id

fenceURL - BD-API gateway URL

token - authorization token

Returns:

metadata in json format

Throws:

org.apache.http.client.ClientProtocolException

IOException

getMetadataJsonLD

public static com.google.gson.JsonElement getMetadataJsonLD(String fileId,
                                            String fenceURL,
                                            String token)
                                                     throws org.apache.http.client.ClientProtocolException,
                                                            IOException

Get metadata for file extraction from api/files/{file-id}/metadata.jsonld

Parameters:

fileId - file id

fenceURL - BD-API gateway URL

token - authorization token

Returns:

metadata in json format

Throws:

org.apache.http.client.ClientProtocolException

IOException

getDAPLogFile

public static String getDAPLogFile(String fileId,
                   String fenceURL,
                   String token)
                            throws org.apache.http.client.ClientProtocolException,
                                   IOException

Throws:

org.apache.http.client.ClientProtocolException

IOException

createCommandlineOption

public static CommandLineOption createCommandlineOption(CommandLineOption.Type type,
                                        String value,
                                        String flag,
                                        String optionId,
                                        CommandLineOption.InputOutput inputOutput,
                                        String filename,
                                        boolean commandline)

Create command line option

Parameters:

type - command line option type

value - initial value of command line option

flag - flag associated with the command line option

optionId - command line option id

inputOutput - specify whether command line option is an input, output or both

filename - filename for command line option, if applicable

commandline - pass option at the command line

Returns:

Command line option

createCommandlineImplementation

public static CommandLineImplementation createCommandlineImplementation(String executable,
                                                        String captureStdOut,
                                                        String captureStdErr,
                                                        boolean joinStdOutStdErr,
                                                        List<CommandLineOption> commandLineOptions,
                                                        Map<String,String> env)

Create command line implementation based on options, standard out/error logs, environment, etc

Parameters:

executable - Executable to run

captureStdOut - data id to capture standard out

captureStdErr - data id to capture standard error

joinStdOutStdErr - Join standard out and error to a single file

commandLineOptions - command line options

env - environment variables to set before execution

Returns:

Commandline implementation description for the tool

getDTSShellScript

public static String getDTSShellScript()

Shell script to run DTS extractor

Returns:

shell script for running DTS extractor

getDAPScript

public static String getDAPScript()

Create DataWolf tool shell script for calling SoftwareServers

Returns:

Shell script for calling SoftwareServers