Working with console version

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Contents

Overview

How to execute flow analysis from console by using Offline version or Clone (See Clone application) is described here.

How to Run

genImg / genImg.ppl using an explanation.

Download of sample flow

If you run as a flow

[Windows case] XiP_console.bat
[UNIX case] XiP_console.sh

Run.

In UNIX case, execution file is written in bash shell script, so you must execute like...

bash ./ XiP_console.sh

Or

chmod 500
./ XiP_console.sh


Option List

You can use the options below.


argument required type description
input yes URI Enter pipeline file of pipeline analysis flow (usually extension, xml, ppl)
propertyFile no URI Batch file to input the information flow analysis for the property specified in the override (usually extension, ppf)
password no String Password input file specified in the flow analysis
preferences no String Preference in the local file path
printPreferences no Used preference settings file will be displayed. Typically, input specified with the option.
override no String Command line argument to override the properties of each component
proxyHost no Proxy server host name
proxyPort no Proxy server port number
R no Choose from on/off/auto. [on]connect to R server, [off]not connect to R server, [auto]connect to R server if R-related components are contained in the executed pipeline flow(default)
uncheckSSLAuth no Input, propertyFile options for the SSL connection is successful even if it is certified sites without permission
logLevel no enum Specifies the log level to perform flow analysis (none: all: trace: debug: info: warn: error: fatal) may specify. defaultはinfo The default info
sample no This example displays the command line
splashScreen no URI Specified will be displayed at startup splashscreen
options no PropertyFile read in the List property. used to retrieve the override key to override the property if each option.
arg : -help
usage: CSMLPLConsole
-gui <gui type [edit|popup|both]>     Indicates if some GUI components
                                      will appers before/during
                                      calculations
-help                                 Prints command line options.
-input <pipeline-file>                Indicates a Pipeline xml file to
                                      execute
-logLevel <log level>                 the level of logging
-options                              Prints properties.
-override <property=value>            use value for given property
-password <password>                  Indicates the password for Pipeline
                                      file. If no argument is provided
                                      the default password will be used
-preferences <preference file>        Indicates local preference file
-printPreferences                     Prints preferences.
-propertyFile <pp-file>               Indicates parameters file, used to
                                      override custom components
                                      properties
-proxyHost <proxy host>               proxy host
-proxyPort <proxy port>               proxy port
-R <R server settings>                Decide whether to connect to R server
-sample                               Prints sample usage.
-splashScreen <splash screen image>   splash screen file to use
-uncheckSSLAuth                       Determines if SSL Authentication
                                      should be checked.

Try running

Let's actually run.

./ XiP_console.sh -input GenImg.ppl

This sample is simple one, in which sample.csml.gz is loaded and sample.png is output. When running, you can see sample.png is output in the same directory as genImg.ppl.

Sample.png

An override option

The flow is assumed in this analysis we want to use to switch the input and output files for each user. In this case, there are two ways.

Option 1-propertyFile second method

The first method, propertyFile propertyFile option to use the bulk using a set of options is a way to override. On XiP, File-> Export-> PPFile by running, genImg.ppl flow analysis of an optional set of Excel, tsv, csv format can be output. (For details of how PPFile see) the actual output file is as follows.


#Pipeline Name
#Short Description
#Long Description
#Creation Date 2010/03/26
#Version
#Author
#Affiliation
#Contact Email
#Model URL
#Model License STANDARD
#Pipeline Version 0.945
Component Name Component Id Property Name Current Value Default Value Level Type Available Items Short Description Long Description Use
Input CSML c1 CSML File Name rel:/GenImg_sample.csml.gz REQUIRED URI CSML File Name CSML File Name true
Input CSML c1 Time Out 0 0 PREFERENCE Integer Time Out Time Out false
Input CSML c1 Time Out Unit SECONDS SECONDS PREFERENCE Enum MICROSECONDS|MILLISECONDS|SECONDS|MINUTES|HOURS|DAYS Time Out Unit Time Out Unit false
Output Image file c2 Image Output File Name rel:/sample.png REQUIRED URI CSML Output File Name CSML Output File Name true
Output Image file c2 save_all_views false false ADVANCED Boolean false Store All View Store All View false
Output Image file c2 Time Out 0 0 PREFERENCE Integer Time Out Time Out false
Output Image file c2 Time Out Unit SECONDS SECONDS PREFERENCE Enum MICROSECONDS|MILLISECONDS|SECONDS|MINUTES|HOURS|DAYS Time Out Unit Time Out Unit false


Property File after editing

This file, Current Value of the portion, rel: / input / sample.csml.gz rel: / output / sample.csml.gz see that there is a file called. Let's rewrite them.For example, rel: / input / sample.csml.gz the http://www.csml.org/download/model/csml30/lysogen_30.csml rel: / output / Sample.csml.gz a rel: / test.png Rewrite or the results are as follows.


#Pipeline Name
#Short Description
#Long Description
#Creation Date 2010/03/26
#Version
#Author
#Affiliation
#Contact Email
#Model URL
#Model License STANDARD
#Pipeline Version 0.945
Component Name Component Id Property Name Current Value Default Value Level Type Available Items Short Description Long Description Use
Input CSML c1 CSML File Name http://www.csml.org/download/model/csml30/lysogen_30.csml REQUIRED URI CSML File Name CSML File Name true
Input CSML c1 Time Out 0 0 PREFERENCE Integer Time Out Time Out false
Input CSML c1 Time Out Unit SECONDS SECONDS PREFERENCE Enum MICROSECONDS|MILLISECONDS|SECONDS|MINUTES|HOURS|DAYS Time Out Unit Time Out Unit false
Output Image file c2 Image Output File Name rel:/test.png REQUIRED URI Image Output File Name Image Output File Name true
Output Image file c2 Save All Views false false ADVANCED Boolean false Store All View Store All View false
Output Image file c2 Time Out 0 0 PREFERENCE Integer Time Out Time Out false
Output Image file c2 Time Out Unit SECONDS SECONDS PREFERENCE Enum MICROSECONDS|MILLISECONDS|SECONDS|MINUTES|HOURS|DAYS Time Out Unit Time Out Unit false


So let's run with this new Property File.

./ XiP_console.sh -input genImg.ppl -propertyFile propertyFile.tsv

After running you can see test.png is output in the same directory as genImg.ppl.

GenImg test.png

Second method 2-override option

-Override individual parameters that you can use the override option.

./ XiP_console.sh  -input genImg.ppl
  -override "c1.CSML File Name=http://www.csml.org/download/model/csml30/lysogen_30.csml"
  -override "c2.Image Output File Name=test.png"

We want you to note, override is how to specify the name of the option, "$ Component Id. $ Property Name" as specified."" If at Kukuranai, $ Property Name and the script must have a space it will not work properly because they are judged as a delimiter.

The type of exclusion override Boolean type option if you are associated to the exclusive control of all the options you need to specify-override option.


In addition,-override option, the following can also override global parameters. In this case, <property=value> in the form of.

property description
Script Language [Auto, JavaScript, Pnuts, JavaFX, Jython] and specify the scripting language
Script Write a script.
The "is \", the new line \ n must be replaced.
Script File Properties are mutually exclusive.
Script File A text file containing the script, URI, in the form.
Script and properties are not mutually exclusive.
./ XiP_console.sh -input genImg.ppl -override "Script File=file:/C:/script/genImgScript.txt"
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