Scripting Integration Workshop Antje Janosch Technology - - PowerPoint PPT Presentation

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Scripting Integration Workshop Antje Janosch Technology - - PowerPoint PPT Presentation

May 04, 2023 448 likes •817 views

KNIME SUMMIT 2016 Scripting Integration Workshop Antje Janosch Technology Development Studio MPI-CBG Dresden History ? ? R-Scrip4ng, Python Scrip4ng, Matlab Scrip4ng 2009 2010 2016 2013 / 2014 2 Antje Janosch, MPI-CBG, Dresden,

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SLIDE 1

KNIME SUMMIT 2016

Antje Janosch – Technology Development Studio MPI-CBG Dresden

Scripting Integration Workshop

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SLIDE 2

History

Antje Janosch, MPI-CBG, Dresden, Germany

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2009 2016

?

R-Scrip4ng, Python Scrip4ng, Matlab Scrip4ng

2010

?

2013 / 2014

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SLIDE 3

General Features

  • Server/Client based solu4on
  • Parallel execu4on
  • Centralized setup
  • Remote template repositories
  • Template configura4on via “KNIME-like” GUI
  • Deployment of KNIME-nodes with scrip4ng

behind

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SLIDE 4

Short news

R

  • RowID support (both direc4ons)
  • Domain values
  • Color / Size / Shape model support
  • Flow variable support
  • Chunked transfer
  • ‘Open external’
  • R-workspace as generic R port

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SLIDE 5

Client-(server) model

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RServe

remote or local

Matlab- Server

local remote or local local

Python- Server

remote or local

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SLIDE 6

Getting started (Client)

  • Install Scrip4ng plugins from “Trusted Community

Contribu4ons” update site (KNIME >= 3.0 recommended)

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SLIDE 7

Preferences

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SLIDE 8

Node Types

  • Plot
  • Snippet
  • (OpenIn… )
  • Generic nodes (R)

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SLIDE 9

Plot / Snippet – Script editor tab

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Column names Scripting area

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SLIDE 10

Plot / Snippet – Template tab

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SLIDE 11

Plot / Snippet – Template tab

Template Repository

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SLIDE 12

Plot / Snippet – Template tab

Template Repository

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SLIDE 13

Plot / Snippet – Template tab

Template Repository

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SLIDE 14

Plot / Snippet – Template tab

Template Repository Template Description / Source

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SLIDE 15

Plot / Snippet – Template tab

Template Repository Template Description / Source

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SLIDE 16

Script editor tab – template view

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SLIDE 17

Script editor tab – template view

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RGG interface of the selected template

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SLIDE 18

Script editor tab – template view

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RGG interface of the selected template

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SLIDE 19

Script editor tab – template view

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RGG interface of the selected template

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SLIDE 20

Script editor tab – template view

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RGG interface of the selected template

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SLIDE 21

Script editor tab – template view

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SLIDE 22

Script editor tab – template view

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modify template (dev)

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SLIDE 23

Script editor tab – template view

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modify template (dev) RGG (XML)

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SLIDE 24

Tips and Tricks for Editing (R)

  • Mouse click = ”Column name”
  • Alt + Mouse click = kIn$”Column name”
  • Ctrl + Mouse click = Displays possible domain values of the

column and offers to insert a selec4on (comma separated

  • Press Apple/Windows key

and select mul4ple = as soon as you release the key, the selected column names will be inserted “column 1”,”column 2”,...

  • FLOWVAR(currentColumnName)

placeholder to enable the use of flow variables

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Plot – Output Options tab

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Placeholders for filename $$DATE$$ - yymmdd $$USER$$ - user name $$WS$$ - knime.workspace FLOWVAR(varName) – flow variable

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SLIDE 26

Plot - View options (R)

  • Dynamic repain4ng acer mouse click

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SLIDE 27

KNIME tables in R

  • Input ports (kIn or kIn1, kIn2, …)
  • R data.frame
  • RowIDs as row names
  • Domain values as factor levels
  • Color model (kIn.color.model)
  • R data.frame
  • Colors as hex-values
  • Shape model (kIn.shape.model)
  • R data.frame
  • Shapes as pch and their KNIME name

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KNIME tables in R

  • Size model (kIn.size.model + kIn.size.model.fun)
  • Name of the column having a size model
  • Func4on to calculate the size

based on the KNIME size model

  • Flow variables

(knime.flow.in)

  • R list

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SLIDE 29

KNIME tables in R

  • Size model (kIn.size.model + kIn.size.model.fun)
  • Name of the column having a size model
  • Func4on to calculate the size

based on the KNIME size model

  • Flow variables

(knime.flow.in)

  • R list

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SLIDE 30

KNIME tables in R

  • Size model (kIn.size.model + kIn.size.model.fun)
  • Name of the column having a size model
  • Func4on to calculate the size

based on the KNIME size model

  • Flow variables

(knime.flow.in)

  • R list

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Template repositories Template.txt

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################################################## # name: A very cool method # author: Antje Janosch # category: KNIME-UGM/ # preview: niceImage.png

  • (optional)
  • This is my template description.

######

  • R/Python/Matlab code

Optionally emmbedded in RGG

  • ##################################################

# name: Another very cool method # author: Antje Janosch ...

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SLIDE 32

RGG

  • R GUI Generator
  • Addi4onal element

<panellistbox label="Label" 
 items="item1,item2,item3" 
 span="full"/>


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http://rgg.r-forge.r-project.org/ RGG: a general GUI Framework for R scripts.BMC Bioinformatics. 2009 Mar 2 ; 10:74. doi: 10.1186/1471-2105-10-74.

<rgg> some interface elements definitions <![CDATA[ R-script ]]> </rgg>

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RGG

  • Placeholders

$$$NUM_ATTRIBUTES$$$ - for all numeric columns
 $$$STR_ATTRIBUTES$$$ - for all string columns
 $$$ALL_ATTRIBUTES$$$ - for all columns

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Demos (R)

  • 1. I want to use templates
  • 2. I want to write my own R-scripts
  • 3. I want to create knimeR-workflows

(generic nodes)

  • 4. I want to create templates
  • 5. I want to create a KNIME node with R

behind

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Outlook

  • Support of row IDs for Python/Matlab and for

both direc4ons

  • Console output view for R nodes
  • Keep offline copy of template files
  • …

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Contact us!

antje.janosch@mpi-cbg.de stoeter@mpi-cbg.de

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