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OR2YW Tool

Project description


Openrefine to Yesworkflow model tool

The Openrefine to Yesworkflow model(OR2YW) toolkit repository contains or2yw-examples folder,in which uses Ecology_Rodents dataset and NYPL(New York Public Library) Menu dataset as examples.




This tool aims to provide an auto-parsing method from Openrefine Operation History JSON file to Yesworklfow model. As we know, the openrefine operation history json file works as a data wrangling workflow. However, the structure of the workflow is not transparent enough, where we can not know the dependency and independency of column operations. And through yw model, it classify Openrefine operations into two levels: schema level and column level.

1.Repo Structure

1.1 or2yw_examples

folder Description
Ecology_rodents Portal_rodents_19772002_scinameUUIDs.csv
NYPL What's on the Menu?

Take NYPL folder as an example:

folder Function
dataset "messy dataset"
facts "File for storing prolog facts about scripts"
gv Save the DOT output to a file
pdf Render gv file as PDF file using Graphviz's dot command
png Render gv file as PNG file using Graphviz's dot command
results Screenshot the models
script Auto-parsing file: Linear/Serial-Parallell and the Openrefine json file
yw The parsed yw comments yw settings for graph(yw) command cheatsheet command

1.2 or2ywtool

This tool is aimed to connect OpenRefine Recipe which is written in JSON format with Yesworkflow, where it can generate the Parallel and Serial conceptual model. And in this way, the depedency relationships between each data cleaning steps can be shown clearly.

2.Toolkit Usage

  1. Python Version : 3+

Install the or2yw package from pip install:

   $ pip  install or2ywtool

(Note: double check the pip version, if pip is for version 2, then use pip3 install...) if you want to upgrade the version for or2ywtool

   $ pip install upgrade or2ywtool
  1. After successfully install the or2yw tool, there are two ways using this tool.

2.1 Generate yw file , copy and paste on Yesworkflow Editor (No need to install other dependency packages)

   $ or2yw
     usage: [-h] [-i INPUT] [-o OUTPUT] [-t TYPE] [-ot OUTPUTTYPE]
               [-j JAVA] [-dot DOT] [-title TITLE] [-desc DESCRIPTION]

      OR2YW v0.0.1

      optional arguments:
        -h, --help            show this help message and exit
        -i INPUT, --input INPUT
                              openrefine json file
        -o OUTPUT, --output OUTPUT
                              yesworkflow output file
        -t TYPE, --type TYPE  Workflow Type, Produce [serial,parallel] workflow,
                              Default: serial
        -ot OUTPUTTYPE, --outputtype OUTPUTTYPE
                              Output Type, Produce output [yw,gv,png,svg,pdf],
                              Default: yw (only yw for now other file type will
                              available in the next release)
        -j JAVA, --java JAVA  Java Path, if not initialized will use the java
                              installation environment path
        -dot DOT, --dot DOT   Dot Path, if not initialized will use the dot
                              installation environment path
        -title TITLE, --title TITLE
                              Title for the Workflow
        -desc DESCRIPTION, --description DESCRIPTION
                              Description for the Workflow

a. Generate Serial yw file:

   $ or2yw -i or2ywtool/test.json -o test.yw

b. Generate Parallel yw file:

   $ or2yw -i or2ywtool/test.json -o test.yw -t parallel

c. Test on Yesworkflow Editor: Yesworkflow

2.2 Generate pdf/png with tool. (**Require Graphviz install)

a. Check your graphviz version:

 $ dot -V 
 dot - graphviz version 2.39.20160823.1445 (20160823.1445)
libdir = "/usr/local/lib/graphviz"
Activated plugin library: libgvplugin_dot_layout.6.dylib
Using layout: dot:dot_layout
Activated plugin library: libgvplugin_core.6.dylib
Using render: dot:core
Using device: dot:dot:core
The plugin configuration file:
    was successfully loaded.
    render	:  dot dot_json fig json json0 map mp pic pov ps quartz svg tk vml xdot xdot_json
    layout	:  circo dot fdp neato nop nop1 nop2 osage patchwork sfdp twopi
    textlayout	:  textlayout
    device	:  bmp canon cgimage cmap cmapx cmapx_np dot dot_json eps exr fig gif gv icns ico imap imap_np ismap jp2 jpe jpeg jpg json json0 mp pct pdf pic pict plain plain-ext png pov ps ps2 psd sgi svg svgz tga tif tiff tk vml vmlz xdot xdot1.2 xdot1.4 xdot_json
    loadimage	:  (lib) bmp eps gif jpe jpeg jpg pdf png ps svg

**Do check your dot information, there may occur some issues like: "Format: pdf/png not recognized...., then make sure the device can support the formats here."

b. Install the latest version Download Graphviz:

1). For Mac users (ex.use Homebrew):

$ brew install graphviz

2). For Windows users, choose one of the methods from the download website

3). For Linux users, choose one of the methods from the download website

c.If the format is not recognized:

d. Use the command to generate the Yesworkflow PDF/PNG file (insert the json file in the correct path, and the output file name):

ex1. Generate **Parallel Yesworkflow model PDF file:

$ or2yw -i or2ywtool/test.json -o testa.pdf -ot pdf -t parallel

ex2. Generate **Parallel Yesworkflow model PNG file:

$ or2yw -i or2ywtool/test.json -o testa.png -ot png -t parallel

ex3. Generate **Linear Yesworkflow model PDF file:

$ or2yw -i or2ywtool/test.json -o testa.pdf -ot pdf

ex4. Generate **Linear Yesworkflow model PNG file:

$ or2yw -i or2ywtool/test.json -o testa.png -ot png

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