jvarkit

KnimeToText

converts a Knime Workflow to a html representation.

Usage

Usage: knime2txt [options] Files
  Options:
    -g, --dot
      graphiz dot file.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• knime
• workflow
• convert

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew knime2txt

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/KnimeToText.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite knime2txt ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

## Example

 $ java -jar dist/knime2txt.jar -g out.dot  knime_3.3.2/workspace/TEST/  | xmllint --format - > out.html
 [INFO][KnimeToText]read XML: knime_3.3.2/workspace/TEST/workflow.knime
[INFO][KnimeToText]read XML: knime_3.3.2/workspace/TEST/Interactive Table (#3)/settings.xml
[INFO][KnimeToText]read XML: knime_3.3.2/workspace/TEST/File Reader (#4)/settings.xml
[INFO][KnimeToText]read XML: knime_3.3.2/workspace/TEST/Java Snippet Row Filter (#5)/settings.xml
[INFO][KnimeToText]read XML: knime_3.3.2/workspace/TEST/Extract Column Header (#6)/settings.xml
[INFO][KnimeToText]read XML: knime_3.3.2/workspace/TEST/Unpivoting (#7)/settings.xml
[INFO][KnimeToText]read XML: knime_3.3.2/workspace/TEST/Java Snippet _simple_ (#8)/settings.xml
[INFO][KnimeToText]read XML: knime_3.3.2/workspace/TEST/Column Filter (#10)/settings.xml
[INFO][KnimeToText]read XML: knime_3.3.2/workspace/TEST/CSV Writer (#9)/settings.xml

$ xmllint out.html  | head
<?xml version="1.0"?>
<div>
  <div>
    <p>Interactive Table (#3)/settings.xml</p>
    <ul>
      <li><b>factory</b>  value:"<i>org.knime.base.node.viz.table.TableNodeFactory</i>"</li>
      <li><b>customDescription</b>  value:"<i/>"</li>
    </ul>
  </div>
  <div>
(...)

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