Icon Validator

What is the Reactome Icon Validator

Reactome improves the graphical representation of higher-level pathways in the Reactome pathway browser with the idea of icon library, this project is meant to validate the structure and value of each icon XML file.

icon XML file

The correct xml file should have the following structure:

<metadata>
    <categories>
        <category>{CATEGORY}</category>
    </categories>
    <person orcid="{ORCID}" role="curator">{CURATOR_NAME}</person>
    <person role="designer" url="{DESIGNER_URL}">{DESIGNER_NAME}</person>
    <name>{ICON_NAME}</name>
    <description>{DESCRIPTION}</description>
    <references>
        <reference>
            <db>{REFERENCE_NAME}</db>
            <id>{REFERENCE_ID}</id>
        </reference>
    </references>
    <synonyms>
        <synonym>{SYNONYM}</synonym>
    </synonyms>
</metadata>

• {CATEGORY} with one or more of the suggested categories: arrow, cell_element, cell_type, compound, human_tissue, protein, receptor and transporter.
• {REFERENCE_NAME} for the name of the resource you have used to find this component (e.g.: UNIPROT, GO, CHEBI … ).
• {SYNONYM} as any synonyms or alternative names your component might be known of.

This validator validates the meaningful value of significant elements like {category}, catch the unmatching end-tags and mistaken attribute specifications, generates a validation log file in the end to display all errors. It won't cause any problems after fixing the errors in the file and then sending them to server.

Installation & Usage

Requirements

1. Maven 3.X - [Installation Guide](http://maven.apache.org/install.html)

Git Clone

git clone https://github.com/reactome/icon-validator.git 
cd icon-validator

Usage

To validate icon files and generate a validation log file, package and use the validator tool as follows:

mvn clean package

then start validating files by using the following line:

java -jar ./target/icon-validator-jar-with-dependencies.jar
      -d path/to/icon/directory
      -r references.txt
      -c categories.txt

the expected result should be as below:

ERROR - Element "synonym" is missing value in R-ICO-013884.xml.
ERROR - The element type "description" must be terminated by the matching end-tag "</description>". File: R-ICO-013655.xml
ERROR - [proteoin] at the element "category" is not in the list CATEGORIES in the R-ICO-013736.xml.
...