Diagram-Core

What is the Diagram Core?

The Diagram core contains a collection of server-side tools, mainly focusing on the generation of a set of JSON files to be consumed by the Pathway Diagram Viewer v3.0. As illustrated in the following figure, the Diagram-core utilises the Reactome-Core to generate two different types of files for every single pathway diagram. The first file includes layout information (nodes, edges, co-ordinates, glyphs, names, shades, etc.), while the second file includes a graph of the pathway diagram and all its contained entities.

How do I generate all pathway diagrams ?

** Maven Setup: https://maven.apache.org/guides/getting-started/maven-in-five-minutes.html.

1. Clone the Diagram-Core repository on your end

   git clone https://github.com/reactome-pwp/diagram-core.git

2. Navigate into diagram-core

3. Package with Maven

   mvn clean package

4. Diagram-core Help: --help

   java -jar target/tools-jar-with-dependencies.jar --help

5. Convert all pathway diagrams

   1. command help (ensure special characters are escaped):

      java -jar target/tools-jar-with-dependencies.jar Convert
           -h dbhost 
           -d dbschema
           -u dbuser
           -p dbpass 
           -o output_folder
           -r list_of_trivial_molecules
           -v 

   2. Please note that the current list of trivial molecules can be found in ./src/main/resources/trivialchemicals.txt

      java -jar target/tools-jar-with-dependencies.jar Convert \
           -h localhost \
           -d reactome \
           -u root \
           -p root \ 
           -o /Users/reactome/diagram/static \
           -r /Users/reactome/diagram/trivialchemicals.txt \
           -v 

How do I generate specific pathway diagrams ?

The user can also specify a target list of diagrams to be generated by using the -t switch and the list of DBIDs like in the example:

java -jar target/tools-jar-with-dependencies.jar Convert \
     -h localhost \
     -d reactome \
     -u root \
     -p root \ 
     -o /Users/reactome/diagram/static \
     -r /Users/reactome/diagram/trivialchemicals.txt \
     -t:5654738,5655291,2219530,5637815
     -v 

Important Notice

In case of connection to a remote server via ssh there might be a "No X11 DISPLAY variable was set" error. Then try unsetting the DISPLAY using the following command:

unset DISPLAY