1. Run run.sh.
2. It will create workflows (with figures) in separate folders for all questions.

To update the tool descriptions and taxonomy, replace the GISTaxonomy.rdf, GISTaxonomy_fl.rdf, ToolDescription_ct.json, and ToolDescription_ct_fl.json files with newly generated ones.

Here's a short explanation of what each file/directory is here for:

• APE-0.9.1.jar: APE jar. See its repository
• run.sh: Bash script for easily running all synthesis.
• clean.sh Bash script for easily removing all output produced by APE.
• evaluation/evaluation.csv: A table with synthesized workflows used in the paper, and evaluations of them using our classification scheme.
• evaluation/diagrams/*.png: Visualizations of the workflows. (The ID's in evaluation/evaluation.csv correspond to the filenames.)
• GISTaxonomy.rdf: Taxonomy used for the CCDT ontology.
• GISTaxonomy_fl.rdf: Taxonomy used for the state-of-the-art (SOTA) ontology.
• ToolDescription_ct.json: Tool descriptions using the CCDT ontology.
• ToolDescription_ct_fl.json: Tool descriptions using the state-of-the-art (SOTA) ontology.
• q[1-5]_(sota|full)(_constrained)?: Directories with APE configuration files for each question and ontology. The output files are also placed here by APE.