GEO GMT (Generic Mapping Tools)

This Geovisualization Case Study (using GMT tools) will demonstrate the sysnthesis functionality provided by APE (the Automated Pipeline Explorer).

The use case aims to demonstrate the usefulness of the synthesis approach for solving a problem of map creation. The scenario was demonstrated in [1], where the full workflows synthesis was accomplished in few incremental synthesis steps. Some of them are given here for demonstration:

E0 use case describes the initial workflow sinthesys step, labeled as E0 in the paper.
E1 use case extends the initial workflow sinthesys step with additional constraints enforcing better map annotations.

E0 - Initial Workflow

In order to run the synthesis APE-<version>.jar needs to be available: https://github.com/sanctuuary/APE.

Note

In order to be able to execute the generated workflows on the machine, GMT set of tools needs to be installed (http://gmt.soest.hawaii.edu/projects/gmt/wiki/Installing) However, this step is not required for the workflow synthesis, considering that the synthesis of conadidate workflows and their execution are 2 separate steps.

In order to use the APE library from the command line, simply run the APE-<version>-executable.jar file using command:

java -jar APE-<version>-executable.jar [path_to_ape_configuration_file]

As an example, if you would download the APE-2.4.0-executable.jar to the root of APE_UseCases repository on your local machine, you could run this demo by executing the following command:

cd ~/git/APE_UseCases
java -jar APE-<version>.jar GeoGMT/E0/config.json

Note

In case the execution fails due to the heap space,

The results of the synthesis would be stored under the directory specified in the configuration file (solutions_dir_path parameter). The results of the synthesis would be:

solutions_dir_path/solutions.txt - First X candidate solutions in textual format, where X is the number of solutions specified in the config file (``solutions`` parameter)
solutions_dir_path/Figures/        - Workflow figures corresponding to the first Y solutions, where Y is the number of solutions specified in the config file (``number_of_generated_graphs`` parameter, 0 if not specified))
solutions_dir_path/Executables/  - Executable shell scripts corresponding to the first Z solution, where Z is the number of solutions specified in the config file (``number_of_execution_scripts`` parameter, 0 if not specified))
solutions_dir_path/CWL/ - CWL files corresponding to the first Q solution, where Q is the number of solutions specified in the config file (``number_of_cwl_files`` parameter, 0 if not specified)

E1 - Additional Constraints

By adding more constraints (constraints_e1.json), we avoid obtaining workflows that are ambiguous, redundant, or not relevant to the domain [1].

Domain Model

Tool Taxonomy

Type Taxonomy