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Update documentation - restructure the documentation and include more examples #9

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Sep 10, 2024
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Improve the demo examples
vedran-kasalica committed Aug 8, 2024

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commit 38e42b0f10de4da1758a89d54a99f526facaa078
13 changes: 9 additions & 4 deletions docs/demo/geo_gmt/geo_gmt.rst
Original file line number Diff line number Diff line change
@@ -54,13 +54,18 @@ you could run this demo by executing the following command:
cd ~/git/APE_UseCases
java -jar APE-<version>.jar GeoGMT/E0/config.json

The results of the synthesis would be:
.. 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:

.. code-block:: shell

GeoGMT/E0/solutions.txt - First 100 candidate solutions in textual format
GeoGMT/E0/Figures/ - Data-flow figures corresponding to the first 10 solutions
GeoGMT/E0/Executables/ - Executable shell scripts corresponding to the first 6 solutions
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
10 changes: 6 additions & 4 deletions docs/demo/imagemagick/imagemagick.rst
Original file line number Diff line number Diff line change
@@ -36,13 +36,15 @@ you could run this demo by executing the following command:
cd ~/git/APE_UseCases
java -jar APE-2.3.0-executable.jar ImageMagick/Example1/config.json

The results of the synthesis would be:
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:

.. code-block:: shell

ImageMagick/Example1/solutions.txt - First 100 candidate solutions in textual format
ImageMagick/Example1/Figures/ - Data-flow figures corresponding to the first solution (config.json specifies that only 1 solution should be found)
ImageMagick/Example1/Executables/ - Executable shell scripts corresponding to the first solution
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)

Domain Model
^^^^^^^^^^^^
12 changes: 7 additions & 5 deletions docs/demo/massspectrometry/massspectrometry.rst
Original file line number Diff line number Diff line change
@@ -34,15 +34,17 @@ you could run this demo by executing the following command:
.. code-block:: shell

cd ~/git/APE_UseCases
java -jar APE-2.3.0-executable.jar MassSpectometry/No1/config.jsonuration
java -jar APE-2.3.0-executable.jar MassSpectometry/No1/config.json

The results of the synthesis would be:
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:

.. code-block:: shell

MassSpectometry/No1/solutions.txt - First 100 candidate solutions in textual format
MassSpectometry/No1/Figures/ - Data-flow figures corresponding to the first 10 solutions
MassSpectometry/No1/Executables/ - Executable shell scripts corresponding to the first 6 solutions
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)

.. [1] Magnus Palmblad, Anna-Lena Lamprecht, Jon Ison, Veit Schwämmle,
Automated workflow composition in mass spectrometry-based proteomics,
3 changes: 2 additions & 1 deletion docs/developers/java.rst
Original file line number Diff line number Diff line change
@@ -103,8 +103,9 @@ Run the Synthesis

// write the solutions to the file system
APE.writeSolutionToFile(solutions); // write solutions to ./sat_solutions.txt
APE.writeDataFlowGraphs(solutions, Rank.RankDir.TOP_TO_BOTTOM); // save images to ./Figures/
APE.writeDataFlowGraphs(solutions, Rank.RankDir.TOP_TO_BOTTOM); // save images to ./Figures/, alternatively APE.writeTavernaDesignGraphs() method can be used to generate workflows that follow the visual design of Taverna workflows
APE.writeExecutableWorkflows(solutions); // save scripts to ./Executables/
APE.writeCWLWorkflows(solutions); // save CWL files to ./CWL/


The API allows to generate and edit the configuration file programmatically between runs:
3 changes: 0 additions & 3 deletions docs/specifications/domain.rst
Original file line number Diff line number Diff line change
@@ -59,8 +59,6 @@ The core configuration is structured as follows:
| | | where the inheritance has to be strictly specified, false if we |
| | | should consider all possible data traces (gives more solutions). |
+---------------------------------+----------+------------------------------------------------------------------+
| ``cwl_annotations_path`` | No | Path to the YAML file that contains CWL tool annotations. |
+---------------------------------+----------+------------------------------------------------------------------+

JSON example:

@@ -72,7 +70,6 @@ JSON example:
"toolsTaxonomyRoot": "ToolsTaxonomy",
"dataDimensionsTaxonomyRoots": ["TypesTaxonomy"],
"tool_annotations_path": "./GeoGMT/tool_annotations.json",
"cwl_annotations_path": "./GeoGTM/cwl_annotations.yaml",
}