SPIF-to-SVIF-Tool

Set up:

1. Setup a local Galaxy instance.
2. Go to the directory galaxy/tools/moonshot/ and clone this repository. (Create the moonshot directory if it doesn't exist yet)
3. Change the galaxy tool configuration at galaxy/config/tool_conf.xml.sample by adding:

   <section name="Moonshot" id="moonshot">
     <tool file="moonshot/SPIF-to-SVIF-Tool/owl_to_json.xml"/>
   </section>
   

How to use the tool:

1. Build and run Galaxy as normal.
2. Navigate on the left Tools column > Moonshot > SPIF-to-SVIF-Tool.
3. Upload and select a SPIF file.
4. Click on "Run Tool" button.

Edge definitions:

• S holds T when Structure S has a variable of Type T.
• S accepts T when Structure S has an operation that has a parameter of Type T.
• S returns T when Structure S has an operation with return Type T.
• S constructs T when Structure S has a script that instantiates Structure T.
• S calls T when Structure S has a script that calls an operation of Structure T. It is what is usually considered in a “dependency graph”.
• S accesses T when Structure S has a script that directly access a field of Structure T.

For more information about the format see the section "LPG schema for abstract structure knowledge" here.

How to run unit tests

Run the command:

python -m unittest discover -s tests

Add -v flag at the end for more detailed testing
Depending on how your python environment is set up the command can also be:

python3 -m unittest discover -s tests

Implementation progress:

Nodes:

• Primitive
• Container
• Structure

Edges:

• contains (container contains structure)
• contains (container contains container)
• contains (structure contains structure)
• holds
• returns
• accepts
• accesses
• calls
• constructs
• extends
• implements

Structure node properties:

The unimplemented ones left are not visualized using ClassViz.

• kind
• isPublic
• isClass
• isInterface
• isAbstract
• isEnum
• isStatic
• sourceText
• isSerializable
• isCollection
• isMap
• isAWTComponent
• namedController
• namedManager
• namedListener
• namedTest
• numFields
• numPublicFields
• numPrivateFields
• numPrimitiveFields
• numCollectionFields
• numIterableFields
• numMapFields
• numAWTComponentFields
• ratioPublicFields
• ratioPrivateFields
• numMethods
• numPublicMethods
• numPrivateMethods
• numAbstractMethods
• numGetters
• numSetters
• ratioPublicMethods
• ratioPrivateMethods
• ratioAbstractMethods
• ratioGetters
• ratioSetters
• ratioGettersToFields
• ratioSettersToFields
• numStatementsInMethods
• averageStatementsPerMethod
• numParametersInMethods
• averageParametersPerMethod
• numBranchingInMethods
• averageBranchingPerMethod
• numLoopsInMethods
• averageLoopsPerMethod
• accessesIO
• maxLoopDepth

Reference

For automated installation of Galaxy and the Moonshot tools (including SPIF-to-SVIF-Tool), see the Andromeda Ansible playbooks: Software-Analytics-Visualisation-Team/andromeda-ansible.