jami-core

[tschaka1904]

General workshop guidance

https://github.com/MICommunity/psi-jami/tree/master/jami-core/src/main/java/psidev/psi/mi/jami

• analysis/graph
  • README.md
  • Test coverage
  • Java example
• binary
  • README.md
  • Test coverage
  • Java example
• datasource
  • README.md
  • Test coverage
  • Java example
• exception
  • README.md
  • Test coverage
  • Java example
• factory
  • README.md
  • Test coverage
  • Java example
• listener
  • README.md
  • Test coverage
  • Java example
• model
  • README.md
  • Test coverage
  • Java example
• utils
  • README.md
  • Test coverage
  • Java example

[tschaka1904]

What are psi-jami/jami-core/src/main/resources/interactorDatabase.properties & interactorType.properties used for? We need description where and for what it is used.

DefaultInteractorFactory.java uses both properties files.

Loads some properties to recognize interactor type from different MI terms

WARNING: These MI terms are hardcoded. Maybe use web services instead? Could cache temp file etc. See #32

[tschaka1904]

Is the a need for the psi-jami/jami-core/src/main/assembly/descriptor.xml?

[tschaka1904]

Should we use a lib for checksum instead of psi-jami/jami-core/src/main/java/psidev/psi/mi/jami/utils/checksum?

[tschaka1904]

jami-core/datasource provides interfaces for of sources and stream to receive interaction data.

[julie-sullivan]

@tschaka1904 That /assembly/description.xml file is a mistake and should be removed. I confirmed this with @danielabutano. Maven has assembly.xml but not description.xml. Why would you need to create a custom zip file anyway?

[julie-sullivan]

Interaction and InteractionEvidence is in the model package. BinaryInteraction and BinaryInteractionEvidence is in the /binary directory. Why?

[julie-sullivan]

Also, the word binary means something in computer science. Having binary directory is confusing! This should be renamed.

[julie-sullivan]

jami-core/analysis/graph is used to calculate cliques, which is used to calculate inferred interactions. This is used when writing interaction XML.

What are inferred interactions used for?

[julie-sullivan]

`jami-core/binary', in addition to having a bunch of classes that should be in the model, also handles the expansion.

[tschaka1904]

Should we refactor utils or do we want to keep it?

[julie-sullivan]

[tschaka1904]

We should move the wrapper classes out of psidev.psi.mi.jami.binary.impl. Maybe into utils?

[julie-sullivan]

binary package is tested well.

[julie-sullivan]

Overall test coverage is okay for psi-core

[julie-sullivan]

jami-core/datasource has no tests, but that's okay. It's just a bunch of interfaces. Same for jami-core/exceptions

[tschaka1904]

About inferred interactions Sandra said:

I think this was the terminology we used for cases such as the curated complexes, or also when we were attempting to add cases where a binding site was created by the binding of 2 molecules then a third protein bound into it.

[julie-sullivan]

Could not run either test in psi-core/factory

Aug 09, 2016 11:58:48 AM psidev.psi.mi.jami.factory.MIDataSourceFactory getMIDataSourceWith
WARNING: We cannot instantiate data source of type class psidev.psi.mi.jami.datasource.MockExperimentDataSource with the given options.
java.lang.IllegalArgumentException: no source option
    at psidev.psi.mi.jami.datasource.MockExperimentDataSource.initialiseContext(MockExperimentDataSource.java:20)
    at psidev.psi.mi.jami.factory.MIDataSourceFactory.instantiateNewDataSource(MIDataSourceFactory.java:156)
    at psidev.psi.mi.jami.factory.MIDataSourceFactory.getMIDataSourceWith(MIDataSourceFactory.java:55)
    at psidev.psi.mi.jami.factory.MiDataSourceFactoryTest.test_missing_file_data_source_options(MiDataSourceFactoryTest.java:35)

See #30

[tschaka1904]

test coverage of model package

[tschaka1904]

test coverage of factory package

[tschaka1904]

test coverage of listener package. There are no tests

[tschaka1904]

test coverage of utils package.

[julie-sullivan]

Datasource is a bad name for this package. (Maybe because a data source is a specific thing in InterMine!).

I would prefer "stream helper" or stream handler. Something that indicates what this package actually does. Even better than documentation!