diff --git a/molgenis-data-omx/doc/molgenis-data-omx.dia b/molgenis-data-omx/doc/molgenis-data-omx.dia new file mode 100644 index 00000000000..df4c6b7b31c Binary files /dev/null and b/molgenis-data-omx/doc/molgenis-data-omx.dia differ diff --git a/molgenis-data-omx/doc/molgenis-data-omx.md b/molgenis-data-omx/doc/molgenis-data-omx.md new file mode 100644 index 00000000000..55b7f7ff8ed --- /dev/null +++ b/molgenis-data-omx/doc/molgenis-data-omx.md @@ -0,0 +1,36 @@ +## Introduction +The molgenis-data-omx package is data backend for Molgenis that uses observe omx `DataSet` matrices. It provides repository wrappers around DataSets so that they can be used like any other repository. The attributes of the repository are the `ObservableFeatures` of the `Protocol` used by the `DataSet`. The values of an entity are the `ObservedValues` of an `ObservationSet` that belongs to the `DataSet`. So one `ObservationSet` represents one `Entity` + +This package depends on molgenis-omx-core, molgenis-data-jpa and molgenis-search. + +## Core molgenis-data-omx classes + + + +**The light grey classes are provided by other molgenis modules** + +### OmxRepository + +`Repository` implementation for an omx `DataSet` matrix. For each `DataSet` there is an `OmxRepository`, the `SearchService` is used to retrieve the attribute values of an entity. So an index needs to be in place to be able to use an `OmxRepository`. The `OmxRepository` uses the `SearchService` for querying and iterating. + +The `OmxRepository` methods returns `MapEntities` as the `Entity` implementation. It implements the `Queryable` interface so you can query it but you can't add, update or delete entities with it. + +The entitynames are the identifiers of the available `DataSets`. The attributenames are de identifiers of the `ObservableFeatures`. + +### OmxEntitySource +There is only one `OmxEntitySource` in an application with url `omx://`. + +### OmxEntitySourceFactory +There can be only one `OmxEntitySourceFactory` in an application, it has the urlprefix `omx://`. + +### OmxDataConfig +This is the spring configuration class for the molgenis-data-omx package. It adds the `OmxEntitySource` and `OmxEntitySourceFactory` to the spring applicationcontext and registers the omx entitysource as a databackend at the `DataService`. + +So when you import tis class in your configuration class or this class is in the componentscan, you automatically can use the omx data classes. + + + + + + + diff --git a/molgenis-data-omx/doc/molgenis-data-omx.png b/molgenis-data-omx/doc/molgenis-data-omx.png new file mode 100644 index 00000000000..446fd035813 Binary files /dev/null and b/molgenis-data-omx/doc/molgenis-data-omx.png differ