DataModels

DB Schema

        classDiagram

   Sample "1" -->"N" Environment

   Sample "1" -->"1" Layer : substrate_layer
   Sample "1" -->"1<=N<=5" Layer : layers

   Layer "1" -->"1" Material : layer_material


   Measurement <|-- Reflectivity
   Measurement <|-- EIS

   Environment "1" -->"1" Material : ambient_medium_material
   Environment "1" -->"N" Measurement

   Sample "1" -->"N" Publication

   class Sample{
       +str description
       +list~Environment~ environments
       +Layer substrate
       +str geometry?
       +str main_composition
       +list~Layer~ layers
       +list~Publication~ publications
   }


   class Layer{
       +str name
       +Material material
       +float thickness
       +float? roughness
   }

   class Material{
       +str:composition
       +float mass?
       +float density?
       +float sld?
       +float isld?
   }

   class Measurement{
       +enum laboratory
       +str run_title
       +str run_number?
       +str proposal_number
       +enum facility
       +enum instrument
       +enum probe
       +enum technique
       +str technique_description
       +bool is_simulated
       +datetime run_start
       +str raw_file_path
   }

   class Reflectivity{
       +float q_1_angstrom
       +float r
       +float d_r
       +float d_q
       +float measurement_geometry
       +datetime reduction_time
       +str reduction_version
   }

   class EIS{
       +float frequency
       +float duration
       +float real_z
       +float imaginery_z
       +float phase
       +str potential

   }


   class Environment{
       +str description
       +Material ambient_medium?
       +float temperature?
       +float pressure?
       +float relative_humidity?
       +list~Measurement~ measurements
       +datetime timestamp

   }


   class Publication{
       +str title
       +str url
       +str abstract
       +str notes
       +list~str~ keywords
   }
    

DataModel ODM vs BaseModel

Classes defined as DataModel are stored in separate collections in the DB. Classes defined as (pydantic) BaseModel are embedded in the outter class’s collections, e.g. JSON schema fields.

        classDiagram

   Sample <|-- DataModel
   Layer <|-- BaseModel
   Material <|-- BaseModel
   Measurement <|-- DataModel
   Environment <|-- DataModel
   Publication <|-- DataModel


   Sample "1" o-- "N" Environment
   Sample "1" *-- "1" Layer : substrate_layer
   Sample "1" *-- "1<=N<=5" Layer : layers

   Layer "1" *-- "1" Material : layer_material

   Measurement <|-- Reflectivity
   Measurement <|-- EIS

   Environment "1" *--"1" Material : ambient_medium_material
   Environment "1" o--"N" Measurement

   Sample "N" o--"N" Publication

   class Sample{
       +$get_foreign_key_fields(cls)
   }

   class Layer{

   }

   class Material{

   }

   class Measurement{

   }

   class Reflectivity{

   }

   class EIS{

   }

   class Environment{

       +$get_foreign_key_fields(cls)
   }

   class DataModel{
       +str: Id
       +datetime: created_at
       +bool: is_deleted
       -$DBstore: _store

       +save(self, session)
       +delete(self,session)
       +restore(self,session)
       +view_object(self)

       +$connect_to_store(cls)
       +$find_by_id(cls, session, doc_id)
       +$find_active(cls, session)
       +$raw_rql(cls, session, query)
       +$get_foreign_key_fields(cls)
       +$validate_main_fields(cls, payload)
       +$get_foreign_key_fields(cls)
       +$validate_foreign_keys(cls,session, foreign_keys,field)
   }

   class BaseModel{

   }
    

Considerations:

• Data Objects that are defined as DataModel (Sample, Measurement, Environment, Publication) are Documents within their DataModel-defined Collections. Relationships with other DataModel classes are defined as aggregation with the current schema. However, they can be deleted programmatically, if needed, in case there is a strong dependency with another DataModel object that needs to be deleted.

• Data Objects that are defined as BaseModel (Layer, Material) by default introduce composition relationships with the associated DataModel classes. Thus layers, substrate and material are unique within the context they live, e.g. a material (ambiant_medium_material) for a specific environment only exists in that environment and no other DataModel object can point and refer to it. While materials with similar properties can exist on different environments, they are considered different (objects) with this schema. Additionally, if the main dataobject, e.g. environment, is deleted the associated BaseModel objects are deleted, too.

• The concepts of DataModel and BaseModel allow for the following:

  • BaseModel objects being embedded into the DataModel ones eliminate joins to retrieve them, while ensuring a standard format of the embedded objects.

  • DataModel Collections are to be used in the DB queries

  • BaseModel dataobjects cannot be queried directly

  • DataModel class enables for unified encapsulated operational and DB-wrapped capabilities

Note: We defined the relationships based on: UML composition models are nested documents with a dependent lifecycle, while aggregation models linked documents that can exist independently. Aggregation and composition are subsets of association.

Software Architecture

Software Architecture

        architecture-beta
    group process(cloud)[WebApplication Process]
    group user(cloud)[api]

    service db(database)[Database]
    service WebServer(server)[WebServer] in process
    service MCPServer(server)[MCPServer] in process

    db:L -- R:WebServer