High Level API

In addition to the old standard pylib API, new versions of pylib ship with a high level API that facilitates usage of CaosDB entities within data analysis scripts. In a nutshell that API exposes all properties of CaosDB Records as standard python attributes making their access easier.

Or to speak it out directly in Python:

import caosdb as db
# Old API:
r = db.Record()
r.add_parent("Experiment")
r.add_property(name="alpha", value=5)
r.get_property("alpha").value = 25 # setting properties (old api)
print(r.get_property("alpha").value + 25) # getting properties (old api)

from caosdb.high_level_api import convert_to_python_entity
obj = convert_to_python_object(r) # create a high level entity
obj.r = 25 # setting properties (new api)
print(obj.r + 25) # getting properties (new api)

Quickstart

The module, needed for the high level API is called: caosdb.high_level_api

There are two functions converting entities between the two representation (old API and new API):

  • convert_to_python_object: Convert entities from old into new representation.

  • convert_to_entity: Convert entities from new into old representation.

Furthermore there are a few utility functions which expose very practical shorthands:

  • new_high_level_entity: Retrieve a record type and create a new high level entity which contains properties of a certain importance level preset.

  • create_record: Create a new high level entity using the name of a record type and a list of key value pairs as properties.

  • load_external_record: Retrieve a record with a specific name and return it as high level entity.

  • create_entity_container: Convert a high level entity into a standard entity including all sub entities.

  • query: Do a CaosDB query and return the result as a container of high level objects.

So as a first example, you could retrieve any record from CaosDB and use it using its high level representation:

from caosdb.high_level_api import query

res = query("FIND Experiment")
experiment = res[0]
# Use a property:
print(experiment.date)

# Use sub properties:
print(experiment.output[0].path)

The latter example demonstrates, that the function query is very powerful. For its default parameter values it automatically resolves and retrieves references recursively, so that sub properties, like the list of output files “output”, become immediately available.

Note that for the old API you were supposed to run the following series of commands to achieve the same result:

import caosdb as db

res = db.execute_query("FIND Experiment")
output = res.get_property("output")
output_file = db.File(id=output.value[0].id).retrieve()
print(output_file.path)

Resolving subproperties makes use of the “resolvereference” function provided by the high level entity class (CaosDBPythonEntity), with the following parameters:

  • deep: Whether to use recursive retrieval

  • references: Whether to use the supplied db.Container to resolve references. This allows offline usage. Set it to None if you want to automatically retrieve entities from the current CaosDB connection.

  • visited: Needed for recursion, set this to None.

Objects in the high level representation can be serialized to a simple yaml form using the function serialize with the following parameters:

  • without_metadata: Set this to True if you don’t want to see property metadata like “unit” or “importance”.

  • visited: Needed for recursion, set this to None.

This function creates a simple dictionary containing a representation of the entity, which can be stored to disk and completely deserialized using the function deserialize.

Furthermore the “str” function is overloaded, so that you can use print to directly inspect high level objects using the following statement:

print(str(obj))

Concepts

As described in the section Quickstart the two functions convert_to_python_object and convert_to_entity convert entities beetween the high level and the standard representation.

The high level entities are represented using the following classes from the module caosdb.high_level_api:

  • CaosDBPythonEntity: Base class of the following entity classes.

  • CaosDBPythonRecord

  • CaosDBPythonRecordType

  • CaosDBPythonProperty

  • CaosDBPythonMultiProperty: WARNING Not implemented yet.

  • CaosDBPythonFile: Used for file entities and provides an additional download function for being able to directly retrieve files from CaosDB.

In addition, there are the following helper structures which are realized as Python data classes:

  • CaosDBPropertyMetaData: For storing meta data about properties.

  • CaosDBPythonUnresolved: The base class of unresolved “things”.

  • CaosDBPythonUnresolvedParent: Parents of entities are stored as unresolved parents by default, storing an id or a name of a parent (or both).

  • CaosDBPythonUnresolvedReference: An unresolved reference is a reference property with an id which has not (yet) been resolved to an Entity.

The function “resolvereferences” can be used to recursively replace CaosDBPythonUnresolvedReferences into members of type CaosDBPythonRecords or CaosDBPythonFile.

Each property stored in a CaosDB record corresponds to:

  • a member attribute of CaosDBPythonRecord and

  • an entry in a dict called “metadata” storing a CaosDBPropertyMetadata object with the following information about proeprties:

    • unit

    • datatype

    • description

    • id

    • importance