From b7c491114f8fa1b9017e2be8d7119ebcfcbc91dd Mon Sep 17 00:00:00 2001
From: Alexander Schlemmer <alexander@mail-schlemmer.de>
Date: Thu, 17 Mar 2022 14:54:19 +0100
Subject: [PATCH] DOC: converted the org-mode documentation file to
restructured text
---
src/doc/high_level_api.org | 121 ---------------------------
src/doc/high_level_api.rst | 162 +++++++++++++++++++++++++++++++++++++
2 files changed, 162 insertions(+), 121 deletions(-)
delete mode 100644 src/doc/high_level_api.org
create mode 100644 src/doc/high_level_api.rst
diff --git a/src/doc/high_level_api.org b/src/doc/high_level_api.org
deleted file mode 100644
index 7df50bb2..00000000
--- a/src/doc/high_level_api.org
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-* 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:
-#+BEGIN_SRC 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)
-
-#+END_SRC
-
-
-* 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:
-#+BEGIN_SRC python
- from caosdb.high_level_api import query
-
- res = query("FIND Record Experiment")
- experiment = res[0]
- # Use a property:
- print(experiment.date)
-
- # Use sub properties:
- print(experiment.output[0].path)
-#+END_SRC
-
-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:
-#+BEGIN_SRC python
- import caosdb as db
-
- res = db.execute_query("FIND Record Experiment")
- output = res.get_property("output")
- output_file = db.File(id=output.value[0].id).retrieve()
- print(output_file.path)
-#+END_SRC
-
-Resolving subproperties makes use of the "resolve_reference" 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:
-#+BEGIN_SRC python
-print(str(obj))
-#+END_SRC
-
-
-* 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 "resolve_references" 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
diff --git a/src/doc/high_level_api.rst b/src/doc/high_level_api.rst
new file mode 100644
index 00000000..46460de1
--- /dev/null
+++ b/src/doc/high_level_api.rst
@@ -0,0 +1,162 @@
+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:
+
+.. code:: 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\ :sub:`levelapi`
+
+There are two functions converting entities between the two
+representation (old API and new API):
+
+- convert\ :sub:`topythonobject`: Convert entities from **old** into
+ **new** representation.
+- convert\ :sub:`toentity`: Convert entities from **new** into **old**
+ representation.
+
+Furthermore there are a few utility functions which expose very
+practical shorthands:
+
+- new\ :sub:`highlevelentity`: Retrieve a record type and create a new
+ high level entity which contains properties of a certain importance
+ level preset.
+- create\ :sub:`record`: Create a new high level entity using the name
+ of a record type and a list of key value pairs as properties.
+- load\ :sub:`externalrecord`: Retrieve a record with a specific name
+ and return it as high level entity.
+- create\ :sub:`entitycontainer`: 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:
+
+.. code:: python
+
+ from caosdb.high_level_api import query
+
+ res = query("FIND Record 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:
+
+.. code:: python
+
+ import caosdb as db
+
+ res = db.execute_query("FIND Record 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 "resolve\ :sub:`reference`"
+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\ :sub:`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:
+
+.. code:: python
+
+ print(str(obj))
+
+Concepts
+========
+
+As described in the section Quickstart the two functions
+"convert\ :sub:`topythonobject`" and "convert\ :sub:`toentity`" 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\ :sub:`levelapi`:
+
+- 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 "resolve\ :sub:`references`" 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
--
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