From de8b26c38f6cc5cf0ab02055d2216f5fdaf4940c Mon Sep 17 00:00:00 2001
From: Alexander Schlemmer <alexander@mail-schlemmer.de>
Date: Fri, 22 Apr 2022 10:52:37 +0200
Subject: [PATCH] DOC: added a real world example for high level API to the
docs
---
src/doc/high_level_api.org | 50 ++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
diff --git a/src/doc/high_level_api.org b/src/doc/high_level_api.org
index c24bc7ba..516df1b4 100644
--- a/src/doc/high_level_api.org
+++ b/src/doc/high_level_api.org
@@ -119,3 +119,53 @@ Each property stored in a CaosDB record corresponds to:
- ~description~
- ~id~
- ~importance~
+
+
+* Example
+
+The following shows a more complex example taken from a real world use case:
+A numerical experiment is created to simulate cardiac electric dynamics. The physical problem
+is modelled using the monodomain equation with the local current term given by the Mitchell
+Schaeffer Model.
+
+The data model for the numerical experiment consists of multiple record types which stores assosciated paremeters:
+- `MonodomainTissueSimulation`
+- `MitchellSchaefferModel`
+- `SpatialExtent2d`
+- `SpatialDimension`
+- `ConstantTimestep`
+- `ConstantDiffusion`
+
+First, the data model will be filled with the parameter values for this specific simulation run. It will be stored in the python variable `MonodomainRecord`. Passing the `MonodomainRecord` through the python functions, the simulation parameters can be easily accessed everywhere in the code when needed.
+
+Records are created by the `create_record` function. Parameter values can be set at record creation and also after creation as python properties of the corresponding record instance. The following example shows how to create a record, how to set the parameter at creation and how to set them as python properties
+
+#+BEGIN_SRC python
+ from caosdb.high_level_api import create_record
+
+ MonodomainRecord = create_record("MonodomainTissueSimulation")
+ MonodomainRecord.LocalModel = create_record("MitchellSchaefferModel")
+ MonodomainRecord.SpatialExtent = create_record(
+ "SpatialExtent2d", spatial_extent_x=100, spatial_extent_y=100)
+ MonodomainRecord.SpatialExtent.cell_sizes = [0.1, 0.1] # parameters can be set as properties
+ MonodomainRecord.SpatialDimension = create_record("SpatialDimension",
+ num_dim=2)
+
+ MonodomainRecord.TimestepInformation = create_record("ConstantTimestep")
+ MonodomainRecord.TimestepInformation.DeltaT = 0.1
+
+ D = create_record("ConstantDiffusion", diffusion_constant=0.1)
+ MonodomainRecord.DiffusionConstantType = D
+ model = MonodomainRecord.LocalModel
+ model.t_close = 150
+ model.t_open = 120
+ model.t_out = 6
+ model.t_in = 0.3
+ model.v_gate = 0.13
+ model.nvars = 2
+#+END_SRC
+
+At any position in the algorithm you are free to:
+- Convert this model to the standard python API and insert or update the records in a running instance of CaosDB.
+- Serialize this model in the high level API yaml format. This enables the CaosDB crawler to pickup the file and synchronize it with a running instance
+of CaosDB.
--
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