From f9c56bf717b40ace289562544cc7bb9aea1ceaaa Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Wed, 11 Sep 2024 06:33:22 +0200
Subject: [PATCH] add figure of multiple tasks

---
 .../_figures/_fig_multiple_task_structure.qmd | 42 +++++++++++++++++++
 documentation/fundamentals/philosophy.qmd     |  3 ++
 2 files changed, 45 insertions(+)
 create mode 100644 documentation/_figures/_fig_multiple_task_structure.qmd

diff --git a/documentation/_figures/_fig_multiple_task_structure.qmd b/documentation/_figures/_fig_multiple_task_structure.qmd
new file mode 100644
index 00000000..d54e2181
--- /dev/null
+++ b/documentation/_figures/_fig_multiple_task_structure.qmd
@@ -0,0 +1,42 @@
+```{mermaid}
+%%| label: fig-task-structure
+%%| fig-cap: "The structure of an OpenProblems task. **Legend**: Grey rectangles are HDF5-backed AnnData (`.h5ad`) files. Purple rhomboids are Viash components."
+%%| cap-location: margin
+graph LR
+  loader[/Dataset<br/>loader/]:::component
+  dataset[Dataset]:::anndata
+  loader --> dataset
+
+  processor0[/Processor/]:::component
+  processed0[Processed<br/>data]:::anndata
+  method0[/Method/]:::component
+  output0[Output]:::anndata
+  metric0[/Metric/]:::component
+  score0[Score]:::anndata
+  dataset --- processor0 --> processed0 --- method0 --> output0 --- metric0 --> score0
+
+  processor1[/Processor/]:::component
+  processed1[Processed<br/>data]:::anndata
+  method1[/Method/]:::component
+  output1[Output]:::anndata
+  metric1[/Metric/]:::component
+  score1[Score]:::anndata
+  dataset --- processor1 --> processed1 --- method1 --> output1 --- metric1 --> score1
+
+  processor2[/Processor/]:::component
+  processed2[Processed<br/>data]:::anndata
+  method2[/Method/]:::component
+  output2[Output]:::anndata
+  metric2[/Metric/]:::component
+  score2[Score]:::anndata
+  dataset --- processor2 --> processed2 --- method2 --> output2 --- metric2 --> score2
+
+  processor3[/Processor/]:::component
+  processed3[Processed<br/>data]:::anndata
+  method3[/Method/]:::component
+  output3[Output]:::anndata
+  metric3[/Metric/]:::component
+  score3[Score]:::anndata
+  dataset --- processor3 --> processed3 --- method3 --> output3 --- metric3 --> score3
+
+```
\ No newline at end of file
diff --git a/documentation/fundamentals/philosophy.qmd b/documentation/fundamentals/philosophy.qmd
index bfed5f26..f067d20c 100644
--- a/documentation/fundamentals/philosophy.qmd
+++ b/documentation/fundamentals/philosophy.qmd
@@ -22,6 +22,9 @@ To define benchmarking tasks, OpenProblems incorporates the principles of the Co
 
 {{< include ../_figures/_fig_task_structure.qmd >}}
 
+{{< include ../_figures/_fig_multiple_task_structure.qmd >}}
+
+
 AnnData, short for "Annotated Data", is a file format designed for handling annotated, high-dimensional biological data [@virshup2021anndataannotateddata]. In OpenProblems, AnnData serves as the standard data format for both input and output files of components, ensuring a consistent and seamless exchange of data between different components of the benchmarking pipelines.
 
 Viash is a meta-framework which allows generating modular {{< glossary Nextflow >}} components and workflows from Python and R scripts [@cannoodt2021viashfromscripts]. Viash components are used in OpenProblems for creating dataset loaders, dataset processors, methods, and metrics, enabling developers to focus on the core functionality of their components without worrying about the chosen pipeline framework (i.e. Nextflow).