diff --git a/how-we-work/create-puml-images.qmd b/how-we-work/create-puml-images.qmd deleted file mode 100644 index 1a0a1052..00000000 --- a/how-we-work/create-puml-images.qmd +++ /dev/null @@ -1,64 +0,0 @@ ---- -title: Creating PlantUML images ---- - -We use [PlantUML](https://plantuml.com) to create diagrams across most -of content, such as: - -1. [C4 diagrams](https://c4model.com) to visualise the software - architecture. -2. [Sequence diagrams](https://plantuml.com/sequence-diagram) that - visualise how and in what order things work together. - -To create PNG images of the PlantUML files, open a Terminal while inside -the project that has the PlantUML files and that has the `justfile`, and -run the command: - -``` bash -just generate-puml-all -``` - -If you want to generate a specific image, run: - -``` bash -just generate-puml PATH/TO/PUML -``` - -You need to have both Docker and Just installed and have Docker running -in the background in order for these commands to work. To see how to -install these programs, check out the entry on [software](software.qmd)) -for more details. - -## Style guide - -When you create a PlantUML diagram, please follow the style guide below: - -1. Use the Seedcase theme, see below. -2. Use sentence case (capitalise the first word only) for diagram - titles and texts. -3. Ensure that you use the same wording and ordering of elements in the - diagram as in the surrounding text. -4. For C4 diagrams, add a legend by writing `SHOW_LEGEND()` or - `SHOW_FLOATING_LEGEND()` at the end of the diagram. - -## Seedcase theme - -We have created a PlantUML theme that we use across all our PlantUML -diagrams. This theme is located in the -[`seedcase-theme`](https://github.com/seedcase-project/seedcase-theme) -repository and is synced to the remaining Seedcase repositories. In -these repositories, the theme is located in the -`_extensions/seedcase-project/seedcase-theme` directory. - -To include the theme in a PlantUML file, add the following line at the -top of the file: - -``` bash -@startuml diagram-name - -!theme seedcase from https://raw.githubusercontent.com/seedcase-project/seedcase-theme/main - -[add your diagram code here] - -@enduml -``` diff --git a/user-tests/sprout.qmd b/user-tests/sprout.qmd deleted file mode 100644 index 72c349c5..00000000 --- a/user-tests/sprout.qmd +++ /dev/null @@ -1,108 +0,0 @@ ---- -title: "Instructions for user tests of Sprout" ---- - -::: callout-warning -🚧 This section is still in active development and is subject to changes -🚧 -::: - -This document provides the context and instructions for users who we ask -to come and test out a demo of Sprout. We intended to use this document -so that a user can read before they come and do a user test. - -For this user test, we've made a basic case example that includes three -simple test data files. - -## About Sprout - -Sprout is a component of the Seedcase software ecosystem, which is a -framework for an open and scalable infrastructure for health data. The -Seedcase ecosystem aims to enable researchers to build, manage, and -(legally) share health data using modern best practices in data -engineering. - -Sprout is the component for building or "growing" data and aims to: - -> Take data created or collected for research studies and "grow" it in a -> structured way using modern best practices for storing data along with -> its metadata. - -## Context - -Imagine you are a researcher collecting data on diabetes patients and -their physical activity. You want to save and structure your data to -ease the process of: - -1. adding more data to your dataset, when more has been collected, and - -2. analysing the data later on. - -You have collected the data across two time periods (in 2023 and 2024), -resulting in a longitudinal study of the same individuals, who tracked -their exercise in March of 2023 and 2024. - -You have two types of files with data: - -1. A `patients` file that describes the patients and includes their - age, sex, height, weight, and diabetes type. The file is called - `patients.csv`. - -| id | age | sex | height | weight | diabetes_type | -|-----|-----|-----|--------|--------|---------------| -| 1 | 54 | F | 167.5 |  70.3 | Type 1 | -| 2 | 66 | M | 175 |  80.5 | Type 2 | - -: Showing the first two rows in the `patients.csv` file. - -2. Two `physical_activity` files that describe their physical activity - patterns, such as when they did activities, what type of activity, - and for how long. The files are called `physical_activity_2023.csv` - and `physical_activity_2024.csv`. - -| id | physical_activity | duration | date | -|-----|-------------------|----------|------------| -| 1 | run | 10 | 01-03-2024 | -| 2 | walk | 25 | 02-04-2024 | - -: Showing the first two rows in the `physical_activity_2024.csv` file. - -Since you want to grow your data in a structured way, you decide to try -out Sprout for handling your data. - -## Tasks - -We want you to do some tasks, that you'll read about below. As you do -it, we want you to tell us your inner dialogue and thought process on -what you're doing and what makes sense, doesn't make sense, is -confusing, or is something you like. - -Throughout, we will refrain from explaining and helping you too much. - -::: callout-note -An important aspect of user testing for you as the user is that **there -are no right or wrong answers.** We are trying to learn how to build a -better tool for you and others like you. So give honest, constructive -feedback! - -If something is unclear to you, it is a great oppurtunity for us to -learn how to make it clearer going forward - this is exactly why user -tests are so helpful for us! -::: - -The tasks we want you to do are: - -1. Download the files from the [data - repository](https://github.com/seedcase-project/data/tree/main/patients). -2. Open up the files on your computer and take a look at them, so you - have a bit of an idea of what the data is. -3. Using Sprout, create the metadata for the `patients.csv` file. -4. Then create the metadata for `physical_activity_2023.csv` and call - it `physical_activity`. -5. Add the data from `physical_activity_2024.csv` to the - `physical_activity` metadata. - -Go through them one at the time and remember to verbally walk through -your thoughts and reactions to us. - -Thank you so much for your help and your time! :relaxed: