SciWIn-Client Demo

This repo contains the scripts to perform a small SciWIn-Client Demo. This instructions file will be updated to use new features when they are available. The commands stated below will perform the operations based on our hello world repo.

Demo Commands

To check if SciWIn is available type s4n --version which should output something like s4n 0.6.0.

Initializing a Project

To begin the journey use s4n init to initialize a project in the current directory.

s4n init

Create a virtual environment

python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

Creation of CommandLineTools

To create the two CommandLineTools needed for the demo you just have to prefix the execution commands with s4n tool create or s4n run.

Calculation

To create the calculation.cwl tool run the following command:

s4n tool create python calculation.py --population population.csv --speakers speakers.csv

which will output something like

📂 The current working directory is /home/ubuntu/sciwin_test
▶️  Executing command: python calculation.py --population population.csv --speakers speakers.csv
Total population: 7694245029
            language    speakers  percentage
0             Bangla   300000000    3.899018
1    Egyptian Arabic   100542400    1.306722
2            English  1132366680   14.717060
3             German   134993040    1.754468
4         Indonesian   198996550    2.586304
5           Japanese   128000000    1.663581
6         Portuguese   475300000    6.177344
7            Punjabi   125000000    1.624591
8            Russian   154000000    2.001496
9  Standard Mandarin  1090951810   14.178803

📜 Found changes:
        - results.csv

📄 Created CWL file workflows/calculation/calculation.cwl

Plot

The Plot tool will use the created results.csv. The creation command is

s4n run python plot.py --results results.csv

which will lead to the following output:

📂 The current working directory is /home/ubuntu/sciwin_test
▶️  Executing command: python plot.py --results results.csv

📜 Found changes:
        - results.svg

📄 Created CWL file workflows/plot/plot.cwl

Workflow Creation

Workflow Creation

To create a Workflow with name demo simply call

s4n workflow create demo

which will output

📄 Created new Workflow file: workflows/demo/demo.cwl

Connecting Tools

To connect the steps in the workflow you need to call s4n workflow connect a couple of times.

Connecting Inputs

First we will connect the calculation tool to the input sockets. The tool has two inputs which we will connect to the speakers and pop input.

s4n workflow connect demo --from @inputs/speakers --to calculation/speakers
s4n workflow connect demo --from @inputs/pop --to calculation/population

An example output looks like

➕ Added step calculation to workflow
➕ Added or updated connection from inputs.speakers to calculation/speakers in workflow
✔️  Updated Workflow workflows/demo/demo.cwl!

Connecting Tools

We now will connect the plot and the calculation tool. We will map results-output to results-input.

s4n workflow connect demo --from calculation/results --to plot/results

An example output looks like

🔗 Found step calculation in workflow. Not changing that!
➕ Added step plot to workflow
✔️  Updated Workflow workflows/demo/demo.cwl!

Connecting to output

To get the results file we will connect the result of the plot step to out.

s4n workflow connect demo --from plot/o_results --to @outputs/out

which outputs

➕ Added or updated connection from plot/results to outputs.out in workflow!
✔️  Updated Workflow workflows/demo/demo.cwl!

To commit a simple call is needed:

s4n workflow save demo

We now have a full workflow which can be executed

s4n execute local workflows/demo/demo.cwl --pop population.csv --speakers speakers_revised.csv

However we did not use Docker containers, so this will work only on our computer. take a look at the other examples to learn how to use Docker with s4n. https://github.com/fairagro/m4.4_sciwin_client_examples