Import CODECHECK metadata from existing codecheck.yml file from GitHub

[dxL1nus]

Relates to #36

Mock Up (Repository List now with Load Metadata Buttons that would retrieve the data from the existing codecheck.yml file and load it into the metadata form:

---

To Do:

• check if repository has correct GitHub format
• find way to download file from GitHub
• retrieve data from this file instead of the loadData() from the submission
• integrate this functionality with the Repository List from Subhan
• Now User should be able to Save this metadata manually

GitHub codecheck.yml download example: https://github.com/codecheckers/lifecycle-journal-codechecks/blob/main/7/codecheck.yml
Easier: https://raw.githubusercontent.com/codecheckers/lifecycle-journal-codechecks/refs/heads/main/7/codecheck.yml
GitHub Code Repository Link example: https://github.com/codecheckers/lifecycle-journal-codechecks/blob/main/7/

Second example for Repository Link: https://github.com/codecheckers/certificate-2025-029

---

• Add Unit Tests

[dxL1nus]

Each Repository now has a LoadMetadata Button, that when pressed checks if the inputted url has the correct zenodo format or not (using php regex).

When the first Load Metadata Button is pressed:

When the second Load Metadata Button is pressed:

[dxL1nus]

Each Repository now has a LoadMetadata Button, that when pressed checks if the inputted url has the correct zenodo format or not (using php regex).

When the first Load Metadata Button is pressed:

When the second Load Metadata Button is pressed:

@nuest could you please tell me if this is a good start, or did I still didn't understand something?

[nuest]

Yes, good start.

Note that in terms of priorities, the majority of codecheck.yml files are stored on GitHub, specifically in the root of projects on GitHub (see column Repository in https://github.com/codecheckers/register/blob/master/register.csv), so that would be the first feature to implement, then OSF projects (again the codecheck.yml is in the root, then GitHub repos with a subpath, and then Zenodo.

But since we're going to get all of them to work, you can also figure out Zenodo first.

[dxL1nus]

Yes, good start.

Note that in terms of priorities, the majority of codecheck.yml files are stored on GitHub, specifically in the root of projects on GitHub (see column Repository in https://github.com/codecheckers/register/blob/master/register.csv), so that would be the first feature to implement, then OSF projects (again the codecheck.yml is in the root, then GitHub repos with a subpath, and then Zenodo.

But since we're going to get all of them to work, you can also figure out Zenodo first.

Okay didn't know that. Then I will just rename the issue for now and look for the GitHub Downloads instead

[dxL1nus]

The script now identifies if just a repository or the path to a specific folder inside the repository was input. It then searches for the codecheck.yml in this directory and if found, it then automatically returns the contents of the codecheck.yml file.

In this example both visible GitHub Links work, although one obviously only specifies a repository while the other also specifies the branch and the path to a specific sub-directory in this branch.

API Answer for the first url:

---

API Answer for the second url:

[dxL1nus]

The contents from the codecheck.yml are now correctly formatted and returned as a metadata array by the API.

[dxL1nus]

Before the content is loaded from the codecheck.yml file:

After the content from the codecheck.yml file is loaded:

After the user saved the metadata, it can now be previewed with the following output:

---
version: https://codecheck.org.uk/spec/config/1.0/
paper:
  title: |
    Systematic evaluation of robustness to cell type mismatch of deconvolution methods for spatial transcriptomics data
  authors:
    - name: Utkarsh M. Mahamune
    - name: Aldo Jongejan
    - name: Antoine van Kampen
    - name: Lisa van Baarsen
    - name: Perry Moerland
manifest:
  - file: Results_figures/Figure_2.png
    comment: manuscript Figure 2
  - file: Results_figures/Figure_3.png
    comment: manuscript Figure 3
  - file: Results_figures/Figure_4a.png
    comment: manuscript Figure 4a
  - file: Results_figures/Figure_4b.png
    comment: manuscript Figure 4b
  - file: Results_figures/Figure_5.png
    comment: manuscript Figure 5
codechecker:
  - name: Bauke van der Velde
  - name: Merel Postema
summary: |
  R and Python code by EDS Bioinformatics Laboratory at Amsterdam UMC;  all manuscript figures successfully reproduced on myDRE
repository: https://github.com/codecheckers/certificate-2025-029
check_time: 2025-07-13T10:00
certificate: 2025-029
report: https://doi.org/10.5281/zenodo.17524536