• Padding
• The footer to the bottom
• Contact info box sizes
• Flip if possible
• Circle next to cohorts
• Make the headers inactive/unclickable for now
• Send Yasi all the pictures so she can help
• Capitalize the modalities
• Highlight the modality button
• Add a link to PASSIONATE
• Add citation to the home component
• Center subpage links in header

list all services, components and their dependencies

To be done at the end:

• Clean up the code
• Add Documentation to the root README.md (Description, how to start, how to run, troubleshooting etc.)
• Draft a 1.0.0 Release

Update the publication number of Prof. Dr. Martin-Hofmann Apitius.

Related to the functionality required in the frontend (#3), define a list of data endpoints / functionalities needed for the retrieval.

Examples

Autocompletion

Select a feature in the frontend that should be based on the reference terms in the PASSIONATE CDM

Endpoint

e.g. GET /features/autocomplete

Input Params

Partial String defined by user input, e.g.

A

Endpoint Output

List of potential matches of reference terms in the CDM, e.g.:

["Age", "Asymmetrical tremor", (...)]

• Decide on DB type
• Find Helm Chart & run in k8s
• Add data

• Scale it based on the actual maximum of features
• get them dynamically fom the api

Add a photo of Marjan Niazpoor for the contact us component whenever it is ready.

Implement the Parkinson's disease data

Create a component called "Longitudinal" to showcase patient drop-out throughout the study both in general and for specific biomarkers.

Depends on #61.

Create the biomarkers component to showcase the distribution of the patient-level data.

Depends on #61.

Change public URLs from k8s.scai.fraunhofer.de to k8s.bio.scai.fraunhofer.de

The y-axis in the drop-off diagrams was labeled as "patient drop-off", whereas it should have been "participant drop-off".

• Alternate between right-hand side and left-hand side for images.
• Align the Explore button to the center of the container rather than the center of the text.

Create a component called "Auto-Harmonization" that will utilize index package to automatically harmonize uploaded variables to PASSIONATE or another terminology.

Depends on #65 and SCAI-BIO/datastew#7.

Create a component called "Ethnicity" to showcase the ethnoracial diversity in each cohort study.

Depends on #61.

Describe the bug
The credentials are not correctly initialized

Is your feature request related to a problem? Please describe.
Current hashing algorithm (sha256) is not strong enough.

Describe the solution you'd like
Upgrade to sha3_512 encryption algorithm.

Describe alternatives you've considered
Alternatives can be other sha3 algorithms or argon2 algorithm.

• Studypicker - Ranked Cohorts

This is only minor; In the README.md it states that the frontend will be running on port 8080 when started locally, the docker-compose.local.yaml starts it on port 3000 - we should explicitly state this in the README so this does not have to be looked up in the docker-compsoe file itself

Implement an encrypted SQL database to store patient-level data as well as the PASSIONATE CDM.

• Cohorts - Spacing between patients needs to be fixed.
• Cohorts - The number of patients per cohort needs to be reduced.
• Mappings - Generate a .png logo.

Issue Title

Summary
Migrate to INDEX API rather than using datastew directly.

Details
We use the functions directly from datastew and develop the same API endpoints for INDEX. Switching to direct usage of INDEX API will solve some of the security issues.

See here:
https://stackoverflow.com/questions/47426721/angular-cli-change-rest-api-url-on-build

• first envirnment should be called dev and point to the development backend url on localhost
• second environment should be called scai and point to k8s URL

We should start with a test deployment to facilitate the actual release & make it possible for members of SCAI to test the current implemented features. We can update the test deployment based on releases we schedule after feature milestones that you define.

Steps would be:

• test containers (pdataviewer/frontend & pdataviewer/backend) @mehmetcanay
• #21
• create SCAI branch with adjusted URLs to backend (for now only internal: pdata.k8s.scai.fraunhofer.de & api.pdata.k8s.scai.fraunhofer.de) @mehmetcanay
• #20
• #18
• setup protection rules for scai branch
• #19
• #25

Doing this ASAP can give us some feedback which may be useful for your thesis and possibly catch potential bugs before the actual release by the time of your submission.

Reformat the code so that it accepts .zip file containing .csv files for easier import of multiple data.

Describe the bug
SQL repository cannot function properly due to dash signs in the table names.

Expected behavior
SQL repository to handle all functions properly

Update the versions of API (in routes.py) and PDataViewer (in package-lock.json) automatically during release.

• How many (and which) datasets will be included?
• What needs to be computed based on these datasets (e.g. summary statistics, models, plots)?

Reproduce:

In root dir calling:

docker-compose -f docker-compose.local.yaml up

will crash with:

  File "/usr/local/lib/python3.12/site-packages/uvicorn/importer.py", line 22, in import_from_string
    raise exc from None
  File "/usr/local/lib/python3.12/site-packages/uvicorn/importer.py", line 19, in import_from_string
    module = importlib.import_module(module_str)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 995, in exec_module
  File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
  File "/api/routes.py", line 4, in <module>
    from functions.visualization import generate_chords
ModuleNotFoundError: No module named 'functions'
exit code: 1
``

• What it is?
• requirements
• how to run
• etc

Add a column called "Data access" and put the application links of each cohort.

Documentation Update

What documentation needs to be updated?
Architecture drawing.

Any chance we can rename this back to "frontend" instead of "pdataviewer" to avoid confusion in the future?

What exact components does Martin want to see in the frontend (Graphs, Plots, Tables etc.) ?

Include number of idiopathic patients in the Cohorts component