diff --git a/README.md b/README.md new file mode 100644 index 0000000..12b9518 --- /dev/null +++ b/README.md @@ -0,0 +1,174 @@ +# FAIR Data Fund — Developer Overview + +This repository contains a small Python web application that powers the FAIR Data Fund application & review workflow. It’s a classic WSGI app built on **Werkzeug** and **Jinja2**, with data stored in / read from a **SPARQL 1.1 endpoint** via **RDFLib**. + +## Tech stack (at a glance) + +- **Language**: Python 3.8+ +- **Web**: Werkzeug (WSGI), Jinja2 templates, static assets (HTML/CSS/JS, jQuery, Quill, Dropzone) +- **Data**: RDF and SPARQL via `rdflib` (uses `SPARQLStore`); defaults to a Virtuoso-style endpoint at `http://127.0.0.1:8890/sparql` +- **Auth**: Optional SAML settings are supported via XML config (no external SAML lib; parsed & validated with `defusedxml`) +- **Email**: SMTP (configurable via XML) +- **Build tooling**: GNU Autotools (`configure.ac`, `Makefile.am`) is used to generate `pyproject.toml` and Makefiles; packaging via `setuptools` +- **CLI entry point**: `fair-data-fund` → `fair_data_fund.ui:main` +- **Key deps** (from `requirements.txt`): Jinja2, rdflib, requests, urllib3, Werkzeug, defusedxml + +## Project structure + +``` +fair-data-fund/ +├─ configure.ac # Autotools: defines Python version & outputs Makefiles/pyproject +├─ Makefile.am # Autotools: top-level build/dist instructions +├─ pyproject.toml.in # Template → becomes pyproject.toml after ./configure +├─ requirements.txt # Runtime dependencies +└─ src/ + ├─ Makefile.am # Autotools: package layout & installables + └─ fair_data_fund/ + ├─ *.py # Application modules (wsgi, ui, database, email, validator, rdf, ...) + └─ resources/ + ├─ html_templates/ # Jinja2 templates (home, application form, review UI, etc.) + ├─ static/ # CSS, JS (jquery, quill, dropzone), fonts, images + └─ sparql_templates/ # Jinja2-templated SPARQL queries +``` + +### Notable modules + +- `fair_data_fund.wsgi`: WSGI app; routing via `werkzeug.routing.Map/Rule`; static files via `SharedDataMiddleware`. +- `fair_data_fund.ui`: CLI entry; starts the dev server with `werkzeug.serving`. Handles `--config-file` and `--initialize`. +- `fair_data_fund.database`: SPARQL client built on `rdflib.plugins.stores.sparqlstore.SPARQLStore`. Uses Jinja2-rendered SPARQL templates. Default endpoint: `http://127.0.0.1:8890/sparql`. SPARQL Update can be configured separately. +- `fair_data_fund.validator`, `formatter`, `email_handler`, `rdf`, `cache`, `convenience`: support logic. + +## Prerequisites + +- Python **3.8+** +- A **SPARQL 1.1 endpoint** with update enabled (e.g. Virtuoso at `:8890` or Jena Fuseki). You can run one locally using Docker; set the endpoint URLs in the XML config below. +- (Optional) SMTP account for outgoing email notifications. +- (Optional) SAML Identity Provider metadata if you want SSO in dev. + +## Local setup (fast path for development) + +You can run the app directly from source without a full Autotools build: + +```bash +# 1) Create and activate a virtual environment +python3 -m venv .venv +source .venv/bin/activate + +# 2) Install Python dependencies +pip install --upgrade pip +pip install -r requirements.txt + +# 3) Create a config file (see example below), then start the server +python -m fair_data_fund.ui --config-file ./dev-config.xml --initialize +# or, after installation via setuptools (see "Autotools build" below): +# fair-data-fund --config-file ./dev-config.xml --initialize +``` + +This starts a dev server (defaults to `127.0.0.1:8080`). The `--initialize` flag will populate the RDF store with default triples (institutions, etc.). + +> **Tip:** If you run from source, `python` needs to see the `src/` tree. From the repo root, `python -m fair_data_fund.ui` works because Python will pick up `src/` automatically when installed in editable mode. If you hit `ModuleNotFoundError`, run `pip install -e .` after generating `pyproject.toml` (see below), or set `PYTHONPATH=src`. + +## Minimal config (XML) + +Create a file `dev-config.xml` in the repo root with something like: + +```xml + + + +
127.0.0.1
+ 8080 + http://127.0.0.1:8080 + 1 + 1 + + + .cache + + + .fdf_storage + + default://graph + http://127.0.0.1:8890/sparql + http://127.0.0.1:8890/sparql + + + + + smtp.example.com + 587 + user + pass + no-reply@example.com + [FDF] + 1 + + + + + https://fdf.local/ + /path/to/sp.pem + /path/to/sp.key + + + https://idp.example.org/ + ...PEM... + + https://idp.example.org/sso + urn:oasis:names:tc:SAML:2.0:bindings:HTTP-Redirect + + + + +``` + +Only the SPARQL settings are required for a functional dev run; email & SAML are optional. + +## Running a local SPARQL endpoint (example) + +**Virtuoso (quick start):** +```bash +docker run -it --name virtuoso -p 8890:8890 -e DBA_PASSWORD=dba openlink/virtuoso-opensource-7:latest +# After it starts, ensure SPARQL Update is enabled and use the endpoints in dev-config.xml. +``` + +**Jena Fuseki (alternative):** +```bash +docker run -it --name fuseki -p 3030:3030 stain/jena-fuseki +# Create a dataset in the UI, then set: +# http://127.0.0.1:3030/your-dataset/sparql +# http://127.0.0.1:3030/your-dataset/update +``` + +## Autotools build (optional, for packaging) + +This repo uses GNU Autotools to generate the packaging metadata (`pyproject.toml`) and Makefiles. If you want to build & install the package the “classic” way, do: + +```bash +# Install autotools if needed (autoconf, automake, libtool) +autoreconf -i # generates ./configure and friends +./configure # writes Makefile(s) and pyproject.toml from pyproject.toml.in +make # builds dist artifacts (and assembles extra resources) +pip install . # installs the package (exposes the 'fair-data-fund' CLI) +# (Optional) make distcheck / make install +``` + +Once installed: +```bash +fair-data-fund --config-file ./dev-config.xml --initialize +``` + +## Common issues + +- **SPARQL endpoint not reachable**: The app will log failures if it cannot connect. Check `rdf-store` URIs, port mappings, and that SPARQL Update is enabled. +- **Missing fonts/static**: Static is served by the WSGI app via `SharedDataMiddleware`; ensure you’re running from an installed layout or from the source tree so resource paths resolve. +- **SAML misconfiguration**: Start without SAML in dev; add it later with correct IdP metadata. +- **Email sending fails**: Verify SMTP credentials; set `1` only if your SMTP server supports it. + +## License + +AGPL-3.0-or-later (see `LICENSE` if included in your dist). + +--- + +_This README was generated from the uploaded repository contents to give you a working starting point._ diff --git a/src/fair_data_fund/resources/html_templates/application-form.html b/src/fair_data_fund/resources/html_templates/application-form.html index 6806716..f531d50 100644 --- a/src/fair_data_fund/resources/html_templates/application-form.html +++ b/src/fair_data_fund/resources/html_templates/application-form.html @@ -50,7 +50,14 @@

Basic information

For example: Quantitive data, qualitative data, research software.
- ∗ + ∗
Include a description of the data (raw, processed, analyzed) and research software as these are currently available. In later questions, you can elaborate on how the FAIR principles will be implemented.