From 3e9427ace276a26574f4d977b227a7ec6648683c Mon Sep 17 00:00:00 2001 From: Heinz-Alexander Fuetterer <fuetterh@posteo.de> Date: Sun, 1 Oct 2023 07:17:58 +0200 Subject: [PATCH] temp --- README.md | 37 +++++++++++++++++-------------------- 1 file changed, 17 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 4bd7bd9f..9e256b82 100644 --- a/README.md +++ b/README.md @@ -19,18 +19,18 @@ Devaraju, A. and Huber, R. (2021). An automated solution for measuring the progr ### Clients and User Interface -A web demo using F-UJI is available at https://www.f-uji.net +A web demo using F-UJI is available at <https://www.f-uji.net>. -An R client package that was generated from the F-UJI OpenAPI definition is available from https://github.com/NFDI4Chem/rfuji. +An R client package that was generated from the F-UJI OpenAPI definition is available from <https://github.com/NFDI4Chem/rfuji>. -An open source web client for F-UJI is available at https://github.com/MaastrichtU-IDS/fairificator. +An open source web client for F-UJI is available at <https://github.com/MaastrichtU-IDS/fairificator>. ## Assessment Scope, Constraint and Limitation The service is **in development** and its assessment depends on several factors. - In the FAIR ecosystem, FAIR assessment must go beyond the object itself. FAIR enabling services and repositories are vital to ensure that research data objects remain FAIR over time. Importantly, machine-readable services (e.g., registries) and documents (e.g., policies) are required to enable automated tests. - In addition to repository and services requirements, automated testing depends on clear machine assessable criteria. Some aspects (rich, plurality, accurate, relevant) specified in FAIR principles still require human mediation and interpretation. -- The tests must focus on generally applicable data/metadata characteristics until domain/community-driven criteria have been agreed (e.g., appropriate schemas and required elements for usage/access control, etc.). For example, for some metrics (i.e., on I and R principles), the automated tests we proposed only inspect the ‘surface’ of criteria to be evaluated. Therefore, tests are designed in consideration of generic cross-domain metadata standards such as dublin core, dcat, datacite, schema.org, etc. -- FAIR assessment is performed based on aggregated metadata; this includes metadata embedded in the data (landing) page, metadata retrieved from a PID provider (e.g., Datacite content negotiation) and other services (e.g., re3data). +- The tests must focus on generally applicable data/metadata characteristics until domain/community-driven criteria have been agreed (e.g., appropriate schemas and required elements for usage/access control, etc.). For example, for some metrics (i.e., on I and R principles), the automated tests we proposed only inspect the ‘surface’ of criteria to be evaluated. Therefore, tests are designed in consideration of generic cross-domain metadata standards such as Dublin Core, DCAT, DataCite, schema.org, etc. +- FAIR assessment is performed based on aggregated metadata; this includes metadata embedded in the data (landing) page, metadata retrieved from a PID provider (e.g., DataCite content negotiation) and other services (e.g., re3data). ![alt text](https://github.com/pangaea-data-publisher/fuji/blob/master/fuji_server/static/main.png?raw=true) @@ -38,9 +38,9 @@ The service is **in development** and its assessment depends on several factors. [Python](https://www.python.org/downloads/) `3.11+` ### Google Dataset Search -* Download the latest Dataset Search corpus file from: https://www.kaggle.com/googleai/dataset-search-metadata-for-datasets +* Download the latest Dataset Search corpus file from: <https://www.kaggle.com/googleai/dataset-search-metadata-for-datasets> * Open file `fuji_server/helper/create_google_cache_db.py` and set variable 'google_file_location' according to the file location of the corpus file -* Run create_google_cache_db.py which creates a SQLite database in the data directory. From root directory run `python3 -m fuji_server.helper.create_google_cache_db`. +* Run `create_google_cache_db.py` which creates a SQLite database in the data directory. From root directory run `python3 -m fuji_server.helper.create_google_cache_db`. The service was generated by the [swagger-codegen](https://github.com/swagger-api/swagger-codegen) project. By using the [OpenAPI-Spec](https://github.com/swagger-api/swagger-core/wiki) from a remote server, you can easily generate a server stub. @@ -55,9 +55,9 @@ To install F-UJI, you may execute the following Python-based or docker-based ins From the fuji source folder run ```bash -pip install . +python -m pip install . ``` -The F-UJI server can now be started with. +The F-UJI server can now be started with: ```bash python -m fuji_server -c fuji_server/config/server.ini ``` @@ -68,17 +68,14 @@ python -m fuji_server -c fuji_server/config/server.ini docker run -d -p 1071:1071 ghcr.io/pangaea-data-publisher/fuji ``` -To access the Swagger user interface, open the URL below in the browser: +To access the Swagger user interface, open the URL below in the browser: + +<http://localhost:1071/fuji/api/v1/ui/> -``` -http://localhost:1071/fuji/api/v1/ui/ -``` Your Swagger definition lives here: -``` -http://localhost:1071/fuji/api/v1/swagger.json -``` +<http://localhost:1071/fuji/api/v1/swagger.json> You can provide a different server config file this way: @@ -95,12 +92,12 @@ docker run -d -p 1071:1071 <tag_name> ### Notes -To avoid tika startup warning message, set environment variable TIKA_LOG_PATH. For more information, see [https://github.com/chrismattmann/tika-python](https://github.com/chrismattmann/tika-python) +To avoid Tika startup warning message, set environment variable `TIKA_LOG_PATH`. For more information, see [https://github.com/chrismattmann/tika-python](https://github.com/chrismattmann/tika-python) -If you receive the exception 'urllib2.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] on MacOS, run the install command shipped with Python : -./Install\ Certificates.command +If you receive the exception `urllib2.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED]` on macOS, run the install command shipped with Python: +`./Install\ Certificates.command`. -F-UJI is using [basic authentication](https://en.wikipedia.org/wiki/Basic_access_authentication), so username and password have to be provided for each REST call which can be configured in fuji_server/config/users.py +F-UJI is using [basic authentication](https://en.wikipedia.org/wiki/Basic_access_authentication), so username and password have to be provided for each REST call which can be configured in `fuji_server/config/users.py`. ## License