diff --git a/Dockerfile b/Dockerfile index ebc5ca80..7f4045b6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # syntax=docker/dockerfile:1.5 -FROM python:3.8-slim +FROM python:3.11-slim WORKDIR /usr/src/app diff --git a/README.md b/README.md index e4c09c8a..000f224c 100644 --- a/README.md +++ b/README.md @@ -8,8 +8,8 @@ Developers: [Robert Huber](mailto:rhuber@marum.de), [Anusuriya Devaraju](mailto: ## Overview -F-UJI is a web service to programatically assess FAIRness of research data objects based on [metrics](https://doi.org/10.5281/zenodo.3775793) developed by the [FAIRsFAIR](https://www.fairsfair.eu/) project. -The service will be applied to demostrate the evaluation of objects in repositories selected for in-depth collaboration with the project. +F-UJI is a web service to programatically assess FAIRness of research data objects based on [metrics](https://doi.org/10.5281/zenodo.3775793) developed by the [FAIRsFAIR](https://www.fairsfair.eu/) project. +The service will be applied to demostrate the evaluation of objects in repositories selected for in-depth collaboration with the project. The '__F__' stands for FAIR (of course) and '__UJI__' means 'Test' in Malay. So __F-UJI__ is a FAIR testing tool. @@ -26,20 +26,16 @@ An R client package that was generated from the F-UJI OpenAPI definition is avai 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 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 of the 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) ## Requirements -Python 3.8+ - -### 308 redirects -In order to deal with 308 redirects, the following patch has to be applied on urrlib: -https://github.com/python/cpython/pull/19588/commits +[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 @@ -47,7 +43,7 @@ https://github.com/python/cpython/pull/19588/commits * 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. +[OpenAPI-Spec](https://github.com/swagger-api/swagger-core/wiki) from a remote server, you can easily generate a server stub. The service uses the [Connexion](https://github.com/spec-first/connexion) library on top of Flask. ## Usage diff --git a/pyproject.toml b/pyproject.toml index b7b7395a..5dacd299 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,9 +11,8 @@ classifiers = [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.11", "Topic :: Scientific/Engineering :: Information Analysis" ] dependencies = [ @@ -58,7 +57,7 @@ keywords = [ license = "MIT" name = "fuji" readme = "README.md" -requires-python = ">=3.8" +requires-python = ">=3.11" version = "3.0.0" [project.optional-dependencies] @@ -94,7 +93,7 @@ Source = "https://github.com/pangaea-data-publisher/fuji" [tool.black] line-length = 120 -target_version = ["py38", "py39", "py310", "py311"] +target_version = ["py311"] [tool.coverage.report] skip_empty = true @@ -144,7 +143,7 @@ line-length = 120 select = [ "I" # isort ] -target-version = "py38" +target-version = "py311" [tool.ruff.isort] known-first-party = ["fuji_server", "tests"] diff --git a/tests/controllers/cassettes/test_fair_check/test_harvest_all_metadata.yaml b/tests/controllers/cassettes/test_fair_check/test_harvest_all_metadata.yaml index f3b3109d..91ba6860 100644 --- a/tests/controllers/cassettes/test_fair_check/test_harvest_all_metadata.yaml +++ b/tests/controllers/cassettes/test_fair_check/test_harvest_all_metadata.yaml @@ -443,7 +443,7 @@ interactions: body: headers: Accept: - - text/turtle, application/turtle, application/x-turtle;q=0.8, application/rdf+xml, text/n3;q=0.9, text/rdf+n3;q=0.9,application/ld+json + - application/ld+json Connection: - close Host: @@ -585,6 +585,60 @@ interactions: status: code: 422 message: Unprocessable Entity +- request: + body: + headers: + Accept: + - text/turtle, application/turtle, application/x-turtle;q=0.8, application/rdf+xml, text/n3;q=0.9, text/rdf+n3;q=0.9,application/ld+json + Connection: + - close + Host: + - doi.pangaea.de + User-Agent: + - F-UJI + method: GET + uri: https://doi.pangaea.de/10.1594/PANGAEA.902845 + response: + body: + string: '{"@context":"http://schema.org/","@id":"https://doi.org/10.1594/PANGAEA.902845","@type":"Dataset","identifier":"https://doi.org/10.1594/PANGAEA.902845","url":"https://doi.pangaea.de/10.1594/PANGAEA.902845","creator":[{"@id":"https://orcid.org/0000-0001-5130-5494","@type":"Person","name":"Konrad Bärfuss","familyName":"Bärfuss","givenName":"Konrad","identifier":"https://orcid.org/0000-0001-5130-5494","email":"k.baerfuss@tu-bs.de"},{"@type":"Person","name":"Rudolf Hankers","familyName":"Hankers","givenName":"Rudolf","email":"r.hankers@tu-bs.de"},{"@type":"Person","name":"Mark Bitter","familyName":"Bitter","givenName":"Mark","email":"mark.bitter@tu-bs.de"},{"@type":"Person","name":"Thomas Feuerle","familyName":"Feuerle","givenName":"Thomas","email":"t.feuerle@tu-bs.de"},{"@type":"Person","name":"Helmut Schulz","familyName":"Schulz","givenName":"Helmut"},{"@type":"Person","name":"Thomas Rausch","familyName":"Rausch","givenName":"Thomas","email":"thomas.rausch@tu-bs.de"},{"@id":"https://orcid.org/0000-0002-9276-3587","@type":"Person","name":"Andreas Platis","familyName":"Platis","givenName":"Andreas","identifier":"https://orcid.org/0000-0002-9276-3587","email":"andreas.platis@uni-tuebingen.de"},{"@id":"https://orcid.org/0000-0003-4075-1573","@type":"Person","name":"Jens Bange","familyName":"Bange","givenName":"Jens","identifier":"https://orcid.org/0000-0003-4075-1573","email":"jens.bange@uni-tuebingen.de"},{"@id":"https://orcid.org/0000-0003-1414-1616","@type":"Person","name":"Astrid Lampert","familyName":"Lampert","givenName":"Astrid","identifier":"https://orcid.org/0000-0003-1414-1616","url":"https://www.tu-braunschweig.de/ilr/dasinstitut/mitarbeiter/ehemaligemitarbeiter/astridlampert","email":"astrid.lampert@tu-bs.de"}],"name":"In-situ airborne measurements of atmospheric and sea surface parameters related to offshore wind parks in the German Bight","publisher":{"@type":"Organization","name":"PANGAEA","disambiguatingDescription":"Data Publisher for Earth & Environmental Science","url":"https://www.pangaea.de/"},"includedInDataCatalog":{"@type":"DataCatalog","name":"PANGAEA","disambiguatingDescription":"Data Publisher for Earth & Environmental Science","url":"https://www.pangaea.de/"},"datePublished":"2019-06-21","description":"Offshore wind parks interact with the marine atmospheric boundary layer and can create long downstream wakes of reduced wind speed and changed turbulence. 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The aircraft recorded in-situ meteorological parameters (wind vector, temperature, humidity) and sea surface properties (temperature, elevation standard deviation)\nThe flights comprise vertical soundings and straight legs upstream, downstream and above wind parks for different synoptic conditions.\n\n\nPlatis\nAndreas\nandreas.platis@uni-tuebingen.de\n0000-0002-9276-3587\n\n\nSiedersleben\nSimon K\n0000-0002-8467-1471\n\n\nBange\nJens\njens.bange@uni-tuebingen.de\n0000-0003-4075-1573\n\n\nLampert\nAstrid\nastrid.lampert@tu-bs.de\nhttps://www.tu-braunschweig.de/ilr/dasinstitut/mitarbeiter/ehemaligemitarbeiter/astridlampert\n0000-0003-1414-1616\n\n\nBärfuss\nKonrad\nk.baerfuss@tu-bs.de\n0000-0001-5130-5494\n\n\nHankers\nRudolf\nr.hankers@tu-bs.de\n\n\nCañadillas\nBeatriz\nb.canadillas@tu-bs.de\n0000-0003-2004-0336\n\n\nForeman\nRichard\n\n\nSchulz-Stellenfleth\nJohannes\n\n\nDjath\nBughsin\n0000-0002-1121-5272\n\n\nNeumann\nThomas\nthomas.neumann@io-warnemuende.de\n\n\nEmeis\nStefan\n0000-0001-6114-6212\n\n2018\nFirst in situ evidence of wakes in the far field behind offshore wind farms\nScientific Reports\n8(1)\nhttps://doi.org/10.1038/s41598-018-20389-y\n\n\n\nSiedersleben\nSimon K\n0000-0002-8467-1471\n\n\nLundquist\nJulie K\n0000-0001-5490-2702\n\n\nPlatis\nAndreas\nandreas.platis@uni-tuebingen.de\n0000-0002-9276-3587\n\n\nBange\nJens\njens.bange@uni-tuebingen.de\n0000-0003-4075-1573\n\n\nBärfuss\nKonrad\nk.baerfuss@tu-bs.de\n0000-0001-5130-5494\n\n\nLampert\nAstrid\nastrid.lampert@tu-bs.de\nhttps://www.tu-braunschweig.de/ilr/dasinstitut/mitarbeiter/ehemaligemitarbeiter/astridlampert\n0000-0003-1414-1616\n\n\nCañadillas\nBeatriz\nb.canadillas@tu-bs.de\n0000-0003-2004-0336\n\n\nNeumann\nThomas\nthomas.neumann@io-warnemuende.de\n\n\nEmeis\nStefan\n0000-0001-6114-6212\n\n2018\nMicrometeorological impacts of offshore wind farms as seen in observations and simulations\nEnvironmental Research Letters\n13(12)\nhttps://doi.org/10.1088/1748-9326/aaea0b\n124012\n\n\n\nSiedersleben\nSimon K\n0000-0002-8467-1471\n\n\nPlatis\nAndreas\nandreas.platis@uni-tuebingen.de\n0000-0002-9276-3587\n\n\nLundquist\nJulie K\n0000-0001-5490-2702\n\n\nLampert\nAstrid\nastrid.lampert@tu-bs.de\nhttps://www.tu-braunschweig.de/ilr/dasinstitut/mitarbeiter/ehemaligemitarbeiter/astridlampert\n0000-0003-1414-1616\n\n\nBärfuss\nKonrad\nk.baerfuss@tu-bs.de\n0000-0001-5130-5494\n\n\nCañadillas\nBeatriz\nb.canadillas@tu-bs.de\n0000-0003-2004-0336\n\n\nDjath\nBughsin\n0000-0002-1121-5272\n\n\nSchulz-Stellenfleth\nJohannes\n\n\nBange\nJens\njens.bange@uni-tuebingen.de\n0000-0003-4075-1573\n\n\nNeumann\nThomas\nthomas.neumann@io-warnemuende.de\n\n\nEmeis\nStefan\n0000-0001-6114-6212\n\n2018\nEvaluation of a Wind Farm Parametrization for Mesoscale Atmospheric Flow Models with Aircraft Measurements\nMeteorologische Zeitschrift\n27(5)\nhttps://doi.org/10.1127/metz/2018/0900\n401-415\n\n\n\n6.516988\n9.158623\n53.452294\n54.993339\n7.542532644354501\n54.10945427946413\n\n\n2016-09-06T12:13:11\n2017-10-15T15:51:13\n\nnot specified\n\n\nWIPAFF\nWind Park Far Field\n\n\n\nFederal Ministry for Economic Affairs and Energy\nBMWi\nhttps://www.bmwi.de/Navigation/EN/Home/home.html\nhttps://doi.org/10.13039/501100006360\n\n0325783B\nWind Park Far Field / Wind Plant Far Field\nhttps://foerderportal.bund.de/foekat/jsp/SucheAction.do?actionMode=view&fkz=0325783B\n\n41\n\nCC-BY-4.0\nCreative Commons Attribution 4.0 International\nhttps://creativecommons.org/licenses/by/4.0/\n\naircraft north | Aircraft velocity, absolute north-south components | Aircraft vel V | aircraft east | Aircraft velocity, absolute east-west components | Aircraft vel U | aircraft down | Aircraft velocity, absolute downward components | Aircraft vel W | Roll angle | Roll | Pitch angle | Pitch | Heading | Head | Pressure, air | Press air | Temperature, air | TTT | Density, air | Density air | Humidity, relative | RH | Dewpoint mirror | Lyman-alpha sensor | northward component | Wind velocity, south-north | V | eastward component | Wind velocity, west-east | U | downward component | Wind velocity, vertical | W | Surface temperature | Surf temp | Radar altitude above ground | Radar altitude | Radar altimeter | Surface elevation, standard deviation | Surf elev std dev | LiDAR (Light Detection And Ranging)\n\ncitable\nairborne measurements\nGerman Bight\nmeteorological parameters\noffshore wind park\nsea surface\nwake\nfeatured\nmethod10325\nmethod10342\nmethod10343\nmethod7376\nparam123717\nparam123718\nparam123719\nparam154943\nparam166609\nparam170894\nparam170895\nparam170896\nparam170897\nparam170898\nparam21892\nparam2219\nparam31368\nparam31369\nparam4610\nparam50171\npi69919\nauthor22721\nauthor32784\nauthor61851\nauthor69919\nauthor69920\nauthor69921\nauthor69922\nauthor69923\nauthor69924\nauthor69925\nauthor69926\nauthor69927\nauthor69928\nauthor69929\nauthor69930\nauthor69931\nauthor70090\naward161\nfunder20684\ngeocode1599\ngeocode1600\ngeocode1601\njournal11153\njournal16727\njournal5064\nlicense21\nproject4330\nref100073\nref100074\nref100075\nterm34421\nterm47227\nterm48504\nterm49558\nterm49559\nterm49560\nterm49561\ntopotype1\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" + string: 10.1594/PANGAEA.902845Bärfuss, KonradKonradBärfuss0000-0001-5130-5494Hankers, RudolfRudolfHankersBitter, MarkMarkBitterFeuerle, ThomasThomasFeuerleSchulz, HelmutHelmutSchulzRausch, ThomasThomasRauschPlatis, AndreasAndreasPlatis0000-0002-9276-3587Bange, JensJensBange0000-0003-4075-1573Lampert, AstridAstridLampert0000-0003-1414-1616In-situ airborne measurements of atmospheric and sea surface parameters related to offshore wind parks in the German BightPANGAEA2019airborne measurementsGerman Bightmeteorological parametersoffshore wind parksea surfacewakeWind Park Far Field (WIPAFF)2016-09-06T12:13:11/2017-10-15T15:51:13enPublication Series of Datasets10.1038/s41598-018-20389-y10.1088/1748-9326/aaea0b10.1127/metz/2018/090041 datasetsapplication/zipCreative Commons Attribution 4.0 InternationalOffshore wind parks interact with the marine atmospheric boundary layer and can create long downstream wakes of reduced wind speed and changed turbulence. During the project WIPAFF (wind park far field) funded by the German Federal Ministry for Economic Affairs and Energy (grant number 0325783B), 41 measurement flights were performed with the research aircraft Dornier-128 of TU Braunschweig between September 2016 and October 2017. The aircraft recorded in-situ meteorological parameters (wind vector, temperature, humidity) and sea surface properties (temperature, elevation standard deviation)
The flights comprise vertical soundings and straight legs upstream, downstream and above wind parks for different synoptic conditions.6.5169889.15862353.45229454.993339Federal Ministry for Economic Affairs and Energyhttps://doi.org/10.13039/5011000063600325783BWind Park Far Field / Wind Plant Far Field headers: Alt-Svc: - h3=":443"; ma=2592000 @@ -703,9 +757,9 @@ interactions: Connection: - close Content-Disposition: - - inline; filename=Baerfuss-etal_2019.panmd.xml + - inline; filename=Baerfuss-etal_2019.datacite.xml Content-Type: - - application/vnd.pangaea.metadata+xml; charset=UTF-8 + - application/vnd.datacite.datacite+xml; charset=UTF-8 Date: - Mon, 25 Sep 2023 18:06:59 GMT Link: @@ -1091,6 +1145,7 @@ interactions: Connection: - close Content-Disposition: + - inline; filename=Baerfuss-etal_2019.datacite.xml Content-Type: - application/vnd.datacite.datacite+xml; charset=UTF-8 diff --git a/tests/functional/cassettes/test_evaluation/test_evaluation.yaml b/tests/functional/cassettes/test_evaluation/test_evaluation.yaml index 24b65d90..3610ff6c 100644 --- a/tests/functional/cassettes/test_evaluation/test_evaluation.yaml +++ b/tests/functional/cassettes/test_evaluation/test_evaluation.yaml @@ -804,7 +804,7 @@ interactions: Referrer-Policy: - strict-origin-when-cross-origin Retry-After: - - '59' + - '60' Server: - nginx Set-Cookie: