fdpAPIconnector.py

Python package for communictaion with a FairDataPoint (FDP) API. This is based on the fairdatapoint-client api client but adapted for FAIRDataTeam/FAIRDataPoint. You can find the fdpAPIconnector package on PyPI.

Install

pip install fdpAPIconnector

Usage

Import the FDPClient within your Python or Jupyter script.

from fdpAPIconnector.fdpclient import FDPClient

Create an instance of the client and login

fdp_baseurl = "http://localhost:8088"
email = "abmin@FDP.org"
password = "SuperSecretePassword"

fdpclient=FDPClient(fdp_baseurl,email,password)

You can also use an api_token

fdpclient=FDPClient(fdp_baseurl,api_token = 'APITOKEN123456789')

You may change the templates used for catalogs, datasets and distributions

fdpclient=FDPClient(fdp_baseurl,email,password,
                    catalog_template='./<pathToTemplates>/catalog_template.ttl',
                    dataset_template='./<pathToTemplates>/dataset_template.ttl,
                    distribution_template='./<pathToTemplates>/distribution_template.ttl
                    )

Create a new Catalog

newcat=fdpclient.createCatalogRDF(DESCRIPTION='My First Catalog',
                               title='My First Catalog',
                               version="1.0.0",
                               ispartof=fdpclient.publicurl,
                               publisher='Projectmanagementteam',
                               LANGUAGE='http://id.loc.gov/vocabulary/iso639-1/en',
                               HOMEPAGE=fdpclient.baseurl)

pprint(newcat)
id=fdpclient.create(type='catalog',data=newcat)
print(id)

Read the created Catalog

cat_meta=fdpclient.read(type='catalog',id=id)
pprint(cat_meta.serialize(format="turtle"))

Update/Modify the created catalog

fdpclient.update(type='catalog', id=id, data=modified.cat_meta.serialize(format="turtle"))

Publish the created catalog

sate_published=json.dumps({"current":"PUBLISHED"})

fdpclient.update(type='catalog',id=id,subtype='meta/state',data=sate_published,format="json-ld")

Delete the created catalog

fdpclient.delete(type='catalog',id=id)

All functions are also available for datasets and distributions e.g. create:

newdat=fdpclient.createDatasetRDF(title="COVAC-DM Study",
                               version="1.0.0",
                               catalogid=id,
                               publishername="Projectmanagementteam",
                               ISSUED=datetime.datetime.now(),
                               MODIFIED=datetime.datetime.now(),
                               LANGUAGE='http://id.loc.gov/vocabulary/iso639-1/en',
                               KEYWORDS=["diabetes mellitus type 1","diabetes mellitus type 2","COVID-19"],
                               DESCRIPTION="<https://biobank.medunigraz.at/.../biobank/pdf/Kohorten/5006_21_COVAC-DM_Study.pdf>",
                               CONTACTPOINT = "patrick.nitsche@medunigraz.at",
                               themes_list=["http://www.w3.org/ns/dcat#theme","http://identifiers.org/icd/Q87.8"])

newdis=fdpclient.createDistributionRDF(title="Distribution", # HTML distribution
                               version="1.0.0",
                               datasetid=dat_id,
                               publishername="Projectmanagementteam",
                               ISSUED=datetime.datetime.now(),
                               MODIFIED=datetime.datetime.now(),
                               LANGUAGE='http://id.loc.gov/vocabulary/iso639-1/en',
                               mediatype="WSI", #text/html
                               FORMAT="SVS",
                               BYTESIZE="10737418240",
                               ACCESSURL="https://youtu.be/dQw4w9WgXcQ", # URL of OS
                               DOWNLOADURL="http://download.url")
dat_id=fdpclient.create(type='dataset',data=newdat)
dis_id=fdpclient.create(type='distribution',data=newdis)

Subtypes

E.g. Get metadata (memberships and state) for Catalog

cat_meta_state=fdpclient.read(type='catalog',id=id,subtype='meta')

Templates

Templates are used to create the RDF turtle format for the FDP resources. You might want to use your own templates:

fdpclient=FDPClient(fdp_baseurl,email,password,
                    catalog_template='./templates/catalog_template.ttl',
                    dataset_template='./templates/dataset_template.ttl',
                    distribution_template='./templates/distribution_template.ttl')

The template should look like this:

# default_catalog_template

@prefix dcat: <http://www.w3.org/ns/dcat#>.
@prefix dct: <http://purl.org/dc/terms/>.
@prefix foaf: <http://xmlns.com/foaf/0.1/>.
@prefix loc: <§§BASEURL/>.
@prefix n0: <http://>.

loc:new
    a dcat:Catalog, dcat:Resource;
    dct:description "§§DESCRIPTION";
    dct:hasVersion "§§VERSION";
    dct:isPartOf <§§ISPARTOF>;
    dct:language <§§LANGUAGE>;
    dct:license <§§LICENSE>;
    dct:publisher [ a foaf:Agent; foaf:name "§§PUBLISHERNAME"];
    dct:rights <§§RIGHTS>;
    dct:title "§§TITLE";
    foaf:homePage <§§HOMEPAGE>;
    .

Variables that will be replaced have the prefix §§.

You might want to extend the information of the publisher:

Important you should only have one variable per line because each line containing a variable that was not set is thrown out.

@prefix dcat: <http://www.w3.org/ns/dcat#>.
@prefix dct: <http://purl.org/dc/terms/>.
@prefix foaf: <http://xmlns.com/foaf/0.1/>.
@prefix loc: <§§BASEURL/>.
@prefix n0: <http://>.

loc:new
    a dcat:Catalog, dcat:Resource;
    dct:description "§§DESCRIPTION";
    dct:hasVersion "§§VERSION";
    dct:isPartOf <§§ISPARTOF>;
    dct:language <§§LANGUAGE>;
    dct:license <§§LICENSE>;
    dct:publisher [ a foaf:Agent; foaf:name "§§PUBLISHERNAME"; 
                                  rdf:Description [
                                      vcard:hasEmail [rdf:resource "§§PUBLISHEREMAIL"]; 
                                      vcard:hasUID [rdf:resource "§§PUBLISHERUID"]
                                  ]
                  ];
    dct:rights <§§RIGHTS>;
    dct:title "§§TITLE";
    foaf:homePage <§§HOMEPAGE>;
    .

Build and upload to PyPI

# Intsall build and twine
python3 -m pip install --upgrade build
python3 -m pip install --upgrade twine

# Build the package
python3 -m build

# to test the package first 
python3 -m twine upload --repository testpypi dist/*
python3 -m pip install --index-url https://test.pypi.org/simple/ --no-deps fdpAPIconnector

# upload the package
python3 -m twine upload dist/*
# username: __token__
# password: For the password, use the token value, including the pypi- prefix

TODOs

• allow "login" via api-token instead of email and password
• auto check for strings and urls(or iri) for RDF turtle creation
• Create a nice documentation