Merge pull request #60 from NLeSC/refine4cloud

Refine4cloud

.gitignore

@@ -24,6 +24,4 @@ playground
 .vscode
 
 # Mac
-.DS_Store
-
-data
+.DS_Store

fdp/api/metadata.py

@@ -106,7 +106,11 @@ def put():
         '''
         Update FDP metadata
         '''
-        return make_response({'message': 'Method Not Allowed'}, 405)
+        targetURI = fairgraph.buildURI('FDP')
+        if not fairgraph.URIexists(targetURI):
+            return make_response({'message': 'Not Found'}, 404)
+        fairgraph.deleteURI(targetURI)
+        return httpResponsePost('FDP')
 
 class Metadata():
 
@@ -135,19 +139,21 @@ def put(self, id):
         '''
         Update Catalog metadata
         '''
-        if not fairgraph.URIexists(fairgraph.buildURI(self.layer, id)):
+        targetURI = fairgraph.buildURI(self.layer, id)
+        if not fairgraph.URIexists(targetURI):
             return make_response({'message': 'Not Found'}, 404)
-        fairgraph.deleteURI(fairgraph.buildURI(self.layer, id))
+        fairgraph.deleteURI(targetURI)
         #TODO validate the id of the request body
         return httpResponsePost(self.layer)
 
     def delete(self, id):
         '''
         Delete the catalog ID and metadata
         '''
-        if not fairgraph.URIexists(fairgraph.buildURI(self.layer, id)):
+        targetURI = fairgraph.buildURI(self.layer, id)
+        if not fairgraph.URIexists(targetURI):
             return make_response({'message': 'Not Found'}, 404)
-        fairgraph.deleteURI(fairgraph.buildURI(self.layer, id))
+        fairgraph.deleteURI(targetURI)
         return make_response('', 204)
 
 Catalog = Metadata('Catalog')

fdp/config.py

@@ -2,9 +2,7 @@
 from fdp.fairgraph import FAIRGraph
 
 def build_base_uri(host, port):
-    if host == 'localhost':
-        host = 'http://127.0.0.1'
-    elif not host.startswith('http'):
+    if not host.startswith('http'):
         host = f'http://{host}'
     if int(port) == 80:
         base_uri = host

fdp/openapi/openapi.yaml

@@ -1,12 +1,21 @@
 openapi: 3.0.0
 info:
-  description:
-    Find more about [FAIR Data Point](https://github.com/NLeSC/fairdatapoint).
+  title: FAIR Data Point
   version: "1.0.0"
-  title: FAIR Data Point REST APIs
+  description: FAIR Data Point is a RESTful web service that enables data owners
+     to describe and to expose their datasets (metadata) as well as data users
+     to discover more information about available datasets according to the
+     [FAIR Data Principles](https://www.force11.org/group/fairgroup/fairprinciples).
+  contact:
+    name: Netherlands eScience Center
+    url: https://www.esciencecenter.nl/
+    email: [email protected]
   license:
     name: Apache 2.0
     url: 'http://www.apache.org/licenses/LICENSE-2.0.html'
+externalDocs:
+  description: Find out more about FAIR Data Point
+  url: https://github.com/NLeSC/fairdatapoint
 servers:
   - description: API version 1
     url: /

tests/data/catalog01_update.ttl

@@ -0,0 +1,17 @@
+@prefix schema: <http://schema.org/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix dcat: <http://www.w3.org/ns/dcat#> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix fdp: <http://rdf.biosemantics.org/ontologies/fdp-o#> .
+@prefix dbp: <http://dbpedia.org/resource/> .
+
+<http://0.0.0.0/catalog/catalog01> a dcat:Catalog ;
+    dcterms:title "First sample catalog";
+    dcterms:hasVersion "2.0" ;
+    dcterms:publisher <http://orcid.org/0000-0002-4368-8058> ;
+    dcterms:isPartOf <http://0.0.0.0/fdp> ;
+    fdp:metadataIdentifier <http://example.org/catalog01> ;
+    fdp:metadataIssued "2016-10-27T00:00:00"^^xsd:dateTime ;
+    fdp:metadataModified "2016-10-27T00:00:00"^^xsd:dateTime ;
+    dcat:dataset <dataset/breedb> ;
+    dcat:themeTaxonomy dbp:Breeding .

tests/data/dataset01_update.ttl

@@ -0,0 +1,17 @@
+@prefix schema: <http://schema.org/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix dcat: <http://www.w3.org/ns/dcat#> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix fdp: <http://rdf.biosemantics.org/ontologies/fdp-o#> .
+@prefix dbp: <http://dbpedia.org/resource/> .
+
+<http://0.0.0.0/dataset/breedb> a dcat:Dataset ;
+    dcterms:title "BreeDB tomato passport dataset"^^xsd:string ;
+    dcterms:publisher <http://orcid.org/0000-0002-4368-8058> ;
+    dcterms:hasVersion "2.0"^^xsd:string ;
+    dcterms:isPartOf <http://0.0.0.0/catalog/catalog01> ;
+    fdp:metadataIdentifier <http://example.org/dataset01> ;
+    fdp:metadataIssued "2016-10-27T09:30:00"^^xsd:dateTime ;
+    fdp:metadataModified "2016-10-27T09:30:00"^^xsd:dateTime ;
+    dcat:distribution <http://0.0.0.0/distribution/breedb-sparql> ;
+    dcat:theme dbp:Plant_breeding .

tests/data/dist01_update.ttl

@@ -0,0 +1,15 @@
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix dcat: <http://www.w3.org/ns/dcat#> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix fdp: <http://rdf.biosemantics.org/ontologies/fdp-o#> .
+
+<http://0.0.0.0/distribution/breedb-sparql> a dcat:Distribution ;
+    dcterms:title "SPARQL endpoint for BreeDB tomato passport data"^^xsd:string ;
+    dcterms:license <http://rdflicense.appspot.com/rdflicense/cc-by-nc-nd3.0> ;
+    dcterms:hasVersion "2.0"^^xsd:string ;
+    dcterms:isPartOf <http://0.0.0.0/dataset/breedb> ;
+    fdp:metadataIdentifier <http://example.org/dist_breedb-sparql> ;
+    fdp:metadataIssued "2016-10-27T09:30:00"^^xsd:dateTime ;
+    fdp:metadataModified "2016-10-27T09:30:00"^^xsd:dateTime ;
+    dcat:mediaType "application/n-triples"^^xsd:string ;
+    dcat:accessURL <http://virtuoso.biotools.nl:8888/sparql> .

tests/data/fdp_update.ttl

@@ -0,0 +1,24 @@
+@prefix ex: <http://example.com/ns#> .
+@prefix fdp: <http://rdf.biosemantics.org/ontologies/fdp-o#> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix lang: <http://id.loc.gov/vocabulary/iso639-1/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix r3d: <http://www.re3data.org/schema/3-0#> .
+
+<http://0.0.0.0/fdp> a r3d:Repository;
+    dcterms:title "FAIR Data Point service of Plant Breeding group at Wageningen University and Research.";
+    dcterms:title "FAIR Data Point service van Plant Breeding group van Wageningen University and Research."@nl;
+    dcterms:hasVersion "0.2";
+    dcterms:description "This service provides machine-readable descriptions about available datasets (metadata).";
+    dcterms:publisher <http://orcid.org/0000-0003-1711-7961> ;
+    dcterms:language lang:en ;
+    dcterms:conformsTo <https://github.com/FAIRDataTeam/FAIRDataPoint-Spec> ;
+    fdp:metadataIdentifier ex:fdp;
+    fdp:metadataIssued "2019-04-09T10:01:00"^^xsd:dateTime;
+    fdp:metadataModified "2019-05-10T09:00:00"^^xsd:dateTime;
+    rdfs:label "FAIR Data Point service of Plant Breeding group at Wageningen University and Research.";
+    r3d:dataCatalog
+        <http://0.0.0.0/catalog/catalog01>,
+        <http://0.0.0.0/catalog/catalog02>;
+    r3d:repositoryIdentifier ex:fdp_repositoryID .

tests/test_endpoints.py

@@ -24,7 +24,7 @@ class TestBaseEndpointTests:
 
     # datadir fixture provided via pytest-datadir-ng
     def test_fdp(self, client, datadir):
-        """Testing post and get to fdp"""
+        """Testing post, get and put to fdp"""
         rv = client.post('/fdp', data=datadir['fdp.ttl'])
         assert rv.status_code == 200
         assert 'message' in rv.json
@@ -38,6 +38,15 @@ def test_fdp(self, client, datadir):
         assert b'hasVersion "0.1"' in rv.data
         assert b'metadataIssued "2019-04-09T10:01:00"^^xsd:dateTime' in rv.data
 
+        rv = client.put('/fdp', data=datadir['fdp_update.ttl'])
+        assert rv.status_code == 200
+        assert 'message' in rv.json
+        assert rv.json['message'] == 'Ok'
+
+        rv = client.get('/fdp')
+        assert rv.status_code == 200
+        assert b'hasVersion "0.2"' in rv.data
+
         rv = client.delete('/fdp')
         assert rv.status_code == 405
 
@@ -80,7 +89,7 @@ def test_fdp_invalid(self, client, datadir):
         assert 'Not allowed RDF type for layer FDP' in rv.json['message']
 
     def test_catalog(self, client, datadir):
-        """Testing post and get to catalog"""
+        """Testing post, get, put and delete to catalog"""
         rv = client.post('/catalog', data=datadir['catalog01.ttl'])
         assert rv.status_code == 200
         assert rv.json['message'] == 'Ok'
@@ -102,6 +111,18 @@ def test_catalog(self, client, datadir):
         assert 'GET' in rv.headers['Allow']
         assert rv.mimetype == 'text/turtle'
         assert b'catalog01' in rv.data
+        assert b'hasVersion "1.0"' in rv.data
+
+        rv = client.put('/catalog/catalog01', data=datadir['catalog01_update.ttl'])
+        # assert rv.status_code == 200
+        # assert rv.json['message'] == 'Ok'
+        print(rv.data)
+        assert rv.json['message'] == 'Ok'
+
+        rv = client.get('/catalog/catalog01')
+        assert rv.status_code == 200
+        assert b'catalog01' in rv.data
+        assert b'hasVersion "2.0"' in rv.data
 
         rv = client.delete('/catalog/catalog01')
         assert rv.status_code == 204
@@ -111,6 +132,11 @@ def test_catalog(self, client, datadir):
         assert 'message' in rv.json
         assert rv.json['message'] == 'Not Found'
 
+        rv = client.put('/catalog/catalog01', data=datadir['catalog01_update.ttl'])
+        assert rv.status_code == 404
+        assert 'message' in rv.json
+        assert rv.json['message'] == 'Not Found'
+
         rv = client.delete('/catalog/catalog01')
         assert rv.status_code == 404
         assert 'message' in rv.json
@@ -134,7 +160,7 @@ def test_catalog_invalid(self, client, datadir):
         assert 'Validation Report\nConforms: False\nResults (9)' in rv.json['message']
 
     def test_dataset(self, client, datadir):
-        """Testing post and get to dataset"""
+        """Testing post, get, put and delete to dataset"""
         rv = client.post('/dataset', data=datadir['dataset01.ttl'])
         assert rv.status_code == 200
         assert rv.json['message'] == 'Ok'
@@ -155,6 +181,16 @@ def test_dataset(self, client, datadir):
         assert 'GET' in rv.headers['Allow']
         assert rv.mimetype == 'text/turtle'
         assert b'breedb' in rv.data
+        assert b'hasVersion "1.0"' in rv.data
+
+        rv = client.put('/dataset/breedb', data=datadir['dataset01_update.ttl'])
+        assert rv.status_code == 200
+        assert rv.json['message'] == 'Ok'
+
+        rv = client.get('/dataset/breedb', )
+        assert rv.status_code == 200
+        assert b'breedb' in rv.data
+        assert b'hasVersion "2.0"' in rv.data
 
         rv = client.delete('/dataset/breedb')
         assert rv.status_code == 204
@@ -164,6 +200,11 @@ def test_dataset(self, client, datadir):
         assert 'message' in rv.json
         assert rv.json['message'] == 'Not Found'
 
+        rv = client.put('/dataset/breedb', data=datadir['dataset01_update.ttl'])
+        assert rv.status_code == 404
+        assert 'message' in rv.json
+        assert rv.json['message'] == 'Not Found'
+
         rv = client.delete('/dataset/breedb')
         assert rv.status_code == 404
         assert 'message' in rv.json
@@ -187,7 +228,7 @@ def test_dataset_invalid(self, client, datadir):
         assert 'Validation Report\nConforms: False\nResults (9)' in rv.json['message']
 
     def test_distribution(self, client, datadir):
-        """Testing post and get to distribution"""
+        """Testing post, get, put and delete to distribution"""
 
         rv = client.post('/distribution', data=datadir['dist01.ttl'])
         assert rv.status_code == 200
@@ -209,6 +250,16 @@ def test_distribution(self, client, datadir):
         assert 'GET' in rv.headers['Allow']
         assert rv.mimetype == 'text/turtle'
         assert b'breedb-sparql' in rv.data
+        assert b'hasVersion "1.0"' in rv.data
+
+        rv = client.put('/distribution/breedb-sparql', data=datadir['dist01_update.ttl'])
+        assert rv.status_code == 200
+        assert rv.json['message'] == 'Ok'
+
+        rv = client.get('/distribution/breedb-sparql')
+        assert rv.status_code == 200
+        assert b'breedb-sparql' in rv.data
+        assert b'hasVersion "2.0"' in rv.data
 
         rv = client.delete('/distribution/breedb-sparql')
         assert rv.status_code == 204
@@ -218,6 +269,11 @@ def test_distribution(self, client, datadir):
         assert 'message' in rv.json
         assert rv.json['message'] == 'Not Found'
 
+        rv = client.put('/distribution/breedb-sparql', data=datadir['dist01_update.ttl'])
+        assert rv.status_code == 404
+        assert 'message' in rv.json
+        assert rv.json['message'] == 'Not Found'
+
         rv = client.get('/distribution')
         assert rv.status_code == 200
         assert b'breedb-sparql' not in rv.data