Merge pull request #25 from fair-workflows/use-test-endpoint

Use test endpoint

conftest.py

@@ -1,3 +1,9 @@
+import pytest
+import requests
+
+from nanopub.nanopub import NANOPUB_TEST_GRLC_URL
+
+
 def pytest_addoption(parser):
     parser.addoption('--no_rsa_key', action='store_true', default=False,
                      help="enable no_rsa_key decorated tests")
@@ -6,3 +12,8 @@ def pytest_addoption(parser):
 def pytest_configure(config):
     if not config.option.no_rsa_key:
         setattr(config.option, 'markexpr', 'not no_rsa_key')
+
+
+skip_if_nanopub_server_unavailable = (
+    pytest.mark.skipif(requests.get(NANOPUB_TEST_GRLC_URL).status_code != 200,
+                       reason='Nanopub server is unavailable'))

nanopub/java_wrapper.py

@@ -4,18 +4,28 @@
 from typing import Union
 
 import rdflib
+import requests
 
 from nanopub.definitions import PKG_FILEPATH
 
 # Location of nanopub tool (currently shipped along with the lib)
 NANOPUB_SCRIPT = str(PKG_FILEPATH / 'np')
+NANOPUB_TEST_SERVER = 'http://test-server.nanopubs.lod.labs.vu.nl/'
 
 
 class JavaWrapper:
     """
     Wrapper around 'np' java tool that is used to sign and publish nanopublications to
     a nanopub server.
     """
+    def __init__(self, use_test_server=False):
+        """Construct JavaWrapper.
+
+        Args:
+            use_test_server: Toggle using the test nanopub server.
+        """
+        self.use_test_server = use_test_server
+
     @staticmethod
     def _run_command(command):
         result = subprocess.run(command, shell=True, stderr=subprocess.PIPE)
@@ -33,7 +43,20 @@ def sign(self, unsigned_file: Union[str, Path]) -> str:
         return self._get_signed_file(unsigned_file)
 
     def publish(self, signed: str):
-        self._run_command(f'{NANOPUB_SCRIPT} publish ' + signed)
+        """ Publish.
+
+        Publish the signed nanopub to the nanopub server. Publishing to the real server depends
+        on nanopub-java, for the test server we do a simple POST request.
+
+        TODO: Use nanopub-java for publishing to test once it supports it.
+        """
+        if self.use_test_server:
+            headers = {'content-type': 'application/x-www-form-urlencoded'}
+            with open(signed, 'rb') as data:
+                r = requests.post(NANOPUB_TEST_SERVER, headers=headers, data=data)
+            r.raise_for_status()
+        else:
+            self._run_command(f'{NANOPUB_SCRIPT} publish ' + signed)
         return self.extract_nanopub_url(signed)
 
     @staticmethod
@@ -47,5 +70,4 @@ def extract_nanopub_url(signed: Union[str, Path]):
     @staticmethod
     def _get_signed_file(unsigned_file: str):
         unsigned_file = Path(unsigned_file)
-
         return str(unsigned_file.parent / f'signed.{unsigned_file.name}')

nanopub/nanopub.py

@@ -19,6 +19,7 @@
                      "https://grlc.nanopubs.knows.idlab.ugent.be/api/local/local/",
                      "http://grlc.np.scify.org/api/local/local/",
                      "http://grlc.np.dumontierlab.com/api/local/local/"]
+NANOPUB_TEST_GRLC_URL = 'http://test-grlc.nanopubs.lod.labs.vu.nl/api/local/local/'
 DEFAULT_URI = 'http://purl.org/nanopub/temp/mynanopub'
 
 
@@ -206,9 +207,18 @@ class NanopubClient:
     Provides utility functions for searching, creating and publishing RDF graphs
     as assertions in a nanopublication.
     """
-    def __init__(self):
-        self.java_wrapper = JavaWrapper()
-        self.grlc_urls = NANOPUB_GRLC_URLS
+    def __init__(self, use_test_server=False):
+        """Construct NanopubClient.
+
+        Args:
+            use_test_server: Toggle using the test nanopub server.
+        """
+        self.use_test_server = use_test_server
+        self.java_wrapper = JavaWrapper(use_test_server=use_test_server)
+        if use_test_server:
+            self.grlc_urls = [NANOPUB_TEST_GRLC_URL]
+        else:
+            self.grlc_urls = NANOPUB_GRLC_URLS
 
     def find_nanopubs_with_text(self, text, max_num_results=1000):
         """

tests/test_java_wrapper.py

@@ -3,6 +3,7 @@
 
 import pytest
 
+from conftest import skip_if_nanopub_server_unavailable
 from nanopub.definitions import TEST_RESOURCES_FILEPATH
 from nanopub.java_wrapper import JavaWrapper
 
@@ -49,3 +50,11 @@ def test_sign_nanopub_no_rsa_key(tmp_path):
     with pytest.raises(RuntimeError) as e:
         java_wrapper.sign(unsigned_file=temp_unsigned_file)
     assert 'RSA key appears to be missing' in str(e.value)
+
+
+@pytest.mark.flaky(max_runs=10)
+@skip_if_nanopub_server_unavailable
+def test_publish():
+    java_wrapper = JavaWrapper(use_test_server=True)
+    pubinfo = java_wrapper.publish(NANOPUB_SAMPLE_SIGNED)
+    assert pubinfo

tests/test_nanopub.py

@@ -1,19 +1,13 @@
 from unittest import mock
-from unittest.mock import patch
 
 import pytest
 import rdflib
-import requests
 from rdflib.namespace import RDF
 
-from nanopub import NanopubClient, namespaces
-from nanopub.nanopub import Nanopub
+from conftest import skip_if_nanopub_server_unavailable
+from nanopub import NanopubClient, namespaces, Nanopub
 
-skip_if_nanopub_server_unavailable = (
-    pytest.mark.skipif(requests.get('http://grlc.nanopubs.lod.labs.vu.nl/').status_code != 200,
-                       reason='Nanopub server is unavailable'))
-
-client = NanopubClient()
+client = NanopubClient(use_test_server=True)
 
 def test_nanopub_construction_with_bnode_introduced_concept():
     """
@@ -34,13 +28,14 @@ def test_nanopub_construction_with_bnode_introduced_concept():
         )
     assert str(nanopub.introduces_concept) == test_concept_uri
 
+
 @pytest.mark.flaky(max_runs=10)
 @skip_if_nanopub_server_unavailable
 def test_find_nanopubs_with_text():
     """
     Check that Nanopub text search is returning results for a few common search terms
     """
-    searches = ['fair', 'heart']
+    searches = ['test', 'US']
 
     for search in searches:
         results = client.find_nanopubs_with_text(search)
@@ -49,15 +44,28 @@ def test_find_nanopubs_with_text():
     assert len(client.find_nanopubs_with_text('')) == 0
 
 
+@pytest.mark.flaky(max_runs=10)
+def test_find_nanopubs_with_text_prod():
+    """
+    Check that Nanopub text search is returning results for a few common search terms on the
+    production nanopub server
+    """
+    prod_client = NanopubClient()
+    searches = ['test', 'US']
+    for search in searches:
+        results = prod_client.find_nanopubs_with_text(search)
+        assert len(results) > 0
+
+
 @pytest.mark.flaky(max_runs=10)
 @skip_if_nanopub_server_unavailable
 def test_find_nanopubs_with_pattern():
     """
         Check that Nanopub pattern search is returning results
     """
     searches = [
-        ('', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'https://www.omg.org/spec/BPMN/scriptTask'),
-        ('http://purl.org/np/RANhYfdZCVDQr8ItxDYCZWhvBhzjJTs9Cq-vPnmSBDd5g', '', '')
+        ('', 'http://example.org/transmits', 'http://example.org/malaria'),
+        ('http://purl.org/np/RA8ui7ddvV25m1qdyxR4lC8q8-G0yb3SN8AC0Bu5q8Yeg', '', '')
     ]
 
     for subj, pred, obj in searches:
@@ -68,18 +76,12 @@ def test_find_nanopubs_with_pattern():
 
 @pytest.mark.flaky(max_runs=10)
 @skip_if_nanopub_server_unavailable
-def test_nanopub_search_things():
+def test_nanopub_find_things():
     """
-        Check that Nanopub 'find_things' search is returning results
+    Check that Nanopub 'find_things' search is returning results
     """
-    searches = [
-        'http://dkm.fbk.eu/index.php/BPMN2_Ontology#ManualTask',
-        'http://purl.org/net/p-plan#Plan'
-    ]
-
-    for thing_type in searches:
-        results = client.find_things(type=thing_type)
-        assert len(results) > 0
+    results = client.find_things(type='http://purl.org/net/p-plan#Plan')
+    assert len(results) > 0
 
     with pytest.raises(Exception):
         client.find_things()