Merge branch 'master' into docco_clean

11 files changed, 150 insertions, 15 deletions

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..62f2d35d
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,12 @@
+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: weekly
+  open-pull-requests-limit: 10
+  ignore:
+  - dependency-name: sphinx
+    versions:
+    - 3.4.3
+    - 3.5.2
diff --git a/docs/sphinx-requirements.txt b/docs/sphinx-requirements.txt
index 403eec52..48ba7549 100644
--- a/docs/sphinx-requirements.txt
+++ b/docs/sphinx-requirements.txt
@@ -1,3 +1,3 @@
-sphinx==3.5.4
+sphinx==4.0.1
 sphinxcontrib-apidoc
 git+https://github.com/gniezen/n3pygments.git
diff --git a/rdflib/graph.py b/rdflib/graph.py
index 9d4431bc..d2a5e872 100644
--- a/rdflib/graph.py
+++ b/rdflib/graph.py
@@ -879,11 +879,11 @@ class Graph(Node):
             for rt_2 in self.transitiveClosure(func, rt, seen):
                 yield rt_2
 
-    def transitive_objects(self, subject, property, remember=None):
-        """Transitively generate objects for the ``property`` relationship
+    def transitive_objects(self, subject, predicate, remember=None):
+        """Transitively generate objects for the ``predicate`` relationship
 
         Generated objects belong to the depth first transitive closure of the
-        ``property`` relationship starting at ``subject``.
+        ``predicate`` relationship starting at ``subject``.
         """
         if remember is None:
             remember = {}
@@ -891,15 +891,15 @@ class Graph(Node):
             return
         remember[subject] = 1
         yield subject
-        for object in self.objects(subject, property):
-            for o in self.transitive_objects(object, property, remember):
+        for object in self.objects(subject, predicate):
+            for o in self.transitive_objects(object, predicate, remember):
                 yield o
 
     def transitive_subjects(self, predicate, object, remember=None):
-        """Transitively generate objects for the ``property`` relationship
+        """Transitively generate subjects for the ``predicate`` relationship
 
-        Generated objects belong to the depth first transitive closure of the
-        ``property`` relationship starting at ``subject``.
+        Generated subjects belong to the depth first transitive closure of the
+        ``predicate`` relationship starting at ``object``.
         """
         if remember is None:
             remember = {}
diff --git a/rdflib/plugins/sparql/results/txtresults.py b/rdflib/plugins/sparql/results/txtresults.py
index 426dd9a1..baa5316b 100644
--- a/rdflib/plugins/sparql/results/txtresults.py
+++ b/rdflib/plugins/sparql/results/txtresults.py
@@ -43,7 +43,7 @@ class TXTResultSerializer(ResultSerializer):
             return "(no results)\n"
         else:
 
-            keys = sorted(self.result.vars)
+            keys = self.result.vars
             maxlen = [0] * len(keys)
             b = [
                 [_termString(r[k], namespace_manager) for k in keys]
diff --git a/rdflib/plugins/stores/sparqlstore.py b/rdflib/plugins/stores/sparqlstore.py
index e021e5df..26436f20 100644
--- a/rdflib/plugins/stores/sparqlstore.py
+++ b/rdflib/plugins/stores/sparqlstore.py
@@ -167,7 +167,7 @@ class SPARQLStore(SPARQLConnector, Store):
         self.debug = DEBUG
         assert isinstance(query, str)
 
-        if initNs is not None:
+        if initNs is not None and len(initNs) > 0:
             query = self._inject_prefixes(query, initNs)
 
         if initBindings:
diff --git a/rdflib/term.py b/rdflib/term.py
index 3a822158..0f627e69 100644
--- a/rdflib/term.py
+++ b/rdflib/term.py
@@ -38,7 +38,6 @@ import logging
 import warnings
 import math
 
-import base64
 import xml.dom.minidom
 
 from datetime import date, time, datetime, timedelta
@@ -53,6 +52,7 @@ from isodate import (
     parse_duration,
     duration_isoformat,
 )
+from base64 import b64decode, b64encode
 from binascii import hexlify, unhexlify
 
 import rdflib
@@ -1435,6 +1435,7 @@ _XSD_DAYTIMEDURATION = URIRef(_XSD_PFX + "dayTimeDuration")
 _XSD_YEARMONTHDURATION = URIRef(_XSD_PFX + "yearMonthDuration")
 
 _OWL_RATIONAL = URIRef("http://www.w3.org/2002/07/owl#rational")
+_XSD_B64BINARY = URIRef(_XSD_PFX + "base64Binary")
 _XSD_HEXBINARY = URIRef(_XSD_PFX + "hexBinary")
 # TODO: gYearMonth, gYear, gMonthDay, gDay, gMonth
 
@@ -1559,6 +1560,8 @@ _GenericPythonToXSDRules = [
 _SpecificPythonToXSDRules = [
     ((str, _XSD_HEXBINARY), hexlify),
     ((bytes, _XSD_HEXBINARY), hexlify),
+    ((str, _XSD_B64BINARY), b64encode),
+    ((bytes, _XSD_B64BINARY), b64encode),
 ]
 
 XSDToPython = {
@@ -1593,7 +1596,7 @@ XSDToPython = {
     URIRef(_XSD_PFX + "unsignedByte"): int,
     URIRef(_XSD_PFX + "float"): float,
     URIRef(_XSD_PFX + "double"): float,
-    URIRef(_XSD_PFX + "base64Binary"): lambda s: base64.b64decode(s),
+    URIRef(_XSD_PFX + "base64Binary"): b64decode,
     URIRef(_XSD_PFX + "anyURI"): None,
     _RDF_XMLLITERAL: _parseXML,
     _RDF_HTMLLITERAL: _parseHTML,
diff --git a/setup.py b/setup.py
index 8dd82c2b..e2edc084 100644
--- a/setup.py
+++ b/setup.py
@@ -16,7 +16,7 @@ kwargs["test_suite"] = "nose.collector"
 kwargs["extras_require"] = {
     "html": ["html5lib"],
     "tests": kwargs["tests_require"],
-    "docs": ["sphinx < 4", "sphinxcontrib-apidoc"],
+    "docs": ["sphinx < 5", "sphinxcontrib-apidoc"],
 }
 
 
diff --git a/test/test_b64_binary.py b/test/test_b64_binary.py
new file mode 100644
index 00000000..b512f29d
--- /dev/null
+++ b/test/test_b64_binary.py
@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+
+import unittest
+import base64 
+from rdflib import Literal, XSD
+
+
+class B64BinaryTestCase(unittest.TestCase):
+
+    def test_unicode(self):
+        str1 = "Test utf-8 string éàë"
+        # u b64string
+        b64_str1 = base64.b64encode(str1.encode("utf-8")).decode()
+        l1 = Literal(b64_str1, datatype=XSD.base64Binary)
+        b_str1 = l1.toPython()
+        self.assertEqual(b_str1.decode("utf-8"), str1)
+        self.assertEqual(str(l1), b64_str1)
+
+        # b b64string
+        b64_str1b = base64.b64encode(str1.encode("utf-8"))
+        l1b = Literal(b64_str1b, datatype=XSD.base64Binary)
+        b_str1b = l1b.toPython()
+        self.assertEqual(b_str1, b_str1b)
+        self.assertEqual(b_str1b.decode("utf-8"), str1)
+        self.assertEqual(str(l1b), b64_str1)
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/test/test_graph.py b/test/test_graph.py
index 93a81df3..9f6d5d9b 100644
--- a/test/test_graph.py
+++ b/test/test_graph.py
@@ -319,6 +319,47 @@ class GraphTestCase(unittest.TestCase):
             # this endpoint is currently not available, ignore this test.
             pass
 
+    def testTransitive(self):
+        person = URIRef("ex:person")
+        dad = URIRef("ex:dad")
+        mom = URIRef("ex:mom")
+        mom_of_dad = URIRef("ex:mom_o_dad")
+        mom_of_mom = URIRef("ex:mom_o_mom")
+        dad_of_dad = URIRef("ex:dad_o_dad")
+        dad_of_mom = URIRef("ex:dad_o_mom")
+
+        parent = URIRef("ex:parent")
+
+        g = Graph()
+        g.add((person, parent, dad))
+        g.add((person, parent, mom))
+        g.add((dad, parent, mom_of_dad))
+        g.add((dad, parent, dad_of_dad))
+        g.add((mom, parent, mom_of_mom))
+        g.add((mom, parent, dad_of_mom))
+
+        # transitive parents of person
+        self.assertEqual(
+            set(g.transitive_objects(subject=person, predicate=parent)),
+            {person, dad, mom_of_dad, dad_of_dad, mom, mom_of_mom, dad_of_mom},
+        )
+        # transitive parents of dad
+        self.assertEqual(
+            set(g.transitive_objects(dad, parent)), {dad, mom_of_dad, dad_of_dad}
+        )
+        # transitive parents of dad_of_dad
+        self.assertEqual(set(g.transitive_objects(dad_of_dad, parent)), {dad_of_dad})
+
+        # transitive children (inverse of parents) of mom_of_mom
+        self.assertEqual(
+            set(g.transitive_subjects(predicate=parent, object=mom_of_mom)),
+            {mom_of_mom, mom, person},
+        )
+        # transitive children (inverse of parents) of mom
+        self.assertEqual(set(g.transitive_subjects(parent, mom)), {mom, person})
+        # transitive children (inverse of parents) of person
+        self.assertEqual(set(g.transitive_subjects(parent, person)), {person})
+
 
 # dynamically create classes for each registered Store
 
diff --git a/test/test_sparql.py b/test/test_sparql.py
index fa548146..6454e7ef 100644
--- a/test/test_sparql.py
+++ b/test/test_sparql.py
@@ -1,8 +1,8 @@
 from rdflib.plugins.sparql import sparql, prepareQuery
 from rdflib import Graph, URIRef, Literal, BNode, ConjunctiveGraph
 from rdflib.namespace import Namespace, RDF, RDFS
-from rdflib.plugins.sparql import prepareQuery
 from rdflib.compare import isomorphic
+from rdflib.term import Variable
 
 from nose.tools import eq_
 
@@ -163,6 +163,43 @@ def test_named_filter_graph_query():
                         initNs={'ex': ex})) == [(Literal('Susan'),)]
 
 
+def test_txtresult():
+    data = f"""\
+    @prefix rdfs: <{str(RDFS)}> .
+    rdfs:Class a rdfs:Class ;
+        rdfs:isDefinedBy <http://www.w3.org/2000/01/rdf-schema#> ;
+        rdfs:label "Class" ;
+        rdfs:comment "The class of classes." ;
+        rdfs:subClassOf rdfs:Resource .
+    """
+    graph = Graph()
+    graph.parse(data=data, format="turtle")
+    result = graph.query(
+        """\
+    SELECT ?class ?superClass ?label ?comment WHERE {
+        ?class rdf:type rdfs:Class.
+        ?class rdfs:label ?label.
+        ?class rdfs:comment ?comment.
+        ?class rdfs:subClassOf ?superClass.
+    }
+    """
+    )
+    vars = [
+        Variable("class"),
+        Variable("superClass"),
+        Variable("label"),
+        Variable("comment"),
+    ]
+    assert result.type == "SELECT"
+    assert len(result) == 1
+    assert result.vars == vars
+    txtresult = result.serialize(format="txt")
+    lines = txtresult.decode().splitlines()
+    assert len(lines) == 3
+    vars_check = [Variable(var.strip()) for var in lines[0].split("|")]
+    assert vars_check == vars
+
+
 if __name__ == "__main__":
     import nose
 
diff --git a/test/test_sparqlstore.py b/test/test_sparqlstore.py
index 8154b10c..8d720de3 100644
--- a/test/test_sparqlstore.py
+++ b/test/test_sparqlstore.py
@@ -67,6 +67,19 @@ class SPARQLStoreDBPediaTestCase(unittest.TestCase):
         for i in res:
             assert type(i[0]) == Literal, i[0].n3()
 
+    def test_query_with_added_rdf_prolog(self):
+        prologue = """\
+        PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+        PREFIX xyzzy: <http://www.w3.org/2004/02/skos/core#>
+        """
+        query = """\
+        SELECT ?label WHERE
+            { ?s a xyzzy:Concept ; xyzzy:prefLabel ?label . } LIMIT 10
+        """
+        res = helper.query_with_retry(self.graph, prologue + query)
+        for i in res:
+            assert type(i[0]) == Literal, i[0].n3()
+
     def test_counting_graph_and_store_queries(self):
         query = """
             SELECT ?s