Use SparqlImplementation with local queries for ttl format files.

Addresses #49

docs/selectors.rst

@@ -22,7 +22,8 @@ Examples of scheme-less descriptors, implicit implementation:
 
 - :code:`tests/input/go-nucleus.obo` - local obo format file loaded with pronto
 - :code:`tests/input/go-nucleus.json` - local obojson format file loaded with pronto
-- :code:`tests/input/go-nucleus.owl` - local OWL rdf/xml format file (loaded with pronto at the moment may change)
+- :code:`tests/input/go-nucleus.owl` - local OWL rdf/xml format file (loaded with rdflib at the moment may change)
+- :code:`tests/input/go-nucleus.owl.ttl` - local OWL turtle format file (loaded with rdflib at the moment may change)
 - :code:`tests/input/go-nucleus.db` - local sqlite3 db loaded with SqlImplementation
 - :code:`http://purl.obolibrary.org/obo/pato.obo` - NOT IMPLEMENTED; download locally for now
 - :code:`http://purl.obolibrary.org/obo/pato.owl` - NOT IMPLEMENTED; download locally for now

pyproject.toml

@@ -12,13 +12,11 @@ nxontology = "^0.4.0"
 pronto = "^2.4.5"
 SPARQLWrapper = "^2.0.0"
 SQLAlchemy = "^1.4.32"
-linkml-runtime = "^1.3.0rc1"
+linkml-runtime = "^1.1.9"
 networkx = "^2.7.1"
 sssom = "^0.3.8"
 ratelimit = "^2.2.1"
 appdirs = "^1.4.4"
-uvicorn = "^0.17.6"
-fastapi = "^0.75.2"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"

src/oaklib/cli.py

@@ -107,8 +107,9 @@ def _shorthand_to_pred_curie(shorthand: str) -> PRED_CURIE:
 @click.option("-v", "--verbose", count=True)
 @click.option("-q", "--quiet")
 @input_option
+@input_type_option
 @add_option
-def main(verbose: int, quiet: bool, input: str, add: List):
+def main(verbose: int, quiet: bool, input: str, input_type: str, add: List):
     """Run the oaklib Command Line.
 
     A subcommand must be passed - for example: ancestors, terms, ...
@@ -134,7 +135,7 @@ def main(verbose: int, quiet: bool, input: str, add: List):
 
     if input:
         impl_class: Type[OntologyInterface]
-        resource = get_resource_from_shorthand(input)
+        resource = get_resource_from_shorthand(input, format=input_type)
         impl_class = resource.implementation_class
         logging.info(f'RESOURCE={resource}')
         settings.impl = impl_class(resource)

tests/test_cli.py

@@ -171,7 +171,8 @@ def test_check_definitions(self):
 
     def test_lexmatch_owl(self):
         outfile = f'{OUTPUT_DIR}/matcher-test-cli.owl.sssom.tsv'
-        result = self.runner.invoke(main, ['-i', f'{INPUT_DIR}/matcher-test.owl', 'lexmatch', '-R', f'{INPUT_DIR}/matcher_rules.yaml',
+        result = self.runner.invoke(main, ['-i', f'pronto:{INPUT_DIR}/matcher-test.owl', 'lexmatch',
+                                           '-R', f'{INPUT_DIR}/matcher_rules.yaml',
                                            '-o', outfile])
         out = result.stdout
         err = result.stderr

tests/test_selector.py

@@ -5,12 +5,12 @@
 from oaklib.implementations.ols.ols_implementation import OlsImplementation
 from oaklib.implementations.ontobee.ontobee_implementation import OntobeeImplementation
 from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation
+from oaklib.implementations.sparql.sparql_implementation import SparqlImplementation
 from oaklib.implementations.sqldb.sql_implementation import SqlImplementation
 from oaklib.implementations.ubergraph import UbergraphImplementation
 from oaklib.selector import get_resource_from_shorthand
 
 
-
 class TestResource(unittest.TestCase):
 
 
@@ -21,6 +21,11 @@ def test_from_descriptor(self):
         self.assertEqual('foo.obo', resource.slug)
         resource = get_resource_from_shorthand('foo.owl')
         # this may change:
+        assert resource.implementation_class == SparqlImplementation
+        resource = get_resource_from_shorthand('foo.ttl')
+        # this may change:
+        assert resource.implementation_class == SparqlImplementation
+        resource = get_resource_from_shorthand('pronto:foo.owl')
         assert resource.implementation_class == ProntoImplementation
         resource = get_resource_from_shorthand('foo.db')
         assert resource.implementation_class == SqlImplementation