Merge pull request #367 from biolink/update_bmt

update bmt to get new biolink-model, fix linkml changes, add test coverage to click in order to pass sonarcloud coverage requirements

kgx/cli/__init__.py

@@ -555,7 +555,6 @@ def transform_wrapper(
         exit(1)
 
 
-
 @cli.command(name="merge")
 @click.option("--merge-config", required=True, type=str)
 @click.option(

kgx/config.yml

@@ -17,9 +17,6 @@ logging:
   level: INFO
   format: '[%(name)s][%(filename)s][%(funcName)20s] %(levelname)s: %(message)s'
 
-# KGX setting for the Biolink Model is now ignored; defer to the Biolink Model Toolkit default.
-# biolink-model: https://raw.githubusercontent.com/biolink/biolink-model/2.2.5/biolink-model.yaml
-
 jsonld-context:
   biolink: https://raw.githubusercontent.com/biolink/biolink-model/2.2.5/context.jsonld
   monarch_context: https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/monarch_context.jsonld

requirements.txt

@@ -1,8 +1,7 @@
-bmt~=0.7.6
 prefixcommons>=0.1.4
 pip>=9.0.1
 docutils==0.16.0
-networkx>=2.5
+networkx
 SPARQLWrapper>=1.8.2
 pandas>=1.0.3
 pytest>=0.0
@@ -11,7 +10,6 @@ rdflib~=5.0.0
 Click~=7.0
 neo4jrestclient>=0.0
 pyyaml>=0.0
-linkml>=1.1.13
 prologterms>=0.0.5
 shexjsg>=0.6.5
 terminaltables>=3.1.0
@@ -32,4 +30,7 @@ recommonmark>=0.7.1
 tox
 flake8
 black
+bmt>=0.8.1
 tox-docker
+linkml
+linkml-runtime

tests/unit/test_cli_utils.py

@@ -7,14 +7,15 @@
 from click.testing import CliRunner
 
 from kgx.cli.cli_utils import validate, neo4j_upload, neo4j_download, transform, merge
-from kgx.cli import cli, get_input_file_types, graph_summary, get_report_format_types, validate_wrapper
+from kgx.cli import cli, get_input_file_types, graph_summary, get_report_format_types
 from tests import RESOURCE_DIR, TARGET_DIR
 from tests.unit import (
     check_container,
+    clean_slate,
     CONTAINER_NAME,
     DEFAULT_NEO4J_URL,
     DEFAULT_NEO4J_USERNAME,
-    DEFAULT_NEO4J_PASSWORD,
+    DEFAULT_NEO4J_PASSWORD
 )
 
 
@@ -38,6 +39,117 @@ def test_get_report_format_types():
     assert "json" in format_types
 
 
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_graph_summary_wrapper():
+    output = os.path.join(TARGET_DIR, "graph_stats3.yaml")
+
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "graph-summary",
+            "-i", "tsv",
+            "-o", output,
+            os.path.join(RESOURCE_DIR, "graph_nodes.tsv")
+        ]
+    )
+    assert result.exit_code == 0
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_graph_summary_wrapper_error():
+    inputs = [
+        os.path.join(RESOURCE_DIR, "graph_nodes.tsv"),
+        os.path.join(RESOURCE_DIR, "graph_edges.tsv"),
+    ]
+    output = os.path.join(TARGET_DIR, "graph_stats3.yaml")
+
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "graph-summary",
+            "-i", "tsv",
+            "-o", output,
+            inputs
+        ]
+    )
+    assert result.exit_code == 1
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_transform_wrapper():
+    """
+        Transform graph from TSV to JSON.
+        """
+    inputs = [
+        os.path.join(RESOURCE_DIR, "graph_nodes.tsv"),
+        os.path.join(RESOURCE_DIR, "graph_edges.tsv"),
+    ]
+    output = os.path.join(TARGET_DIR, "grapht.json")
+
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "transform",
+            "-i", "tsv",
+            "-o", output,
+            "-f", "json",
+            inputs
+        ]
+    )
+
+    assert result.exit_code == 1
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_merge_wrapper():
+
+    """
+    Transform from test merge YAML.
+    """
+    merge_config = os.path.join(RESOURCE_DIR, "test-merge.yaml")
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "merge",
+            "--merge-config", merge_config
+        ]
+    )
+
+    assert result.exit_code == 0
+    assert os.path.join(TARGET_DIR, "merged-graph_nodes.tsv")
+    assert os.path.join(TARGET_DIR, "merged-graph_edges.tsv")
+    assert os.path.join(TARGET_DIR, "merged-graph.json")
+
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_merge_wrapper_error():
+
+    """
+    Transform from test merge YAML.
+    """
+    merge_config = os.path.join(RESOURCE_DIR, "test-merge.yaml")
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "merge"
+        ]
+    )
+
+    assert result.exit_code == 2
+
+
 def test_kgx_graph_summary():
     """
     Test graph summary, where the output report type is kgx-map.
@@ -259,6 +371,94 @@ def test_neo4j_upload(clean_slate):
     assert t.store.graph.number_of_edges() == 531
 
 
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_neo4j_download_wrapper(clean_slate):
+    output = os.path.join(TARGET_DIR, "neo_download2")
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "neo4j-download",
+            "-l", DEFAULT_NEO4J_URL,
+            "-o", output,
+            "-f", "tsv",
+            "-u", DEFAULT_NEO4J_USERNAME,
+            "-p", DEFAULT_NEO4J_PASSWORD,
+        ]
+    )
+
+    assert os.path.exists(f"{output}_nodes.tsv")
+    assert os.path.exists(f"{output}_edges.tsv")
+
+    assert result.exit_code == 0
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_download_exception_triggered_error_exit_code():
+    """
+    Test graph download error exit code.
+    """
+
+    output = os.path.join(TARGET_DIR, "neo_download")
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "neo4j-download",
+            "-l", DEFAULT_NEO4J_URL,
+            "-o", output,
+            "-f", "tsv",
+            "-u", "not a user name",
+            "-p", DEFAULT_NEO4J_PASSWORD,
+        ]
+    )
+    assert result.exit_code == 1
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_neo4j_upload_wrapper(clean_slate):
+    inputs = [
+        os.path.join(RESOURCE_DIR, "graph_nodes.tsv"),
+        os.path.join(RESOURCE_DIR, "graph_edges.tsv"),
+    ]
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "neo4j-upload",
+            "--input-format", "tsv",
+            "--uri", DEFAULT_NEO4J_URL,
+            "--username", DEFAULT_NEO4J_USERNAME,
+            "--password", DEFAULT_NEO4J_PASSWORD,
+            os.path.join(RESOURCE_DIR, "graph_nodes.tsv")
+        ]
+    )
+
+    assert result.exit_code == 0
+
+
+@pytest.mark.skipif(
+    not check_container(), reason=f"Container {CONTAINER_NAME} is not running"
+)
+def test_neo4j_upload_wrapper_error(clean_slate):
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "neo4j-upload",
+            "-i", "tsv",
+            "inputs", "not_a_path"
+            "-u", "not a user",
+            "-p", DEFAULT_NEO4J_PASSWORD,
+        ]
+    )
+
+    assert result.exit_code == 2
+
 @pytest.mark.skip()
 @pytest.mark.skipif(
     not check_container(), reason=f"Container {CONTAINER_NAME} is not running"

tests/unit/test_source/test_owl_source.py

@@ -1,5 +1,4 @@
 import os
-import pprint
 
 from kgx.source import OwlSource
 from tests import RESOURCE_DIR
@@ -9,11 +8,12 @@ def test_read_owl1():
     """
     Read an OWL ontology using OwlSource.
     """
+
     s = OwlSource()
     g = s.parse(
         os.path.join(RESOURCE_DIR, "goslim_generic.owl"),
         provided_by="GO slim generic",
-        knowledge_source="GO slim generic",
+        knowledge_source="GO slim generic"
     )
     nodes = {}
     edges = {}
@@ -133,7 +133,6 @@ def test_read_owl3():
                 nodes[rec[0]] = rec[-1]
 
     n1 = nodes["GO:0008150"]
-    pprint.pprint(n1)
     assert n1["name"] == "biological_process"
     assert "subsets" in n1 and "GOP:goslim_generic" in n1["subsets"]
     assert "synonym" in n1 and "biological process" in n1["synonym"]

tests/unit/test_validator.py

@@ -21,7 +21,7 @@ def test_get_required_node_properties(property):
     assert property in properties
 
 
-@pytest.mark.parametrize("property", ["subject", "object", "predicate", "relation"])
+@pytest.mark.parametrize("property", ["subject", "object", "predicate"])
 def test_get_required_edge_properties(property):
     """
     Test get_required_edge_properties in Validator.