Merge pull request #260 from biolink/knowledge-map-cli

Add ability to generate summary report in different formats via KGX CLI

kgx/cli/__init__.py

@@ -4,7 +4,7 @@
 
 from kgx.config import get_logger, get_config
 from kgx.cli.cli_utils import get_file_types, get_transformer, parse_source, apply_operations, graph_summary, validate, \
-    neo4j_download, neo4j_upload, transform, merge
+    neo4j_download, neo4j_upload, transform, merge, summary_report_types
 
 log = get_logger()
 config = get_config()
@@ -31,9 +31,10 @@ def cli():
 @click.option('--input-format', required=True, help=f'The input format. Can be one of {get_file_types()}')
 @click.option('--input-compression', required=False, help='The input compression type')
 @click.option('--output', required=True, type=click.Path(exists=False))
+@click.option('--report-type', required=False, type=str, help=f'The summary report type. Can be one of {summary_report_types.keys()}', default='kgx-map')
 @click.option('--node-facet-properties', required=False, multiple=True, help='A list of node properties from which to generate counts per value for those properties')
 @click.option('--edge-facet-properties', required=False, multiple=True, help='A list of edge properties from which to generate counts per value for those properties')
-def graph_summary_wrapper(inputs: List[str], input_format: str, input_compression: str, output: str, node_facet_properties: Optional[Set], edge_facet_properties: Optional[Set]):
+def graph_summary_wrapper(inputs: List[str], input_format: str, input_compression: str, output: str, report_type: str, node_facet_properties: Optional[Set], edge_facet_properties: Optional[Set]):
     """
     Loads and summarizes a knowledge graph from a set of input files.
     \f
@@ -48,12 +49,14 @@ def graph_summary_wrapper(inputs: List[str], input_format: str, input_compressio
         The input compression type
     output: str
         Where to write the output (stdout, by default)
+    report_type: str
+        The summary report type
     node_facet_properties: Optional[Set]
         A list of node properties from which to generate counts per value for those properties. For example, ``['provided_by']``
     edge_facet_properties: Optional[Set]
         A list of edge properties from which to generate counts per value for those properties. For example, ``['provided_by']``
     """
-    graph_summary(inputs, input_format, input_compression, output, node_facet_properties=list(node_facet_properties), edge_facet_properties=list(edge_facet_properties))
+    graph_summary(inputs, input_format, input_compression, output, report_type, node_facet_properties=list(node_facet_properties), edge_facet_properties=list(edge_facet_properties))
 
 
 @cli.command('validate')

kgx/cli/cli_utils.py

@@ -5,14 +5,16 @@
 from typing import List, Tuple, Any, Optional, Dict, Set
 
 import yaml
+
+from kgx.operations import knowledge_map
 from kgx.transformers.sssom_transformer import SssomTransformer
 
 from kgx import PandasTransformer, NeoTransformer, Validator, RdfTransformer, NtTransformer, RsaTransformer, \
     RdfOwlTransformer, ObographJsonTransformer, JsonlTransformer, JsonTransformer, Transformer
 from kgx.config import get_logger
 from kgx.graph.base_graph import BaseGraph
 from kgx.operations.graph_merge import merge_all_graphs
-from kgx.operations.summarize_graph import summarize_graph
+from kgx.operations import summarize_graph
 
 _transformers = {
     'tar': PandasTransformer,
@@ -30,6 +32,11 @@
     'sssom': SssomTransformer
 }
 
+summary_report_types = {
+    'kgx-map': summarize_graph.summarize_graph,
+    'knowledge-map': knowledge_map.summarize_graph
+}
+
 log = get_logger()
 
 
@@ -72,7 +79,7 @@ def get_file_types() -> Tuple:
     return tuple(_transformers.keys())
 
 
-def graph_summary(inputs: List[str], input_format: str, input_compression: Optional[str], output: Optional[str], node_facet_properties: Optional[List] = None, edge_facet_properties: Optional[List] = None) -> Dict:
+def graph_summary(inputs: List[str], input_format: str, input_compression: Optional[str], output: Optional[str], report_type: str, node_facet_properties: Optional[List] = None, edge_facet_properties: Optional[List] = None) -> Dict:
     """
     Loads and summarizes a knowledge graph from a set of input files.
 
@@ -86,6 +93,8 @@ def graph_summary(inputs: List[str], input_format: str, input_compression: Optio
         The input compression type
     output: Optional[str]
         Where to write the output (stdout, by default)
+    report_type: str
+        The summary report type
     node_facet_properties: Optional[List]
         A list of node properties from which to generate counts per value for those properties. For example, ``['provided_by']``
     edge_facet_properties: Optional[List]
@@ -101,7 +110,10 @@ def graph_summary(inputs: List[str], input_format: str, input_compression: Optio
     for file in inputs:
         transformer.parse(file, input_format=input_format, compression=input_compression)
 
-    stats = summarize_graph(transformer.graph, name='Graph', node_facet_properties=node_facet_properties, edge_facet_properties=edge_facet_properties)
+    if report_type in summary_report_types:
+        stats = summary_report_types[report_type](graph=transformer.graph, name='Graph', node_facet_properties=node_facet_properties, edge_facet_properties=edge_facet_properties)
+    else:
+        raise ValueError(f"report_type must be one of {summary_report_types.keys()}")
     if output:
         WH = open(output, 'w')
         WH.write(yaml.dump(stats))

kgx/operations/knowledge_map.py

@@ -31,7 +31,7 @@ def generate_knowledge_map(graph: BaseGraph, name: str, filename: str) -> None:
     json.dump(knowledge_map, WH, indent=4)
 
 
-def summarize_graph(graph: BaseGraph, name: str = None) -> Dict:
+def summarize_graph(graph: BaseGraph, name: str = None, **kwargs) -> Dict:
     """
     Generate a knowlege map that describes the composition of the graph.
 
@@ -41,8 +41,8 @@ def summarize_graph(graph: BaseGraph, name: str = None) -> Dict:
         The graph
     name: Optional[str]
         Name for the graph
-    filename: str
-        The file to write the knowledge map to
+    kwargs: Dict
+        Any additional arguments
 
     Returns
     -------

tests/unit/test_cli_utils.py

@@ -37,13 +37,13 @@ def test_get_file_types():
     assert 'ttl' in file_types
 
 
-def test_graph_summary():
+def test_graph_summary1():
     inputs = [
         os.path.join(resource_dir, 'graph_nodes.tsv'),
         os.path.join(resource_dir, 'graph_edges.tsv')
     ]
-    output = os.path.join(target_dir, 'graph_stats.yaml')
-    summary_stats = graph_summary(inputs, 'tsv', None, output)
+    output = os.path.join(target_dir, 'graph_stats1.yaml')
+    summary_stats = graph_summary(inputs, 'tsv', None, output, report_type='kgx-map')
     pprint.pprint(summary_stats)
 
     assert os.path.exists(output)
@@ -58,6 +58,22 @@ def test_graph_summary():
     assert 'biolink:interacts_with' in summary_stats['edge_stats']['predicates']
 
 
+def test_graph_summary2():
+    inputs = [
+        os.path.join(resource_dir, 'graph_nodes.tsv'),
+        os.path.join(resource_dir, 'graph_edges.tsv')
+    ]
+    output = os.path.join(target_dir, 'graph_stats2.yaml')
+    summary_stats = graph_summary(inputs, 'tsv', None, output, report_type='knowledge-map')
+    pprint.pprint(summary_stats)
+
+    assert os.path.exists(output)
+    assert summary_stats
+    assert 'knowledge_map' in summary_stats
+    assert 'nodes' in summary_stats['knowledge_map']
+    assert 'edges' in summary_stats['knowledge_map']
+
+
 def test_validate():
     inputs = [
         os.path.join(resource_dir, 'valid.json'),