Merge pull request #28 from nlesc-nano/dev

Improve documentation and query results

ceibacli/actions/query.py

@@ -41,6 +41,7 @@ def query_collection_properties(opts: Options) -> pd.DataFrame:
     # Transform the JSON reply into a DataFrame
     properties = reply["properties"]
     df = json_properties_to_dataframe(properties)
-    df.to_csv(opts.output_file)
-    print(f"Requested properties has been save to: {opts.output_file}")
+    output_file = f"{opts.collection_name}.csv"
+    df.to_csv(output_file)
+    print(f"Requested properties has been save to: {output_file}")
     return df

ceibacli/cli.py

@@ -71,7 +71,6 @@ def parse_user_arguments() -> Tuple[str, Options]:
     query_parser = subparsers.add_parser(
         "query", help="Query some properties from the database",
         parents=[common_parser])
-    query_parser.add_argument("-o", "--output", help="File to store the properties", default="output_properties.csv")
 
     # Manage the Jobs status
     subparsers.add_parser(
@@ -91,7 +90,7 @@ def handle_input(args: argparse.Namespace) -> Options:
     """Check user input."""
     input_file = getattr(args, "input", None)
     if input_file is None:
-        user_input = {key: value for key, value in vars(args).items() if key not in {"command", "input", "output"}}
+        user_input = {key: value for key, value in vars(args).items() if key not in {"command", "input"}}
         input_file = Path(tempfile.gettempdir()) / "user_input.yml"
         with open(input_file, 'w') as handler:
             yaml.dump(user_input, handler)

ceibacli/input_validation.py

@@ -71,10 +71,7 @@ def is_in_array_uppercase(array: Iterable[str]) -> Schema:
     Optional("web", default=DEFAULT_WEB): str,
 
     # Name to which the property belongs. e.g. Theory level
-    Optional("collection_name", default=None): Or(str, None),
-
-    # Name to store the properties as csv
-    Optional("output_file", default="output_properties.csv"): str
+    Optional("collection_name", default=None): Or(str, None)
 })
 
 ADD_SCHEMA = Schema({

docs/query.rst

@@ -29,5 +29,5 @@ To request all the datasets available in a given collection, you just need to ru
    
    ceibacli query -w http://yourCeibaInstance:8080/grapqhl -c simulation2
 
-That command will write into your current work directory a file called ``output_properties.csv``
+That command will write into your current work directory a file called ``simulation2.csv``
 containing the properties in the requested collection.

tests/files/input_test_query.yml

@@ -1 +1 @@
-collection_name: "functional/basisset"
+collection_name: "example_collection"

tests/test_query.py

@@ -15,14 +15,18 @@ def test_query(mocker: MockFixture, tmp_path: Path):
     # Read and Validate user input
     path_input = PATH_TEST / "input_test_query.yml"
     opts = validate_input(path_input, "query")
-    opts.output_file = (tmp_path / "output.csv").absolute().as_posix()
 
     # Mock the server call
     mocker.patch("ceibacli.actions.query.query_server",
                  return_value=read_mocked_reply("query_mocked.json"))
 
-    df = query_properties(opts)
-    assert len(df) == 10
+    try:
+        df = query_properties(opts)
+        assert len(df) == 10
+    finally:
+        path = Path("example_collection.csv")
+        if path.exists():
+            path.unlink()
 
 
 def test_query_collections(mocker: MockFixture):