feat: adds ability to parse dot information from json file

tantri/cli/file_importer.py

@@ -1,5 +1,8 @@
 import json
 import logging
+import tantri.cli.input_files
+from typing import Sequence
+import tantri.dipoles
 
 _logger = logging.getLogger(__name__)
 
@@ -8,8 +11,14 @@ _logger = logging.getLogger(__name__)
 # TODO: if this ever matters, can improve file handling.
 
 
-def read_json_file(filename):
+def read_data_from_filename(filename: str):
 	try:
-		return json.load(filename)
+		with open(filename, "r") as file:
-	except Exception:
+			return json.load(file)
-		_logger.exception(f"failed on reading filename {filename}")
+	except Exception as e:
+		_logger.error(f"failed to read the file {filename}, raising and aborting", exc_info=e)
+
+
+def read_dots_json_file(filename: str) -> Sequence[tantri.dipoles.DotPosition]:
+	data = read_data_from_filename(filename)
+	return tantri.cli.input_files.rows_to_dots(data)

tantri/cli/input_files/__init__.py

@@ -0,0 +1,5 @@
+from tantri.cli.input_files.read_dots import rows_to_dots
+
+__all__ = [
+	"rows_to_dots"
+]

tantri/cli/input_files/json_dots.py

@@ -1 +0,0 @@
-import tantri

tantri/cli/input_files/read_dots.py

@@ -0,0 +1,16 @@
+import tantri.dipoles
+import numpy
+from typing import Sequence
+
+
+def row_to_dot(input_dict: dict) -> tantri.dipoles.DotPosition:
+	r = input_dict["r"]
+	if len(r) != 3:
+		raise ValueError(f"r parameter in input_dict [{input_dict}] does not have length 3")
+	label = input_dict["label"]
+
+	return tantri.dipoles.DotPosition(numpy.array(r), label)
+
+
+def rows_to_dots(dot_dict_array: Sequence[dict]) -> Sequence[tantri.dipoles.DotPosition]:
+	return [row_to_dot(input_dict) for input_dict in dot_dict_array]

tests/cli/__snapshots__/test_read_dots_json.ambr

@@ -0,0 +1,10 @@
+# serializer version: 1
+# name: test_from_json_string
+  list([
+    DotPosition(r=array([0. , 1.5, 2. ]), label='dot1'),
+    DotPosition(r=array([-5.,  3., -1.]), label='dot2'),
+  ])
+# ---
+# name: test_parse_one_dot
+  DotPosition(r=array([1.5, 0. , 1. ]), label='dot1')
+# ---

tests/cli/test_read_dots_json.py

@@ -0,0 +1,63 @@
+import json
+import tantri.cli.input_files.read_dots as dots
+import pytest
+
+
+def test_parse_one_dot_failures():
+
+	dict = {
+		"r": [1.5, 0, 1]
+		# missing label
+	}
+
+	with pytest.raises(KeyError, match=r".*label.*"):
+		dots.row_to_dot(dict)
+
+	dict = {
+		# missing r
+		"label": "label"
+	}
+
+	with pytest.raises(KeyError, match=r".*r.*"):
+		dots.row_to_dot(dict)
+
+
+def test_parse_one_dot(snapshot):
+
+	dict = {
+		"r": [1.5, 0, 1],
+		"label": "dot1",
+	}
+
+	transformed = dots.row_to_dot(dict)
+	assert transformed == snapshot
+
+
+def test_dot_r_wrong_length():
+
+	dict = {
+		"r": [1.5, 0],
+		"label": "dot1",
+	}
+
+	with pytest.raises(ValueError, match=r".*does not have length 3.*"):
+		dots.row_to_dot(dict)
+
+
+def test_from_json_string(snapshot):
+	dots_json = """[
+		{
+			"r": [0, 1.5, 2],
+			"label": "dot1"
+		},
+		{
+			"r": [-5, 3, -1.0],
+			"label": "dot2"
+		}
+	]
+	"""
+
+	parsed = json.loads(dots_json)
+	transformed = dots.rows_to_dots(parsed)
+
+	assert transformed == snapshot