update API and tests

chem_spectra/controller/spectra_layout_api.py

@@ -1,6 +1,7 @@
 import json
 from flask import jsonify, Blueprint
 import os
+import shutil
 
 spectra_layout_api = Blueprint('spectra_layout_api', __name__)
 script_dir = os.path.dirname(__file__)
@@ -11,10 +12,10 @@ def load_data_types():
         with open(data_type_json_path, 'r') as mapping_file:
             return json.load(mapping_file)
     except FileNotFoundError:
-        with open(data_type_json_path, 'w') as new_mapping_file:
-            initial_data = {"datatypes": {}}
-            json.dump(initial_data, new_mapping_file, indent=4)
-            return initial_data
+        example_json_path = os.path.join(script_dir, '../lib/converter/jcamp/data_type.json.example')
+        shutil.copy(example_json_path, data_type_json_path)
+        with open(data_type_json_path, 'r') as mapping_file:
+            return json.load(mapping_file)
 
 @spectra_layout_api.route('/spectra_layouts', methods=['GET'])
 def get_spectra_layouts():

chem_spectra/controller/spectra_type_api.py

@@ -1,6 +1,7 @@
 import json
 import os
 from flask import request, jsonify, Blueprint
+import shutil
 
 spectra_type_api = Blueprint('spectra_type_api', __name__)
 
@@ -12,35 +13,41 @@ def load_data_types():
         with open(data_type_json_path, 'r') as mapping_file:
             return json.load(mapping_file)
     except FileNotFoundError:
-        return {"datatypes": {}}
+        example_json_path = os.path.join(script_dir, '../lib/converter/jcamp/data_type.json.example')
+        shutil.copy(example_json_path, data_type_json_path)
+        with open(data_type_json_path, 'r') as mapping_file:
+            return json.load(mapping_file)
 
 def save_data_types(data_types):
     with open(data_type_json_path, 'w') as mapping_file:
         json.dump(data_types, mapping_file, indent=4)
 
 @spectra_type_api.route('/data_type', methods=['POST'])
-def create_or_update_data_type():
+def create_data_type():
     request_data = request.get_json()
     new_data_type_mapping = request_data.get("new_data_type")
     existing_data_types = load_data_types()
-
-    for data_type, layout in new_data_type_mapping.items():
-        if data_type in existing_data_types["datatypes"]:
+
+    for layout, data_type in new_data_type_mapping.items():
+        if layout in existing_data_types["datatypes"] and data_type not in existing_data_types['datatypes'][layout]:
+            existing_data_types["datatypes"][layout].append(data_type)
+        elif layout in existing_data_types["datatypes"] and data_type in existing_data_types['datatypes'][layout]:
             return jsonify({"message": f"Data type '{data_type}' already exists"}), 400
-
-    existing_data_types["datatypes"].update(new_data_type_mapping)
+        else:
+            return jsonify({"message": f"Layout '{layout}' does not exist"}), 400
 
     save_data_types(existing_data_types)
 
-    return jsonify({"message": "Data type created/updated successfully"}), 200
+    return jsonify({"message": "Data type created successfully"}), 200
 
 @spectra_type_api.route('/data_type/<data_type>', methods=['DELETE'])
 def delete_data_type(data_type):
     existing_data_types = load_data_types()
-
-    if data_type in existing_data_types["datatypes"]:
-        del existing_data_types["datatypes"][data_type]
-        save_data_types(existing_data_types)
-        return jsonify({"message": f"Data type '{data_type}' deleted successfully"}), 200
-    else:
-        return jsonify({"message": f"Data type '{data_type}' not found"}), 404
+
+    for layout, data_types in existing_data_types['datatypes'].items():
+        if data_type in data_types:
+            data_types.remove(data_type)
+            save_data_types(existing_data_types)
+            return jsonify({"message": f"Data type '{data_type}' deleted successfully"}), 200
+
+    return jsonify({"message": f"Data type '{data_type}' not found"}), 404

chem_spectra/lib/converter/jcamp/data_type.json.example

@@ -0,0 +1,19 @@
+{
+  "datatypes": {
+      "NMR": ["NMR SPECTRUM", "NMRSPECTRUM"],
+      "INFRARED": ["INFRARED SPECTRUM"],
+      "RAMAN": ["RAMAN SPECTRUM"],
+      "MS": ["MASS SPECTRUM"],
+      "HPLC UVVIS": ["HPLC UV/VIS SPECTRUM", "HPLC UV-VIS"],
+      "UVVIS": ["UV/VIS SPECTRUM", "UV-VIS", "ULTRAVIOLET SPECTRUM"],
+      "THERMOGRAVIMETRIC ANALYSIS": ["THERMOGRAVIMETRIC ANALYSIS"],
+      "X-RAY DIFFRACTION": ["X-RAY DIFFRACTION"],
+      "CYCLIC VOLTAMMETRY": ["CYCLIC VOLTAMMETRY"],
+      "SIZE EXCLUSION CHROMATOGRAPHY": ["SIZE EXCLUSION CHROMATOGRAPHY"],
+      "CIRCULAR DICHROISM SPECTROSCOPY": ["CIRCULAR DICHROISM SPECTROSCOPY"],
+      "SORPTION-DESORPTION MEASUREMENT": ["SORPTION-DESORPTION MEASUREMENT"],
+      "Emissions": ["Emissions", "EMISSIONS", "FLUORESCENCE SPECTRUM", "FL SPECTRUM"],
+      "DLS ACF": ["DLS ACF"],
+      "DLS intensity": ["DLS INTENSITY", "DLS intensity"]
+  }
+}

tests/controller/test_spectra_layout_api.py

@@ -7,17 +7,8 @@ def test_get_spectra_layouts_with_data(client):
     response_data = response.json()
     assert response.status_code == 200
     assert response_data == {
-        "NMRSPECTRUM": "NMR",
-        "INFRARED SPECTRUM": "INFRARED"
-        }
-
-def test_get_spectra_layouts_without_data(client):
-    data_type_json_path = './tests/fixtures/result/spectralayout_test_data.json'
-
-    response = client.get('/spectra_layouts')
-    response_data = response.json()
-    assert response.status_code == 200
-    assert response_data == {}
-
-    if os.path.exists(data_type_json_path):
-        os.remove(data_type_json_path)
+        "INFRARED": ["INFRARED SPECTRUM"],
+        "MS": ["MASS SPECTRUM"],
+        "NMR": ["NMR SPECTRUM", "NMRSPECTRUM"],
+        "RAMAN": ["RAMAN"]
+        }

tests/controller/test_spectra_type_api.py

@@ -3,25 +3,25 @@
 
 data_type_json_path = './tests/fixtures/test_data_types.json'
 
-def test_create_or_update_data_type(client):
+def test_create_data_type(client):
     new_data_type = {
         "new_data_type": {
-            "MASS SPECTRUM": "MS"
+            "MS": "MASS SPEC"
         }
     }
 
     response = client.post('/data_type', json=new_data_type)
     assert response.status_code == 200
 
     response_data = response.json()
-    assert response_data.get("datatypes") is not None
-    assert response_data["datatypes"].get("MASS SPECTRUM") == "MS"
+    assert "message" in response_data
+    response_data["message"] == "Data type created successfully"
 
-def test_create_or_update_data_type_unchanged(client):    
+def test_create_data_type_unchanged(client):    
     # data type already exists in JSON
     new_data_type = {
         "new_data_type": {
-             "INFRARED SPECTRUM": "INFRARED"
+             "INFRARED": "INFRARED SPECTRUM"
         }
     }
 
@@ -33,35 +33,35 @@ def test_create_or_update_data_type_unchanged(client):
     assert "message" in response_data
     assert response_data["message"] == "Data type 'INFRARED SPECTRUM' already exists"
 
-def test_create_or_update_data_type_file_not_found(client):
-    data_type_json_path = './tests/fixtures/result/spectratype_test_data.json'
-
+def test_create_data_type_layout_does_not_exist(client):
     new_data_type = {
         "new_data_type": {
-            "RAMAN SPECTRUM": "RAMAN"
+             "UNKNOWN": "NA"
         }
     }
 
     response = client.post('/data_type', json=new_data_type)
-    assert response.status_code == 200
-    response_data = response.json()
-    assert len(response_data.get("datatypes")) == 1
-    assert response_data["datatypes"].get("RAMAN SPECTRUM") == "RAMAN"
+    assert response.status_code == 400
 
-    if os.path.exists(data_type_json_path):
-        os.remove(data_type_json_path)
+    response_data = response.json()
+
+    assert "message" in response_data
+    assert response_data["message"] == "Layout 'UNKNOWN' does not exist"
 
 def test_delete_data_type(client):
     # create a new data type
     new_data_type = {
         "new_data_type": {
-            "FLUORESCENCE": "FLUORESCENCE SPECTRUM"
+            "INFRARED": "IR"
         }
     }
     response = client.post('/data_type', json=new_data_type)
     assert response.status_code == 200
 
     # delete the new data type
-    response = client.delete('/data_type/FLUORESCENCE')
+    response = client.delete('/data_type/IR')
     assert response.status_code == 200
+    response_data = response.json()
 
+    assert "message" in response_data
+    assert response_data["message"] == "Data type 'IR' deleted successfully"

tests/fixtures/test_data_types.json

@@ -1,6 +1,8 @@
 {
-    "datatypes": {
-      "NMRSPECTRUM": "NMR",
-      "INFRARED SPECTRUM": "INFRARED"
+  "datatypes": {
+    "NMR": ["NMR SPECTRUM", "NMRSPECTRUM"],
+    "INFRARED": ["INFRARED SPECTRUM"],
+    "RAMAN": ["RAMAN"],
+    "MS": ["MASS SPECTRUM"]
   }
 }