Update the way to handle spectra type (#133)

* Map data types and spectra layouts

* FIx: process lower/mixed case data types

chem_spectra/__init__.py

@@ -1,6 +1,8 @@
 import os
 
 from flask import Flask
+from flask_jwt_extended import JWTManager
+from datetime import timedelta
 
 import logging
 
@@ -23,6 +25,11 @@ def create_app(test_config=None):
     except OSError:
         pass
 
+    app.config["JWT_ACCESS_TOKEN_EXPIRES"] = timedelta(days=1)
+    app.config["JWT_REFRESH_TOKEN_EXPIRES"] = timedelta(days=30)
+
+    jwt = JWTManager(app)
+
     #create logging
     logger = logging.getLogger(__name__)
     logger.setLevel(logging.INFO)
@@ -39,6 +46,10 @@ def create_app(test_config=None):
     @app.route('/ping')
     def ping():
         return 'pong'
+
+    # Refresh token api
+    from chem_spectra.controller.refresh_token_api import refresh_token_api
+    app.register_blueprint(refresh_token_api)
 
     # file api
     from chem_spectra.controller.file_api import file_api
@@ -52,4 +63,8 @@ def ping():
     from chem_spectra.controller.transform_api import trans_api
     app.register_blueprint(trans_api)
 
+    # spectra layout api
+    from chem_spectra.controller.spectra_layout_api import spectra_layout_api
+    app.register_blueprint(spectra_layout_api)
+
     return app

chem_spectra/controller/refresh_token_api.py

@@ -0,0 +1,19 @@
+from flask import jsonify, Blueprint
+from flask_jwt_extended import jwt_required, create_access_token, get_jwt_identity, create_refresh_token
+
+
+refresh_token_api = Blueprint('refresh_token_api', __name__)
+
+@refresh_token_api.route("/api/v1/chemspectra/login", methods=["POST"])
+def login():
+    access_token = create_access_token(identity="user")
+    refresh_token = create_refresh_token(identity="user")
+    return jsonify(access_token=access_token, refresh_token=refresh_token)
+
+
+@refresh_token_api.route("/api/v1/chemspectra/refresh", methods=["POST"])
+@jwt_required(refresh=True)
+def refresh():
+    identity = get_jwt_identity()
+    access_token = create_access_token(identity=identity)
+    return jsonify(access_token=access_token)

chem_spectra/controller/spectra_layout_api.py

@@ -0,0 +1,65 @@
+import json
+from flask import jsonify, Blueprint, request
+import os
+import shutil
+from flask_jwt_extended import jwt_required
+
+spectra_layout_api = Blueprint('spectra_layout_api', __name__)
+script_dir = os.path.dirname(__file__)
+data_type_json_path = os.path.join(script_dir, '../lib/converter/jcamp/data_type.json')
+
+def load_data_types():
+    try:
+        with open(data_type_json_path, 'r') as mapping_file:
+            return json.load(mapping_file)
+    except FileNotFoundError:
+        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_layout_api.route('/api/v1/chemspectra/spectra_layouts', methods=['GET', 'PUT', 'DELETE'])
+@jwt_required()
+def update_or_fetch_mapping():
+    if request.method == 'GET':
+         existing_data_types = load_data_types()
+         return jsonify(existing_data_types["datatypes"]), 200   
+
+    elif request.method == 'PUT':
+        request_data = request.get_json()
+        new_data_type_mapping = request_data.get("new_data_type")
+        existing_data_types = load_data_types()
+
+        for layout, data_type in new_data_type_mapping.items():
+            if data_type == '':
+                return jsonify({"message": "Invalid Data Type"}), 400
+            elif 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
+            else:
+                return jsonify({"message": f"Layout '{layout}' does not exist"}), 400
+
+        save_data_types(existing_data_types)
+        return jsonify({"message": "Data type created successfully"}), 200
+
+    elif request.method == 'DELETE':
+        request_data = request.get_json()
+        data_type_mapping = request_data.get("data_type")
+        existing_data_types = load_data_types()
+        for layout, data_type in data_type_mapping.items():
+            if layout in existing_data_types["datatypes"]:
+                if data_type in existing_data_types['datatypes'][layout]:
+                    existing_data_types['datatypes'][layout].remove(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 in layout '{layout}'"}), 404
+            else:
+                return jsonify({"message": f"Layout '{layout}' does not exist"}), 400
+    else:
+        return jsonify({"message": "Method not allowed"}), 405

chem_spectra/lib/converter/jcamp/base.py

@@ -1,6 +1,10 @@
 import nmrglue as ng
+import json
 
 from chem_spectra.lib.converter.share import parse_params, parse_solvent
+import os
+
+data_type_json = os.path.join(os.path.dirname(__file__), 'data_type.json')
 
 
 class JcampBaseConverter:
@@ -43,82 +47,36 @@ def __read(self, path):
 
     def __set_datatype(self):
         dts = self.datatypes
-        if 'NMR SPECTRUM' in dts:
-            return 'NMR SPECTRUM'
-        elif 'NMRSPECTRUM' in dts:  # MNova
-            return 'NMR SPECTRUM'
-        elif 'INFRARED SPECTRUM' in dts:
-            return 'INFRARED SPECTRUM'
-        elif 'RAMAN SPECTRUM' in dts:
-            return 'RAMAN SPECTRUM'
-        elif 'MASS SPECTRUM' in dts:
-            return 'MASS SPECTRUM'
-        elif 'HPLC UV/VIS SPECTRUM' in dts:
-            return 'HPLC UV/VIS SPECTRUM'
-        elif 'HPLC UV-VIS' in dts:
-            return 'HPLC UV/VIS SPECTRUM'
-        elif 'UV/VIS SPECTRUM' in dts:
-            return 'UV/VIS SPECTRUM'
-        elif 'UV-VIS' in dts:
-            return 'UV/VIS SPECTRUM'
-        elif 'ULTRAVIOLET SPECTRUM' in dts:
-            return 'UV/VIS SPECTRUM'
-        elif 'THERMOGRAVIMETRIC ANALYSIS' in dts:
-            return 'THERMOGRAVIMETRIC ANALYSIS'
-        elif 'X-RAY DIFFRACTION' in dts:
-            return 'X-RAY DIFFRACTION'
-        elif 'CYCLIC VOLTAMMETRY' in dts:
-            return 'CYCLIC VOLTAMMETRY'
-        elif 'SIZE EXCLUSION CHROMATOGRAPHY' in dts:
-            return 'SIZE EXCLUSION CHROMATOGRAPHY'
-        elif 'CIRCULAR DICHROISM SPECTROSCOPY' in dts:
-            return 'CIRCULAR DICHROISM SPECTROSCOPY'
-        elif 'SORPTION-DESORPTION MEASUREMENT' in dts:
-            return 'SORPTION-DESORPTION MEASUREMENT'
-        elif 'Emissions' in dts or 'EMISSIONS' in dts or 'FLUORESCENCE SPECTRUM' in dts or 'FL SPECTRUM' in dts:
-            return 'Emissions'
-        elif 'DLS ACF' in dts:
-            return 'DLS ACF'
-        elif 'DLS INTENSITY' in dts or 'DLS intensity' in dts:
-            return 'DLS intensity'
+        dt_dict = {
+            'NMR': 'NMR SPECTRUM',
+            'INFRARED': 'INFRARED SPECTRUM',
+            'RAMAN': 'RAMAN SPECTRUM',
+            'MS': 'MASS SPECTRUM',
+            'HPLC UVVIS': 'HPLC UV/VIS SPECTRUM',
+            'UVVIS': 'UV/VIS SPECTRUM',
+        }
+
+        with open(data_type_json, 'r') as mapping_file:
+            data_type_mappings = json.load(mapping_file)["datatypes"]
+        for key, values in data_type_mappings.items():
+            values = [value.upper() for value in values]
+            for dt in dts:
+                if dt in values and key in dt_dict:
+                    return dt_dict[key]
+                elif dt in values and not key in dt_dict:
+                    return key
         return ''
 
     def __typ(self):
         dt = self.datatype
-        if 'NMR SPECTRUM' == dt:
-            return 'NMR'
-        elif 'NMRSPECTRUM' == dt:  # MNova
-            return 'NMR'
-        elif 'INFRARED SPECTRUM' == dt:
-            return 'INFRARED'  # TBD
-        elif 'RAMAN SPECTRUM' == dt:
-            return 'RAMAN'  # TBD
-        elif 'MASS SPECTRUM' == dt:
-            return 'MS'
-        elif 'HPLC UV/VIS SPECTRUM' == dt:
-            return 'HPLC UVVIS'
-        elif 'HPLC UV-VIS' == dt:
-            return 'HPLC UVVIS'
-        elif 'UV/VIS SPECTRUM' == dt or 'UV-VIS' == dt or 'ULTRAVIOLET SPECTRUM' == dt:
-            return 'UVVIS'
-        elif 'THERMOGRAVIMETRIC ANALYSIS' == dt:
-            return 'THERMOGRAVIMETRIC ANALYSIS'
-        elif 'X-RAY DIFFRACTION' == dt:
-            return 'X-RAY DIFFRACTION'
-        elif 'CYCLIC VOLTAMMETRY' in dt:
-            return 'CYCLIC VOLTAMMETRY'
-        elif 'SIZE EXCLUSION CHROMATOGRAPHY' in dt:
-            return 'SIZE EXCLUSION CHROMATOGRAPHY'
-        elif 'CIRCULAR DICHROISM SPECTROSCOPY' in dt:
-            return 'CIRCULAR DICHROISM SPECTROSCOPY'
-        elif 'SORPTION-DESORPTION MEASUREMENT' in dt:
-            return 'SORPTION-DESORPTION MEASUREMENT'
-        elif 'Emissions' in dt or 'EMISSIONS' in dt or 'FLUORESCENCE SPECTRUM' in dt or 'FL SPECTRUM' in dt:
-            return 'Emissions'
-        elif 'DLS ACF' in dt:
-            return 'DLS ACF'
-        elif 'DLS INTENSITY' in dt or 'DLS intensity' in dt:
-            return 'DLS intensity'
+
+        with open(data_type_json, 'r') as mapping_file:
+            data_type_mappings = json.load(mapping_file)["datatypes"]
+
+        for key, values in data_type_mappings.items():
+            values = [value.upper() for value in values]
+            if dt.upper() in values:
+                return key
         return ''
 
     def __set_dataclass(self):
@@ -140,12 +98,10 @@ def __is_em_wave(self):
         return self.typ in ['INFRARED', 'RAMAN', 'UVVIS']
 
     def __non_nmr(self):
-        return self.typ in [
-            'INFRARED', 'RAMAN', 'UVVIS', 'HPLC UVVIS',
-            'THERMOGRAVIMETRIC ANALYSIS', 'MS', 'X-RAY DIFFRACTION',
-            'CYCLIC VOLTAMMETRY', 'SIZE EXCLUSION CHROMATOGRAPHY',
-            'CIRCULAR DICHROISM SPECTROSCOPY', 'SORPTION-DESORPTION MEASUREMENT', 'Emissions', 
-            'DLS ACF', 'DLS intensity']
+        with open(data_type_json, 'r') as mapping_file:
+            data_type_mappings = json.load(mapping_file).get("datatypes")
+        dts = [dt for dt in data_type_mappings.keys() if dt != 'NMR']
+        return self.typ in dts
 
     def __is_ir(self):
         return self.typ in ['INFRARED']
@@ -175,13 +131,13 @@ def __is_aif(self):
         return self.typ in ['SORPTION-DESORPTION MEASUREMENT']
 
     def __is_emissions(self):
-        return self.typ in ['Emissions', 'EMISSIONS', 'FLUORESCENCE SPECTRUM', 'FL SPECTRUM']
+        return self.typ in ['Emissions']
 
     def __is_dls_acf(self):
         return self.typ in ['DLS ACF']
 
     def __is_dls_intensity(self):
-        return self.typ in ['DLS INTENSITY', 'DLS intensity']
+        return self.typ in ['DLS intensity']
 
     def __ncl(self):
         try:

chem_spectra/lib/converter/jcamp/data_type.json

@@ -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"]
+  }
+}

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"]
+  }
+}