update mapping

chem_spectra/lib/converter/jcamp/base.py

@@ -2,6 +2,9 @@
 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:
@@ -44,21 +47,35 @@ def __read(self, path):
 
     def __set_datatype(self):
         dts = self.datatypes
-
-        with open('data_type.json', 'r') as mapping_file:
+        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 dt in dts:
-            if dt in data_type_mappings:
-                return data_type_mappings[dt]
+        for key, values in data_type_mappings.items():
+            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
 
-        with open('data_type.json', 'r') as mapping_file:
+        with open(data_type_json, 'r') as mapping_file:
             data_type_mappings = json.load(mapping_file)["datatypes"]
 
-        return data_type_mappings.get(dt, '')
+        for key, values in data_type_mappings.items():
+            if dt in values:
+                return key
+        return ''
 
     def __set_dataclass(self):
         data_class = self.dataclasses
@@ -79,10 +96,9 @@ def __is_em_wave(self):
         return self.typ in ['INFRARED', 'RAMAN', 'UVVIS']
 
     def __non_nmr(self):
-        with open('data_type.json', 'r') as mapping_file:
+        with open(data_type_json, 'r') as mapping_file:
             data_type_mappings = json.load(mapping_file).get("datatypes")
-        dts = set(data_type_mappings.values())
-        dts.discard('NMR')
+        dts = [dt for dt in data_type_mappings.keys() if dt != 'NMR']
         return self.typ in dts
 
     def __is_ir(self):

chem_spectra/lib/converter/jcamp/data_type.json

@@ -1,27 +1,19 @@
 {
-    "datatypes": {
-      "NMR SPECTRUM": "NMR",
-      "NMRSPECTRUM": "NMR",
-      "INFRARED SPECTRUM": "INFRARED",
-      "RAMAN SPECTRUM": "RAMAN",
-      "MASS SPECTRUM": "MS",
-      "HPLC UV/VIS SPECTRUM": "HPLC UVVIS",
-      "HPLC UV-VIS": "HPLC UVVIS",
-      "UV/VIS SPECTRUM": "UVVIS",
-      "UV-VIS": "UVVIS",
-      "ULTRAVIOLET SPECTRUM": "UVVIS",
-      "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": "Emissions",
-      "FLUORESCENCE SPECTRUM": "Emissions",
-      "FL SPECTRUM": "Emissions",
-      "DLS ACF": "DLS ACF",
-      "DLS INTENSITY": "DLS intensity",
-      "DLS intensity": "DLS intensity"
+  "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/ni.py

@@ -5,6 +5,7 @@
 from chem_spectra.lib.shared.calc import to_float
 from chem_spectra.lib.converter.jcamp.data_parse import make_ni_data_ys, make_ni_data_xs
 import json
+import os
 
 THRESHOLD_IR = 0.93
 THRESHOLD_RAMAN = 0.07
@@ -14,7 +15,7 @@
 THRESHOLD_TGA = 1.05
 THRESHOLD_XRD = 1.00
 THRESHOLD_EMISSION = 0.5
-
+data_type_json = os.path.join(os.path.dirname(__file__), 'data_type.json')
 
 class JcampNIConverter:  # nmr & IR
     def __init__(self, base):
@@ -74,31 +75,33 @@ def __init__(self, base):
 
     def __thres(self):
         dt = self.datatype
-        with open('data_type.json', 'r') as mapping_file:
+        threshold_values = {
+            "NMR": THRESHOLD_NMR,
+            "INFRARED": THRESHOLD_IR,
+            "RAMAN": THRESHOLD_RAMAN,
+            "MS": THRESHOLD_MS,
+            "HPLC UVVIS": THRESHOLD_UVVIS,
+            "UVVIS": THRESHOLD_UVVIS,
+            "THERMOGRAVIMETRIC ANALYSIS": THRESHOLD_TGA,
+            "DLS ACF": THRESHOLD_TGA,
+            "X-RAY DIFFRACTION": THRESHOLD_XRD,
+            "CIRCULAR DICHROISM SPECTROSCOPY": THRESHOLD_XRD,
+            "CYCLIC VOLTAMMETRY": THRESHOLD_XRD,
+            "SORPTION-DESORPTION MEASUREMENT": THRESHOLD_XRD,
+            "DLS intensity": THRESHOLD_XRD,
+            "Emissions": THRESHOLD_EMISSION
+        }
+        with open(data_type_json, 'r') as mapping_file:
             data_type_mappings = json.load(mapping_file)["datatypes"]
-
-        if data_type_mappings.get(dt) == "NMR":
-            return THRESHOLD_NMR
-        elif data_type_mappings.get(dt) == "INFRARED":
-            return THRESHOLD_IR
-        elif data_type_mappings.get(dt) == "RAMAN":
-            return THRESHOLD_RAMAN
-        elif data_type_mappings.get(dt) == "MS":
-            return THRESHOLD_MS
-        elif data_type_mappings.get(dt) in ["HPLC UVVIS", 'UVVIS']:
-            return THRESHOLD_UVVIS
-        elif data_type_mappings.get(dt) in ['THERMOGRAVIMETRIC ANALYSIS', 'DLS ACF']:
-            return THRESHOLD_TGA
-        elif data_type_mappings.get(dt) in ['X-RAY DIFFRACTION', 'CIRCULAR DICHROISM SPECTROSCOPY', 'CYCLIC VOLTAMMETRY', 
-                                            'SORPTION-DESORPTION MEASUREMENT', 'DLS intensity']:
-            return THRESHOLD_XRD
-        elif data_type_mappings.get(dt) in ['Emissions']:
-            return THRESHOLD_EMISSION
-        return 0.5
+        key = next((k for k, v in data_type_mappings.items() if dt in v), None)
+
+        return threshold_values.get(key, 0.5)
+
 
     def __index_target(self):
-        with open('data_type.json', 'r') as mapping_file:
-            target_topics = json.load(mapping_file).get("datatypes")
+        with open(data_type_json, 'r') as mapping_file:
+            target = json.load(mapping_file).get("datatypes").values()
+            target_topics = [value for values in target for value in values]
 
         for tp in target_topics:
             if tp in self.datatypes: