fix and refactor: fix generated jcamp for nmrium and change label for…

… CV layout (#171)

fix: fixed generated jcamp file cannot be read by nmrium

refactor: change label name for CV data

chem_spectra/lib/composer/base.py

@@ -134,6 +134,7 @@ def generate_original_metadata(self):
             content.append(
                 '###{}= {}\n'.format(str_key.upper(), str_value)
             )
+        content.append('\n\n')
         return content
     def gen_ending(self):
         return [

chem_spectra/lib/composer/ms.py

@@ -79,7 +79,6 @@ def __compose(self):
         meta.extend(self.__gen_ntuples_end())
 
         meta.extend(self.generate_original_metadata())
-        meta.extend(self.gen_ending())
 
         meta.extend(self.gen_ending())
         return meta

chem_spectra/lib/composer/ni.py

@@ -225,7 +225,6 @@ def __compose(self):
         meta.extend(self.gen_ending())
 
         meta.extend(self.generate_original_metadata())
-        meta.extend(self.gen_ending())
 
         meta.extend(self.gen_ending())
         return meta
@@ -490,26 +489,26 @@ def tf_img(self):
 
     def __prepare_metadata_info_for_csv(self, csv_writer: csv.DictWriter):
         csv_writer.writerow({
-            'Ox E(V)': 'Measurement type',
-            'Red E(V)': 'Cyclic Voltammetry',
+            'Anodic E(V)': 'Measurement type',
+            'Cathodic E(V)': 'Cyclic Voltammetry',
         })
         csv_writer.writerow({
-            'Ox E(V)': 'Measurement type ID',
+            'Anodic E(V)': 'Measurement type ID',
         })
         csv_writer.writerow({
-            'Ox E(V)': 'Sample ID',
+            'Anodic E(V)': 'Sample ID',
         })
         csv_writer.writerow({
-            'Ox E(V)': 'Analysis ID',
+            'Anodic E(V)': 'Analysis ID',
         })
         csv_writer.writerow({
-            'Ox E(V)': 'Dataset ID',
+            'Anodic E(V)': 'Dataset ID',
         })
         csv_writer.writerow({
-            'Ox E(V)': 'Dataset name',
+            'Anodic E(V)': 'Dataset name',
         })
         csv_writer.writerow({
-            'Ox E(V)': 'Link to sample',
+            'Anodic E(V)': 'Link to sample',
         })
         csv_writer.writerow({
         })
@@ -527,7 +526,7 @@ def tf_csv(self):
             listMaxMinPeaks = self.core.params['list_max_min_peaks']
 
         with open(tf_csv.name, 'w', newline='', encoding='utf-8') as csvfile:
-            fieldnames = ['Ox E(V)', 'Ox I(A)', 'Red E(V)', 'Red I(A)', 'I lambda0(A)', 'I ratio', 'E1/2(V)', 'Delta Ep(mV)']
+            fieldnames = ['Anodic E(V)', 'Anodic I(A)', 'Cathodic E(V)', 'Cathodic I(A)', 'I lambda0(A)', 'I ratio', 'E1/2(V)', 'Delta Ep(mV)']
             writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
 
             self.__prepare_metadata_info_for_csv(writer)
@@ -577,10 +576,10 @@ def tf_csv(self):
                         y_pecker = ''
 
                 writer.writerow({
-                    'Ox E(V)': '{x_max}'.format(x_max=x_max_peak),
-                    'Ox I(A)': '{y_max}'.format(y_max=y_max_peak),
-                    'Red E(V)': '{x_min}'.format(x_min=x_min_peak),
-                    'Red I(A)': '{y_min}'.format(y_min=y_min_peak),
+                    'Anodic E(V)': '{x_max}'.format(x_max=x_max_peak),
+                    'Anodic I(A)': '{y_max}'.format(y_max=y_max_peak),
+                    'Cathodic E(V)': '{x_min}'.format(x_min=x_min_peak),
+                    'Cathodic I(A)': '{y_min}'.format(y_min=y_min_peak),
                     'I lambda0(A)': '{y_pecker}'.format(y_pecker=y_pecker),
                     'I ratio': '{ratio}'.format(ratio=ratio),
                     'E1/2(V)': '{e12}'.format(e12=e12),

tests/fixtures/result/edit/edit_meta_13C-DEPT135

@@ -685,7 +685,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###$CSSOLVENTNAME= DMSO-d6
 ###$CSSOLVENTVALUE= 39.52
 ###$CSSOLVENTX= 0
-##END=
+
 
 ##END=
 

tests/fixtures/result/edit/edit_meta_1H

@@ -698,7 +698,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###$CSSOLVENTNAME= DMSO-d6 (quin)
 ###$CSSOLVENTVALUE= 2.5
 ###$CSSOLVENTX= 0
-##END=
+
 
 ##END=
 

tests/fixtures/result/edit/edit_meta_IR

@@ -102,7 +102,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###$CSTHRESHOLD= 0.8, 0.8
 ###MAXX= 3997.453, 3997.453
 ###MINX= 373.96442, 373.96442
-##END=
+
 
 ##END=
 

tests/fixtures/result/im/im_meta_1H

@@ -754,7 +754,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###$CSSOLVENTNAME= DMSO-d6 (quin)
 ###$CSSOLVENTVALUE= 2.5
 ###$CSSOLVENTX= 0
-##END=
+
 
 ##END=
 

tests/fixtures/result/im/im_meta_IR

@@ -156,7 +156,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###MAXY= 1.0055419
 ###MINY= 0.27871406
 ###NPOINTS= 2559
-##END=
+
 
 ##END=
 

tests/fixtures/result/meta_13C-CPD

@@ -702,7 +702,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###$CSSOLVENTNAME= DMSO-d6
 ###$CSSOLVENTVALUE= 39.52
 ###$CSSOLVENTX= 0
-##END=
+
 
 ##END=
 

tests/fixtures/result/meta_1H

@@ -747,7 +747,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###$CSSOLVENTNAME= DMSO-d6 (quin)
 ###$CSSOLVENTVALUE= 2.5
 ###$CSSOLVENTX= 0
-##END=
+
 
 ##END=
 

tests/fixtures/result/meta_IR

@@ -156,7 +156,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###MAXY= 1.0055419
 ###MINY= 0.27871406
 ###NPOINTS= 2559
-##END=
+
 
 ##END=
 

tests/fixtures/result/meta_SVS-790A_13C

@@ -219,7 +219,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###$CSSOLVENTNAME= Chloroform-d (t)
 ###$CSSOLVENTVALUE= 77.16
 ###$CSSOLVENTX= 0
-##END=
+
 
 ##END=
 

tests/fixtures/result/ps/ps_meta_IR

@@ -159,7 +159,7 @@ $$ === CHEMSPECTRA ORIGINAL METADATA ===
 ###MAXY= 1.0055419
 ###MINY= 0.27871406
 ###NPOINTS= 2559
-##END=
+
 
 ##END=
 

tests/lib/composer/test_base_composer.py

@@ -36,4 +36,5 @@ def test_base_composer_generate_original_metadata(jcamp_file_1h):
       '###.AVERAGES= 16\n',
       '###.SHIFT REFERENCE= INTERNAL, CDCl3, 1, 15.91938\n',
       '###.AVERAGES= 16\n',
+      '\n\n'
     ]