fix: store molfile data into nmrium

chem_spectra/controller/transform_api.py

@@ -14,6 +14,7 @@
 
 from chem_spectra.model.transformer import TransformerModel as TraModel
 from chem_spectra.lib.converter.bagit.base import BagItBaseConverter
+from chem_spectra.model.molecule import MoleculeModel
 
 
 trans_api = Blueprint('transform_api', __name__)
@@ -33,7 +34,8 @@ def zip_jcamp_n_img():
     molfile = FileContainer(request.files.get('molfile'))
     params = extract_params(request)
     if file:  # and allowed_file(file):
-        cmpsr, invalid_molfile = TraModel(file, molfile=molfile, params=params).to_composer()
+        transform_model = TraModel(file, molfile=molfile, params=params)
+        cmpsr, invalid_molfile = transform_model.to_composer()
         if (not cmpsr):
             abort(403)
 
@@ -79,7 +81,14 @@ def zip_jcamp_n_img():
             )
             rsp.headers['X-Extra-Info-JSON'] = json.dumps({'spc_type': spc_type, 'invalid_molfile': invalid_molfile})
         else:
-            tf_jcamp, tf_img, tf_csv, tf_nmrium = cmpsr.tf_jcamp(), cmpsr.tf_img(), cmpsr.tf_csv(), cmpsr.generate_nmrium()
+            tf_jcamp, tf_img, tf_csv = cmpsr.tf_jcamp(), cmpsr.tf_img(), cmpsr.tf_csv()
+            tf_nmrium = None
+            try:
+                molecule_model = MoleculeModel(molfile, cmpsr.core.ncl, decorate=False)
+                tf_nmrium = cmpsr.generate_nmrium(molfile_data=molecule_model.moltxt)
+            except Exception:
+                pass
+
             spc_type = cmpsr.core.ncl if cmpsr.core.typ == 'NMR' else cmpsr.core.typ
             if (tf_csv is not None and tf_csv != False):
                 memory = to_zip_response([tf_jcamp, tf_img, tf_csv])

chem_spectra/lib/composer/ni.py

@@ -587,15 +587,15 @@ def tf_csv(self):
                 })
         return tf_csv
 
-    def generate_nmrium(self, version=4):
+    def generate_nmrium(self, version=4, molfile_data=None):
         typ = self.core.typ
         if 'NMR' != typ:
             return None
 
         if version == 3:
-            dic_data = self.__generate_nmrium_version_3()
+            dic_data = self.__generate_nmrium_version_3(molfile_data=molfile_data)
         else:
-            dic_data = self.__generate_nmrium_data(version)
+            dic_data = self.__generate_nmrium_data(version=version, molfile_data=molfile_data)
 
         json_data = json.dumps(dic_data)
 
@@ -604,16 +604,18 @@ def generate_nmrium(self, version=4):
         tf_nmrium.seek(0)
         return tf_nmrium
 
-    def __generate_nmrium_version_3(self):
+    def __generate_nmrium_version_3(self, molfile_data=None):
         dic_data = {'actionType': 'INITIATE', 'version': 3}
         spectra = self.__generate_nmrim_spectra()
         dic_data['spectra'] = spectra
+        dic_data['molecules'] = self.__generate_molecules(molfile_data)
         return dic_data
 
-    def __generate_nmrium_data(self, version):
+    def __generate_nmrium_data(self, version, molfile_data=None):
         dic_data = {'version': version, 'data': {}, 'view': {}}
         spectra = self.__generate_nmrim_spectra()
         dic_data['data']['spectra'] = spectra
+        dic_data['data']['molecules'] = self.__generate_molecules(molfile_data)
         return dic_data
 
     def __generate_nmrim_spectra(self):
@@ -793,3 +795,16 @@ def __generate_nmrim_ranges(self):
             dic_ranges['values'].append(rang_item)
 
         return dic_ranges
+
+    def __generate_molecules(self, molfile_data):
+        if molfile_data is None:
+          return []
+
+        molecule_id = str(uuid.uuid4())
+        return [
+            {
+                'id': molecule_id,
+                'label': 'P1',
+                'molfile': molfile_data
+            }
+        ]

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name='chem-spectra-app',
-    version='1.1.1',
+    version='1.1.2',
     packages=find_packages(),
     include_package_data=True,
     zip_safe=False,

tests/fixtures/source/nmrium/nmrium_data_schema_v3.json

@@ -1,5 +1,6 @@
 {
   "version": 3,
   "actionType": "",
-  "spectra": []
+  "spectra": [],
+  "molecules": []
 }

tests/fixtures/source/nmrium/nmrium_data_schema_v4.json

@@ -1,7 +1,8 @@
 {
   "version": 4,
   "data": {
-    "spectra": []
+    "spectra": [],
+    "molecules": []
   },
   "view": {}
 }

tests/fixtures/source/nmrium/nmrium_data_schema_v5.json

@@ -1,7 +1,8 @@
 {
   "version": 5,
   "data": {
-    "spectra": []
+    "spectra": [],
+    "molecules": []
   },
   "view": {}
 }

tests/lib/composer/test_ni_composer.py

@@ -4,10 +4,12 @@
 from chem_spectra.lib.converter.jcamp.base import JcampBaseConverter
 from chem_spectra.lib.converter.jcamp.ni import JcampNIConverter
 from chem_spectra.lib.composer.ni import NIComposer
+from chem_spectra.controller.helper.file_container import FileContainer
 
 source_nmr = './tests/fixtures/source/1H.dx'
 source_nmr_edit = './tests/fixtures/source/1H.edit.jdx'
 source_ir = './tests/fixtures/source/IR.dx'
+source_dir_molfile = './tests/fixtures/source/molfile/c60h57fn4.mol'
 
 @pytest.fixture
 def data_schema():
@@ -29,6 +31,15 @@ def jcamp_file_1h_edit():
 def jcamp_file_ir():
     return source_ir
 
+@pytest.fixture
+def molfile_data():
+    molfile = open(source_dir_molfile, "r")
+    molfile_str = molfile.read()
+    return molfile_str
+    # molfile.close()
+    # molfile_data = FileContainer().from_str(molfile_str)
+    # return molfile_data
+
 def test_init_ni_composer_failed():
     with pytest.raises(Exception) as error:
         _ = NIComposer(None)
@@ -203,3 +214,42 @@ def test_ni_composer_generate_nmrium(jcamp_file_1h):
         y_value = xy_points['re']
         assert len(x_values) == 65536
         assert len(y_value) == 65536
+
+def test_ni_composer_generate_nmrium_without_molfile(jcamp_file_1h):
+    base_converter = JcampBaseConverter(jcamp_file_1h)
+    ni_converter = JcampNIConverter(base=base_converter)
+    ni_composer = NIComposer(core=ni_converter)
+    nmrium_file = ni_composer.generate_nmrium()
+
+    assert nmrium_file is not None
+    with open(nmrium_file.name) as file:
+        file_content = file.read()
+        assert file_content != ""
+
+        dic_content = json.loads(file_content)
+        dic_data = dic_content['data']
+        molecules = dic_data['molecules']
+        assert molecules is not None
+        assert len(molecules) == 0
+
+def test_ni_composer_generate_nmrium_with_molfile(jcamp_file_1h, molfile_data):
+    base_converter = JcampBaseConverter(jcamp_file_1h)
+    ni_converter = JcampNIConverter(base=base_converter)
+    ni_composer = NIComposer(core=ni_converter)
+    nmrium_file = ni_composer.generate_nmrium(molfile_data=molfile_data)
+
+    assert nmrium_file is not None
+    with open(nmrium_file.name) as file:
+        file_content = file.read()
+        assert file_content != ""
+
+        dic_content = json.loads(file_content)
+        dic_data = dic_content['data']
+        molecules = dic_data['molecules']
+        assert molecules is not None
+        assert len(molecules) == 1
+
+        molecule_data = molecules[0]
+        assert 'id' in molecule_data.keys()
+        assert molecule_data['label'] == 'P1'
+        assert molecule_data['molfile'] == molfile_data