Update to version 1.1.2

.github/workflows/unit_test.yml

@@ -1,21 +1,24 @@
-name: Test with pytest
+name: Tests
 
 on: [push]
 
 jobs:
-  build-linux:
+  run-unit-tests:
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python 3.8
       uses: actions/setup-python@v4
       with:
         python-version: 3.8
     - name: Install dependencies
-      run: |
-        $CONDA/bin/conda env update --file environment.yml --name base
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        activate-environment: python-v38
+        environment-file: environment.yml
+        miniforge-version: latest
     - name: Test with pytest
+      shell: bash -el {0}
       run: |
-        # pip install -r requirements.txt
-        $CONDA/bin/python -m pytest
+        conda activate python-v38
+        python -m pytest

README.md

@@ -2,6 +2,9 @@
 
 This backend web service provides NMR/IR/MS processing for jcamp/RAW/mzML files.
 
+![Python 3.8](https://img.shields.io/badge/python-3.8-blue.svg)
+![Testing](https://github.com/ComPlat/chem-spectra-app/actions/workflows/unit_test.yml/badge.svg)
+
 The frontend is provided by chem-spectra-client.
 
 ### Install

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

@@ -587,21 +587,36 @@ def tf_csv(self):
                 })
         return tf_csv
 
-    def generate_nmrium(self):
+    def generate_nmrium(self, version=4, molfile_data=None):
         typ = self.core.typ
         if 'NMR' != typ:
             return None
 
-        dic_data = {'actionType': 'INITIATE', 'version': 3}
-        spectra = self.__generate_nmrim_spectra()
-        dic_data['spectra'] = spectra
+        if version == 3:
+            dic_data = self.__generate_nmrium_version_3(molfile_data=molfile_data)
+        else:
+            dic_data = self.__generate_nmrium_data(version=version, molfile_data=molfile_data)
 
         json_data = json.dumps(dic_data)
 
         tf_nmrium = tempfile.NamedTemporaryFile(suffix='.nmrium')
         tf_nmrium.write(bytes(json_data, 'UTF-8'))
         tf_nmrium.seek(0)
         return tf_nmrium
+
+    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, 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):
         spectra = []
@@ -780,3 +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
+            }
+        ]

environment.yml

@@ -4,64 +4,70 @@ channels:
 dependencies:
   - _libgcc_mutex=0.1=main
   - _openmp_mutex=5.1=1_gnu
-  - ca-certificates=2023.08.22=h06a4308_0
+  - ca-certificates=2024.3.11=h06a4308_0
   - ld_impl_linux-64=2.38=h1181459_1
-  - libffi=3.4.4=h6a678d5_0
+  - libffi=3.4.4=h6a678d5_1
   - libgcc-ng=11.2.0=h1234567_1
   - libgomp=11.2.0=h1234567_1
   - libstdcxx-ng=11.2.0=h1234567_1
   - ncurses=6.4=h6a678d5_0
-  - openssl=3.0.11=h7f8727e_2
-  - pip=23.3=py38h06a4308_0
-  - python=3.8.18=h955ad1f_0
+  - openssl=3.0.13=h7f8727e_1
+  - pip=24.0=py38h06a4308_0
+  - python=3.8.19=h955ad1f_0
   - readline=8.2=h5eee18b_0
-  - setuptools=68.0.0=py38h06a4308_0
-  - sqlite=3.41.2=h5eee18b_0
-  - tk=8.6.12=h1ccaba5_0
-  - wheel=0.41.2=py38h06a4308_0
-  - xz=5.4.2=h5eee18b_0
-  - zlib=1.2.13=h5eee18b_0
+  - setuptools=69.5.1=py38h06a4308_0
+  - sqlite=3.45.3=h5eee18b_0
+  - tk=8.6.14=h39e8969_0
+  - wheel=0.43.0=py38h06a4308_0
+  - xz=5.4.6=h5eee18b_1
+  - zlib=1.2.13=h5eee18b_1
   - pip:
-      - atomicwrites==1.3.0
-      - attrs==23.1.0
-      - certifi==2023.7.22
+      - astroid==2.15.8
+      - atomicwrites==1.4.1
+      - attrs==23.2.0
+      - certifi==2024.2.2
       - cftime==1.6.3
-      - chardet==3.0.4
+      - chardet==5.2.0
       - charset-normalizer==3.3.2
-      - click==8.0.0
+      - click==8.1.7
       - contourpy==1.1.1
-      - coverage==4.5.3
-      - cycler==0.10.0
+      - coverage==7.5.1
+      - coverage-badge==1.1.1
+      - cycler==0.12.1
+      - dill==0.3.8
       - entrypoints==0.3
-      - exceptiongroup==1.1.3
-      - flake8==3.7.7
+      - exceptiongroup==1.2.1
+      - flake8==3.7.9
       - flask==2.2.5
       - flask-jwt-extended==4.5.2
-      - fonttools==4.43.1
-      - gunicorn==19.9.0
-      - idna==2.7
+      - fonttools==4.51.0
+      - gunicorn==22.0.0
+      - idna==3.7
       - importlib-metadata==3.6.0
       - importlib-resources==5.1.3
       - iniconfig==2.0.0
+      - isort==5.13.2
       - itsdangerous==2.0.0
-      - jinja2==3.1.2
+      - jinja2==3.1.4
       - kiwisolver==1.4.5
+      - lazy-object-proxy==1.10.0
       - markupsafe==2.1.2
       - matplotlib==3.7.3
       - mccabe==0.6.1
       - more-itertools==7.2.0
       - netcdf4==1.5.3
       - numpy==1.22.4
       - olefile==0.46
-      - packaging==23.2
+      - packaging==24.0
       - pandas==2.0.3
       - pathlib2==2.3.4
-      - pillow==10.0.1
+      - pillow==10.3.0
+      - platformdirs==4.2.1
       - pluggy==0.12.0
-      - py==1.11.0
       - pycodestyle==2.5.0
       - pyflakes==2.1.1
       - pyjwt==2.8.0
+      - pylint==2.17.7
       - pymzml==2.5.2
       - pyopenms==2.6.0
       - pyparsing==2.4.2
@@ -74,9 +80,12 @@ dependencies:
       - scipy==1.7.3
       - six==1.11.0
       - tomli==2.0.1
-      - tzdata==2023.3
+      - tomlkit==0.12.4
+      - typing-extensions==4.11.0
+      - tzdata==2024.1
       - urllib3==1.26.18
-      - werkzeug==3.0.1
+      - werkzeug==3.0.3
+      - wrapt==1.16.0
       - zipp==0.5.2
       - -e git+https://github.com/ComPlat/nmrglue.git@e6e8a63b1848ae0525f07de0a6ec0cfdb900ba60#egg=nmrglue
 prefix: /home/eln/anaconda3/envs/python-v38

requirements.txt

@@ -1,19 +1,19 @@
 rdkit==2023.9.1
-atomicwrites==1.3.0
-attrs==23.1.0
-certifi==2023.7.22
-chardet==3.0.4
-Click==8.0
-coverage==4.5.3
-cycler==0.10.0
+atomicwrites==1.4.1
+attrs==23.2.0
+certifi==2024.2.2
+chardet==5.2.0
+Click==8.1.7
+coverage==7.5.1
+cycler==0.12.1
 entrypoints==0.3
-flake8==3.7.7
+flake8==3.7.9
 Flask==2.2.5
-gunicorn==19.9.0
-idna==2.7
+gunicorn==22.0.0
+idna==3.7
 importlib-metadata==3.6.0
 itsdangerous==2.0
-Jinja2==3.1.2
+Jinja2==3.1.4
 MarkupSafe==2.1.2
 matplotlib==3.7.3
 mccabe==0.6.1
@@ -25,7 +25,7 @@ numpy==1.22.4
 olefile==0.46
 pandas==2.0.3
 pathlib2==2.3.4
-Pillow==10.0.1
+Pillow==10.3.0
 pluggy==0.12.0
 pycodestyle==2.5.0
 pyflakes==2.1.1
@@ -39,7 +39,7 @@ requests==2.31.0
 scipy==1.7.3
 six==1.11.0
 urllib3==1.26.18
-Werkzeug==3.0.1
+Werkzeug==3.0.3
 zipp==0.5.2
 pyopenms==2.6.0
 PyJWT==2.8.0

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

@@ -0,0 +1,6 @@
+{
+  "version": 3,
+  "actionType": "",
+  "spectra": [],
+  "molecules": []
+}

tests/fixtures/source/nmrium/nmrium_data_schema_v4.json

@@ -0,0 +1,8 @@
+{
+  "version": 4,
+  "data": {
+    "spectra": [],
+    "molecules": []
+  },
+  "view": {}
+}

tests/fixtures/source/nmrium/nmrium_data_schema_v5.json

@@ -0,0 +1,8 @@
+{
+  "version": 5,
+  "data": {
+    "spectra": [],
+    "molecules": []
+  },
+  "view": {}
+}