feat: process generate nmrium data schema v3 and v4, v5

.github/workflows/unit_test.yml

@@ -3,19 +3,22 @@ name: Test with pytest
 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

chem_spectra/lib/composer/ni.py

@@ -587,21 +587,34 @@ def tf_csv(self):
                 })
         return tf_csv
 
-    def generate_nmrium(self):
+    def generate_nmrium(self, version=4):
         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()
+        else:
+            dic_data = self.__generate_nmrium_data(version)
 
         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):
+        dic_data = {'actionType': 'INITIATE', 'version': 3}
+        spectra = self.__generate_nmrim_spectra()
+        dic_data['spectra'] = spectra
+        return dic_data
+
+    def __generate_nmrium_data(self, version):
+        dic_data = {'version': version, 'data': {}, 'view': {}}
+        spectra = self.__generate_nmrim_spectra()
+        dic_data['data']['spectra'] = spectra
+        return dic_data
 
     def __generate_nmrim_spectra(self):
         spectra = []

environment.yml

@@ -22,6 +22,7 @@ dependencies:
   - xz=5.4.2=h5eee18b_0
   - zlib=1.2.13=h5eee18b_0
   - pip:
+      - astroid==2.15.8
       - atomicwrites==1.3.0
       - attrs==23.1.0
       - certifi==2023.7.22
@@ -32,6 +33,7 @@ dependencies:
       - contourpy==1.1.1
       - coverage==4.5.3
       - cycler==0.10.0
+      - dill==0.3.7
       - entrypoints==0.3
       - exceptiongroup==1.1.3
       - flake8==3.7.7
@@ -43,9 +45,11 @@ dependencies:
       - 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
       - kiwisolver==1.4.5
+      - lazy-object-proxy==1.10.0
       - markupsafe==2.1.2
       - matplotlib==3.7.3
       - mccabe==0.6.1
@@ -57,11 +61,13 @@ dependencies:
       - pandas==2.0.3
       - pathlib2==2.3.4
       - pillow==10.0.1
+      - platformdirs==4.1.0
       - 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
+      - tomlkit==0.12.3
+      - typing-extensions==4.9.0
       - tzdata==2023.3
       - urllib3==1.26.18
       - werkzeug==3.0.1
+      - 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

tests/fixtures/source/nmrium/nmrium_data_schema_v3.json

@@ -0,0 +1,5 @@
+{
+  "version": 3,
+  "actionType": "",
+  "spectra": []
+}

tests/fixtures/source/nmrium/nmrium_data_schema_v4.json

@@ -0,0 +1,7 @@
+{
+  "version": 4,
+  "data": {
+    "spectra": []
+  },
+  "view": {}
+}

tests/fixtures/source/nmrium/nmrium_data_schema_v5.json

@@ -0,0 +1,7 @@
+{
+  "version": 5,
+  "data": {
+    "spectra": []
+  },
+  "view": {}
+}

tests/lib/composer/test_ni_composer.py

@@ -1,5 +1,6 @@
 import json
 import pytest
+import numpy as np
 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
@@ -8,6 +9,14 @@
 source_nmr_edit = './tests/fixtures/source/1H.edit.jdx'
 source_ir = './tests/fixtures/source/IR.dx'
 
+@pytest.fixture
+def data_schema():
+  return [
+        './tests/fixtures/source/nmrium/nmrium_data_schema_v3.json',
+        './tests/fixtures/source/nmrium/nmrium_data_schema_v4.json',
+        './tests/fixtures/source/nmrium/nmrium_data_schema_v5.json'
+    ]
+
 @pytest.fixture
 def jcamp_file_1h():
     return source_nmr
@@ -67,6 +76,63 @@ def test_ni_composer_generate_nmrium_not_nmr(jcamp_file_ir):
 
     assert nmrium_file is None
 
+def test_ni_composer_check_schema_v3(data_schema, jcamp_file_1h):
+    schema_source = data_schema[0]
+    schema = ''
+    with open(schema_source, 'r') as f:
+        schema = f.read()
+    dic_schema = json.loads(schema)
+    expected_schema_keys = np.array(dic_schema.keys())
+
+    base_converter = JcampBaseConverter(jcamp_file_1h)
+    ni_converter = JcampNIConverter(base=base_converter)
+    ni_composer = NIComposer(core=ni_converter)
+    nmrium_file = ni_composer.generate_nmrium(version=3)
+    with open(nmrium_file.name, 'r') as f:
+        nmrium = f.read()
+        nmrium_spectra = json.loads(nmrium)
+        nmrium_spectra_keys = np.array(nmrium_spectra.keys())
+        assert np.array_equal(expected_schema_keys, nmrium_spectra_keys)
+        assert nmrium_spectra['version'] == 3
+
+def test_ni_composer_check_schema_v4(data_schema, jcamp_file_1h):
+    schema_source = data_schema[1]
+    schema = ''
+    with open(schema_source, 'r') as f:
+        schema = f.read()
+    dic_schema = json.loads(schema)
+    expected_schema_keys = np.array(dic_schema.keys())
+
+    base_converter = JcampBaseConverter(jcamp_file_1h)
+    ni_converter = JcampNIConverter(base=base_converter)
+    ni_composer = NIComposer(core=ni_converter)
+    nmrium_file = ni_composer.generate_nmrium()
+    with open(nmrium_file.name, 'r') as f:
+        nmrium = f.read()
+        nmrium_spectra = json.loads(nmrium)
+        nmrium_spectra_keys = np.array(nmrium_spectra.keys())
+        assert np.array_equal(expected_schema_keys, nmrium_spectra_keys)
+        assert nmrium_spectra['version'] == 4
+
+def test_ni_composer_check_schema_v5(data_schema, jcamp_file_1h):
+    schema_source = data_schema[2]
+    schema = ''
+    with open(schema_source, 'r') as f:
+        schema = f.read()
+    dic_schema = json.loads(schema)
+    expected_schema_keys = np.array(dic_schema.keys())
+
+    base_converter = JcampBaseConverter(jcamp_file_1h)
+    ni_converter = JcampNIConverter(base=base_converter)
+    ni_composer = NIComposer(core=ni_converter)
+    nmrium_file = ni_composer.generate_nmrium(version=5)
+    with open(nmrium_file.name, 'r') as f:
+        nmrium = f.read()
+        nmrium_spectra = json.loads(nmrium)
+        nmrium_spectra_keys = np.array(nmrium_spectra.keys())
+        assert np.array_equal(expected_schema_keys, nmrium_spectra_keys)
+        assert nmrium_spectra['version'] == 5
+
 def test_ni_composer_nmrium_spectra(jcamp_file_1h):
     base_converter = JcampBaseConverter(jcamp_file_1h)
     ni_converter = JcampNIConverter(base=base_converter)
@@ -129,9 +195,10 @@ def test_ni_composer_generate_nmrium(jcamp_file_1h):
         assert file_content != ""
 
         dic_content = json.loads(file_content)
-        assert dic_content['spectra'] is not None
+        dic_data = dic_content['data']
+        assert dic_data['spectra'] is not None
 
-        xy_points = dic_content['spectra'][0]['data']
+        xy_points = dic_data['spectra'][0]['data']
         x_values = xy_points['x']
         y_value = xy_points['re']
         assert len(x_values) == 65536

tests/lib/converter/nmrium/test_nmrium_base.py

@@ -3,13 +3,20 @@
 from chem_spectra.controller.helper.file_container import FileContainer
 from chem_spectra.lib.converter.nmrium.base import NMRiumDataConverter
 
-source = './tests/fixtures/source/nmrium/nmrium_test.nmrium'
+source_files = [
+    './tests/fixtures/source/nmrium/nmrium_test_v3.nmrium',
+    './tests/fixtures/source/nmrium/nmrium_test_v4.nmrium',
+    './tests/fixtures/source/nmrium/nmrium_test_v5.nmrium'
+]
 
 @pytest.fixture
-def nmrium_file():
-    with open(source, 'rb') as f:
-        nmriumFile = FileContainer(FileStorage(f))
-    return nmriumFile
+def nmrium_files():
+    files = []
+    for source in source_files:
+        with open(source, 'rb') as f:
+            nmriumFile = FileContainer(FileStorage(f))
+            files.append(nmriumFile)
+    return files
 
 @pytest.fixture
 def parsed_json_nmrium_data():
@@ -77,17 +84,19 @@ def test_parsing_spectra(parsed_json_nmrium_data):
     assert spectrum_data != None
     assert spectrum_data == expected_value
 
-def test_read_file(nmrium_file):
-    nmrium_converter = NMRiumDataConverter()
-    nmrium_converter.file = nmrium_file
-    spectrum_data = nmrium_converter._NMRiumDataConverter__read_file()
-    assert spectrum_data != None
-
-def test_read_file_content(nmrium_file):
-    nmrium_converter = NMRiumDataConverter(nmrium_file)
-    assert nmrium_converter.data != None
-    assert len(nmrium_converter.data['x']) == 65536
-    assert len(nmrium_converter.data['x']) == len(nmrium_converter.data['y'])
+def test_read_file(nmrium_files):
+    for file in nmrium_files:
+        nmrium_converter = NMRiumDataConverter()
+        nmrium_converter.file = file
+        spectrum_data = nmrium_converter._NMRiumDataConverter__read_file()
+        assert spectrum_data is not None
+
+def test_read_file_content(nmrium_files):
+    for file in nmrium_files:
+        nmrium_converter = NMRiumDataConverter(file)
+        assert nmrium_converter.data != None
+        assert len(nmrium_converter.data['x']) == 65536
+        assert len(nmrium_converter.data['x']) == len(nmrium_converter.data['y'])
 
 def test_read_xy_values_failed():
     nmrium_converter = NMRiumDataConverter()