Features of version 1.2.1 (#203)

* feat: show peak info, move integrals value to bottom (#181)

* docs: update automatic startup info (#202)

* feat: process DSC layout (#197)

* fix: fixed cannot save nmrium

INSTALL.md

@@ -149,6 +149,26 @@ logger.error('message to log')
 ```
 Note: You need to use function as the same as your logger level, which named as lowercased of level's name, to write your log message to the logs file
 
+
+### 2.3. Automatic startup in crontab
+
+To make sure ChemSpectra is started on reboot you can use this BASH script in your root crontab (if required, adapt Chemotion ELN username and home directory):
+
+```sh
+#!/bin/bash
+
+sudo -H -u production bash -c "cd /home/production/chem-spectra-app && \
+  source /home/production/anaconda3/bin/activate chem-spectra && \
+  gunicorn -w 4 -b 0.0.0.0:3007 server:app --daemon"
+
+# Remember to modify path according to your installation
+docker run --detach --name msconvert_docker \
+    --rm -it \
+    -e WINEDEBUG=-all \
+    -v /home/production/chem-spectra-app/chem_spectra/tmp:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses \
+    bash
+```
+
 ## 3. Run test
 
 ```

chem_spectra/controller/helper/share.py

@@ -107,6 +107,7 @@ def extract_params(request):
     list_file_names = request.form.getlist('list_file_names[]')
     data_type_mapping = request.form.get('data_type_mapping', default='')
     detector = request.form.get('detector', default=None)
+    dsc_meta_data = request.form.get('dsc_meta_data', default=None)
 
     params = {
         'peaks_str': request.form.get('peaks_str', default=None),
@@ -131,6 +132,7 @@ def extract_params(request):
         'axesUnits': axesUnits,
         'data_type_mapping': data_type_mapping,
         'detector': detector,
+        'dsc_meta_data': dsc_meta_data,
     }
     has_params = (
         params.get('peaks_str') or

chem_spectra/lib/converter/jcamp/base.py

@@ -34,6 +34,7 @@ def __init__(self, path, params=False):
         self.is_emissions = self.__is_emissions()
         self.is_dls_acf = self.__is_dls_acf()
         self.is_dls_intensity = self.__is_dls_intensity()
+        self.is_dsc = self.__is_dsc()
         self.non_nmr = self.__non_nmr()
         self.ncl = self.__ncl()
         self.simu_peaks = self.__read_simu_peaks()
@@ -156,6 +157,9 @@ def __is_dls_acf(self):
 
     def __is_dls_intensity(self):
         return self.typ in ['DLS intensity']
+
+    def __is_dsc(self):
+        return self.typ in ['DIFFERENTIAL SCANNING CALORIMETRY']
 
     def __ncl(self):
         try:

chem_spectra/lib/converter/jcamp/data_type.json

@@ -14,6 +14,7 @@
         "SORPTION-DESORPTION MEASUREMENT": ["SORPTION-DESORPTION MEASUREMENT"],
         "Emissions": ["Emissions", "EMISSIONS", "FLUORESCENCE SPECTRUM", "FL SPECTRUM"],
         "DLS ACF": ["DLS ACF"],
-        "DLS intensity": ["DLS INTENSITY", "DLS intensity"]
+        "DLS intensity": ["DLS INTENSITY", "DLS intensity"],
+        "DIFFERENTIAL SCANNING CALORIMETRY": ["DIFFERENTIAL SCANNING CALORIMETRY"]
     }
 }

chem_spectra/lib/converter/jcamp/data_type.json.example

@@ -14,6 +14,7 @@
       "SORPTION-DESORPTION MEASUREMENT": ["SORPTION-DESORPTION MEASUREMENT"],
       "Emissions": ["Emissions", "EMISSIONS", "FLUORESCENCE SPECTRUM", "FL SPECTRUM"],
       "DLS ACF": ["DLS ACF"],
-      "DLS intensity": ["DLS INTENSITY", "DLS intensity"]
+      "DLS intensity": ["DLS INTENSITY", "DLS intensity"],
+      "DIFFERENTIAL SCANNING CALORIMETRY": ["DIFFERENTIAL SCANNING CALORIMETRY"]
   }
 }

chem_spectra/lib/converter/jcamp/ni.py

@@ -43,6 +43,7 @@ def __init__(self, base):
         self.is_emissions = base.is_emissions if hasattr(base, 'is_emissions') else False
         self.is_dls_acf = base.is_dls_acf if hasattr(base, 'is_dls_acf') else False
         self.is_dls_intensity = base.is_dls_intensity if hasattr(base, 'is_dls_intensity') else False
+        self.is_dsc = base.is_dsc if hasattr(base, 'is_dsc') else False
         self.non_nmr = base.non_nmr
         self.ncl = base.ncl
         self.is_dept = base.is_dept
@@ -98,7 +99,8 @@ def __thres(self):
             "CYCLIC VOLTAMMETRY": THRESHOLD_XRD,
             "SORPTION-DESORPTION MEASUREMENT": THRESHOLD_XRD,
             "DLS intensity": THRESHOLD_XRD,
-            "Emissions": THRESHOLD_EMISSION
+            "Emissions": THRESHOLD_EMISSION,
+            "DIFFERENTIAL SCANNING CALORIMETRY": THRESHOLD_TGA,
         }
 
         if self.params.get('user_data_type_mapping'):

chem_spectra/lib/converter/nmrium/base.py

@@ -46,6 +46,8 @@ def __init__(self, file=None):
 
         self.simu_peaks = []
         self.is_cyclic_volta = False
+        self.is_sec = False
+        self.is_dsc = False
         self.typ = ''
         self.threshold = 1.0
 

chem_spectra/lib/converter/share.py

@@ -25,6 +25,7 @@ def parse_params(params):
             'jcamp_idx': 0,
             'axesUnits': None,
             'detector': None,
+            'dsc_meta_data': None,
         }
 
     select_x = params.get('select_x', None)
@@ -68,6 +69,8 @@ def parse_params(params):
     user_data_type_mapping = params.get('data_type_mapping')
     detector = params.get('detector')
     detector = json.loads(detector) if detector else None
+    dsc_meta_data = params.get('dsc_meta_data')
+    dsc_meta_data = json.loads(dsc_meta_data) if dsc_meta_data else None
     if (cyclicvolta is not None):
         spectraList = cyclicvolta['spectraList']
         if (len(spectraList) > 0):
@@ -101,6 +104,7 @@ def parse_params(params):
         'axesUnits': axesUnits,
         'user_data_type_mapping': user_data_type_mapping,
         'detector': detector,
+        'dsc_meta_data': dsc_meta_data,
     }
 
 

environment.yml

@@ -4,24 +4,25 @@ channels:
 dependencies:
   - _libgcc_mutex=0.1=main
   - _openmp_mutex=5.1=1_gnu
-  - ca-certificates=2024.3.11=h06a4308_0
+  - ca-certificates=2023.08.22=h06a4308_0
   - ld_impl_linux-64=2.38=h1181459_1
-  - libffi=3.4.4=h6a678d5_1
+  - libffi=3.4.4=h6a678d5_0
   - 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=3.0.13=h7f8727e_1
-  - pip=24.0=py38h06a4308_0
-  - python=3.8.19=h955ad1f_0
+  - openssl=3.0.11=h7f8727e_2
+  - pip=23.3=py38h06a4308_0
+  - python=3.8.18=h955ad1f_0
   - readline=8.2=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
+  - 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
   - pip:
+      - adjusttext==1.1.1
       - astroid==2.15.8
       - atomicwrites==1.4.1
       - attrs==23.2.0
@@ -32,15 +33,14 @@ dependencies:
       - click==8.1.7
       - contourpy==1.1.1
       - coverage==7.5.1
-      - coverage-badge==1.1.1
       - cycler==0.12.1
-      - dill==0.3.8
+      - dill==0.3.7
       - entrypoints==0.3
-      - exceptiongroup==1.2.1
+      - exceptiongroup==1.1.3
       - flake8==3.7.9
       - flask==2.2.5
       - flask-jwt-extended==4.5.2
-      - fonttools==4.51.0
+      - fonttools==4.43.1
       - gunicorn==22.0.0
       - idna==3.7
       - importlib-metadata==3.6.0
@@ -58,12 +58,13 @@ dependencies:
       - netcdf4==1.5.3
       - numpy==1.22.4
       - olefile==0.46
-      - packaging==24.0
+      - packaging==23.2
       - pandas==2.0.3
       - pathlib2==2.3.4
       - pillow==10.3.0
-      - platformdirs==4.2.1
+      - platformdirs==4.1.0
       - pluggy==0.12.0
+      - py==1.11.0
       - pycodestyle==2.5.0
       - pyflakes==2.1.1
       - pyjwt==2.8.0
@@ -76,14 +77,14 @@ dependencies:
       - pytz==2023.3
       - rdkit==2023.9.1
       - regex==2019.4.9
-      - requests==2.31.0
+      - requests==2.32.2
       - scipy==1.7.3
       - six==1.11.0
       - tomli==2.0.1
-      - tomlkit==0.12.4
-      - typing-extensions==4.11.0
-      - tzdata==2024.1
-      - urllib3==1.26.18
+      - tomlkit==0.12.3
+      - typing-extensions==4.9.0
+      - tzdata==2023.3
+      - urllib3==1.26.19
       - werkzeug==3.0.3
       - wrapt==1.16.0
       - zipp==0.5.2

requirements.txt

@@ -18,7 +18,6 @@ MarkupSafe==2.1.2
 matplotlib==3.7.3
 mccabe==0.6.1
 more-itertools==7.2.0
-# -e git+https://github.com/ComPlat/nmrglue.git@c5a7d4d0073fedff68808b4e9c95836a8c20413e#egg=nmrglue
 -e git+https://github.com/ComPlat/nmrglue.git@e6e8a63b1848ae0525f07de0a6ec0cfdb900ba60#egg=nmrglue
 netCDF4==1.5.3
 numpy==1.22.4
@@ -35,10 +34,10 @@ pytest==7.2.0
 python-dateutil==2.8.2
 pytz==2023.3
 regex==2019.4.9
-requests==2.31.0
+requests==2.32.2
 scipy==1.7.3
 six==1.11.0
-urllib3==1.26.18
+urllib3==1.26.19
 Werkzeug==3.0.3
 zipp==0.5.2
 pyopenms==2.6.0

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name='chem-spectra-app',
-    version='1.2.0',
+    version='1.2.1',
     packages=find_packages(),
     include_package_data=True,
     zip_safe=False,

tests/lib/converter/bagit/test_bagit_base_converter.py

@@ -10,6 +10,7 @@
 emissions_layout_path = target_dir + 'emissions/emissions.zip'
 dls_acf_layout_path = target_dir + 'dls_acf/dls_acf.zip'
 dls_intensity_layout_path = target_dir + 'dls_intensity/dls_intensity.zip'
+dsc_layout_path = target_dir + 'dsc/dsc.zip'
 
 def assertFileType(file, mimeStr):
     assert mimetypes.guess_type(file.name)[0] == mimeStr
@@ -144,3 +145,12 @@ def test_bagit_has_one_file_no_combined_image():
 
         converter = BagItConveter(td)
         assert converter.combined_image is None
+
+def test_bagit_convert_to_jcamp_dsc_layout():
+    with tempfile.TemporaryDirectory() as td:
+        with zipfile.ZipFile(dsc_layout_path, 'r') as z:
+            z.extractall(td)
+
+        converter = BagItConveter(td)
+        jcamp = converter.data[0]
+        assertJcampContent(jcamp, '##DATA TYPE=DIFFERENTIAL SCANNING CALORIMETRY')

tests/lib/converter/jcamp/test_jcamp_ni_converter.py

@@ -20,4 +20,10 @@ def test_init_jcamp_ni_success(jcamp_file_1h):
 
     assert ni_converter is not None
     assert ni_converter.base == base_converter
+
+def test_init_jcamp_ni_nmr_label(jcamp_file_1h):
+    base_converter = JcampBaseConverter(jcamp_file_1h)
+    ni_converter = JcampNIConverter(base=base_converter)
+
+    assert ni_converter.label == {'x': 'PPM', 'y': 'ARBITRARY'}
 

tests/lib/converter/test_share.py

@@ -28,6 +28,7 @@ def expected_default_params():
         'jcamp_idx': 0,
         'axesUnits': None,
         'detector': None,
+        'dsc_meta_data': None,
     }
 
 def test_parse_params_without_params(expected_default_params):
@@ -222,6 +223,11 @@ def test_parse_params_detector():
 def test_parse_solvent():
     #TODO: need to be updated
     assert 1==1
+
+def test_parse_dsc_meta_data():
+    params = {'dsc_meta_data': '{"meltingPoint": "1.0", "tg": "1.0"}'}
+    parsed_data = parse_params(params)
+    assert parsed_data['dsc_meta_data'] == {"meltingPoint": "1.0", "tg": "1.0"}
 
 def test_reduce_pts_when_does_not_have_any_x():
     array_data = []