Merge branch '101-new-hplc-reader' into dev

.github/workflows/pylint.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: [ "3.10", "3.11" ]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -16,7 +16,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        pip install wheel setuptools pip pybind11 --upgrade
         pip install -r ./requirements/dev.txt
         pip install pylint
     - name: Analysing the code with pylint

.github/workflows/pytest.yml

@@ -16,7 +16,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        pip install wheel setuptools pip pybind11 --upgrade
         pip install -r ./requirements/dev.txt
         pip install pytest
     - name: Build tests

converter_app/readers/hplc.py

@@ -0,0 +1,75 @@
+import logging
+import os
+import shutil
+import tempfile
+import tarfile
+import hplc as ph
+from converter_app.readers.helper.base import Reader
+from converter_app.readers.helper.reader import Readers
+
+logger = logging.getLogger(__name__)
+
+
+class HplcReader(Reader):
+    """
+    Reads tarballed hplc files with extension .tar.gz
+    """
+    identifier = 'hplc_reader'
+    priority = 5
+
+    def __init__(self, file):
+        super().__init__(file)
+        self.df = None
+        self.temp_dir = None
+
+    def check(self):
+        """
+        :return: True if it fits
+        """
+        result = self.file.name.endswith(".tar.gz") or self.file.name.endswith(".tar")
+        if result:
+            with  tempfile.TemporaryDirectory() as temp_dir:
+                self.temp_dir = temp_dir
+            with tempfile.NamedTemporaryFile(delete=True) as temp_pdf:
+                try:
+                    # Save the contents of FileStorage to the temporary file
+                    self.file.fp.save(temp_pdf.name)
+                    if self.file.name.endswith("tar.gz"):
+                        mode = "r:gz"
+                    elif self.file.name.endswith("tar"):
+                        mode = "r:"
+                    else:
+                        return False
+                    with tarfile.open(temp_pdf.name, mode) as tar:
+                        tar.extractall(self.temp_dir)
+                        tar.close()
+
+                    for p in os.listdir(self.temp_dir):
+                        file_path = os.path.join(self.temp_dir, p)
+                        self.df = ph.read_chromatograms(file_path)
+                        break
+                except ValueError:
+                    return False
+        if not result and self.temp_dir is not None and os.path.exists(self.temp_dir) and os.path.isdir(self.temp_dir):
+            shutil.rmtree(self.temp_dir)
+        return result
+
+    def prepare_tables(self):
+        tables = []
+        table = self.append_table(tables)
+
+        keys = list(self.df.keys())
+        values = [self.df[x] for x in keys]
+        for i in range(len(values[0])):
+            table['rows'].append([])
+            for x in values:
+                table['rows'][-1].append(float(x[i]))
+
+        table['columns'] = [{
+            'key': str(idx),
+            'name': f'{value}'
+        } for idx, value in enumerate(keys)]
+        return tables
+
+
+Readers.instance().register(HplcReader)

requirements/common.txt

@@ -12,4 +12,5 @@ Werkzeug~=2.2.2
 jcamp~=1.2.2
 PyMuPDF==1.23.7
 pylint==3.0.3
-str2bool~=1.1
+str2bool~=1.1
+parser-binary @ git+https://github.com/ComPlat/BinaryParser@main