Add agilent rdl (#20)

* added agilent rdl * updated docs * Bump version to 0.9.6 in pyproject.toml * fixed unicode decode error * added debug print * Fix debug print statement and update file path string formatting * Update pytest command to include verbose output * Update pytest command to include verbose output * Fix assertion error in test_windows * Refactor debug print statements and flush output in analyzer.py * Refactor debug print statements and flush output in analyzer.py * Refactor debug print statements and improve error handling in analyzer.py * Refactor debug print statements and add error handling in analyzer.py * Refactor file reading in AgilentRDLReader to specify UTF-8 encoding * Refactor debug print statements and remove unnecessary variables in analyzer.py * Refactor debug print statements and update error handling in analyzer.py * Refactor debug print statements and update error handling in analyzer.py * Refactor error handling in analyzer.py
FAIRChemistry · Oct 25, 2024 · d21576d · d21576d
1 parent b790f6e
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diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml
@@ -27,4 +27,4 @@ jobs:
 
       - name: Run tests with pytest
         run: |
-          poetry run pytest --nbval-lax
+          poetry run pytest --nbval-lax -s
diff --git a/chromatopy/readers/abstractreader.py b/chromatopy/readers/abstractreader.py
@@ -290,7 +290,7 @@ def read(self) -> list[Measurement]:
 
     def print_success(self, n_measurement_objects: int) -> None:
         """Prints a success message."""
-        print(f"✅ Loaded {n_measurement_objects} chromatograms.")
+        print(f" Loaded {n_measurement_objects} chromatograms.")
 
 
 if __name__ == "__main__":

diff --git a/chromatopy/readers/agilent_csv.py b/chromatopy/readers/agilent_csv.py
@@ -21,8 +21,6 @@ def read(self) -> list[Measurement]:
         'RESULTS.CSV' files {len(self.file_paths)}.
         """
 
-        print(self.file_paths)
-
         measurements = []
         for path_idx, csv_path in enumerate(self.file_paths):
             peaks = self._read_peaks_from_csv(csv_path)

diff --git a/chromatopy/readers/agilent_rdl.py b/chromatopy/readers/agilent_rdl.py
@@ -0,0 +1,115 @@
+import re
+from typing import Tuple
+
+from chromatopy.model import Chromatogram, Data, Measurement, Peak
+from chromatopy.readers.abstractreader import AbstractReader
+
+
+class AgilentRDLReader(AbstractReader):
+    def read(self):
+        measurements = []
+        for path_id, path in enumerate(self.file_paths):
+            lines = self.read_file(path)
+
+            peak_data, sample_name, signal = self.extract_information(lines)
+
+            peak_data = [
+                self.align_and_concatenate_columns(*pair) for pair in peak_data
+            ]
+            peaks = [self.map_peak(peak) for peak in peak_data]
+
+            sample_name = self.align_and_concatenate_columns(*sample_name)[1]
+
+            wavelength = self.extract_wavelength(signal)
+
+            data = Data(
+                value=self.values[path_id],
+                unit=self.unit,
+                data_type=self.mode,
+            )
+
+            chromatogram = Chromatogram(peaks=peaks, wavelength=wavelength)
+
+            measurements.append(
+                Measurement(
+                    id=f"m{path_id}",
+                    chromatograms=[chromatogram],
+                    temperature=self.temperature,
+                    temperature_unit=self.temperature_unit,
+                    ph=self.ph,
+                    data=data,
+                )
+            )
+
+        if not self.silent:
+            self.print_success(len(measurements))
+
+        return measurements
+
+    @staticmethod
+    def read_file(file_path: str) -> list[str]:
+        with open(file_path, "r", encoding="utf-8") as file:
+            lines = file.readlines()
+
+        return lines
+
+    @staticmethod
+    def extract_information(lines: list[str]) -> Tuple[list[list[str]], list[str], str]:
+        data = []
+        for i, line in enumerate(lines):
+            # Check for first line with float values after space and pipe characters
+            if re.search(r"^\s{2}│\s+\d+\.\d+\s+│", line):
+                line_pair = [line]
+
+                if lines[i + 1].startswith("  │"):
+                    line_pair.append(lines[i + 1])
+                else:
+                    line_pair.append("")
+
+                data.append(line_pair)
+
+            if "│Sample Name     │" in line:
+                sample_name = [line]
+                if lines[i + 1].startswith("   │"):
+                    sample_name.append(lines[i + 1])
+                else:
+                    sample_name.append("")
+
+            if "│Signal:│" in line:
+                signal = line
+
+        return data, sample_name, signal
+
+    @staticmethod
+    def extract_wavelength(line: str) -> int | None:
+        pattern = r"Sig=(\d+)"
+
+        match = re.search(pattern, line)
+        if match:
+            return int(match.group(1))
+        else:
+            return None
+
+    @staticmethod
+    def align_and_concatenate_columns(row1, row2):
+        # Split each string by the vertical bar '│' and strip whitespace from each column
+        row1_columns = [col.strip() for col in re.split(r"│", row1) if col]
+        row2_columns = [col.strip() for col in re.split(r"│", row2) if col]
+
+        # Concatenate aligned columns
+        aligned_columns = [
+            f"{col1}{col2}".strip() for col1, col2 in zip(row1_columns, row2_columns)
+        ]
+
+        return aligned_columns[1:-1]
+
+    @staticmethod
+    def map_peak(peak_list: list[str]) -> Peak:
+        return Peak(
+            retention_time=float(peak_list[0]),
+            type=peak_list[1],
+            width=float(peak_list[2]),
+            area=float(peak_list[3]),
+            amplitude=float(peak_list[4]),
+            percent_area=float(peak_list[5]),
+        )
diff --git a/chromatopy/tools/analyzer.py b/chromatopy/tools/analyzer.py
@@ -486,10 +486,15 @@ def read_agilent(
             ChromAnalyzer: ChromAnalyzer object containing the measurements.
         """
         from chromatopy.readers.agilent_csv import AgilentCSVReader
+        from chromatopy.readers.agilent_rdl import AgilentRDLReader
         from chromatopy.readers.agilent_txt import AgilentTXTReader
 
         directory = Path(path)
 
+        txt_paths = []
+        csv_paths = []
+        rdl_paths = []
+
         txt_paths = [
             str(f.absolute())
             for f in directory.rglob("Report.TXT")
@@ -500,6 +505,24 @@ def read_agilent(
             for f in directory.rglob("RESULTS.CSV")
             if f.parent.parent == directory
         ]
+        rdl_paths = []
+
+        try:
+            txt_path = next(directory.rglob("*.txt"))
+            print("sole path: ", txt_path, flush=True)
+            print(f"all txt paths: {list(directory.rglob('*.txt'))}", flush=True)
+            print(f"everything: {directory.rglob('*')}", flush=True)
+            try:
+                lines = AgilentRDLReader.read_file(str(txt_path))
+                if lines[0].startswith("┌─────"):
+                    rdl_paths = [str(f.absolute()) for f in directory.rglob("*.txt")]
+                else:
+                    txt_paths = txt_paths
+            except UnicodeDecodeError:
+                txt_paths = txt_paths
+
+        except StopIteration:
+            txt_paths = txt_paths
 
         data = {
             "dirpath": path,
@@ -512,9 +535,13 @@ def read_agilent(
             "mode": mode,
         }
 
-        if not csv_paths and txt_paths:
+        if rdl_paths:
+            data["file_paths"] = rdl_paths  # type: ignore
+            reader = AgilentRDLReader(**data)
+            measurements = reader.read()  # type: ignore
+        elif not csv_paths and txt_paths:
             data["file_paths"] = txt_paths  # type: ignore
-            reader = AgilentTXTReader(**data)
+            reader = AgilentTXTReader(**data)  # type: ignore
             measurements = reader.read()  # type: ignore
         elif csv_paths and not txt_paths:
             data["file_paths"] = csv_paths  # type: ignore

diff --git a/docs/examples/data/agilent_rdl/M2_MJ_100_min.txt b/docs/examples/data/agilent_rdl/M2_MJ_100_min.txt
@@ -0,0 +1,40 @@
+┌──────────────────────────────────────────────────────────────────────────────┐
+│Cross Sequence Summary Report                                                 │
+└──────────────────────────────────────────────────────────────────────────────┘
+   ┌────────────────┬──────────────────────────────────────────────────────────┐
+   │Sample Name     │M2_MJ_                                                    │
+   │                │100_min                                                   │
+   └────────────────┴──────────────────────────────────────────────────────────┘
+  ┌───────┬────────────────────────────────────────────────────────────────────┐
+  │Signal:│DAD1A,Sig=254,4  Ref=360,100                                        │
+  └───────┴────────────────────────────────────────────────────────────────────┘
+  ┌───────┬───┬────────┬────────┬───────┬────────┬─────────────────────────────┐
+  │    RT │Typ│  Width │   Area │ Height│  Area% │Name                         │
+  │ [min] │e  │  [min] │        │       │        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 0.698 │BV │ 0.4062 │    53. │ 7.2642│ 0.3671 │                             │
+  │       │   │        │   0992 │       │        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 1.169 │VV │ 0.8468 │  6094. │   783.│    42. │AMP@1,169min                 │
+  │       │   │        │   3336 │   0775│   1289 │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 2.756 │VB │ 0.4315 │    14. │ 1.9341│ 0.0982 │                             │
+  │       │   │        │   2114 │       │        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 3.331 │BV │ 0.7823 │  7620. │   925.│    52. │ADP@3,327min                 │
+  │       │   │        │   7030 │   5433│   6804 │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 3.974 │VB │ 1.5648 │   381. │    55.│ 2.6397 │                             │
+  │       │   │        │   8593 │   0016│        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 5.770 │BB │ 1.0452 │   301. │    22.│ 2.0856 │ATP@5,720min                 │
+  │       │   │        │   7014 │   1066│        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │       │   │    Sum │ 14465. │       │        │                             │
+  │       │   │        │   9079 │       │        │                             │
+  └───────┴───┴────────┴────────┴───────┴────────┴─────────────────────────────┘
+┌───────────────────────────┬────────────────────────────────┬─────────────────┐
+│D:\CDSProjects\JNS\Report  │     Printed:  2024-10-20       │    Page 1 of 1  │
+│Templates\Export_for_      │        16:25:44+02:00          │                 │
+│python.rdl [Rev. 2.0]      │                                │                 │
+════════════════════════════════════════════════════════════════════════════════
diff --git a/docs/examples/data/agilent_rdl/M3_102_min.txt b/docs/examples/data/agilent_rdl/M3_102_min.txt
@@ -0,0 +1,40 @@
+┌──────────────────────────────────────────────────────────────────────────────┐
+│Cross Sequence Summary Report                                                 │
+└──────────────────────────────────────────────────────────────────────────────┘
+   ┌────────────────┬──────────────────────────────────────────────────────────┐
+   │Sample Name     │M2_MJ_                                                    │
+   │                │100_min                                                   │
+   └────────────────┴──────────────────────────────────────────────────────────┘
+  ┌───────┬────────────────────────────────────────────────────────────────────┐
+  │Signal:│DAD1A,Sig=254,4  Ref=360,100                                        │
+  └───────┴────────────────────────────────────────────────────────────────────┘
+  ┌───────┬───┬────────┬────────┬───────┬────────┬─────────────────────────────┐
+  │    RT │Typ│  Width │   Area │ Height│  Area% │Name                         │
+  │ [min] │e  │  [min] │        │       │        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 0.698 │BV │ 0.4062 │    53. │ 7.2642│ 0.3671 │                             │
+  │       │   │        │   0992 │       │        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 1.169 │VV │ 0.8468 │  6094. │   783.│    42. │AMP@1,169min                 │
+  │       │   │        │   3336 │   0775│   1289 │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 2.756 │VB │ 0.4315 │    14. │ 1.9341│ 0.0982 │                             │
+  │       │   │        │   2114 │       │        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 3.331 │BV │ 0.7823 │  7620. │   925.│    52. │ADP@3,327min                 │
+  │       │   │        │   7030 │   5433│   6804 │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 3.974 │VB │ 1.5648 │   381. │    55.│ 2.6397 │                             │
+  │       │   │        │   8593 │   0016│        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │ 5.770 │BB │ 1.0452 │   301. │    22.│ 2.0856 │ATP@5,720min                 │
+  │       │   │        │   7014 │   1066│        │                             │
+  ├───────┼───┼────────┼────────┼───────┼────────┼─────────────────────────────┤
+  │       │   │    Sum │ 14465. │       │        │                             │
+  │       │   │        │   9079 │       │        │                             │
+  └───────┴───┴────────┴────────┴───────┴────────┴─────────────────────────────┘
+┌───────────────────────────┬────────────────────────────────┬─────────────────┐
+│D:\CDSProjects\JNS\Report  │     Printed:  2024-10-20       │    Page 1 of 1  │
+│Templates\Export_for_      │        16:25:44+02:00          │                 │
+│python.rdl [Rev. 2.0]      │                                │                 │
+════════════════════════════════════════════════════════════════════════════════