pychemstation 0.9.0__py3-none-any.whl → 0.9.1__py3-none-any.whl

pychemstation/analysis/process_report.py

@@ -15,6 +15,7 @@ from aghplctools.ingestion.text import (
     _signal_table_re,
     chunk_string,
 )
+from pandas._libs.parsers import EmptyDataError
 from result import Err, Ok, Result
 
 from ..analysis.chromatogram import AgilentHPLCChromatogram
@@ -69,6 +70,16 @@ class CSVProcessor(ReportProcessor):
         """
         super().__init__(path)
 
+    def find_csv_prefix(self) -> str:
+        files = [f for f in os.listdir(self.path) if os.path.isfile(os.path.join(self.path, f))]
+        for file in files:
+            if "00" in file:
+                name, _, file_extension = file.partition(".")
+                if "00" in name and file_extension.lower() == "csv":
+                    prefix, _, _ = name.partition("00")
+                    return prefix
+        raise FileNotFoundError("Couldn't find the prefix for CSV")
+
     def process_report(self) -> Result[AgilentReport, AnyStr]:
         """
         Method to parse details from CSV report.
@@ -76,8 +87,11 @@ class CSVProcessor(ReportProcessor):
         :return: subset of complete report details, specifically the sample location, solvents in pumps,
          and list of peaks at each wavelength channel.
         """
-        labels = os.path.join(self.path, "REPORT00.CSV")
-        if os.path.exists(labels):
+        prefix = self.find_csv_prefix()
+        labels = os.path.join(self.path, f"{prefix}00.CSV")
+        if not os.path.exists(labels):
+            raise ValueError("CSV reports do not exist, make sure to turn on the post run CSV report option!")
+        elif os.path.exists(labels):
             df_labels: Dict[int, Dict[int:AnyStr]] = pd.read_csv(
                 labels, encoding="utf-16", header=None
             ).to_dict()
@@ -93,12 +107,15 @@ class CSVProcessor(ReportProcessor):
                 elif val == "Number of Signals":
                     num_signals = int(df_labels[1][pos])
                     for s in range(1, num_signals + 1):
-                        df = pd.read_csv(
-                            os.path.join(self.path, f"REPORT0{s}.CSV"),
-                            encoding="utf-16",
-                            header=None,
-                        )
-                        peaks = df.apply(lambda row: AgilentPeak(*row), axis=1)
+                        try:
+                            df = pd.read_csv(
+                                os.path.join(self.path, f"{prefix}0{s}.CSV"),
+                                encoding="utf-16",
+                                header=None,
+                            )
+                            peaks = df.apply(lambda row: AgilentPeak(*row), axis=1)
+                        except EmptyDataError:
+                            peaks = []
                         try:
                             wavelength = df_labels[1][pos + s].partition(",4 Ref=off")[0][
                                 -3:

{pychemstation-0.9.0.dist-info → pychemstation-0.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.9.0
+Version: 0.9.1
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Project-URL: Documentation, https://pychemstation-e5a086.gitlab.io/pychemstation.html
 Project-URL: Repository, https://gitlab.com/heingroup/device-api/pychemstation
@@ -8,10 +8,11 @@ Author-email: lucyhao <hao.lucyy@gmail.com>
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >=3.9
+Requires-Python: ~=3.9
 Requires-Dist: aghplctools==4.8.6
 Requires-Dist: coverage>=7.6.1
 Requires-Dist: matplotlib>=3.7.5

{pychemstation-0.9.0.dist-info → pychemstation-0.9.1.dist-info}/RECORD

@@ -2,7 +2,7 @@ pychemstation/__init__.py,sha256=Sc4z8LRVFMwJUoc_DPVUriSXTZ6PO9MaJ80PhRbKyB8,34
 pychemstation/analysis/__init__.py,sha256=dcX7OeHoKdyrECHRCSXgKZN81nOXSAmZRxXzRT0jpDc,126
 pychemstation/analysis/base_spectrum.py,sha256=t_VoxAtBph1V7S4fOsziERHiOBkYP0_nH7LTwbTEvcE,16529
 pychemstation/analysis/chromatogram.py,sha256=cBfLh58PrBZMg9-u5o_Q-FCuu3MlB0q0ZFm9_2uaciU,3270
-pychemstation/analysis/process_report.py,sha256=Bts92n_Cm5BuDAPvemblCbs-KBWivEouRMN_ddX4ezo,12498
+pychemstation/analysis/process_report.py,sha256=uW5sqAIw_YR3-MHaid1dDEF8qdys-ZEZfa-1vqV-nms,13363
 pychemstation/control/README.md,sha256=_7ITj4hD17YIwci6UY6xBebC9gPCBpzBFTB_Gx0eJBc,3124
 pychemstation/control/__init__.py,sha256=uzfsVAGDhMP6SyV10KAH264ytDLMsMRZXRK5XhWS-rc,102
 pychemstation/control/hplc.py,sha256=mV-IO-6wdzB7MuV5LcZYwb4yZibBgEKX2LtbJ9WiKNw,12304
@@ -31,7 +31,7 @@ pychemstation/utils/sequence_types.py,sha256=T0IP2iMqorUrdzH4at9Vsmmb3SCAEmN4z1c
 pychemstation/utils/spec_utils.py,sha256=lS27Xi4mFNDWBfmBqOoxTcVchPAkLK2mSdoaWDOfaPI,10211
 pychemstation/utils/table_types.py,sha256=inOVpwSsic31VdVdJkfuq35QfKd7PoNoXY1QnOxZ6Sw,3235
 pychemstation/utils/tray_types.py,sha256=9yLRIBn3IPVMbhrFqJQJ5gCQJI7H9DD2cdIFQDp2-8k,5184
-pychemstation-0.9.0.dist-info/METADATA,sha256=Kjo6hY93bhBfQiiqcQb69tAZEIiqrW0D5jfZ_l6LxEk,5931
-pychemstation-0.9.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-pychemstation-0.9.0.dist-info/licenses/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
-pychemstation-0.9.0.dist-info/RECORD,,
+pychemstation-0.9.1.dist-info/METADATA,sha256=ypplz0GWS-erPPVfmLxVQXR6vm7__Mo8UIoSs1VD24o,5981
+pychemstation-0.9.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+pychemstation-0.9.1.dist-info/licenses/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.9.1.dist-info/RECORD,,