pychemstation 0.8.6__py3-none-any.whl → 0.8.7__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 +70,37 @@ 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 report_contains(self, labels: List[str], want: List[str]):
+        for label in labels:
+            if label in want:
+                want.remove(label)
+
+        all_labels_seen = False
+        if len(want) != 0:
+            for want_label in want:
+                label_seen = False
+                for label in labels:
+                    if want_label in label or want_label == label:
+                        label_seen = True
+                all_labels_seen = label_seen
+        else:
+            return True
+        return all_labels_seen
+
     def process_report(self) -> Result[AgilentReport, AnyStr]:
         """
         Method to parse details from CSV report.
@@ -76,15 +108,30 @@ 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):
-            df_labels: Dict[int, Dict[int:AnyStr]] = pd.read_csv(
+        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):
+            LOCATION = "Location"
+            NUM_SIGNALS = "Number of Signals"
+            SOLVENT = "Solvent"
+            df_labels: Dict[int, Dict[int, str]] = pd.read_csv(
                 labels, encoding="utf-16", header=None
             ).to_dict()
-            vial_location = []
-            signals = {}
-            solvents = {}
-            for pos, val in df_labels[0].items():
+            vial_location: str = ""
+            signals: Dict[int, list[AgilentPeak]] = {}
+            solvents: Dict[str, str] = {}
+            report_labels: Dict[int, str] = df_labels[0]
+
+            if not self.report_contains(
+                    list(report_labels.values()), [LOCATION, NUM_SIGNALS, SOLVENT]
+            ):
+                return Err(f"Missing one of: {LOCATION}, {NUM_SIGNALS}, {SOLVENT}")
+
+            for pos, val in report_labels.items():
                 if val == "Location":
                     vial_location = df_labels[1][pos]
                 elif "Solvent" in val:
@@ -93,18 +140,20 @@ 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:]
-                            wavelength = int(wavelength)
-                            signals[wavelength] = list(peaks)
+                                             0
+                                         ][-3:]
+                            signals[int(wavelength)] = list(peaks)
                         except (IndexError, ValueError):
                             # TODO: Ask about the MS signals
                             pass

{pychemstation-0.8.6.dist-info → pychemstation-0.8.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.8.6
+Version: 0.8.7
 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

{pychemstation-0.8.6.dist-info → pychemstation-0.8.7.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=9QTIyml4hmyCBd5QaylO9WzBCnQtatMcFRPerOpP90o,12498
+pychemstation/analysis/process_report.py,sha256=UvDhz90OprP9GLgYotfVsKrFiPOtP1BBL-R6cV71JVk,14410
 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-0.8.6.dist-info/METADATA,sha256=UO8aoaIh7ntSKC6vFLYGlFhIqijy-Nal55pnPePuQ0Y,6032
-pychemstation-0.8.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-pychemstation-0.8.6.dist-info/licenses/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
-pychemstation-0.8.6.dist-info/RECORD,,
+pychemstation-0.8.7.dist-info/METADATA,sha256=gUIv5hJpPnqyuVsfq91lDL_deVNU2BM1klYuW7BE_KI,6032
+pychemstation-0.8.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+pychemstation-0.8.7.dist-info/licenses/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.8.7.dist-info/RECORD,,