initial commit

src/submissions/backend/excel/parser.py

@@ -0,0 +1,122 @@
+import pandas as pd
+from pathlib import Path
+from datetime import datetime
+import logging
+from collections import OrderedDict
+import re
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+class SheetParser(object):
+
+    def __init__(self, filepath:Path|None = None, **kwargs):
+        for kwarg in kwargs:
+            setattr(self, f"_{kwarg}", kwargs[kwarg])
+        if filepath == None:
+            self.xl = None
+        else:
+            try:
+                self.xl = pd.ExcelFile(filepath.__str__())
+            except ValueError:
+                self.xl = None
+        self.sub = OrderedDict()
+        self.sub['submission_type'] = self._type_decider()        
+        parse = getattr(self, f"_parse_{self.sub['submission_type'].lower()}")
+        parse()
+
+    def _type_decider(self):
+        try:
+            for type in self._submission_types:
+                if self.xl.sheet_names == self._submission_types[type]['excel_map']:
+                    return type.title()
+            return "Unknown"
+        except:
+            return "Unknown"
+
+
+    def _parse_unknown(self):
+        self.sub = None
+    
+
+    def _parse_generic(self, sheet_name:str):
+        submission_info = self.xl.parse(sheet_name=sheet_name)
+        self.sub['submitter_plate_num'] = submission_info.iloc[0][1]
+        self.sub['rsl_plate_num'] = str(submission_info.iloc[10][1])
+        self.sub['submitted_date'] = submission_info.iloc[1][1].date()#.strftime("%Y-%m-%d")
+        self.sub['submitting_lab'] = submission_info.iloc[0][3]
+        self.sub['sample_count'] = str(submission_info.iloc[2][3])
+        self.sub['extraction_kit'] = submission_info.iloc[3][3]
+        return submission_info
+
+
+    def _parse_bacterial_culture(self):
+        # submission_info = self.xl.parse("Sample List")
+        submission_info = self._parse_generic("Sample List")
+        # iloc is [row][column] and the first row is set as header row so -2
+        tech = str(submission_info.iloc[11][1])
+        if tech == "nan":
+            tech = "Unknown"
+        elif len(tech.split(",")) > 1:
+            tech_reg = re.compile(r"[A-Z]{2}")
+            tech = ", ".join(tech_reg.findall(tech))
+        self.sub['technician'] = tech
+        # reagents
+        self.sub['lot_wash_1'] = submission_info.iloc[1][6]
+        self.sub['lot_wash_2'] = submission_info.iloc[2][6]
+        self.sub['lot_binding_buffer'] = submission_info.iloc[3][6]
+        self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6]
+        self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6]
+        self.sub['lot_elution_buffer'] = submission_info.iloc[6][6]
+        self.sub['lot_isopropanol'] = submission_info.iloc[9][6]
+        self.sub['lot_ethanol'] = submission_info.iloc[10][6]
+        self.sub['lot_positive_control'] = submission_info.iloc[103][1]
+        self.sub['lot_plate'] = submission_info.iloc[12][6]
+        
+
+    def _parse_wastewater(self):
+        # submission_info = self.xl.parse("WW Submissions (ENTER HERE)")
+        submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
+        enrichment_info = self.xl.parse("Enrichment Worksheet")
+        extraction_info = self.xl.parse("Extraction Worksheet")
+        qprc_info = self.xl.parse("qPCR Worksheet")
+        # iloc is [row][column] and the first row is set as header row so -2
+        # self.sub['submitter_plate_num'] = submission_info.iloc[0][1]
+        # self.sub['rsl_plate_num'] = str(submission_info.iloc[10][1])
+        # self.sub['submitted_date'] = submission_info.iloc[1][1].date()#.strftime("%Y-%m-%d")
+        # self.sub['submitting_lab'] = submission_info.iloc[0][3]
+        # self.sub['sample_count'] = str(submission_info.iloc[2][3])
+        # self.sub['extraction_kit'] = submission_info.iloc[3][3]
+        self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}"
+        # reagents
+        self.sub['lot_lysis_buffer'] = enrichment_info.iloc[0][14]
+        self.sub['lot_proteinase_K'] = enrichment_info.iloc[1][14]
+        self.sub['lot_magnetic_virus_particles'] = enrichment_info.iloc[2][14]
+        self.sub['lot_enrichment_reagent_1'] = enrichment_info.iloc[3][14]
+        self.sub['lot_binding_buffer'] = extraction_info.iloc[0][14]
+        self.sub['lot_magnetic_beads'] = extraction_info.iloc[1][14]
+        self.sub['lot_wash'] = extraction_info.iloc[2][14]
+        self.sub['lot_ethanol'] = extraction_info.iloc[3][14]
+        self.sub['lot_elution_buffer'] = extraction_info.iloc[4][14]
+        self.sub['lot_master_mix'] = qprc_info.iloc[0][14]
+        self.sub['lot_pre_mix_1'] = qprc_info.iloc[1][14]
+        self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14]
+        self.sub['lot_positive_control'] = qprc_info.iloc[3][14]
+        self.sub['lot_ddh2o'] = qprc_info.iloc[4][14]
+        # tech = str(submission_info.iloc[11][1])
+        # if tech == "nan":
+        #     tech = "Unknown"
+        # elif len(tech.split(",")) > 1:
+        #     tech_reg = re.compile(r"[A-Z]{2}")
+        #     tech = ", ".join(tech_reg.findall(tech))
+        
+        
+        # self.sub['lot_wash_1'] = submission_info.iloc[1][6]
+        # self.sub['lot_wash_2'] = submission_info.iloc[2][6]
+        # self.sub['lot_binding_buffer'] = submission_info.iloc[3][6]
+        # self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6]
+        # self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6]
+        # self.sub['lot_elution_buffer'] = submission_info.iloc[6][6]
+        # self.sub['lot_isopropanol'] = submission_info.iloc[9][6]
+        # self.sub['lot_ethanol'] = submission_info.iloc[10][6]
+        # self.sub['lot_positive_control'] = None #submission_info.iloc[103][1]
+        # self.sub['lot_plate'] = submission_info.iloc[12][6]