add sample material column and rewrite inosticID column

qubittool/rowmodel.py

@@ -4,7 +4,10 @@ class RowModel:
         self.coordinate = coordinate
         self.accessionid = accessionid
         self.customerid = None
+<<<<<<< HEAD
         self.materialid = None
+=======
+>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
         self.plasmavolml = float(0.0)
         self.qubitrunid = None
         self.qubitassay = None
@@ -40,6 +43,7 @@ class RowModel:
 
     def get_customerid(self):
         return self.customerid
+<<<<<<< HEAD
 
     def set_materialid(self, matrlid:str):
         self.materialid = matrlid
@@ -47,6 +51,9 @@ class RowModel:
     def get_materialid(self):
         return self.materialid
 
+=======
+    
+>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
     def set_qubitassay(self, assay:str):
         self.qubitassay = assay
 

qubittool/tool.py

@@ -11,10 +11,13 @@ from openpyxl.styles import PatternFill, Border, Side, Alignment
 
 from rowmodel import RowModel
 
+<<<<<<< HEAD
 codex:dict = {"cfDNA from Plasma":None}
 codex.update ( {"gDNA from cells":"BM"} )
 codex.update({"gDNA from Buffy Coat":"BC"})
 
+=======
+>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
 def read_qubit_doc_by_accession(keys:dict, path:str):
     # collect values_by_sample_names string ids #
     with open(path, 'r', newline='', encoding='utf-8') as csvfile:
@@ -88,8 +91,12 @@ def write_run_doc(dm:dict, path:str):
     for r in dm:
         model:RowModel = dm[r]
         ix=ix+1
+<<<<<<< HEAD
         fmtId = formatInosticsId( model.get_Id(), model.get_materialid() )
         ws.append([ix, "", fmtId, model.get_customerid(), model.get_plasmavolml(), model.get_qubitrunid(), 
+=======
+        ws.append([ix, "", model.get_Id(), model.get_customerid(), model.get_plasmavolml(), model.get_qubitrunid(), 
+>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
         model.get_sampleconc(), convert_to_GE(model.get_sampleconc())])
 
     grayFill = PatternFill(start_color='D0CECE', end_color='D0CECE',
@@ -103,6 +110,7 @@ def write_run_doc(dm:dict, path:str):
     wb.close()
     return
 
+<<<<<<< HEAD
 def formatInosticsId(id:str=None, matrl:str=None):
     iid = id.split("-", 1)[0]
     ncd:str = ""
@@ -117,6 +125,8 @@ def formatInosticsId(id:str=None, matrl:str=None):
         pass
     return iid
 
+=======
+>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
 def convert_to_numeric(vlu, stndv:float=0.0):
     try:
         return float(vlu)
@@ -139,7 +149,10 @@ def read_collect_run_doc_name_strids(min_col:int=1, path:str=None):
     InosticsID = None
     CustomerID = None
     PlasmaID = None
+<<<<<<< HEAD
     MaterialID = None
+=======
+>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
     InosticsIDKeys = {}
     for row in ws.iter_rows(max_row=30, min_col=min_col):
         for cell in row:
@@ -155,10 +168,13 @@ def read_collect_run_doc_name_strids(min_col:int=1, path:str=None):
                 PlasmaID = cell.column
                 continue
             
+<<<<<<< HEAD
             if MaterialID==None and cell.value and isinstance(cell.value, str) and "Sample Material" in cell.value:
                 MaterialID = cell.column
                 continue
 
+=======
+>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
             if cell.value and InosticsID == cell.column:
                 InosticsIDKeys[cell.value] = RowModel(cell.coordinate, cell.value)
                 rmv:RowModel = InosticsIDKeys[cell.value]
@@ -183,6 +199,7 @@ def read_collect_run_doc_name_strids(min_col:int=1, path:str=None):
                         rmv.set_plasmavolml( convert_to_numeric(cell.value) )
                 except:
                     pass
+<<<<<<< HEAD
 
             if cell.value and MaterialID == cell.column:
                 print(F"{cell.coordinate}:{cell.row}x{cell.column}={cell.value}") 
@@ -192,5 +209,7 @@ def read_collect_run_doc_name_strids(min_col:int=1, path:str=None):
                         rmv.set_materialid( cell.value )
                 except:
                     pass
+=======
+>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a
     wb.close()
     return InosticsIDKeys