add sample material column and rewrite inosticID column

qubittool/rowmodel.py

@@ -4,6 +4,7 @@ class RowModel:
         self.coordinate = coordinate
         self.accessionid = accessionid
         self.customerid = None
+        self.materialid = None
         self.plasmavolml = float(0.0)
         self.qubitrunid = None
         self.qubitassay = None
@@ -39,7 +40,13 @@ class RowModel:
 
     def get_customerid(self):
         return self.customerid
-    
+
+    def set_materialid(self, matrlid:str):
+        self.materialid = matrlid
+
+    def get_materialid(self):
+        return self.materialid
+
     def set_qubitassay(self, assay:str):
         self.qubitassay = assay
 

qubittool/tool.py

@@ -11,6 +11,9 @@ from openpyxl.styles import PatternFill, Border, Side, Alignment
 
 from rowmodel import RowModel
 
+codex:dict = {"gDNA from cells":"BM"}
+codex.update({"gDNA from Buffy Coat":"BC"})
+
 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:
@@ -84,7 +87,8 @@ def write_run_doc(dm:dict, path:str):
     for r in dm:
         model:RowModel = dm[r]
         ix=ix+1
-        ws.append([ix, "", model.get_Id(), model.get_customerid(), model.get_plasmavolml(), model.get_qubitrunid(), 
+        fmtId = formatInosticsId( model.get_Id(), model.get_materialid() )
+        ws.append([ix, "", fmtId, model.get_customerid(), model.get_plasmavolml(), model.get_qubitrunid(), 
         model.get_sampleconc(), convert_to_GE(model.get_sampleconc())])
 
     grayFill = PatternFill(start_color='D0CECE', end_color='D0CECE',
@@ -98,6 +102,20 @@ def write_run_doc(dm:dict, path:str):
     wb.close()
     return
 
+def formatInosticsId(id:str=None, matrl:str=None):
+    iid = id.split("-", 1)[0]
+    ncd:str = ""
+    try:
+        if codex[matrl] is None: 
+            ncd =  "" 
+        else: 
+            ncd = codex[matrl]  
+        if iid:
+            return iid + ncd 
+    except Exception as e:
+        pass
+    return iid
+
 def convert_to_numeric(vlu, stndv:float=0.0):
     try:
         return float(vlu)
@@ -120,6 +138,7 @@ def read_collect_run_doc_name_strids(min_col:int=1, path:str=None):
     InosticsID = None
     CustomerID = None
     PlasmaID = None
+    MaterialID = None
     InosticsIDKeys = {}
     for row in ws.iter_rows(max_row=30, min_col=min_col):
         for cell in row:
@@ -135,6 +154,10 @@ def read_collect_run_doc_name_strids(min_col:int=1, path:str=None):
                 PlasmaID = cell.column
                 continue
             
+            if MaterialID==None and cell.value and isinstance(cell.value, str) and "Sample Material" in cell.value:
+                MaterialID = cell.column
+                continue
+
             if cell.value and InosticsID == cell.column:
                 InosticsIDKeys[cell.value] = RowModel(cell.coordinate, cell.value)
                 rmv:RowModel = InosticsIDKeys[cell.value]
@@ -159,5 +182,14 @@ def read_collect_run_doc_name_strids(min_col:int=1, path:str=None):
                         rmv.set_plasmavolml( convert_to_numeric(cell.value) )
                 except:
                     pass
+
+            if cell.value and MaterialID == cell.column:
+                print(F"{cell.coordinate}:{cell.row}x{cell.column}={cell.value}") 
+                try:
+                    if InosticsIDKeys[row[InosticsID-1].value] != None: 
+                        rmv:RowModel = InosticsIDKeys[row[InosticsID-1].value]
+                        rmv.set_materialid( cell.value )
+                except:
+                    pass
     wb.close()
     return InosticsIDKeys