From 3d2f3fdf2f03ab54c461d182090b17093935fd7b Mon Sep 17 00:00:00 2001 From: Sherwin Price Date: Tue, 21 Nov 2023 07:36:56 -0500 Subject: [PATCH] add sample material column and rewrite inosticID column --- README.md | 10 ++++++++++ pyproject.toml | 5 +++++ qubittool/rowmodel.py | 7 +++++++ qubittool/tool.py | 19 +++++++++++++++++++ setup.cfg | 17 +++++++++++++++++ 5 files changed, 58 insertions(+) diff --git a/README.md b/README.md index 07d910c..8a4da18 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,4 @@ +<<<<<<< HEAD Qubit Tool Read Qubit CSV dump. @@ -5,3 +6,12 @@ Read Qubit CSV dump. Search dump for matching data and include in output. Format Output and add to Excel Document Output Tab. +======= +Qubit Tool + +Read Qubit CSV dump. + +Search dump for matching data and include in output. + +Format Output and add to Excel Document Output Tab. +>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a diff --git a/pyproject.toml b/pyproject.toml index 7fd26b9..634c1c6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,8 @@ +<<<<<<< HEAD [build-system] requires = ["setuptools"] +======= +[build-system] +requires = ["setuptools"] +>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a build-backend = "setuptools.build_meta" \ No newline at end of file diff --git a/qubittool/rowmodel.py b/qubittool/rowmodel.py index 7309151..4086f42 100644 --- a/qubittool/rowmodel.py +++ b/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 diff --git a/qubittool/tool.py b/qubittool/tool.py index c608137..21e0357 100644 --- a/qubittool/tool.py +++ b/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 diff --git a/setup.cfg b/setup.cfg index b0d3e4a..b33d278 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,3 +1,4 @@ +<<<<<<< HEAD [metadata] name = qubittool version = 0.1.0 @@ -12,4 +13,20 @@ install_requires = pandas [options.package_data] +======= +[metadata] +name = qubittool +version = 0.1.0 + +[options] +packages = find: +zip_safe = True +include_package_data = True +install_requires = + PySimpleGUI >= 4.60 + openpyxl >= 3.1 + pandas + +[options.package_data] +>>>>>>> d07459290f0590ab07c6c3fdca43ff95ec80057a * = README.md \ No newline at end of file