Plate map in procedure details.

CHANGELOG.md

@@ -1,3 +1,7 @@
+# 202509.02
+
+- First Useable updated version.
+
 # 202504.04
 
 - Added html links for equipment/processes/tips.

src/submissions/backend/db/models/__init__.py

@@ -5,7 +5,6 @@ from __future__ import annotations
 import sys, logging, json, inspect
 from datetime import datetime, date
 from pprint import pformat
-
 from dateutil.parser import parse
 from jinja2 import TemplateNotFound, Template
 from pandas import DataFrame
@@ -19,7 +18,7 @@ from sqlalchemy.exc import ArgumentError
 from typing import Any, List, ClassVar
 from pathlib import Path
 from sqlalchemy.orm.relationships import _RelationshipDeclared
-from tools import report_result, list_sort_dict, jinja_template_loading, Report, Result
+from tools import report_result, list_sort_dict, jinja_template_loading, Report, Result, ctx
 
 # NOTE: Load testing environment
 if 'pytest' in sys.modules:
@@ -92,10 +91,6 @@ class BaseClass(Base):
         Returns:
             Session: DB session from ctx settings.
         """
-        if 'pytest' not in sys.modules:
-            from tools import ctx
-        else:
-            from test_settings import ctx
         return ctx.database_session
 
     @classmethod
@@ -107,10 +102,6 @@ class BaseClass(Base):
         Returns:
             Path: Location of the Submissions directory in Settings object
         """
-        if 'pytest' not in sys.modules:
-            from tools import ctx
-        else:
-            from test_settings import ctx
         return ctx.directory_path
 
     @classmethod
@@ -122,10 +113,6 @@ class BaseClass(Base):
         Returns:
             Path: Location of the Submissions backup directory in Settings object
         """
-        if 'pytest' not in sys.modules:
-            from tools import ctx
-        else:
-            from test_settings import ctx
         return ctx.backup_path
 
     def __init__(self, *args, **kwargs):
@@ -284,7 +271,7 @@ class BaseClass(Base):
                 if issubclass(v.__class__, PydBaseClass):
                     setattr(instance, k, v.to_sql())
         instance._misc_info.update(outside_kwargs)
-        logger.info(f"Instance from query or create: {instance}, new: {new}")
+        # logger.info(f"Instance from query or create: {instance}, new: {new}")
         return instance, new
 
     @classmethod

src/submissions/backend/db/models/procedures.py

@@ -87,7 +87,7 @@ class ReagentRole(BaseClass):
             new = True
         for k, v in sanitized_kwargs.items():
             setattr(instance, k, v)
-        logger.info(f"Instance from query or create: {instance}")
+        # logger.info(f"Instance from query or create: {instance}")
         return instance, new
 
     @classmethod
@@ -785,7 +785,7 @@ class ProcedureType(BaseClass):
         )
         return PydProcedure(**output)
 
-    def construct_plate_map(self, sample_dicts: List["PydSample"]) -> str:
+    def construct_plate_map(self, sample_dicts: List["PydSample"], creation:bool=True, vw_modifier:float=1.0) -> str:
         """
         Constructs an html based plate map for procedure details.
 
@@ -800,13 +800,13 @@ class ProcedureType(BaseClass):
         if self.plate_rows == 0 or self.plate_columns == 0:
             return "<br/>"
         sample_dicts = self.pad_sample_dicts(sample_dicts=sample_dicts)
-        vw = round((-0.07 * len(sample_dicts)) + 12.2, 1)
+        vw = round((-0.07 * len(sample_dicts)) + (12.2 * vw_modifier), 1)
         # NOTE: An overly complicated list comprehension create a list of sample locations
         # NOTE: next will return a blank cell if no value found for row/column
         env = jinja_template_loading()
         template = env.get_template("support/plate_map.html")
         html = template.render(plate_rows=self.plate_rows, plate_columns=self.plate_columns, samples=sample_dicts,
-                               vw=vw)
+                               vw=vw, creation=creation)
         return html + "<br/>"
 
     def pad_sample_dicts(self, sample_dicts: List["PydSample"]):
@@ -985,6 +985,7 @@ class Procedure(BaseClass):
         output['sample_count'] = len(active_samples)
         output['clientlab'] = self.run.clientsubmission.clientlab.name
         output['cost'] = 0.00
+        output['platemap'] = self.make_procedure_platemap()
         return output
 
     def to_pydantic(self, **kwargs):
@@ -1038,6 +1039,12 @@ class Procedure(BaseClass):
             output = {k: v for k, v in dicto.items()}
         return output
 
+    def make_procedure_platemap(self):
+        dicto = [sample.to_pydantic() for sample in self.proceduresampleassociation]
+        html = self.proceduretype.construct_plate_map(sample_dicts=dicto, creation=False, vw_modifier=1.15)
+        return html
+
+
 
 class ProcedureTypeReagentRoleAssociation(BaseClass):
     """
@@ -1143,7 +1150,7 @@ class ProcedureTypeReagentRoleAssociation(BaseClass):
                 case _:
                     pass
             setattr(instance, k, v)
-        logger.info(f"Instance from query or create: {instance.__dict__}\nis new: {new}")
+        # logger.info(f"Instance from query or create: {instance.__dict__}\nis new: {new}")
         return instance, new
 
     @classmethod
@@ -1423,7 +1430,7 @@ class EquipmentRole(BaseClass):
             new = True
         for k, v in sanitized_kwargs.items():
             setattr(instance, k, v)
-        logger.info(f"Instance from query or create: {instance}")
+        # logger.info(f"Instance from query or create: {instance}")
         return instance, new
 
     @classmethod
@@ -1816,6 +1823,9 @@ class Process(BaseClass):
 
 
 class ProcessVersion(BaseClass):
+
+    pyd_model_name = "Process"
+
     id = Column(INTEGER, primary_key=True)  #: Process id, primary key
     version = Column(FLOAT(2), default=1.00)  #: Version number
     date_verified = Column(TIMESTAMP)  #: Date this version was deemed worthy
@@ -1867,7 +1877,7 @@ class ProcessVersion(BaseClass):
               version: str | float | None = None,
               name: str | None = None,
               limit: int = 0,
-              **kwargs) -> ReagentLot | List[ReagentLot]:
+              **kwargs) -> ProcessVersion | List[ProcessVersion]:
         query: Query = cls.__database_session__.query(cls)
         match name:
             case str():
@@ -1881,6 +1891,9 @@ class ProcessVersion(BaseClass):
                 pass
         return cls.execute_query(query=query, limit=limit)
 
+    # def to_pydantic(self, pyd_model_name: str | None = None, **kwargs):
+    #     output = super().to_pydantic(pyd_model_name=pyd_model_name, **kwargs)
+
 
 class Tips(BaseClass):
     """

src/submissions/backend/db/models/submissions.py

@@ -879,7 +879,7 @@ class Run(BaseClass, LogMixin):
         Returns:
             PydSubmission: converted object.
         """
-        from backend.validators import PydRun
+        from backend.validators import PydClientSubmission, PydRun
         dicto = self.details_dict(full_data=True, backup=backup)
         new_dict = {}
         for key, value in dicto.items():
@@ -1916,6 +1916,8 @@ class ProcedureSampleAssociation(BaseClass):
         misc = output['misc_info']
         output.update(relevant)
         output['misc_info'] = misc
+        output['row'] = self.row
+        output['column'] = self.column
         output['results'] = [result.details_dict() for result in output['results']]
         return output
 

src/submissions/backend/excel/__init__.py

@@ -2,7 +2,6 @@
 Contains pandas and openpyxl convenience functions for interacting with excel workbooks
 """
 
-# from backend.excel.parsers.clientsubmission_parser import ClientSubmissionInfoParser, ClientSubmissionSampleParser
 from .parsers import (
     DefaultParser, DefaultKEYVALUEParser, DefaultTABLEParser,
     ProcedureInfoParser, ProcedureSampleParser, ProcedureReagentParser, ProcedureEquipmentParser,

src/submissions/backend/excel/reports.py

@@ -8,7 +8,7 @@ from pathlib import Path
 from datetime import date
 from typing import Tuple, List
 from backend.db.models import Procedure, Run
-from tools import jinja_template_loading, get_first_blank_df_row, row_map, flatten_list
+from tools import jinja_template_loading, get_first_blank_df_row, row_map, flatten_list, ctx
 from PyQt6.QtWidgets import QWidget
 from openpyxl.worksheet.worksheet import Worksheet
 
@@ -173,10 +173,6 @@ class TurnaroundMaker(ReportArchetype):
         Returns:
 
         """
-        if 'pytest' not in sys.modules:
-            from tools import ctx
-        else:
-            from test_settings import ctx
         days = sub.turnaround_time
         try:
             tat = sub.get_default_info("turnaround_time")

src/submissions/backend/excel/writers/__init__.py

@@ -36,7 +36,6 @@ class DefaultWriter(object):
                     value = value['name']
                 except (KeyError, ValueError):
                     return
-        # logger.debug(f"Value type: {type(value)}")
         match value:
             case x if issubclass(value.__class__, BaseClass):
                 value = value.name
@@ -81,7 +80,6 @@ class DefaultWriter(object):
         self.worksheet = self.prewrite(self.worksheet, start_row=start_row)
         self.start_row = self.delineate_start_row(start_row=start_row)
         self.end_row = self.delineate_end_row(start_row=start_row)
-        logger.debug(f"Rows for {self.__class__.__name__}:\tstart: {self.start_row}, end: {self.end_row}")
         return workbook
 
     def delineate_start_row(self, start_row: int = 1) -> int:
@@ -93,7 +91,6 @@ class DefaultWriter(object):
         Returns:
             int
         """
-        logger.debug(f"{self.__class__.__name__} will start looking for blank rows at {start_row}")
         for iii, row in enumerate(self.worksheet.iter_rows(min_row=start_row), start=start_row):
             if all([item.value is None for item in row]):
                 return iii
@@ -146,7 +143,6 @@ class DefaultKEYVALUEWriter(DefaultWriter):
         dictionary =  sort_dict_by_list(dictionary=dictionary, order_list=self.key_order)
         for ii, (k, v) in enumerate(dictionary.items(), start=self.start_row):
             value = self.stringify_value(value=v)
-            logger.debug(f"{self.__class__.__name__} attempting to write {value}")
             if value is None:
                 continue
             self.worksheet.cell(column=1, row=ii, value=self.prettify_key(k))
@@ -172,7 +168,6 @@ class DefaultTABLEWriter(DefaultWriter):
 
     def delineate_end_row(self, start_row: int = 1) -> int:
         end_row = start_row + len(self.pydant_obj) + 1
-        logger.debug(f"End row has been delineated as {start_row} + {len(self.pydant_obj)} + 1 = {end_row}")
         return end_row
 
     def pad_samples_to_length(self, row_count,
@@ -220,7 +215,6 @@ class DefaultTABLEWriter(DefaultWriter):
                         value = object.improved_dict()[header.lower().replace(" ", "_")]
                     except (AttributeError, KeyError):
                         value = ""
-                # logger.debug(f"{self.__class__.__name__} attempting to write {value}")
                 self.worksheet.cell(row=write_row, column=column, value=self.stringify_value(value))
         self.worksheet = self.postwrite(self.worksheet)
         return workbook

src/submissions/backend/excel/writers/procedure_writers/__init__.py

@@ -1,5 +1,5 @@
 """
-Default
+Default writers for procedures.
 """
 from __future__ import annotations
 import logging, sys
@@ -18,9 +18,7 @@ class ProcedureInfoWriter(DefaultKEYVALUEWriter):
                'reagentrole', 'results', 'sample', 'tips', 'reagentlot']
 
     def __init__(self, pydant_obj, *args, **kwargs):
-
         super().__init__(pydant_obj=pydant_obj, *args, **kwargs)
-
         self.fill_dictionary = {k: v for k, v in self.fill_dictionary.items() if k not in self.__class__.exclude}
 
     def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,

src/submissions/backend/excel/writers/results_writers/pcr_results_writer.py

@@ -1,5 +1,5 @@
 """
-
+Writers for PCR results from Design and Analysis Software
 """
 from __future__ import annotations
 import logging

src/submissions/frontend/widgets/procedure_creation.py

@@ -69,13 +69,10 @@ class ProcedureCreation(QDialog):
                                         equipment['name'] == relevant_procedure_item.name))
                 equipmentrole['equipment'].insert(0, equipmentrole['equipment'].pop(
                     equipmentrole['equipment'].index(item_in_er_list)))
-        # proceduretype_dict['equipment_section'] = EquipmentUsage.construct_html(procedure=self.procedure, child=True)
         proceduretype_dict['equipment'] = [sanitize_object_for_json(object) for object in proceduretype_dict['equipment']]
-        self.update_equipment = EquipmentUsage.update_equipment
         regex = re.compile(r".*R\d$")
         proceduretype_dict['previous'] = [""] + [item.name for item in self.run.procedure if item.proceduretype == self.proceduretype and not bool(regex.match(item.name))]
-        logger.debug(f"Procedure:\n{pformat(self.procedure.__dict__)}")
+        # sys.exit(f"ProcedureDict:\n{pformat(proceduretype_dict)}")
-        logger.debug(f"ProcedureType:\n{pformat(proceduretype_dict)}")
         html = render_details_template(
             template_name="procedure_creation",
             js_in=["procedure_form", "grid_drag", "context_menu"],
@@ -88,8 +85,9 @@ class ProcedureCreation(QDialog):
         self.webview.setHtml(html)
 
     @pyqtSlot(str, str, str, str)
-    def update_equipment(self, equipmentrole: str, equipment: str, process: str, tips: str):
+    def update_equipment(self, equipmentrole: str, equipment: str, processversion: str, tips: str):
         from backend.db.models import Equipment, ProcessVersion, TipsLot
+        logger.debug(f"\n\nEquipmentRole: {equipmentrole}, Equipment: {equipment}, Process: {processversion}, Tips: {tips}\n\n")
         try:
             equipment_of_interest = next(
                 (item for item in self.procedure.equipment if item.equipmentrole == equipmentrole))
@@ -103,9 +101,9 @@ class ProcedureCreation(QDialog):
         eoi.name = equipment.name
         eoi.asset_number = equipment.asset_number
         eoi.nickname = equipment.nickname
-        process_name, version = process.split("-v")
+        process_name, version = processversion.split("-v")
-        process = ProcessVersion.query(name=process_name, version=version, limit=1)
+        processversion = ProcessVersion.query(name=process_name, version=version, limit=1)
-        eoi.process = process
+        eoi.processversion = processversion.to_pydantic()
         try:
             tips_manufacturer, tipsref, lot = [item if item != "" else None for item in tips.split("-")]
             tips = TipsLot.query(manufacturer=tips_manufacturer, ref=tipsref, lot=lot)

src/submissions/templates/procedure_details.html

@@ -56,10 +56,15 @@
     {% endif %}
     {% if procedure['sample'] %}
     <button type="button"><h3><u>Procedure Samples:</u></h3></button>
+    {% if procedure['platemap']|length > 5 %}
+    <br>
+    {{ procedure['platemap'] }}
+    {% else %}
     <p>{% for sample in procedure['sample'] %}
-        &nbsp;&nbsp;&nbsp;&nbsp;<a class="{% if sample['active'] %}data-link {% else %}unused {% endif %}sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
+        <a class="{% if sample['active'] %}data-link {% else %}unused {% endif %}sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
     {% endfor %}</p>
     {% endif %}
+    {% endif %}
     {% endblock %}
 {% if not child %}
 </body>

src/submissions/templates/support/plate_map.html

@@ -1,7 +1,11 @@
         <div class="plate" id="plate-container" style="grid-template-columns: repeat({{ plate_columns }}, {{ vw }}vw);grid-template-rows: repeat({{ plate_rows }}, {{ vw }}vw);">
             {% for sample in samples %}
-                <div class="well" draggable="true" id="{{ sample['well_id'] }}" style="background-color: {{ sample['background_color'] }};">
+                <div class="well" draggable="true" id="{{ sample['sample_id'] }}" style="background-color: {{ sample['background_color'] }};">
-                  <p style="font-size: 0.7em; text-align: center; word-wrap: break-word;">{{ sample['sample_id'] }}</p>
+                  {% if creation %}
+                    <p style="font-size: 0.7em; text-align: center; word-wrap: break-word;">{{ sample['sample_id'] }}</p>
+                  {% else %}
+                    <a class="data-link sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
+                  {% endif %}
                 </div>
             {% endfor %}
         </div>

src/submissions/tools/__init__.py

@@ -8,6 +8,7 @@ from copy import copy
 from collections import OrderedDict
 from datetime import date, datetime, timedelta
 from json import JSONDecodeError
+from pprint import pformat
 from threading import Thread
 from inspect import getmembers, isfunction, stack
 from dateutil.easter import easter
@@ -1039,7 +1040,7 @@ def flatten_list(input_list: list) -> list:
     return list(itertools.chain.from_iterable(input_list))
 
 
-def sanitize_object_for_json(input_dict: dict) -> dict:
+def sanitize_object_for_json(input_dict: dict) -> dict | str:
     """
     Takes an object and makes sure its components can be converted to JSON
 
@@ -1057,8 +1058,12 @@ def sanitize_object_for_json(input_dict: dict) -> dict:
                 try:
                     input_dict = json.dumps(input_dict)
                 except TypeError:
-                    input_dict = str(input_dict)
+                    match input_dict:
-        return input_dict
+                        case str():
+                            pass
+                        case _:
+                            input_dict = str(input_dict)
+        return input_dict.strip('\"')
     output = {}
     for key, value in input_dict.items():
         match value:
@@ -1070,7 +1075,13 @@ def sanitize_object_for_json(input_dict: dict) -> dict:
                 try:
                     value = json.dumps(value)
                 except TypeError:
-                    value = str(value)
+                    match value:
+                        case str():
+                            pass
+                        case _:
+                            value = str(value)
+        if isinstance(value, str):
+            value = value.strip('\"')
         output[key] = value
     return output