Update of Reagent usage ui for addition of new reagents.

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

@@ -603,7 +603,7 @@ class BaseClass(Base):
             pyd = getattr(pydant, pyd_model_name)
         except AttributeError:
             raise AttributeError(f"Could not get pydantic class {pyd_model_name}")
-        return pyd(**self.details_dict())
+        return pyd(**self.details_dict(**kwargs))
 
     def show_details(self, obj):
         logger.debug("Show Details")

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

@@ -5,13 +5,11 @@ from __future__ import annotations
 import zipfile, logging, re
 from operator import itemgetter
 from pprint import pformat
-
 import numpy as np
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.ext.associationproxy import association_proxy
 from datetime import date, datetime, timedelta
-
 from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, timezone, \
     jinja_template_loading, flatten_list
 from typing import List, Literal, Generator, Any, Tuple, TYPE_CHECKING
@@ -562,7 +560,8 @@ class ReagentRole(BaseClass):
 
     def get_reagents(self, kittype: str | KitType | None = None):
         if not kittype:
-            return [f"{reagent.name} - {reagent.lot}" for reagent in self.reagent]
+            # return [f"{reagent.name} - {reagent.lot} - {reagent.expiry}" for reagent in self.reagent]
+            return [reagent.to_pydantic() for reagent in self.reagent]
         if isinstance(kittype, str):
             kittype = KitType.query(name=kittype)
         assoc = next((item for item in self.reagentrolekittypeassociation if item.kittype == kittype), None)
@@ -571,7 +570,8 @@ class ReagentRole(BaseClass):
             last_used = Reagent.query(name=assoc.last_used)
             if last_used:
                 reagents.insert(0, reagents.pop(reagents.index(last_used)))
-        return [f"{reagent.name} - {reagent.lot}" for reagent in reagents]
+        # return [f"{reagent.name} - {reagent.lot} - {reagent.expiry}" for reagent in reagents]
+        return [reagent.to_pydantic(reagentrole=self.name) for reagent in reagents]
 
 
 class Reagent(BaseClass, LogMixin):
@@ -680,24 +680,24 @@ class Reagent(BaseClass, LogMixin):
         report.add_result(Result(msg=f"Updating last used {rt} was not performed.", status="Information"))
         return report
 
-    @classmethod
+    # @classmethod
-    def query_or_create(cls, **kwargs) -> Reagent:
+    # def query_or_create(cls, **kwargs) -> Reagent:
-        from backend.validators.pydant import PydReagent
+    #     from backend.validators.pydant import PydReagent
-        new = False
+    #     new = False
-        disallowed = ['expiry']
+    #     disallowed = ['expiry']
-        sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
+    #     sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
-        instance = cls.query(**sanitized_kwargs)
+    #     instance = cls.query(**sanitized_kwargs)
-        if not instance or isinstance(instance, list):
+    #     if not instance or isinstance(instance, list):
-            if "reagentrole" not in kwargs:
+    #         if "reagentrole" not in kwargs:
-                try:
+    #             try:
-                    kwargs['reagentrole'] = kwargs['name']
+    #                 kwargs['reagentrole'] = kwargs['name']
-                except KeyError:
+    #             except KeyError:
-                    pass
+    #                 pass
-            instance = PydReagent(**kwargs)
+    #         instance = PydReagent(**kwargs)
-            new = True
+    #         new = True
-            instance = instance.to_sql()
+    #         instance = instance.to_sql()
-        logger.info(f"Instance from query or create: {instance}")
+    #     logger.info(f"Instance from query or create: {instance}")
-        return instance, new
+    #     return instance, new
 
     @classmethod
     @setup_lookup
@@ -800,6 +800,12 @@ class Reagent(BaseClass, LogMixin):
             expiry="Use exact date on reagent.\nEOL will be calculated from kittype automatically"
         )
 
+    def details_dict(self, reagentrole:str|None=None, **kwargs):
+        output = super().details_dict()
+        if reagentrole:
+            output['reagentrole'] = reagentrole
+        return output
+
 
 class Discount(BaseClass):
     """
@@ -1278,7 +1284,7 @@ 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)
-        logger.debug(f"Sample dicts: {pformat(sample_dicts)}")
+        # logger.debug(f"Sample dicts: {pformat(sample_dicts)}")
         vw = round((-0.07 * len(sample_dicts)) + 12.2, 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
@@ -1291,14 +1297,14 @@ class ProcedureType(BaseClass):
     def pad_sample_dicts(self, sample_dicts: List["PydSample"]):
         from backend.validators.pydant import PydSample
         output = []
-        logger.debug(f"Rows: {self.plate_rows}")
+        # logger.debug(f"Rows: {self.plate_rows}")
-        logger.debug(f"Columns: {self.plate_columns}")
+        # logger.debug(f"Columns: {self.plate_columns}")
         for row, column in self.ranked_plate.values():
             sample = next((sample for sample in sample_dicts if sample.row == row and sample.column == column),
                           PydSample(**dict(sample_id="", row=row, column=column, enabled=False)))
             sample.background_color = "#6ffe1d" if sample.enabled else "#ffffff"
             output.append(sample)
-            logger.debug(f"Appending {sample} at row {row}, column {column}")
+            # logger.debug(f"Appending {sample} at row {row}, column {column}")
         return output
 
 
@@ -1453,6 +1459,8 @@ class Procedure(BaseClass):
         dlg = ProcedureCreation(parent=obj, procedure=self.to_pydantic(), edit=True)
         if dlg.exec():
             logger.debug("Edited")
+            sql, _ = dlg.return_sql()
+            sql.save()
 
     def add_comment(self, obj):
         logger.debug("Add Comment!")

src/submissions/backend/validators/pydant.py

@@ -183,7 +183,7 @@ class PydReagent(PydBaseClass):
                 case _:
                     return convert_nans_to_nones(str(value))
         if value is None:
-            value = date.today()
+            value = datetime.combine(date.today(), datetime.max.time())
         return value
 
     @field_validator("expiry")
@@ -201,6 +201,11 @@ class PydReagent(PydBaseClass):
         else:
             return values.data['reagentrole'].strip()
 
+    # @field_validator("reagentrole", mode="before")
+    # @classmethod
+    # def rescue_reagentrole(cls, value):
+    #     if
+
     def improved_dict(self) -> dict:
         """
         Constructs a dictionary consisting of model.fields and model.extras
@@ -226,23 +231,26 @@ class PydReagent(PydBaseClass):
         report = Report()
         if self.model_extra is not None:
             self.__dict__.update(self.model_extra)
-        reagent = Reagent.query(lot=self.lot, name=self.name)
+        reagent, new = Reagent.query_or_create(lot=self.lot, name=self.name)
         # logger.debug(f"Reagent: {reagent}")
-        if reagent is None:
+        # if reagent is None:
-            reagent = Reagent()
+        #     reagent = Reagent()
-            for key, value in self.__dict__.items():
+        #     for key, value in self.__dict__.items():
-                if isinstance(value, dict):
+        #         if isinstance(value, dict):
-                    value = value['value']
+        #             if key == "misc_info":
-                # NOTE: reagent method sets fields based on keys in dictionary
+        #                 value = value
-                reagent.set_attribute(key, value)
+        #             else:
-                if procedure is not None and reagent not in procedure.reagents:
+        #                 value = value['value']
-                    assoc = ProcedureReagentAssociation(reagent=reagent, procedure=procedure)
+        #         # NOTE: reagent method sets fields based on keys in dictionary
-                    assoc.comments = self.comment
+        #         reagent.set_attribute(key, value)
-                else:
+        #         if procedure is not None and reagent not in procedure.reagents:
-                    assoc = None
+        #             assoc = ProcedureReagentAssociation(reagent=reagent, procedure=procedure)
-        else:
+        #             assoc.comments = self.comment
-            if submission is not None and reagent not in submission.reagents:
+        #         else:
-                submission.update_reagentassoc(reagent=reagent, role=self.role)
+        #             assoc = None
+        # else:
+        #     if submission is not None and reagent not in submission.reagents:
+        #         submission.update_reagentassoc(reagent=reagent, role=self.role)
         return reagent, report
 
 
@@ -1486,8 +1494,10 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
         if isinstance(kittype, str):
             kittype_obj = KitType.query(name=kittype)
         try:
-            self.reagentrole = {item.name: item.get_reagents(kittype=kittype_obj) + ["New"] for item in
+            self.reagentrole = {
-                                kittype_obj.get_reagents(proceduretype=self.proceduretype)}
+                item.name: item.get_reagents(kittype=kittype_obj) + [PydReagent(name="--New--", lot="", reagentrole="")]
+                for item in
+                kittype_obj.get_reagents(proceduretype=self.proceduretype)}
         except AttributeError:
             self.reagentrole = {}
 
@@ -1511,19 +1521,19 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
         logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
         for sample_dict in sample_list:
             if sample_dict['sample_id'].startswith("blank_"):
-                continue
+                sample_dict['sample_id'] = ""
             row, column = self.proceduretype.ranked_plate[sample_dict['index']]
             logger.debug(f"Row: {row}, Column: {column}")
             try:
                 sample = next(
-                    (item for item in self.samples if item.sample_id.upper() == sample_dict['sample_id'].upper()))
+                    (item for item in self.sample if item.sample_id.upper() == sample_dict['sample_id'].upper()))
             except StopIteration:
                 # NOTE: Code to check for added controls.
                 logger.debug(
                     f"Sample not found by name: {sample_dict['sample_id']}, checking row {row} column {column}")
                 try:
                     sample = next(
-                        (item for item in self.samples if item.row == row and item.column == column))
+                        (item for item in self.sample if item.row == row and item.column == column))
                 except StopIteration:
                     logger.error(f"Couldn't find sample: {pformat(sample_dict)}")
                     continue
@@ -1532,7 +1542,23 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
             sample.well_id = sample_dict['sample_id']
             sample.row = row
             sample.column = column
-        logger.debug(f"Updated samples:\n{pformat(self.samples)}")
+        # logger.debug(f"Updated samples:\n{pformat(self.sample)}")
+
+    def update_reagents(self, reagentrole: str, name: str, lot: str, expiry: str):
+        removable = next((item for item in self.reagent if item.reagentrole == reagentrole), None)
+        if removable:
+            idx = self.reagent.index(removable)
+            self.reagent.remove(removable)
+        else:
+            idx = 0
+        insertable = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
+        self.reagent.insert(idx, insertable)
+        logger.debug(self.reagent)
+
+    @classmethod
+    def update_new_reagents(cls, reagent: PydReagent):
+        reg = reagent.to_sql()
+        reg.save()
 
     def to_sql(self):
         from backend.db.models import RunSampleAssociation, ProcedureSampleAssociation
@@ -1540,12 +1566,24 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
         # for result in self.results:
         #     result, _ = result.to_sql()
         sql = super().to_sql()
-        logger.debug(f"Initial PYD: {pformat(self.__dict__)}")
+        # logger.debug(f"Initial PYD: {pformat(self.__dict__)}")
         # sql.results = [result.to_sql() for result in self.results]
         if self.run:
             sql.run = self.run
         if self.proceduretype:
             sql.proceduretype = self.proceduretype
+        # Note: convert any new reagents to sql and save
+        for reagentrole, reagents in self.reagentrole.items():
+            for reagent in reagents:
+                if not reagent.lot or reagent.name == "--New--":
+                    continue
+                self.update_new_reagents(reagent)
+        # NOTE: reset reagent associations.
+        sql.procedurereagentassociation = []
+        for reagent in self.reagent:
+            reagent = reagent.to_sql()
+            if reagent not in sql.reagent:
+                reagent_assoc = ProcedureReagentAssociation(reagent=reagent, procedure=sql)
         try:
             start_index = max([item.id for item in ProcedureSampleAssociation.query()]) + 1
         except ValueError:
@@ -1571,13 +1609,15 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
             kittype = KitType.query(name=self.kittype['value'], limit=1)
             if kittype:
                 sql.kittype = kittype
+        logger.debug(self.reagent)
         for equipment in self.equipment:
             equip = Equipment.query(name=equipment.name)
             if equip not in sql.equipment:
-                equip_assoc = ProcedureEquipmentAssociation(equipment=equip, procedure=sql, equipmentrole=equip.equipmentrole[0])
+                equip_assoc = ProcedureEquipmentAssociation(equipment=equip, procedure=sql,
+                                                            equipmentrole=equip.equipmentrole[0])
                 process = equipment.process.to_sql()
                 equip_assoc.process = process
-        logger.debug(f"Output sql: {[pformat(item.__dict__) for item in sql.procedureequipmentassociation]}")
+        # logger.debug(f"Output sql: {[pformat(item.__dict__) for item in sql.procedureequipmentassociation]}")
         return sql, None
 
 

src/submissions/frontend/widgets/procedure_creation.py

@@ -3,6 +3,7 @@
 """
 from __future__ import annotations
 
+import datetime
 import os
 import sys, logging
 from pathlib import Path
@@ -122,6 +123,24 @@ class ProcedureCreation(QDialog):
     def log(self, logtext: str):
         logger.debug(logtext)
 
+    @pyqtSlot(str, str, str, str)
+    def add_new_reagent(self, reagentrole: str, name: str, lot: str, expiry: str):
+        from backend.validators.pydant import PydReagent
+        expiry = datetime.datetime.strptime(expiry, "%Y-%m-%d")
+        pyd = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
+        logger.debug(pyd)
+        self.procedure.reagentrole[reagentrole].insert(0, pyd)
+        logger.debug(pformat(self.procedure.__dict__))
+        self.set_html()
+
+    @pyqtSlot(str, str)
+    def update_reagent(self, reagentrole:str, name_lot_expiry:str):
+        try:
+            name, lot, expiry = name_lot_expiry.split(" - ")
+        except ValueError:
+            return
+        self.procedure.update_reagents(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
+
     def return_sql(self):
         return self.procedure.to_sql()
 

src/submissions/frontend/widgets/submission_table.py

@@ -296,7 +296,7 @@ class SubmissionsTree(QTreeView):
         self.setAlternatingRowColors(True)
         self.setIndentation(20)
         self.setItemsExpandable(True)
-        self.expanded.connect(self.expand_item)
+        # self.expanded.connect(self.expand_item)
 
         for ii in range(2):
             self.resizeColumnToContents(ii)

src/submissions/templates/js/grid_drag.js

@@ -32,24 +32,24 @@ gridContainer.addEventListener("drop", (e) => {
     targetItem !== draggedItem //&&
     //targetItem.classList.contains("well")
   ) {
-    backend.log(targetItem.id);
+//    backend.log(targetItem.id);
     const draggedIndex = [...gridContainer.children].indexOf(draggedItem);
     const targetIndex = [...gridContainer.children].indexOf(targetItem);
     if (draggedIndex < targetIndex) {
-      backend.log(draggedIndex.toString() + " " + targetIndex.toString() + " Lesser");
+//      backend.log(draggedIndex.toString() + " " + targetIndex.toString() + " Lesser");
       gridContainer.insertBefore(draggedItem, targetItem.nextSibling);
 
     } else {
-      backend.log(draggedIndex.toString() + " " + targetIndex.toString() + " Greater");
+//      backend.log(draggedIndex.toString() + " " + targetIndex.toString() + " Greater");
       gridContainer.insertBefore(draggedItem, targetItem);
 
     }
-//    output = [];
+    output = [];
-//    fullGrid = [...gridContainer.children];
+    fullGrid = [...gridContainer.children];
-//    fullGrid.forEach(function(item, index) {
+    fullGrid.forEach(function(item, index) {
-//        output.push({sample_id: item.id, index: index + 1})
+        output.push({sample_id: item.id, index: index + 1})
-//    });
+    });
-//    backend.rearrange_plate(output);
+    backend.rearrange_plate(output);
-    rearrange_plate();
+//    rearrange_plate();
   }
 });

src/submissions/templates/js/procedure_form.js

@@ -21,45 +21,39 @@ for(let i = 0; i < formtexts.length; i++) {
   })
 };
 
+var changed_it = new Event('change');
+
 var reagentRoles = document.getElementsByClassName("reagentrole");
 
 for(let i = 0; i < reagentRoles.length; i++) {
   reagentRoles[i].addEventListener("change", function() {
-    if (reagentRoles[i].value === "New") {
+    if (reagentRoles[i].value.includes("--New--")) {
-
         var br = document.createElement("br");
         var new_reg = document.getElementById("new_" + reagentRoles[i].id);
-        console.log(new_reg.id);
         var new_form = document.createElement("form");
-
+        new_form.setAttribute("class", "new_reagent_form")
+        new_form.setAttribute("id", reagentRoles[i].id + "_addition")
         var rr_name = document.createElement("input");
         rr_name.setAttribute("type", "text");
         rr_name.setAttribute("id", "new_" + reagentRoles[i].id + "_name");
-
         var rr_name_label = document.createElement("label");
         rr_name_label.setAttribute("for", "new_" + reagentRoles[i].id + "_name");
         rr_name_label.innerHTML = "Name:";
-
         var rr_lot = document.createElement("input");
         rr_lot.setAttribute("type", "text");
         rr_lot.setAttribute("id", "new_" + reagentRoles[i].id + "_lot");
-
         var rr_lot_label = document.createElement("label");
         rr_lot_label.setAttribute("for", "new_" + reagentRoles[i].id + "_lot");
         rr_lot_label.innerHTML = "Lot:";
-
         var rr_expiry = document.createElement("input");
         rr_expiry.setAttribute("type", "date");
         rr_expiry.setAttribute("id", "new_" + reagentRoles[i].id + "_expiry");
-
         var rr_expiry_label = document.createElement("label");
         rr_expiry_label.setAttribute("for", "new_" + reagentRoles[i].id + "_expiry");
         rr_expiry_label.innerHTML = "Expiry:";
-
         var submit_btn = document.createElement("input");
         submit_btn.setAttribute("type", "submit");
         submit_btn.setAttribute("value", "Submit");
-
         new_form.appendChild(br.cloneNode());
         new_form.appendChild(rr_name_label);
         new_form.appendChild(rr_name);
@@ -72,19 +66,27 @@ for(let i = 0; i < reagentRoles.length; i++) {
         new_form.appendChild(br.cloneNode());
         new_form.appendChild(submit_btn);
         new_form.appendChild(br.cloneNode());
-
         new_form.onsubmit = function(event) {
             event.preventDefault();
-            alert(reagentRoles[i].id);
             name = document.getElementById("new_" + reagentRoles[i].id + "_name").value;
             lot = document.getElementById("new_" + reagentRoles[i].id + "_lot").value;
             expiry = document.getElementById("new_" + reagentRoles[i].id + "_expiry").value;
-            alert("Submitting: " + name + ", " + lot);
+            backend.add_new_reagent(reagentRoles[i].id, name, lot, expiry);
-            backend.log(name + " " + lot + " " + expiry);
+            new_form.remove();
+            reagentRoles[i].dispatchEvent(changed_it);
         }
-
         new_reg.appendChild(new_form);
+    } else {
+        newregform = document.getElementById(reagentRoles[i].id + "_addition");
+        newregform.remove();
+        backend.update_reagent(reagentRoles[i].id, reagentRoles[i].value)
     }
-  })
+  });
 };
 
+window.onload = function() {
+    for(let i = 0; i < reagentRoles.length; i++) {
+        backend.update_reagent(reagentRoles[i].id, reagentRoles[i].value);
+    }
+}
+

src/submissions/templates/procedure_creation.html

@@ -31,12 +31,14 @@
                       {% endfor %}
                   </select><br>
                   {% if procedure['reagentrole'] %}
-                    <br><hr><br>
+                    <br>
+                    <h1><u>Reagents</u></h1>
+                    <hr>
                     {% for key, value in procedure['reagentrole'].items() %}
                     <label for="{{ key }}">{{ key }}:</label><br>
                     <select class="reagentrole dropdown" id="{{ key }}" name="{{ key }}"><br>
                         {% for reagent in value %}
-                        <option value="{{ reagent }}">{{ reagent }}</option>
+                        <option value="{{ reagent.name }} {% if reagent.lot %}- {{ reagent.lot }} - {{ reagent.expiry.date() }}{% endif %}">{{ reagent.name }} {% if reagent.lot %}- {{ reagent.lot }} - {{ reagent.expiry.date() }}{% endif %}</option>
                         {% endfor %}
                     </select>
                     <div class="new_reagent" id="new_{{ key }}"></div>