Update of Equipment usage UI

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

@@ -5,6 +5,7 @@ from __future__ import annotations
 
 import sys, logging, json
 
+import sqlalchemy.exc
 from dateutil.parser import parse
 from pandas import DataFrame
 from pydantic import BaseModel
@@ -239,14 +240,23 @@ class BaseClass(Base):
         allowed = [k for k, v in cls.__dict__.items() if isinstance(v, InstrumentedAttribute)]
         # and not isinstance(v.property, _RelationshipDeclared)]
         sanitized_kwargs = {k: v for k, v in kwargs.items() if k in allowed}
-        logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
+        # logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
         instance = cls.query(**sanitized_kwargs)
         if not instance or isinstance(instance, list):
             instance = cls()
             new = True
         for k, v in sanitized_kwargs.items():
-            logger.debug(f"QorC Setting {k} to {v}")
-            setattr(instance, k, v)
+            # logger.debug(f"QorC Setting {k} to {v}")
+            if k == "id":
+                continue
+            try:
+                setattr(instance, k, v)
+            except AttributeError as e:
+                from backend.validators.pydant import PydBaseClass
+                if issubclass(v.__class__, PydBaseClass):
+                    setattr(instance, k, v.to_sql())
+                else:
+                    logger.error(f"Could not set {k} due to {e}")
         logger.info(f"Instance from query or create: {instance}, new: {new}")
         return instance, new
 
@@ -315,9 +325,13 @@ class BaseClass(Base):
         try:
             self.__database_session__.add(self)
             self.__database_session__.commit()
+        # except sqlalchemy.exc.IntegrityError as i:
+        #     logger.error(f"Integrity error saving {self} due to: {i}")
+        #     logger.error(pformat(self.__dict__))
         except Exception as e:
-            logger.critical(f"Problem saving object: {e}")
+            logger.critical(f"Problem saving {self} due to: {e}")
             logger.error(f"Error message: {type(e)}")
+            logger.error(pformat(self.__dict__))
             self.__database_session__.rollback()
             report.add_result(Result(msg=e, status="Critical"))
             return report
@@ -484,9 +498,9 @@ class BaseClass(Base):
                     # logger.debug(f"Setting ColumnProperty to {value}")
                     return super().__setattr__(key, value)
                 case _RelationshipDeclared():
-                    logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
+                    # logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
                     if field_type.property.uselist:
-                        logger.debug(f"Setting with uselist")
+                        # logger.debug(f"Setting with uselist")
                         existing = self.__getattribute__(key)
                         # NOTE: This is causing problems with removal of items from lists. Have to overhaul it.
                         if existing is not None:
@@ -502,8 +516,11 @@ class BaseClass(Base):
                                 pass
                             else:
                                 value = [value]
-                        value = list(set(value))
-                        logger.debug(f"Final value for {key}: {value}")
+                        try:
+                            value = list(set(value))
+                        except TypeError:
+                            pass
+                        # logger.debug(f"Final value for {key}: {value}")
                         return super().__setattr__(key, value)
                     else:
                         if isinstance(value, list):
@@ -514,7 +531,7 @@ class BaseClass(Base):
                         try:
                             return super().__setattr__(key, value)
                         except AttributeError:
-                            logger.debug(f"Possible attempt to set relationship {key} to simple var type. {value}")
+                            logger.warning(f"Possible attempt to set relationship {key} to simple var type. {value}")
                             relationship_class = field_type.property.entity.entity
                             value = relationship_class.query(name=value)
                             try:
@@ -555,7 +572,7 @@ class BaseClass(Base):
         output_date = datetime.combine(output_date, addition_time).strftime("%Y-%m-%d %H:%M:%S")
         return output_date
 
-    def details_dict(self):
+    def details_dict(self, **kwargs):
         relevant = {k: v for k, v in self.__class__.__dict__.items() if
                     isinstance(v, InstrumentedAttribute) or isinstance(v, AssociationProxy)}
         output = {}
@@ -578,6 +595,16 @@ class BaseClass(Base):
             output[k.strip("_")] = value
         return output
 
+    def to_pydantic(self, **kwargs):
+        from backend.validators import pydant
+        pyd_model_name = f"Pyd{self.__class__.__name__}"
+        logger.debug(f"Looking for pydant model {pyd_model_name}")
+        try:
+            pyd = getattr(pydant, pyd_model_name)
+        except AttributeError:
+            raise AttributeError(f"Could not get pydantic class {pyd_model_name}")
+        return pyd(**self.details_dict())
+
     def show_details(self, obj):
         logger.debug("Show Details")
         from frontend.widgets.submission_details import SubmissionDetails

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

@@ -4,14 +4,16 @@ All kittype and reagent related models
 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
+    jinja_template_loading, flatten_list
 from typing import List, Literal, Generator, Any, Tuple, TYPE_CHECKING
 from pandas import ExcelFile
 from pathlib import Path
@@ -20,6 +22,7 @@ from io import BytesIO
 
 if TYPE_CHECKING:
     from backend.db.models.submissions import Run, ProcedureSampleAssociation
+    from backend.validators.pydant import PydSample, PydResults
 
 logger = logging.getLogger(f'procedure.{__name__}')
 
@@ -127,6 +130,11 @@ class KitType(BaseClass):
     process = relationship("Process", back_populates="kittype",
                            secondary=kittype_process)  #: equipment process used by this kittype
 
+    proceduretypeequipmentroleassociation = relationship("ProcedureTypeEquipmentRoleAssociation", back_populates="kittype",
+        cascade="all, delete-orphan",)
+
+    equipmentrole = association_proxy("proceduretypeequipmentroleassociation", "equipmentrole")
+
     kittypereagentroleassociation = relationship(
         "KitTypeReagentRoleAssociation",
         back_populates="kittype",
@@ -148,6 +156,8 @@ class KitType(BaseClass):
                                       creator=lambda ST: ProcedureTypeKitTypeAssociation(
                                           submissiontype=ST))  #: Association proxy to SubmissionTypeKitTypeAssociation
 
+
+
     @classproperty
     def aliases(cls) -> List[str]:
         """
@@ -174,17 +184,30 @@ class KitType(BaseClass):
         """
         match proceduretype:
             case ProcedureType():
-                relevant_associations = [item for item in self.kittypereagentroleassociation if
+                relevant_associations = [assoc for assoc in self.kittypereagentroleassociation if
+                                         assoc.proceduretype == proceduretype]
+            case str():
+                relevant_associations = [assoc for assoc in self.kittypereagentroleassociation if
+                                         assoc.proceduretype.name == proceduretype]
+            case _:
+                relevant_associations = [assoc for assoc in self.kittypereagentroleassociation]
+        if required_only:
+            return (assoc.reagentrole for assoc in relevant_associations if assoc.required == 1)
+        else:
+            return (assoc.reagentrole for assoc in relevant_associations)
+
+    def get_equipmentroles(self, proceduretype: str| ProcedureType | None = None) -> Generator[ReagentRole, None, None]:
+        match proceduretype:
+            case ProcedureType():
+                relevant_associations = [item for item in self.proceduretypeequipmentroleassociation if
                                          item.proceduretype == proceduretype]
             case str():
-                relevant_associations = [item for item in self.kittypereagentroleassociation if
+                relevant_associations = [item for item in self.proceduretypeequipmentroleassociation if
                                          item.proceduretype.name == proceduretype]
             case _:
-                relevant_associations = [item for item in self.kittypereagentroleassociation]
-        if required_only:
-            return (item.reagentrole for item in relevant_associations if item.required == 1)
-        else:
-            return (item.reagentrole for item in relevant_associations)
+                relevant_associations = [item for item in self.proceduretypeequipmentroleassociation]
+        return (assoc.equipmentrole for assoc in relevant_associations)
+
 
     def construct_xl_map_for_use(self, proceduretype: str | SubmissionType) -> Tuple[dict | None, KitType]:
         """
@@ -1223,26 +1246,24 @@ class ProcedureType(BaseClass):
         output = super().details_dict(**kwargs)
         output['kittype'] = [item.details_dict() for item in output['kittype']]
         # output['process'] = [item.details_dict() for item in output['process']]
-        output['equipment'] = [item.details_dict() for item in output['equipment']]
+        output['equipment'] = [item.details_dict(proceduretype=self) for item in output['equipment']]
         return output
 
-
-
-    def construct_dummy_procedure(self, run: Run|None=None):
+    def construct_dummy_procedure(self, run: Run | None = None):
         from backend.validators.pydant import PydProcedure
         if run:
             samples = run.constuct_sample_dicts_for_proceduretype(proceduretype=self)
+        else:
+            samples = []
         output = dict(
             proceduretype=self,
-            #name=dict(value=self.name, missing=True),
-            #possible_kits=[kittype.name for kittype in self.kittype],
             repeat=False,
-            # plate_map=plate_map
-            run=run
+            run=run,
+            sample=samples
         )
         return PydProcedure(**output)
 
-    def construct_plate_map(self, sample_dicts: List[dict]) -> str:
+    def construct_plate_map(self, sample_dicts: List["PydSample"]) -> str:
         """
         Constructs an html based plate map for procedure details.
 
@@ -1256,23 +1277,31 @@ class ProcedureType(BaseClass):
         """
         if self.plate_rows == 0 or self.plate_columns == 0:
             return "<br/>"
-        # plate_rows = range(1, self.plate_rows + 1)
-        # plate_columns = range(1, self.plate_columns + 1)
-        # total_wells = self.plate_columns * self.plate_rows
+        sample_dicts = self.pad_sample_dicts(sample_dicts=sample_dicts)
+        logger.debug(f"Sample dicts: {pformat(sample_dicts)}")
         vw = round((-0.07 * len(sample_dicts)) + 12.2, 1)
-        # sample_dicts = run.constuct_sample_dicts_for_proceduretype(proceduretype=self)
-        # output_samples = [next((item for item in sample_dicts if item['row'] == row and item['column'] == column),
-        #                        dict(sample_id="", row=row, column=column, background_color="#ffffff"))
-        #                   for row in plate_rows
-        #                   for column in plate_columns]
-        # logger.debug(f"Output samples:\n{pformat(output_samples)}")
         # 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)
+        html = template.render(plate_rows=self.plate_rows, plate_columns=self.plate_columns, samples=sample_dicts,
+                               vw=vw)
         return html + "<br/>"
 
+    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"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}")
+        return output
+
+
     @property
     def ranked_plate(self):
         matrix = np.array([[0 for yyy in range(1, self.plate_rows + 1)] for xxx in range(1, self.plate_columns + 1)])
@@ -1318,7 +1347,7 @@ class Procedure(BaseClass):
     )  #: Relation to ProcedureReagentAssociation
 
     reagent = association_proxy("procedurereagentassociation",
-                                 "reagent", creator=lambda reg: ProcedureReagentAssociation(
+                                "reagent", creator=lambda reg: ProcedureReagentAssociation(
             reagent=reg))  #: Association proxy to RunReagentAssociation.reagent
 
     procedureequipmentassociation = relationship(
@@ -1365,7 +1394,7 @@ class Procedure(BaseClass):
                 pass
         return cls.execute_query(query=query, limit=limit)
 
-    def to_dict(self, full_data: bool=False):
+    def to_dict(self, full_data: bool = False):
         output = dict()
         output['name'] = self.name
         return output
@@ -1381,7 +1410,7 @@ class Procedure(BaseClass):
         names = ["Add Results", "Add Equipment", "Edit", "Add Comment", "Show Details", "Delete"]
         return {item: self.__getattribute__(item.lower().replace(" ", "_")) for item in names}
 
-    def add_results(self, obj, resultstype_name:str):
+    def add_results(self, obj, resultstype_name: str):
         logger.debug(f"Add Results! {resultstype_name}")
         from ...managers import results
         results_class = getattr(results, resultstype_name)
@@ -1395,30 +1424,35 @@ class Procedure(BaseClass):
             obj (_type_): parent widget
         """
         logger.debug(f"Add equipment")
-        from frontend.widgets.equipment_usage import EquipmentUsage
-        dlg = EquipmentUsage(parent=obj, procedure=self)
+        from frontend.widgets.equipment_usage_2 import EquipmentUsage
+        dlg = EquipmentUsage(parent=obj, procedure=self.to_pydantic())
         if dlg.exec():
-            equipment = dlg.parse_form()
-            for equip in equipment:
-                logger.debug(f"Parsed equipment: {equip}")
-                _, assoc = equip.to_sql(procedure=self)
-                logger.debug(f"Got equipment association: {assoc} for {equip}")
-                try:
-                    assoc.save()
-                except AttributeError as e:
-                    logger.error(f"Couldn't save association with {equip} due to {e}")
-                if equip.tips:
-                    for tips in equip.tips:
-                        # logger.debug(f"Attempting to add tips assoc: {tips} (pydantic)")
-                        tassoc, _ = tips.to_sql(procedure=self)
-                        # logger.debug(f"Attempting to add tips assoc: {tips.__dict__} (sql)")
-                        if tassoc not in self.proceduretipsassociation:
-                            tassoc.save()
-                        else:
-                            logger.error(f"Tips already found in submission, skipping.")
+            # equipment = dlg.parse_form()
+            # for equip in equipment:
+            #     logger.debug(f"Parsed equipment: {equip}")
+            #     _, assoc = equip.to_sql(procedure=self)
+            #     logger.debug(f"Got equipment association: {assoc} for {equip}")
+            #     try:
+            #         assoc.save()
+            #     except AttributeError as e:
+            #         logger.error(f"Couldn't save association with {equip} due to {e}")
+            #     if equip.tips:
+            #         for tips in equip.tips:
+            #             # logger.debug(f"Attempting to add tips assoc: {tips} (pydantic)")
+            #             tassoc, _ = tips.to_sql(procedure=self)
+            #             # logger.debug(f"Attempting to add tips assoc: {tips.__dict__} (sql)")
+            #             if tassoc not in self.proceduretipsassociation:
+            #                 tassoc.save()
+            #             else:
+            #                 logger.error(f"Tips already found in submission, skipping.")
+            dlg.save_procedure()
 
     def edit(self, obj):
+        from frontend.widgets.procedure_creation import ProcedureCreation
         logger.debug("Edit!")
+        dlg = ProcedureCreation(parent=obj, procedure=self.to_pydantic())
+        if dlg.exec():
+            logger.debug("Edited")
 
     def add_comment(self, obj):
         logger.debug("Add Comment!")
@@ -1439,7 +1473,8 @@ class Procedure(BaseClass):
                           if sample.sample.sample_id in [s.sample_id for s in run_samples]]
         for sample in active_samples:
             sample['active'] = True
-        inactive_samples = [sample.details_dict() for sample in run_samples if sample.name not in [s['sample_id'] for s in active_samples]]
+        inactive_samples = [sample.details_dict() for sample in run_samples if
+                            sample.name not in [s['sample_id'] for s in active_samples]]
         # logger.debug(f"Inactive samples:{pformat(inactive_samples)}")
         for sample in inactive_samples:
             sample['active'] = False
@@ -1451,10 +1486,30 @@ class Procedure(BaseClass):
         output['tips'] = [tips.details_dict() for tips in output['proceduretipsassociation']]
         output['repeat'] = bool(output['repeat'])
         output['excluded'] = ['id', "results", "proceduresampleassociation", "sample", "procedurereagentassociation",
-                              "procedureequipmentassociation", "proceduretipsassociation", "reagent", "equipment", "tips",
+                              "procedureequipmentassociation", "proceduretipsassociation", "reagent", "equipment",
+                              "tips",
                               "excluded"]
         return output
 
+    def to_pydantic(self, **kwargs):
+        from backend.validators.pydant import PydResults
+        output = super().to_pydantic()
+        output.kittype = dict(value=output.kittype['name'], missing=False)
+        results = []
+        for result in output.results:
+            match result:
+                case dict():
+                    results.append(PydResults(**result))
+                case PydResults():
+                    results.append(result)
+                case _:
+                    pass
+        output.results = results
+        # for sample in output.sample:
+        #     sample.enabled = True
+        return output
+
+
 class ProcedureTypeKitTypeAssociation(BaseClass):
     """
     Abstract of relationship between kits and their procedure type.
@@ -2046,11 +2101,16 @@ class Equipment(BaseClass, LogMixin):
             PydEquipment: pydantic equipment object
         """
         from backend.validators.pydant import PydEquipment
+        creation_dict = self.details_dict()
         processes = self.get_processes(proceduretype=proceduretype, kittype=kittype,
                                        equipmentrole=equipmentrole)
+        logger.debug(f"Processes: {processes}")
+        creation_dict['processes'] = processes
         logger.debug(f"EquipmentRole: {equipmentrole}")
-        return PydEquipment(processes=processes, equipmentrole=equipmentrole,
-                            **self.to_dict(processes=False))
+        creation_dict['equipmentrole'] = equipmentrole or creation_dict['equipmentrole']
+        # return PydEquipment(process=processes, equipmentrole=equipmentrole,
+        #                     **self.to_dict(processes=False))
+        return PydEquipment(**creation_dict)
 
     @classproperty
     def manufacturer_regex(cls) -> re.Pattern:
@@ -2267,11 +2327,43 @@ class EquipmentRole(BaseClass):
         return OmniEquipmentRole(instance_object=self, name=self.name)
 
     def details_dict(self, **kwargs):
+        if "proceduretype" in kwargs:
+            proceduretype = kwargs['proceduretype']
+        else:
+            proceduretype = None
+        match proceduretype:
+            case ProcedureType():
+                pass
+            case str():
+                proceduretype = ProcedureType.query(name=proceduretype, limit=1)
+            case _:
+                proceduretype = None
         output = super().details_dict(**kwargs)
+        # Note con
         output['equipment'] = [item.details_dict() for item in output['equipment']]
+        output['equipment_json'] = []
+        equip = []
+        for eq in output['equipment']:
+            dicto = dict(name=eq['name'], asset_number=eq['asset_number'])
+            dicto['processes'] = [dict(name=process.name, tiprole=process.tiprole) for process in eq['process'] if proceduretype in process.proceduretype]
+            for process in dicto['processes']:
+                try:
+                    process['tips'] = flatten_list([[tips.name for tips in tr.tips]for tr in process['tiprole']])
+                except KeyError:
+                    logger.debug(f"process: {pformat(process)}")
+                    raise KeyError()
+                del process['tiprole']
+            equip.append(dicto)
+        output['equipment_json'].append(dict(name=self.name, equipment=equip))
         output['process'] = [item.details_dict() for item in output['process']]
+        try:
+            output['tips'] = [item.details_dict() for item in output['tips']]
+        except KeyError:
+            # logger.error(pformat(output))
+            pass
         return output
 
+
 class ProcedureEquipmentAssociation(BaseClass):
     """
     Abstract association between BasicRun and Equipment
@@ -2297,7 +2389,8 @@ class ProcedureEquipmentAssociation(BaseClass):
         except AttributeError:
             return "<ProcedureEquipmentAssociation(Unknown)>"
 
-    def __init__(self, procedure=None, equipment=None, procedure_id:int|None=None, equipment_id:int|None=None, equipmentrole: str = "None"):
+    def __init__(self, procedure=None, equipment=None, procedure_id: int | None = None, equipment_id: int | None = None,
+                 equipmentrole: str = "None"):
         if not procedure:
             if procedure_id:
                 procedure = Procedure.query(id=procedure_id)
@@ -2310,8 +2403,16 @@ class ProcedureEquipmentAssociation(BaseClass):
             else:
                 logger.error("Creation error")
         self.equipment = equipment
+        if isinstance(equipmentrole, list):
+            equipmentrole = equipmentrole[0]
+        if isinstance(equipmentrole, EquipmentRole):
+            equipmentrole = equipmentrole.name
         self.equipmentrole = equipmentrole
 
+    @property
+    def name(self):
+        return f"{self.procedure.name} & {self.equipment.name}"
+
     @property
     def process(self):
         return Process.query(id=self.process_id)
@@ -2379,6 +2480,7 @@ class ProcedureEquipmentAssociation(BaseClass):
         output['process'] = self.process.details_dict()
         return output
 
+
 class ProcedureTypeEquipmentRoleAssociation(BaseClass):
     """
     Abstract association between SubmissionType and EquipmentRole
@@ -2386,6 +2488,8 @@ class ProcedureTypeEquipmentRoleAssociation(BaseClass):
     equipmentrole_id = Column(INTEGER, ForeignKey("_equipmentrole.id"), primary_key=True)  #: id of associated equipment
     proceduretype_id = Column(INTEGER, ForeignKey("_proceduretype.id"),
                               primary_key=True)  #: id of associated procedure
+    kittype_id = Column(INTEGER, ForeignKey("_kittype.id"),
+                              primary_key=True)
     uses = Column(JSON)  #: locations of equipment on the procedure type excel sheet.
     static = Column(INTEGER,
                     default=1)  #: if 1 this piece of equipment will always be used, otherwise it will need to be selected from list?
@@ -2396,6 +2500,8 @@ class ProcedureTypeEquipmentRoleAssociation(BaseClass):
     equipmentrole = relationship(EquipmentRole,
                                  back_populates="equipmentroleproceduretypeassociation")  #: associated equipment
 
+    kittype = relationship(KitType, back_populates="proceduretypeequipmentroleassociation")
+
     @validates('static')
     def validate_static(self, key, value):
         """
@@ -2781,6 +2887,10 @@ class Tips(BaseClass, LogMixin):
     #         template = env.get_template("tips_details.html")
     #     return template
 
+    def to_pydantic(self, **kwargs):
+        output = super().to_pydantic()
+        return output
+
 
 class ProcedureTypeTipRoleAssociation(BaseClass):
     """
@@ -2828,7 +2938,7 @@ class ProcedureTipsAssociation(BaseClass):
 
     @classmethod
     @setup_lookup
-    def query(cls, tips: int|Tips, tiprole: str, procedure: int | Procedure | None = None, limit: int = 0, **kwargs) \
+    def query(cls, tips: int | Tips, tiprole: str, procedure: int | Procedure | None = None, limit: int = 0, **kwargs) \
             -> Any | List[Any]:
         query: Query = cls.__database_session__.query(cls)
         match tips:
@@ -2873,15 +2983,15 @@ class ProcedureTipsAssociation(BaseClass):
 
 
 class Results(BaseClass):
-
     id = Column(INTEGER, primary_key=True)
     result_type = Column(String(32))
     result = Column(JSON)
+    date_analyzed = Column(TIMESTAMP)
     procedure_id = Column(INTEGER, ForeignKey("_procedure.id", ondelete='SET NULL',
-                                                name="fk_RES_procedure_id"))
+                                              name="fk_RES_procedure_id"))
     procedure = relationship("Procedure", back_populates="results")
     assoc_id = Column(INTEGER, ForeignKey("_proceduresampleassociation.id", ondelete='SET NULL',
-                                                name="fk_RES_ASSOC_id"))
+                                          name="fk_RES_ASSOC_id"))
     sampleprocedureassociation = relationship("ProcedureSampleAssociation", back_populates="results")
     _img = Column(String(128))
 
@@ -2900,5 +3010,3 @@ class Results(BaseClass):
     @image.setter
     def image(self, value):
         self._img = value
-
-

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

@@ -398,6 +398,10 @@ class Run(BaseClass, LogMixin):
     def name(self):
         return self.rsl_plate_number
 
+    @hybrid_property
+    def plate_number(self):
+        return self.rsl_plate_number
+
     @classmethod
     def get_default_info(cls, *args, submissiontype: SubmissionType | None = None) -> dict:
         """
@@ -602,6 +606,7 @@ class Run(BaseClass, LogMixin):
 
     def details_dict(self, **kwargs):
         output = super().details_dict()
+        output['plate_number'] = self.plate_number
         submission_samples = [sample for sample in self.clientsubmission.sample]
         # logger.debug(f"Submission samples:{pformat(submission_samples)}")
         active_samples = [sample.details_dict() for sample in output['runsampleassociation']
@@ -1174,7 +1179,7 @@ class Run(BaseClass, LogMixin):
         from frontend.widgets.procedure_creation import ProcedureCreation
         procedure_type = next((proceduretype for proceduretype in self.allowed_procedures if proceduretype.name == proceduretype_name))
         logger.debug(f"Got ProcedureType: {procedure_type}")
-        dlg = ProcedureCreation(parent=obj, run=self, proceduretype=procedure_type)
+        dlg = ProcedureCreation(parent=obj, procedure=procedure_type.construct_dummy_procedure(run=self))
         if dlg.exec():
             sql, _ = dlg.return_sql()
             logger.debug(f"Output run samples:\n{pformat(sql.run.sample)}")
@@ -1358,12 +1363,12 @@ class Run(BaseClass, LogMixin):
             row, column = plate_dict[submission_rank]
             ranked_samples.append(
                 dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank,
-                     background_color="#6ffe1d"))
+                     background_color="#6ffe1d", enabled=True))
         padded_list = []
         for iii in range(1, proceduretype.total_wells+1):
             row, column = proceduretype.ranked_plate[iii]
             sample = next((item for item in ranked_samples if item['submission_rank']==iii),
-                          dict(well_id=f"blank_{iii}", sample_id="", row=row, column=column, submission_rank=iii, background_color="#ffffff")
+                          dict(well_id=f"blank_{iii}", sample_id="", row=row, column=column, submission_rank=iii, background_color="#ffffff", enabled=False)
                           )
             padded_list.append(sample)
         # logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")

src/submissions/backend/validators/pydant.py

@@ -9,6 +9,8 @@ from dateutil.parser import parse
 from dateutil.parser import ParserError
 from typing import List, Tuple, Literal
 from types import GeneratorType
+
+import backend
 from . import RSLNamer
 from pathlib import Path
 from tools import check_not_nan, convert_nans_to_nones, Report, Result, timezone
@@ -31,7 +33,11 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
     def prevalidate(cls, data):
         sql_fields = [k for k, v in cls._sql_object.__dict__.items() if isinstance(v, InstrumentedAttribute)]
         output = {}
-        for key, value in data.items():
+        try:
+            items = data.items()
+        except AttributeError:
+            return data
+        for key, value in items:
             new_key = key.replace("_", "")
             if new_key in sql_fields:
                 output[new_key] = value
@@ -104,11 +110,14 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
     def to_sql(self):
         dicto = self.improved_dict(dictionaries=False)
         logger.debug(f"Dicto: {dicto}")
-        sql, _ = self._sql_object().query_or_create(**dicto)
+        # sql, new = self._sql_object().query_or_create(**dicto)
+        sql, new = self._sql_object.query_or_create(**dicto)
+        if new:
+            logger.warning(f"Creating new {self._sql_object} with values:\n{pformat(dicto)}")
         return sql
 
 
-class PydReagent(BaseModel):
+class PydReagent(PydBaseClass):
     lot: str | None
     reagentrole: str | None
     expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
@@ -269,6 +278,7 @@ class PydSample(PydBaseClass):
             value = row_keys[value]
         return value
 
+
 class PydTips(BaseModel):
     name: str
     lot: str | None = Field(default=None)
@@ -277,6 +287,13 @@ class PydTips(BaseModel):
     @field_validator('tiprole', mode='before')
     @classmethod
     def get_role_name(cls, value):
+        if isinstance(value, list):
+            output = []
+            for tiprole in value:
+                if isinstance(tiprole, TipRole):
+                    tiprole = tiprole.name
+                    return tiprole
+            value = output
         if isinstance(value, TipRole):
             value = value.name
         return value
@@ -304,13 +321,21 @@ class PydEquipment(BaseModel, extra='ignore'):
     asset_number: str
     name: str
     nickname: str | None
-    process: List[str] | None
-    equipmentrole: str | None
-    tips: List[PydTips] | None = Field(default=None)
+    # process: List[dict] | None
+    process: PydProcess | None
+    equipmentrole: str | PydEquipmentRole | None
+    tips: List[PydTips] | None = Field(default=[])
 
     @field_validator('equipmentrole', mode='before')
     @classmethod
     def get_role_name(cls, value):
+        match value:
+            case list():
+                value = value[0]
+            case GeneratorType():
+                value = next(value)
+            case _:
+                pass
         if isinstance(value, EquipmentRole):
             value = value.name
         return value
@@ -325,12 +350,24 @@ class PydEquipment(BaseModel, extra='ignore'):
         value = convert_nans_to_nones(value)
         if not value:
             value = ['']
+        logger.debug(value)
         try:
-            value = [item.strip() for item in value]
+            # value = [item.strip() for item in value]
+            value = next((PydProcess(**process.details_dict()) for process in value))
         except AttributeError:
             pass
         return value
 
+    @field_validator('tips', mode='before')
+    @classmethod
+    def tips_to_pydantic(cls, value):
+        output = []
+        for tips in value:
+            if isinstance(tips, Tips):
+                tips = tips.to_pydantic()
+            output.append(tips)
+        return output
+
     @report_result
     def to_sql(self, procedure: Procedure | str = None, kittype: KitType | str = None) -> Tuple[
         Equipment, ProcedureEquipmentAssociation]:
@@ -357,7 +394,7 @@ class PydEquipment(BaseModel, extra='ignore'):
             # NOTE: Need to make sure the same association is not added to the procedure
             try:
                 assoc, new = ProcedureEquipmentAssociation.query_or_create(equipment=equipment, procedure=procedure,
-                                                            equipmentrole=self.equipmentrole, limit=1)
+                                                                           equipmentrole=self.equipmentrole, limit=1)
             except TypeError as e:
                 logger.error(f"Couldn't get association due to {e}, returning...")
                 return None, None
@@ -1282,8 +1319,14 @@ class PydProcess(BaseModel, extra="allow"):
     @classmethod
     def enforce_list(cls, value):
         if not isinstance(value, list):
-            return [value]
-        return value
+            value = [value]
+        output = []
+        for v in value:
+            if issubclass(v.__class__, BaseClass):
+                output.append(v.name)
+            else:
+                output.append(v)
+        return output
 
     @report_result
     def to_sql(self):
@@ -1356,7 +1399,28 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
     plate_map: str | None = Field(default=None)
     reagent: list | None = Field(default=[])
     reagentrole: dict | None = Field(default={}, validate_default=True)
-    samples: List[PydSample] = Field(default=[])
+    sample: List[PydSample] = Field(default=[])
+    equipment: List[PydEquipment] = Field(default=[])
+    results: List[PydResults] | List[dict] = Field(default=[])
+
+    @field_validator("name", "technician", "kittype", mode="before")
+    @classmethod
+    def convert_to_dict(cls, value):
+        if isinstance(value, str):
+            value = dict(value=value, missing=False)
+        return value
+
+    @field_validator("proceduretype", mode="before")
+    @classmethod
+    def lookup_proceduretype(cls, value):
+        match value:
+            case dict():
+                value = ProcedureType.query(name=value['name'])
+            case str():
+                value = ProcedureType.query(name=value)
+            case _:
+                pass
+        return value
 
     @field_validator("name")
     @classmethod
@@ -1378,25 +1442,41 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
     @classmethod
     def rescue_possible_kits(cls, value, values):
         if not value:
-            if values.data['proceduretype']:
-                value = [kittype.name for kittype in values.data['proceduretype'].kittype]
+            try:
+                if values.data['proceduretype']:
+                    value = [kittype.__dict__['name'] for kittype in values.data['proceduretype'].kittype]
+            except KeyError:
+                pass
         return value
 
     @field_validator("name", "technician", "kittype")
     @classmethod
     def set_colour(cls, value):
-        if value["missing"]:
-            value["colour"] = "FE441D"
-        else:
-            value["colour"] = "6ffe1d"
+        try:
+            if value["missing"]:
+                value["colour"] = "FE441D"
+            else:
+                value["colour"] = "6ffe1d"
+        except KeyError:
+            pass
         return value
 
     @field_validator("reagentrole")
     @classmethod
     def rescue_reagentrole(cls, value, values):
         if not value:
-            if values.data['kittype']['value'] != cls.model_fields['kittype'].default['value']:
-                kittype = KitType.query(name=values.data['kittype']['value'])
+            match values.data['kittype']:
+                case dict():
+                    if "value" in values.data['kittype'].keys():
+                        roi = values.data['kittype']['value']
+                    elif "name" in values.data['kittype'].keys():
+                        roi = values.data['kittype']['name']
+                    else:
+                        raise KeyError(f"Couldn't find kittype name in the dictionary: {values.data['kittype']}")
+                case str():
+                    roi = values.data['kittype']
+            if roi != cls.model_fields['kittype'].default['value']:
+                kittype = KitType.query(name=roi)
                 value = {item.name: item.reagent for item in kittype.reagentrole}
         return value
 
@@ -1413,6 +1493,19 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
         self.kittype['value'] = kittype
         self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
 
+    def update_kittype_equipmentroles(self, kittype: str | KitType):
+        if kittype == self.__class__.model_fields['kittype'].default['value']:
+            return
+        if isinstance(kittype, str):
+            kittype_obj = KitType.query(name=kittype)
+        try:
+            self.equipment = {item.name: item.get_reagents(kittype=kittype_obj) for item in
+                              kittype_obj.get_reagents(proceduretype=self.proceduretype)}
+        except AttributeError:
+            self.reagentrole = {}
+        self.kittype['value'] = kittype
+        self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
+
     def update_samples(self, sample_list: List[dict]):
         logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
         for sample_dict in sample_list:
@@ -1425,7 +1518,8 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
                     (item for item in self.samples 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}")
+                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))
@@ -1441,7 +1535,12 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
 
     def to_sql(self):
         from backend.db.models import RunSampleAssociation, ProcedureSampleAssociation
+        # results = []
+        # for result in self.results:
+        #     result, _ = result.to_sql()
         sql = super().to_sql()
+        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:
@@ -1450,27 +1549,37 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
             start_index = max([item.id for item in ProcedureSampleAssociation.query()]) + 1
         except ValueError:
             start_index = 1
-        relevant_samples = [sample for sample in self.samples if not sample.sample_id.startswith("blank_") and not sample.sample_id == ""]
+        relevant_samples = [sample for sample in self.sample if
+                            not sample.sample_id.startswith("blank_") and not sample.sample_id == ""]
         logger.debug(f"start index: {start_index}")
-        assoc_id_range = range(start_index, start_index + len(relevant_samples)+1)
+        assoc_id_range = range(start_index, start_index + len(relevant_samples) + 1)
         logger.debug(f"Association id range: {assoc_id_range}")
         for iii, sample in enumerate(relevant_samples):
             sample_sql = sample.to_sql()
             if sql.run:
                 if sample_sql not in sql.run.sample:
                     logger.debug(f"sample {sample_sql} not found in {sql.run.sample}")
-                    run_assoc = RunSampleAssociation(sample=sample_sql, run=self.run, row=sample.row, column=sample.column)
+                    run_assoc = RunSampleAssociation(sample=sample_sql, run=self.run, row=sample.row,
+                                                     column=sample.column)
                 else:
                     logger.debug(f"sample {sample_sql} found in {sql.run.sample}")
-            proc_assoc = ProcedureSampleAssociation(new_id=assoc_id_range[iii], procedure=sql, sample=sample_sql, row=sample.row, column=sample.column)
+            if sample_sql not in sql.sample:
+                proc_assoc = ProcedureSampleAssociation(new_id=assoc_id_range[iii], procedure=sql, sample=sample_sql,
+                                                        row=sample.row, column=sample.column)
         if self.kittype['value'] not in ["NA", None, ""]:
             kittype = KitType.query(name=self.kittype['value'], limit=1)
             if kittype:
                 sql.kittype = kittype
+        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])
+                process = equipment.process.to_sql()
+                equip_assoc.process = process
+        logger.debug(f"Output sql: {[pformat(item.__dict__) for item in sql.procedureequipmentassociation]}")
         return sql, None
 
 
-
 class PydClientSubmission(PydBaseClass):
     # sql_object: ClassVar = ClientSubmission
 
@@ -1549,15 +1658,34 @@ class PydClientSubmission(PydBaseClass):
 
 
 class PydResults(PydBaseClass, arbitrary_types_allowed=True):
-
     results: dict = Field(default={})
     results_type: str = Field(default="NA")
     img: None | bytes = Field(default=None)
-    parent: Procedure|ProcedureSampleAssociation|None = Field(default=None)
+    parent: Procedure | ProcedureSampleAssociation | None = Field(default=None)
+    date_analyzed: datetime | None = Field(default=None)
+
+    @field_validator("date_analyzed")
+    @classmethod
+    def set_today(cls, value):
+        match value:
+            case str():
+                value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S")
+            case datetime():
+                pass
+            case _:
+                value = datetime.now()
+        return value
 
     def to_sql(self):
-        sql = Results(results_type=self.results_type, result=self.results)
-        sql.image = self.img
+        sql, _ = Results.query_or_create(results_type=self.results_type, result=self.results)
+        try:
+            check = sql.image
+        except FileNotFoundError:
+            check = False
+        if not check:
+            sql.image = self.img
+        if not sql.date_analyzed:
+            sql.date_analyzed = self.date_analyzed
         match self.parent:
             case ProcedureSampleAssociation():
                 sql.sampleprocedureassociation = self.parent
@@ -1566,4 +1694,3 @@ class PydResults(PydBaseClass, arbitrary_types_allowed=True):
             case _:
                 logger.error("Improper association found.")
         return sql
-

src/submissions/frontend/widgets/app.py

@@ -13,7 +13,7 @@ from PyQt6.QtGui import QAction
 from pathlib import Path
 from markdown import markdown
 from pandas import ExcelWriter
-from backend import Reagent, Sample, ClientSubmission, KitType, Run
+from backend.db.models import Reagent, Sample, ClientSubmission, KitType, Run
 from tools import (
     check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user,
     under_development

src/submissions/frontend/widgets/equipment_usage.py

@@ -127,7 +127,7 @@ class RoleComboBox(QWidget):
         logger.debug(f"Equip2: {equip2}")
         with QSignalBlocker(self.process) as blocker:
             self.process.clear()
-        self.process.addItems([item for item in equip2.processes if item in self.role.process])
+        self.process.addItems([item for item in equip2.process if item in self.role.process])
 
     def update_tips(self):
         """

src/submissions/frontend/widgets/procedure_creation.py

@@ -14,27 +14,28 @@ from PyQt6.QtWebChannel import QWebChannel
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import QDialog, QGridLayout, QMenu, QDialogButtonBox
 from typing import TYPE_CHECKING, Any
-
 if TYPE_CHECKING:
-    from backend.db.models import Run, ProcedureType
+    from backend.db.models import Run, Procedure
+    from backend.validators import PydProcedure
 from tools import jinja_template_loading, get_application_from_parent, render_details_template
-from backend.validators import PydProcedure
+
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
 class ProcedureCreation(QDialog):
 
-    def __init__(self, parent, run: Run, proceduretype: ProcedureType):
+    def __init__(self, parent, procedure: PydProcedure):
         super().__init__(parent)
-        self.run = run
-        self.proceduretype = proceduretype
-        self.setWindowTitle(f"New {proceduretype.name} for { run.rsl_plate_number }")
-        self.created_procedure = self.proceduretype.construct_dummy_procedure(run=self.run)
-        self.created_procedure.update_kittype_reagentroles(kittype=self.created_procedure.possible_kits[0])
-        self.created_procedure.samples = self.run.constuct_sample_dicts_for_proceduretype(proceduretype=self.proceduretype)
+        self.run = procedure.run
+        self.procedure = procedure
+        self.proceduretype = procedure.proceduretype
+        self.setWindowTitle(f"New {self.proceduretype.name} for { self.run.rsl_plate_number }")
+        # self.created_procedure = self.proceduretype.construct_dummy_procedure(run=self.run)
+        self.procedure.update_kittype_reagentroles(kittype=self.procedure.possible_kits[0])
+        # self.created_procedure.samples = self.run.constuct_sample_dicts_for_proceduretype(proceduretype=self.proceduretype)
         # logger.debug(f"Samples to map\n{pformat(self.created_procedure.samples)}")
-        self.plate_map = self.proceduretype.construct_plate_map(sample_dicts=self.created_procedure.samples)
+        self.plate_map = self.proceduretype.construct_plate_map(sample_dicts=self.procedure.sample)
         # logger.debug(f"Plate map: {self.plate_map}")
         # logger.debug(f"Created dummy: {self.created_procedure}")
         self.app = get_application_from_parent(parent)
@@ -61,46 +62,56 @@ class ProcedureCreation(QDialog):
         self.layout.addWidget(self.buttonBox, 11, 1, 1, 1)
 
     def set_html(self):
+        from .equipment_usage_2 import EquipmentUsage
+        proceduretype_dict = self.proceduretype.details_dict()
+        if self.procedure.equipment:
+            for equipmentrole in proceduretype_dict['equipment']:
+                # NOTE: Check if procedure equipment is present and move to head of the list if so.
+                try:
+                    relevant_procedure_item = next((equipment for equipment in self.procedure.equipment if equipment.equipmentrole == equipmentrole['name']))
+                except StopIteration:
+                    continue
+                item_in_er_list = next((equipment for equipment in equipmentrole['equipment'] if 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)
         html = render_details_template(
             template_name="procedure_creation",
             # css_in=['new_context_menu'],
             js_in=["procedure_form", "grid_drag", "context_menu"],
-            proceduretype=self.proceduretype.details_dict(),
+            proceduretype=proceduretype_dict,
             run=self.run.details_dict(),
-            procedure=self.created_procedure.__dict__,
+            procedure=self.procedure.__dict__,
             plate_map=self.plate_map
         )
-        # with open("procedure.html", "w") as f:
-        #     f.write(html)
         self.webview.setHtml(html)
 
     @pyqtSlot(str, str)
     def text_changed(self, key: str, new_value: str):
         logger.debug(f"New value for {key}: {new_value}")
-        attribute = getattr(self.created_procedure, key)
+        attribute = getattr(self.procedure, key)
         attribute['value'] = new_value.strip('\"')
 
     @pyqtSlot(str, bool)
     def check_toggle(self, key: str, ischecked: bool):
         # logger.debug(f"{key} is checked: {ischecked}")
-        setattr(self.created_procedure, key, ischecked)
+        setattr(self.procedure, key, ischecked)
 
     @pyqtSlot(str)
     def update_kit(self, kittype):
-        self.created_procedure.update_kittype_reagentroles(kittype=kittype)
-        logger.debug({k: v for k, v in self.created_procedure.__dict__.items() if k != "plate_map"})
+        self.procedure.update_kittype_reagentroles(kittype=kittype)
+        logger.debug({k: v for k, v in self.procedure.__dict__.items() if k != "plate_map"})
         self.set_html()
 
     @pyqtSlot(list)
     def rearrange_plate(self, sample_list: list):
-        self.created_procedure.update_samples(sample_list=sample_list)
+        self.procedure.update_samples(sample_list=sample_list)
 
     @pyqtSlot(str)
     def log(self, logtext: str):
         logger.debug(logtext)
 
     def return_sql(self):
-        return self.created_procedure.to_sql()
+        return self.procedure.to_sql()
 
 
 # class ProcedureWebViewer(QWebEngineView):

src/submissions/templates/css/styles.css

@@ -179,3 +179,7 @@ ul.no-bullets {
   text-decoration-color: red;
 }
 
+.grid-container {
+          display: grid;
+          grid-auto-flow: column;
+        }

src/submissions/templates/js/equipment.js

@@ -0,0 +1,89 @@
+const equipment_json = {{ proceduretype['equipment_json'] }};
+
+window.addEventListener('load', function () {
+    equipment_json.forEach(startup);
+})
+
+function startup(equipmentrole) {
+    updateEquipmentChoices(equipmentrole);
+    var eq_dropdown = document.getElementById(equipmentrole.name);
+    eq_dropdown.addEventListener("change", function(event){
+        updateProcessChoices(equipmentrole);
+        updateBackend(equipmentrole);
+    });
+    var process_dropdown = document.getElementById(equipmentrole.name + "_process");
+    process_dropdown.addEventListener("change", function(event){
+        updateTipChoices(equipmentrole);
+        updateBackend(equipmentrole);
+    });
+    var tips_dropdown = document.getElementById(equipmentrole.name + "_tips");
+    tips_dropdown.addEventListener("change", function(event){
+        updateBackend(equipmentrole);
+    });
+}
+
+function updateEquipmentChoices(equipmentrole) {
+    console.log("Updating equipment choices.");
+    var dropdown_oi = document.getElementById(equipmentrole.name);
+    while (dropdown_oi.options.length > 0) {
+        dropdown_oi.remove(0);
+    }
+    dropdown_oi.json = equipmentrole;
+    for (let iii = 0; iii < equipmentrole.equipment.length; iii++) {
+        var opt = document.createElement('option');
+        opt.value = equipmentrole.equipment[iii].name;
+        opt.innerHTML = equipmentrole.equipment[iii].name;
+        dropdown_oi.appendChild(opt);
+    }
+    updateProcessChoices(equipmentrole);
+}
+
+function updateProcessChoices(equipmentrole) {
+    console.log("Updating process choices.");
+    var dropdown_oi = document.getElementById(equipmentrole.name + "_process");
+    while (dropdown_oi.options.length > 0) {
+        dropdown_oi.remove(0);
+    }
+    dropdown_oi.json = equipmentrole;
+    var equipment_name = document.getElementById(equipmentrole.name).value;
+    var equipment = equipmentrole.equipment.filter(function(x){ return x.name == equipment_name })[0];
+    for (let iii = 0; iii < equipment.processes.length; iii++) {
+        var opt = document.createElement('option');
+        opt.value = equipment.processes[iii].name;
+        opt.innerHTML = equipment.processes[iii].name;
+        dropdown_oi.appendChild(opt);
+    }
+    updateTipChoices(equipmentrole);
+}
+
+function updateTipChoices(equipmentrole) {
+    console.log("Updating tip choices.");
+    var dropdown_oi = document.getElementById(equipmentrole.name + "_tips");
+    dropdown_oi.innerHTML = "";
+    dropdown_oi.json = equipmentrole;
+    var equipment_name = document.getElementById(equipmentrole.name).value;
+    var process_name = document.getElementById(equipmentrole.name + "_process").value;
+    console.log(process_name);
+    var equipment = equipmentrole.equipment.filter(function(x){ return x.name == equipment_name })[0];
+    console.log(equipment);
+    var process = equipment.processes.filter(function(x){ return x.name == process_name })[0];
+    console.log(process);
+    for (let iii = 0; iii < process.tips.length; iii++) {
+        var opt = document.createElement('option');
+        opt.value = process.tips[iii];
+        opt.innerHTML = process.tips[iii];
+        dropdown_oi.appendChild(opt);
+    }
+}
+
+function updateBackend(equipmentrole) {
+    alert("Updating Backend");
+    var equipmentrole_name = equipmentrole.name
+    var dropdown_oi = document.getElementById(equipmentrole.name);
+    var equipment_name = dropdown_oi.value;
+    dropdown_oi = document.getElementById(equipmentrole.name + "_process");
+    var process_name = dropdown_oi.value;
+    dropdown_oi = document.getElementById(equipmentrole.name + "_tips");
+    var tips_name = dropdown_oi.value;
+    backend.update_equipment(equipmentrole_name, equipment_name, process_name, tips_name)
+}

src/submissions/templates/procedure_creation.html

@@ -28,24 +28,13 @@
                     <br><hr><br>
                     {% for key, value in procedure['reagentrole'].items() %}
                     <label for="{{ key }}">{{ key }}:</label><br>
-                    <datalist class="reagentrole dropdown" id="{{ key }}" name="{{ reagentrole }}"><br>
+                    <select class="reagentrole dropdown" id="{{ key }}" name="{{ key }}"><br>
                         {% for reagent in value %}
                         <option value="{{ reagent }}">{{ reagent }}</option>
                         {% endfor %}
-                    </datalist>
-                    {% endfor %}
-                  {% endif %}
-                  {% if proceduretype['equipment'] %}
-                    <br><hr><br>
-                    {% for equipmentrole in proceduretype['equipment'] %}
-                    <label for="{{ equipmentrole['name'] }}">{{ equipmentrole['name'] }}:</label><br>
-                    <select class="equipmentrole dropdown" id="{{ equipmentrole['name'] }}" name="{{ equipmentrole['name'] }}"><br>
-                        {% for equipment in equipmentrole['equipment'] %}
-                        <option value="{{ equipment['name'] }}">{{ equipment['name'] }}</option>
-                        {% endfor %}
                     </select>
                     {% endfor %}
-                  {% endif%}
+                  {% endif %}
                 </form>
             </div>
             <div class="right">
@@ -55,6 +44,9 @@
                 {% endif %}
             </div>
         </div>
+        {% with proceduretype=proceduretype, child=True %}
+            {% include "support/equipment_usage.html" %}
+        {% endwith %}
         {% include 'support/context_menu.html' %}
         {% endblock %}
 

src/submissions/templates/support/equipment_usage.html

@@ -0,0 +1,141 @@
+{% if not child %}
+<html lang="en">
+<head>
+    {% block head %}
+    <meta charset="UTF-8">
+    {% if css %}
+    <style>
+        {% for c in css %}
+        {{ c }}
+        {% endfor %}
+    </style>
+    {% endif %}
+    {% endblock %}
+<script src="qrc:///qtwebchannel/qwebchannel.js"></script>
+</head>
+<body>
+{% endif %}
+
+
+<h1><u>Equipment</u></h1>
+<br><hr><br>
+{% for equipmentrole in proceduretype['equipment_json'] %}
+    <div class="grid-container">
+        <div>
+            <label for="{{ equipmentrole['name'] }}">{{ equipmentrole['name'] }}:</label><br>
+            <select class="equipmentrole dropdown" id="{{ equipmentrole['name'] }}" name="{{ equipmentrole['name'] }}">
+            </select>
+        </div>
+        <div>
+            <label for="{{ equipmentrole['name'] }}_process">Process:</label><br>
+            <select class="process dropdown" id="{{ equipmentrole['name'] }}_process" name="{{ equipmentrole['name'] }}_process">
+            </select>
+        </div>
+        <div>
+            <label for="{{ equipmentrole['name'] }}_tips">Tips:</label><br>
+            <select class="tips dropdown" id="{{ equipmentrole['name'] }}_tips" name="{{ equipmentrole['name'] }}_tips">
+            </select>
+        </div>
+
+    </div>
+{% endfor %}
+
+{% if not child %}
+{% for j in js%}
+<script>
+    {{ j }}
+</script>
+{% endfor %}
+{% endif %}
+<script>
+    const equipment_json = {{ proceduretype['equipment_json'] }};
+
+    window.addEventListener('load', function () {
+        equipment_json.forEach(startup);
+    })
+
+    function startup(equipmentrole) {
+        updateEquipmentChoices(equipmentrole);
+        var eq_dropdown = document.getElementById(equipmentrole.name);
+        eq_dropdown.addEventListener("change", function(event){
+            updateProcessChoices(equipmentrole);
+            updateBackend(equipmentrole);
+        });
+        var process_dropdown = document.getElementById(equipmentrole.name + "_process");
+        process_dropdown.addEventListener("change", function(event){
+            updateTipChoices(equipmentrole);
+            updateBackend(equipmentrole);
+        });
+        var tips_dropdown = document.getElementById(equipmentrole.name + "_tips");
+        tips_dropdown.addEventListener("change", function(event){
+            updateBackend(equipmentrole);
+        });
+        updateBackend(equipmentrole);
+    }
+
+    function updateEquipmentChoices(equipmentrole) {
+        console.log("Updating equipment choices.");
+        var dropdown_oi = document.getElementById(equipmentrole.name);
+        while (dropdown_oi.options.length > 0) {
+            dropdown_oi.remove(0);
+        }
+        dropdown_oi.json = equipmentrole;
+        for (let iii = 0; iii < equipmentrole.equipment.length; iii++) {
+            var opt = document.createElement('option');
+            opt.value = equipmentrole.equipment[iii].name;
+            opt.innerHTML = equipmentrole.equipment[iii].name;
+            dropdown_oi.appendChild(opt);
+        }
+        updateProcessChoices(equipmentrole);
+    }
+
+    function updateProcessChoices(equipmentrole) {
+        console.log("Updating process choices.");
+        var dropdown_oi = document.getElementById(equipmentrole.name + "_process");
+        while (dropdown_oi.options.length > 0) {
+            dropdown_oi.remove(0);
+        }
+        dropdown_oi.json = equipmentrole;
+        var equipment_name = document.getElementById(equipmentrole.name).value;
+        var equipment = equipmentrole.equipment.filter(function(x){ return x.name == equipment_name })[0];
+        for (let iii = 0; iii < equipment.processes.length; iii++) {
+            var opt = document.createElement('option');
+            opt.value = equipment.processes[iii].name;
+            opt.innerHTML = equipment.processes[iii].name;
+            dropdown_oi.appendChild(opt);
+        }
+        updateTipChoices(equipmentrole);
+    }
+
+    function updateTipChoices(equipmentrole) {
+        console.log("Updating tip choices.");
+        var dropdown_oi = document.getElementById(equipmentrole.name + "_tips");
+        dropdown_oi.innerHTML = "";
+        dropdown_oi.json = equipmentrole;
+        var equipment_name = document.getElementById(equipmentrole.name).value;
+        var process_name = document.getElementById(equipmentrole.name + "_process").value;
+        console.log(process_name);
+        var equipment = equipmentrole.equipment.filter(function(x){ return x.name == equipment_name })[0];
+        console.log(equipment);
+        var process = equipment.processes.filter(function(x){ return x.name == process_name })[0];
+        console.log(process);
+        for (let iii = 0; iii < process.tips.length; iii++) {
+            var opt = document.createElement('option');
+            opt.value = process.tips[iii];
+            opt.innerHTML = process.tips[iii];
+            dropdown_oi.appendChild(opt);
+        }
+    }
+
+    function updateBackend(equipmentrole) {
+        var equipmentrole_name = equipmentrole.name
+        var dropdown_oi = document.getElementById(equipmentrole.name);
+        var equipment_name = dropdown_oi.value;
+        dropdown_oi = document.getElementById(equipmentrole.name + "_process");
+        var process_name = dropdown_oi.value;
+        dropdown_oi = document.getElementById(equipmentrole.name + "_tips");
+        var tips_name = dropdown_oi.value;
+        backend.update_equipment(equipmentrole_name, equipment_name, process_name, tips_name)
+    }
+
+</script>