Basic Procedure addition working.

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

@@ -555,6 +555,8 @@ class BaseClass(Base):
         return output_date
 
 
+
+
 class LogMixin(Base):
     tracking_exclusion: ClassVar = ['artic_technician', 'clientsubmissionsampleassociation',
                                     'submission_reagent_associations', 'submission_equipment_associations',

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

@@ -14,12 +14,15 @@ from sqlalchemy.ext.hybrid import hybrid_property
 from datetime import date, datetime, timedelta
 from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, yaml_regex_creator, timezone, \
     jinja_template_loading
-from typing import List, Literal, Generator, Any, Tuple
+from typing import List, Literal, Generator, Any, Tuple, TYPE_CHECKING
 from pandas import ExcelFile
 from pathlib import Path
 from . import Base, BaseClass, ClientLab, LogMixin
 from io import BytesIO
 
+if TYPE_CHECKING:
+    from backend.db.models.submissions import Run
+
 logger = logging.getLogger(f'procedure.{__name__}')
 
 reagentrole_reagent = Table(
@@ -159,7 +162,7 @@ class KitType(BaseClass):
 
     def get_reagents(self,
                      required_only: bool = False,
-                     proceduretype: str | SubmissionType | None = None
+                     proceduretype: str | ProcedureType | None = None
                      ) -> Generator[ReagentRole, None, None]:
         """
         Return ReagentTypes linked to kittype through KitTypeReagentTypeAssociation.
@@ -181,9 +184,9 @@ class KitType(BaseClass):
             case _:
                 relevant_associations = [item for item in self.kittypereagentroleassociation]
         if required_only:
-            return (item.reagent_role for item in relevant_associations if item.required == 1)
+            return (item.reagentrole for item in relevant_associations if item.required == 1)
         else:
-            return (item.reagent_role for item in relevant_associations)
+            return (item.reagentrole for item in relevant_associations)
 
     def construct_xl_map_for_use(self, proceduretype: str | SubmissionType) -> Tuple[dict | None, KitType]:
         """
@@ -536,6 +539,9 @@ class ReagentRole(BaseClass):
         logger.debug(f"Constructing OmniReagentRole with name {self.name}")
         return OmniReagentRole(instance_object=self, name=self.name, eol_ext=self.eol_ext)
 
+    @property
+    def reagents(self):
+        return [f"{reagent.name} - {reagent.lot}" for reagent in self.reagent]
 
 class Reagent(BaseClass, LogMixin):
     """
@@ -1034,7 +1040,8 @@ class ProcedureType(BaseClass):
     id = Column(INTEGER, primary_key=True)
     name = Column(String(64))
     reagent_map = Column(JSON)
-    plate_size = Column(INTEGER, default=0)
+    plate_columns = Column(INTEGER, default=0)
+    plate_rows = Column(INTEGER, default=0)
 
     procedure = relationship("Procedure",
                              back_populates="proceduretype")  #: Concrete control of this type.
@@ -1140,6 +1147,54 @@ class ProcedureType(BaseClass):
                 raise TypeError(f"Type {type(equipmentrole)} is not allowed")
         return list(set([item for items in relevant for item in items if item is not None]))
 
+    @property
+    def as_dict(self):
+        return dict(
+            name=self.name,
+            kittype=[item.name for item in self.kittype]
+        )
+
+    def construct_dummy_procedure(self):
+        from backend.validators.pydant import PydProcedure
+        output = dict(
+            proceduretype=self,
+            #name=dict(value=self.name, missing=True),
+            #possible_kits=[kittype.name for kittype in self.kittype],
+            repeat=False,
+            plate_map=self.construct_plate_map()
+        )
+        return PydProcedure(**output)
+
+    def construct_plate_map(self) -> str:
+        """
+        Constructs an html based plate map for procedure details.
+
+        Args:
+            sample_list (list): List of procedure sample
+            plate_rows (int, optional): Number of rows in the plate. Defaults to 8.
+            plate_columns (int, optional): Number of columns in the plate. Defaults to 12.
+
+        Returns:
+            str: html output string.
+        """
+        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
+        vw = round((-0.07 * total_wells) + 12.2, 1)
+
+
+        wells = [dict(name="", row=row, column=column, background_color="#ffffff")
+                          for row in plate_rows
+                          for column in plate_columns]
+        # 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("plate_map.html")
+        html = template.render(plate_rows=self.plate_rows, plate_columns=self.plate_columns, samples=wells, vw=vw)
+        return html + "<br/>"
+
 
 class Procedure(BaseClass):
     id = Column(INTEGER, primary_key=True)
@@ -1164,7 +1219,8 @@ class Procedure(BaseClass):
     )  #: Relation to ProcedureReagentAssociation
 
     reagents = association_proxy("procedurereagentassociation",
-                                 "reagent", creator=lambda reg: ProcedureReagentAssociation(reagent=reg))  #: Association proxy to RunReagentAssociation.reagent
+                                 "reagent", creator=lambda reg: ProcedureReagentAssociation(
+            reagent=reg))  #: Association proxy to RunReagentAssociation.reagent
 
     procedureequipmentassociation = relationship(
         "ProcedureEquipmentAssociation",
@@ -1193,7 +1249,8 @@ class Procedure(BaseClass):
 
     @classmethod
     @setup_lookup
-    def query(cls, id: int|None = None, name: str | None = None, limit: int = 0, **kwargs) -> Procedure | List[Procedure]:
+    def query(cls, id: int | None = None, name: str | None = None, limit: int = 0, **kwargs) -> Procedure | List[
+        Procedure]:
         query: Query = cls.__database_session__.query(cls)
         match id:
             case int():
@@ -2431,7 +2488,8 @@ class Tips(BaseClass, LogMixin):
         )
         if full_data:
             subs = [
-                dict(plate=item.procedure.procedure.rsl_plate_num, role=item.role_name, sub_date=item.procedure.procedure.clientsubmission.submitted_date)
+                dict(plate=item.procedure.procedure.rsl_plate_num, role=item.role_name,
+                     sub_date=item.procedure.procedure.clientsubmission.submitted_date)
                 for item in self.tipsprocedureassociation]
             output['procedure'] = sorted(subs, key=itemgetter("sub_date"), reverse=True)
             output['excluded'] = ['missing', 'procedure', 'excluded', 'editable']
@@ -2466,7 +2524,8 @@ class ProcedureTypeTipRoleAssociation(BaseClass):
     proceduretype_id = Column(INTEGER, ForeignKey("_proceduretype.id"),
                               primary_key=True)  #: id of associated procedure
     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?
+    static = Column(INTEGER,
+                    default=1)  #: if 1 this piece of equipment will always be used, otherwise it will need to be selected from list?
     proceduretype = relationship(ProcedureType,
                                  back_populates="proceduretypetiproleassociation")  #: associated procedure
     tiprole = relationship(TipRole,

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

@@ -15,8 +15,6 @@ from operator import itemgetter
 from pprint import pformat
 from pandas import DataFrame
 from sqlalchemy.ext.hybrid import hybrid_property
-
-
 from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func, Table
 from sqlalchemy.orm import relationship, validates, Query
@@ -1122,8 +1120,13 @@ class Run(BaseClass, LogMixin):
         return output
 
     def add_procedure(self, obj, proceduretype_name: str):
+        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)
+        if dlg.exec():
+            pass
+
 
     def delete(self, obj=None):
         """

src/submissions/backend/validators/__init__.py

@@ -208,4 +208,4 @@ class RSLNamer(object):
 
 
 from .pydant import PydSubmission, PydKitType, PydContact, PydOrganization, PydSample, PydReagent, PydReagentRole, \
-    PydEquipment, PydEquipmentRole, PydTips, PydProcess, PydElastic, PydClientSubmission
+    PydEquipment, PydEquipmentRole, PydTips, PydProcess, PydElastic, PydClientSubmission, PydProcedure

src/submissions/backend/validators/pydant.py

@@ -24,7 +24,6 @@ logger = logging.getLogger(f"procedure.{__name__}")
 
 
 class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
-
     _sql_object: ClassVar = None
 
     @model_validator(mode="before")
@@ -240,7 +239,6 @@ class PydReagent(BaseModel):
 
 
 class PydSample(PydBaseClass):
-
     sample_id: str
     sampletype: str | None = Field(default=None)
     submission_rank: int | List[int] | None = Field(default=0, validate_default=True)
@@ -1336,8 +1334,65 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
 
 # NOTE: Generified objects below:
 
-class PydClientSubmission(PydBaseClass):
+class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
+    proceduretype: ProcedureType | None = Field(default=None)
+    name: dict = Field(default=dict(value="NA", missing=True), validate_default=True)
+    technician: dict = Field(default=dict(value="NA", missing=True))
+    repeat: bool = Field(default=False)
+    kittype: dict = Field(default=dict(value="NA", missing=True))
+    possible_kits: list | None = Field(default=[], validate_default=True)
+    plate_map: str | None = Field(default=None)
+    reagent: list | None = Field(default=[])
+    reagentrole: dict | None = Field(default={}, validate_default=True)
 
+    @field_validator("name")
+    @classmethod
+    def rescue_name(cls, value, values):
+        if value['value'] == cls.model_fields['name'].default['value']:
+            if values.data['proceduretype']:
+                value['value'] = values.data['proceduretype'].name
+        return value
+
+    @field_validator("possible_kits")
+    @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]
+        return value
+
+    @field_validator("name", "technician", "kittype")
+    @classmethod
+    def set_colour(cls, value):
+        if value["missing"]:
+            value["colour"] = "FE441D"
+        else:
+            value["colour"] = "6ffe1d"
+        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'])
+                value = {item.name: item.reagents for item in kittype.reagentrole}
+        return value
+
+    def update_kittype_reagentroles(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.reagentrole = {item.name: item.reagents for item in
+                                kittype_obj.get_reagents(proceduretype=self.proceduretype)}
+        except AttributeError:
+            self.reagentrole = {}
+        self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
+
+
+class PydClientSubmission(PydBaseClass):
     # sql_object: ClassVar = ClientSubmission
 
     filepath: Path
@@ -1412,5 +1467,3 @@ class PydClientSubmission(PydBaseClass):
         """
         from frontend.widgets.submission_widget import ClientSubmissionFormWidget
         return ClientSubmissionFormWidget(parent=parent, clientsubmission=self, samples=samples, disable=disable)
-
-

src/submissions/templates/css/styles.css

@@ -40,4 +40,47 @@
   cursor: pointer;
 }
 
+div.procedure_creation_leftright {
+  width:100%;
+  overflow:auto;
+  border-style: solid;
+  border-width: 2px;
+  background-color: #FFFFFF;
+  display: flex;
+}
 
+div.procedure_creation_leftright div.left {
+  height: 100%;
+  width:15%;
+  float:left;
+  border-style: solid;
+  border-width: 1px;
+  background-color: #FFF4A3;
+  padding: 5px;
+  flex: 0.25;
+}
+
+div.procedure_creation_leftright div.right {
+  height: 100%;
+  width:84%;
+  float:left;
+  border-style: solid;
+  border-width: 1px;
+  background-color:#D9EEE1;
+  padding: 5px;
+  flex: 0.75;
+  object-fit: contain;
+}
+
+.dropdown {
+  width: 100%;
+}
+
+.form_text {
+  width: 97%;
+}
+
+div.gallery {
+  width: 100%;
+  object-fit: contain;
+}

src/submissions/templates/plate_map.html

@@ -1,6 +1,6 @@
-        <div class="gallery" style="display: grid;grid-template-columns: repeat({{ PLATE_COLUMNS }}, 7.5vw);grid-template-rows: repeat({{ PLATE_ROWS }}, 7.5vw);grid-gap: 2px;">
+        <div class="gallery" style="display: grid;grid-template-columns: repeat({{ plate_columns }}, {{ vw }}vw);grid-template-rows: repeat({{ plate_rows }}, {{ vw }}vw);grid-gap: 2px;">
             {% for sample in samples %}
-                <div class="well data-link sample" id="{{sample['submitter_id']}}" style="background-color: {{sample['background_color']}};
+                <div class="well data-link sample" id="{{sample['submitter_id']}}" style="background-color: {{ sample['background_color'] }};
                 border: 1px solid #000;
                 padding: 20px;
                 grid-column-start: {{sample['column']}};