Adding equipment usage.

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

@@ -1320,11 +1320,20 @@ class Procedure(BaseClass):
         Returns:
             dict: dictionary of functions
         """
-        names = ["Add Results", "Edit", "Add Comment", "Show Details", "Delete"]
+        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):
         logger.debug(f"Add Results! {resultstype_name}")
+        from frontend.widgets import results
+        results_class = getattr(results, resultstype_name)
+        rs = results_class(procedure=self, parent=obj)
+
+    def add_equipment(self, obj):
+        from frontend.widgets.equipment_usage import EquipmentUsage
+        dlg = EquipmentUsage(parent=obj, procedure=self)
+        if dlg.exec():
+            pass
 
     def edit(self, obj):
         logger.debug("Edit!")
@@ -2668,7 +2677,6 @@ class Results(BaseClass):
     procedure = relationship("Procedure", back_populates="results")
     assoc_id = Column(INTEGER, ForeignKey("_proceduresampleassociation.id", ondelete='SET NULL',
                                                 name="fk_RES_ASSOC_id"))
-
     sampleprocedureassociation = relationship("ProcedureSampleAssociation", back_populates="results")
     _img = Column(String(128))
 

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

@@ -314,6 +314,7 @@ class ClientSubmission(BaseClass, LogMixin):
                 assoc.save()
         else:
             logger.warning("Run cancelled.")
+        obj.set_data()
 
 
     def edit(self, obj):
@@ -1138,8 +1139,7 @@ class Run(BaseClass, LogMixin):
             sql, _ = dlg.return_sql()
             logger.debug(f"Output run samples:\n{pformat(sql.run.sample)}")
             sql.save()
-
+        obj.set_data()
-
 
     def delete(self, obj=None):
         """
@@ -2029,7 +2029,7 @@ class RunSampleAssociation(BaseClass):
 
 class ProcedureSampleAssociation(BaseClass):
 
-    id = Column(INTEGER, primary_key=True)
+    id = Column(INTEGER, unique=True, nullable=False)
     procedure_id = Column(INTEGER, ForeignKey("_procedure.id"), primary_key=True)  #: id of associated procedure
     sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True)  #: id of associated equipment
     row = Column(INTEGER)
@@ -2042,15 +2042,34 @@ class ProcedureSampleAssociation(BaseClass):
 
     results = relationship("Results", back_populates="sampleprocedureassociation")
 
+    @classmethod
+    def query(cls, sample: Sample|str|None=None, procedure: Procedure|str|None=None, limit: int=0, **kwargs):
+        query = cls.__database_session__.query(cls)
+        match sample:
+            case Sample():
+                query = query.filter(cls.sample==sample)
+            case str():
+                query = query.join(Sample).filter(Sample.sample_id==sample)
+            case _:
+                pass
+        match procedure:
+            case Procedure():
+                query = query.filter(cls.procedure == procedure)
+            case str():
+                query = query.join(Procedure).filter(Procedure.name == procedure)
+            case _:
+                pass
+        if sample and procedure:
+            limit = 1
+        return cls.execute_query(query=query, limit=limit, **kwargs)
 
 
-    # def __init__(self, new_id:int|None=None, **kwarg):
+    def __init__(self, new_id:int|None=None, **kwarg):
-    #     if new_id:
+        if new_id:
-    #         self.id = new_id
+            self.id = new_id
-    #     else:
+        else:
-    #         self.id = self.__class__.autoincrement_id()
+            self.id = self.__class__.autoincrement_id()
-    #     # new_id = self.__class__.autoincrement_id()
+        super().__init__(**kwarg)
-    #     super().__init__(**kwarg)
 
 
     @classmethod

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

@@ -7,6 +7,7 @@ from typing import Generator, Tuple
 from openpyxl import load_workbook
 from pandas import DataFrame
 from backend.validators import pydant
+from backend.db.models import Procedure
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -15,7 +16,8 @@ class DefaultParser(object):
     def __repr__(self):
         return f"{self.__class__.__name__}<{self.filepath.stem}>"
 
-    def __init__(self, filepath: Path | str, range_dict: dict | None = None, *args, **kwargs):
+    def __init__(self, filepath: Path | str, procedure: Procedure|None=None, range_dict: dict | None = None, *args, **kwargs):
+        self.procedure = procedure
         try:
             self._pyd_object = getattr(pydant, f"Pyd{self.__class__.__name__.replace('Parser', '')}")
         except AttributeError:

src/submissions/backend/excel/parsers/pcr_parser.py

@@ -8,44 +8,14 @@ from typing import Generator, Tuple
 
 from openpyxl import load_workbook
 
-from backend.db.models import Run, Sample
+from backend.db.models import Run, Sample, Procedure, ProcedureSampleAssociation
 from . import DefaultKEYVALUEParser, DefaultTABLEParser
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
-class PCRSampleParser(DefaultTABLEParser):
-    """Object to pull data from Design and Analysis PCR export file."""
-
-    default_range_dict = [dict(
-        header_row=25,
-        sheet="Results"
-    )]
-
-    @property
-    def parsed_info(self):
-        output = [item for item in super().parsed_info]
-        merge_column = "sample"
-        sample_names = list(set([item['sample'] for item in output]))
-        for sample in sample_names:
-            multi = dict()
-            sois = (item for item in output if item['sample']==sample)
-            for soi in sois:
-                multi[soi['target']] = {k:v for k, v in soi.items() if k != "target"}
-            yield (sample, multi)
-
-    def to_pydantic(self):
-        for key, sample_info in self.parsed_info:
-            sample_obj = Sample.query(sample_id=key)
-            if sample_obj and not isinstance(sample_obj, list):
-                yield self._pyd_object(results=sample_info, parent=sample_obj)
-            else:
-                continue
-
-
 
 class PCRInfoParser(DefaultKEYVALUEParser):
-
     default_range_dict = [dict(
         start_row=1,
         end_row=24,
@@ -72,11 +42,10 @@ class PCRInfoParser(DefaultKEYVALUEParser):
     #
 
     def to_pydantic(self):
-        from backend.db.models import Procedure
+        # from backend.db.models import Procedure
         data = {key: value for key, value in self.parsed_info}
         data['filepath'] = self.filepath
-        return self._pyd_object(**data, parent=Procedure)
+        return self._pyd_object(**data, parent=self.procedure)
-
 
     # @property
     # def pcr_info(self) -> dict:
@@ -97,3 +66,36 @@ class PCRInfoParser(DefaultKEYVALUEParser):
     #         pcr[key] = value
     #     pcr['imported_by'] = getuser()
     #     return pcr
+
+
+class PCRSampleParser(DefaultTABLEParser):
+    """Object to pull data from Design and Analysis PCR export file."""
+
+    default_range_dict = [dict(
+        header_row=25,
+        sheet="Results"
+    )]
+
+    @property
+    def parsed_info(self):
+        output = [item for item in super().parsed_info]
+        merge_column = "sample"
+        sample_names = list(set([item['sample'] for item in output]))
+        for sample in sample_names:
+            multi = dict()
+            sois = [item for item in output if item['sample'] == sample]
+            for soi in sois:
+                multi[soi['target']] = {k: v for k, v in soi.items() if k != "target" and k != "sample"}
+            yield {sample: multi}
+
+    def to_pydantic(self):
+        logger.debug(f"running to pydantic")
+        for item in self.parsed_info:
+            sample_obj = Sample.query(sample_id=list(item.keys())[0])
+            logger.debug(f"Sample object {sample_obj}")
+            assoc = ProcedureSampleAssociation.query(sample=sample_obj, procedure=self.procedure)
+            if assoc and not isinstance(assoc, list):
+                yield self._pyd_object(results=list(item.values())[0], parent=assoc)
+            else:
+                continue
+

src/submissions/backend/validators/pydant.py

@@ -1436,9 +1436,15 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
             sql.run = self.run
         if self.proceduretype:
             sql.proceduretype = self.proceduretype
-        for sample in self.samples:
+        try:
-            if sample.sample_id.startswith("blank_") or sample.sample_id == "":
+            start_index = max([item.id for item in ProcedureSampleAssociation.query()]) + 1
-                continue
+        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 == ""]
+        logger.debug(f"start index: {start_index}")
+        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:
@@ -1446,7 +1452,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
                     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(procedure=sql, sample=sample_sql, row=sample.row, column=sample.column)
+            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:
@@ -1535,5 +1541,17 @@ class PydClientSubmission(PydBaseClass):
 class PydResults(PydBaseClass, arbitrary_types_allowed=True):
 
     results: dict = Field(default={})
-    parent: Sample|Procedure
+    img: None = Field(default=None)
+    parent: Procedure|ProcedureSampleAssociation|None = Field(default=None)
+
+    def to_sql(self):
+        sql = Results(result=self.results)
+        match self.parent:
+            case ProcedureSampleAssociation():
+                sql.sampleprocedureassociation = self.parent
+            case Procedure():
+                sql.procedure = self.parent
+            case _:
+                logger.error("Improper association found.")
+        return sql
 

src/submissions/frontend/widgets/equipment_usage.py

@@ -19,7 +19,7 @@ class EquipmentUsage(QDialog):
     def __init__(self, parent, procedure: Procedure):
         super().__init__(parent)
         self.procedure = procedure
-        self.setWindowTitle(f"Equipment Checklist - {procedure.rsl_plate_num}")
+        self.setWindowTitle(f"Equipment Checklist - {procedure.name}")
         self.used_equipment = self.procedure.equipment
         self.kit = self.procedure.kittype
         self.opt_equipment = procedure.proceduretype.get_equipment()

src/submissions/frontend/widgets/functions.py

@@ -39,6 +39,7 @@ def select_open_file(obj: QMainWindow, file_extension: str | None = None) -> Pat
             logger.warning(f"No file selected, cancelling.")
             return
     obj.last_dir = fname.parent
+    logger.debug(f"File selected: {fname}")
     return fname
 
 

src/submissions/frontend/widgets/procedure_creation.py

@@ -70,8 +70,8 @@ class ProcedureCreation(QDialog):
             procedure=self.created_procedure.__dict__,
             plate_map=self.plate_map
         )
-        with open("procedure.html", "w") as f:
+        # with open("procedure.html", "w") as f:
-            f.write(html)
+        #     f.write(html)
         self.webview.setHtml(html)
 
     @pyqtSlot(str, str)

src/submissions/frontend/widgets/results/PCR.py

@@ -1,26 +0,0 @@
-"""
-
-"""
-from pathlib import Path
-from backend.validators import PydResults
-from backend.db.models import Procedure, Results
-from backend.excel.parsers.pcr_parser import PCRSampleParser, PCRInfoParser
-from frontend.widgets.functions import select_open_file
-from . import DefaultResults
-
-class PCR(DefaultResults):
-
-    def __init__(self, procedure: Procedure, fname:Path|str|None=None):
-        self.procedure = procedure
-        if not fname:
-            self.fname = select_open_file(file_extension="xlsx")
-        elif isinstance(fname, str):
-            self.fname = Path(fname)
-        self.info_parser = PCRInfoParser(filepath=fname)
-        self.sample_parser = PCRSampleParser(filepath=fname)
-
-    def build_procedure(self):
-        results = PydResults(parent=self.procedure)
-        results.results =
-
-

src/submissions/frontend/widgets/results/__init__.py

@@ -4,4 +4,4 @@ class DefaultResults(object):
 
     pass
 
-from .PCR import pcr
+from .pcr import PCR

src/submissions/frontend/widgets/results/pcr.py

@@ -0,0 +1,39 @@
+"""
+
+"""
+import logging
+from pathlib import Path
+from backend.validators import PydResults
+from backend.db.models import Procedure, Results
+from backend.excel.parsers.pcr_parser import PCRSampleParser, PCRInfoParser
+from frontend.widgets.functions import select_open_file
+from tools import get_application_from_parent
+from . import DefaultResults
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+class PCR(DefaultResults):
+
+    def __init__(self, procedure: Procedure, parent, fname:Path|str|None=None):
+        logger.debug(f"FName before correction: {fname}")
+        self.procedure = procedure
+        if not fname:
+            self.fname = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
+        elif isinstance(fname, str):
+            self.fname = Path(fname)
+        logger.debug(f"FName after correction: {fname}")
+        self.info_parser = PCRInfoParser(filepath=self.fname, procedure=self.procedure)
+        self.sample_parser = PCRSampleParser(filepath=self.fname, procedure=self.procedure)
+        self.build_procedure()
+        self.build_samples()
+
+    def build_procedure(self):
+        procedure_info = self.info_parser.to_pydantic()
+        procedure_sql = procedure_info.to_sql()
+        procedure_sql.save()
+
+    def build_samples(self):
+        samples = self.sample_parser.to_pydantic()
+        for sample in samples:
+            sql = sample.to_sql()
+            sql.save()

src/submissions/frontend/widgets/submission_table.py

@@ -321,14 +321,11 @@ class SubmissionsTree(QTreeView):
             event (_type_): the item of interest
         """
         indexes = self.selectedIndexes()
-
         dicto = next((item.data(1) for item in indexes if item.data(1)))
         query_obj = dicto['item_type'].query(name=dicto['query_str'], limit=1)
         logger.debug(query_obj)
-
         # NOTE: Convert to data in id column (i.e. column 0)
         # id = id.sibling(id.row(), 0).data()
-
         # logger.debug(id.model().query_group_object(id.row()))
         # clientsubmission = id.model().query_group_object(id.row())
         self.menu = QMenu(self)
@@ -403,8 +400,6 @@ class SubmissionsTree(QTreeView):
             if isinstance(children, List):
                 self._populateTree(child, child_item)
 
-
-
     def clear(self):
         if self.model != None:
             # self.model.clear()       # works
@@ -415,7 +410,6 @@ class SubmissionsTree(QTreeView):
         # NOTE: Convert to data in id column (i.e. column 0)
         # id = id.sibling(id.row(), 1)
         indexes = self.selectedIndexes()
-
         dicto = next((item.data(1) for item in indexes if item.data(1)))
         logger.debug(dicto)
         # try: