Adding equipment usage.

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:
-            f.write(html)
+        # with open("procedure.html", "w") as f:
+        #     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: