Pre code cleanup

src/submissions/frontend/widgets/app.py

@@ -1,7 +1,7 @@
 """
 Constructs main application.
 """
-import yaml
+from pprint import pformat
 from PyQt6.QtWidgets import (
     QTabWidget, QWidget, QVBoxLayout,
     QHBoxLayout, QScrollArea, QMainWindow, 
@@ -12,17 +12,17 @@ from pathlib import Path
 
 from markdown import markdown
 from __init__ import project_path
-from tools import check_if_app, Settings, Report, jinja_template_loading
-from .functions import select_save_file
+from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization
+from .functions import select_save_file,select_open_file
 from datetime import date
-from .pop_ups import HTMLPop
+from .pop_ups import HTMLPop, AlertPop
 from .misc import LogParser
 import logging, webbrowser, sys, shutil
 from .submission_table import SubmissionsSheet
 from .submission_widget import SubmissionFormContainer
 from .controls_chart import ControlsViewer
 from .kit_creator import KitAdder
-from .submission_type_creator import SubmissionTypeAdder
+from .submission_type_creator import SubmissionTypeAdder, SubmissionType
 from .sample_search import SearchBox
 
 logger = logging.getLogger(f'submissions.{__name__}')
@@ -76,7 +76,8 @@ class App(QMainWindow):
         helpMenu.addAction(self.docsAction)
         helpMenu.addAction(self.githubAction)
         fileMenu.addAction(self.importAction)
-        fileMenu.addAction(self.yamlAction)
+        fileMenu.addAction(self.yamlExportAction)
+        fileMenu.addAction(self.yamlImportAction)
         methodsMenu.addAction(self.searchLog)
         methodsMenu.addAction(self.searchSample)
         reportMenu.addAction(self.generateReportAction)
@@ -111,7 +112,8 @@ class App(QMainWindow):
         self.searchLog = QAction("Search Log", self)
         self.searchSample = QAction("Search Sample", self)
         self.githubAction = QAction("Github", self)
-        self.yamlAction = QAction("Export Type Template", self)
+        self.yamlExportAction = QAction("Export Type Example", self)
+        self.yamlImportAction = QAction("Import Type Template", self)
 
     def _connectActions(self):
         """
@@ -128,7 +130,8 @@ class App(QMainWindow):
         self.searchLog.triggered.connect(self.runSearch)
         self.searchSample.triggered.connect(self.runSampleSearch)
         self.githubAction.triggered.connect(self.openGithub)
-        self.yamlAction.triggered.connect(self.export_ST_yaml)
+        self.yamlExportAction.triggered.connect(self.export_ST_yaml)
+        self.yamlImportAction.triggered.connect(self.import_ST_yaml)
 
     def showAbout(self):
         """
@@ -207,11 +210,31 @@ class App(QMainWindow):
             yaml_path = Path(sys._MEIPASS).joinpath("resources", "viral_culture.yml")
         else:
             yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
-        with open(yaml_path, "r") as f:
-            data = yaml.safe_load(f)
+        # with open(yaml_path, "r") as f:
+        #     data = yaml.safe_load(f)
         fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
-        with open(fname, "w") as f:
-            yaml.safe_dump(data=data, stream=f)
+        # with open(fname, "w") as f:
+        #     yaml.safe_dump(data=data, stream=f)
+        shutil.copyfile(yaml_path, fname)
+
+    @check_authorization
+    def import_ST_yaml(self, *args, **kwargs):
+        fname = select_open_file(obj=self, file_extension="yml")
+        if not fname:
+            logger.info(f"Import cancelled.")
+            return
+        ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
+        ap.exec()
+        st = SubmissionType.import_from_json(filepath=fname)
+        if st:
+            print(pformat(st.to_export_dict()))
+            choice = input("Save the above submission type? [y/N]: ")
+            if choice.lower() == "y":
+                # st.save()
+                pass
+            else:
+                logger.warning("Save of submission type cancelled.")
+
 
 
 class AddSubForm(QWidget):

src/submissions/frontend/widgets/functions.py

@@ -31,6 +31,11 @@ def select_open_file(obj: QMainWindow, file_extension: str | None = None) -> Pat
     else:
         fname = Path(
             QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter=f"{file_extension}(*.{file_extension})")[0])
+        if not fname.exists():
+            raise FileNotFoundError(f"File {fname.__str__()} could not be found.")
+        if fname.__str__() == ".":
+            logger.warning(f"No file selected, cancelling.")
+            return
     obj.last_dir = fname.parent
     return fname
 

src/submissions/frontend/widgets/submission_widget.py

@@ -1,6 +1,8 @@
 '''
 Contains all submission related frontend functions
 '''
+import sys
+
 from PyQt6.QtWidgets import (
     QWidget, QPushButton, QVBoxLayout,
     QComboBox, QDateEdit, QLineEdit, QLabel
@@ -96,6 +98,7 @@ class SubmissionFormContainer(QWidget):
         self.import_submission_function(fname)
         return self.report
 
+    @report_result
     def import_submission_function(self, fname: Path | None = None):
         """
         Import a new submission to the app window
@@ -119,7 +122,7 @@ class SubmissionFormContainer(QWidget):
         if isinstance(fname, bool) or fname is None:
             fname = select_open_file(self, file_extension="xlsx")
         # logger.debug(f"Attempting to parse file: {fname}")
-        if not fname.exists():
+        if not fname:
             report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
             return report
         # NOTE: create sheetparser using excel sheet and context from gui
@@ -347,9 +350,14 @@ class SubmissionFormWidget(QWidget):
         # logger.debug(f"SQL object: {pformat(base_submission.__dict__)}")
         # logger.debug(f"Base submission: {base_submission.to_dict()}")
         # NOTE: check output message for issues
+        # logger.debug(f"Result of to_sql: {result}")
         try:
-            code = report.results[-1].code
-        except IndexError:
+            trigger = result.results[-1]
+            code = trigger.code
+            # logger.debug(f"Code from return: {code}")
+        except IndexError as e:
+            logger.error(result.results)
+            logger.error(f"Problem getting error code: {e}")
             code = 0
         match code:
             # NOTE: code 0: everything is fine.
@@ -357,7 +365,7 @@ class SubmissionFormWidget(QWidget):
                 pass
             # NOTE: code 1: ask for overwrite
             case 1:
-                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
+                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=trigger.msg)
                 if dlg.exec():
                     # NOTE: Do not add duplicate reagents.
                     pass