Moved to error reporting framework.

CHANGELOG.md

@@ -1,6 +1,7 @@
 ## 202409.03
 
-- Improved error messaging when saving submissions.
+- Upgraded sample search to (semi) realtime search.
+- Improved error messaging.
 
 ## 202409.02
 

src/submissions/__init__.py

@@ -19,7 +19,7 @@ def get_week_of_month() -> int:
 __project__ = "submissions"
 __version__ = f"{year}{str(month).zfill(2)}.{get_week_of_month()}b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
-__copyright__ = f"2022-{date.today().year}, Government of Canada"
+__copyright__ = f"2022-{year}, Government of Canada"
 __github__ = "https://github.com/landowark/submissions"
 
 project_path = Path(__file__).parents[2].absolute()

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

@@ -167,20 +167,20 @@ class BaseClass(Base):
         except Exception as e:
             logger.critical(f"Problem saving object: {e}")
             logger.error(f"Error message: {type(e)}")
-            match e:
+            # match e:
-                case sqlalcIntegrityError():
+            #     case sqlalcIntegrityError():
-                    origin = e.orig.__str__().lower()
+            #         origin = e.orig.__str__().lower()
-                    logger.debug(f"Exception origin: {origin}")
+            #         logger.error(f"Exception origin: {origin}")
-                    if "unique constraint failed:" in origin:
+            #         if "unique constraint failed:" in origin:
-                        field = origin.split(".")[1].replace("_", " ").upper()
+            #             field = " ".join(origin.split(".")[1:]).replace("_", " ").upper()
-                        logger.debug(field)
+            #             # logger.debug(field)
-                        msg = f"{field} doesn't have a unique value.\nIt must be changed."
+            #             msg = f"{field} doesn't have a unique value.\nIt must be changed."
-                    else:
+            #         else:
-                        msg = f"Got unknown integrity error: {e}"
+            #             msg = f"Got unknown integrity error: {e}"
-                case _:
+            #     case _:
-                    msg = f"Got generic error: {e}"
+            #         msg = f"Got generic error: {e}"
             self.__database_session__.rollback()
-            report.add_result(Result(msg=msg, status="Critical"))
+            report.add_result(Result(msg=e, status="Critical"))
             return report
 
 

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

@@ -9,7 +9,7 @@ from operator import itemgetter
 from . import BaseClass
 from tools import setup_lookup
 from datetime import date, datetime
-from typing import List
+from typing import List, Literal
 from dateutil.parser import parse
 from re import Pattern
 
@@ -53,7 +53,7 @@ class ControlType(BaseClass):
                 pass
         return cls.execute_query(query=query, limit=limit)
 
-    def get_subtypes(self, mode: str) -> List[str]:
+    def get_subtypes(self, mode: Literal['kraken', 'matches', 'contains']) -> List[str]:
         """
         Get subtypes associated with this controltype (currently used only for Kraken)
 
@@ -161,7 +161,7 @@ class Control(BaseClass):
         }
         return output
 
-    def convert_by_mode(self, mode: str) -> list[dict]:
+    def convert_by_mode(self, mode: Literal['kraken', 'matches', 'contains']) -> list[dict]:
         """
         split this instance into analysis types for controls graphs
 
@@ -195,7 +195,7 @@ class Control(BaseClass):
             output.append(_dict)
         # logger.debug("Have to triage kraken data to keep program from getting overwhelmed")
         if "kraken" in mode:
-            output = sorted(output, key=lambda d: d[f"{mode}_count"], reverse=True)[:49]
+            output = sorted(output, key=lambda d: d[f"{mode}_count"], reverse=True)[:50]
         return output
 
     @classmethod

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

@@ -7,6 +7,7 @@ import datetime
 import json
 from pprint import pprint, pformat
 
+import yaml
 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
@@ -873,7 +874,12 @@ class SubmissionType(BaseClass):
             logging.critical(f"Given file could not be found.")
             return None
         with open(filepath, "r") as f:
+            if filepath.suffix == ".json":
                 import_dict = json.load(fp=f)
+            elif filepath.suffix == ".yml":
+                import_dict = yaml.safe_load(stream=f)
+            else:
+                raise Exception(f"Filetype {filepath.suffix} not supported.")
         logger.debug(pformat(import_dict))
         submission_type = cls.query(name=import_dict['name'])
         if submission_type:

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

@@ -2425,15 +2425,18 @@ class BasicSample(BaseClass):
             case _:
                 model = cls.find_polymorphic_subclass(attrs=kwargs)
             # logger.debug(f"Length of kwargs: {len(kwargs)}")
+        # logger.debug(f"Fuzzy search received sample type: {sample_type}")
         query: Query = cls.__database_session__.query(model)
+        # logger.debug(f"Queried model. Now running searches in {kwargs}")
         for k, v in kwargs.items():
+            # logger.debug(f"Running fuzzy search for attribute: {k} with value {v}")
             search = f"%{v}%"
             try:
                 attr = getattr(model, k)
                 query = query.filter(attr.like(search))
             except (ArgumentError, AttributeError) as e:
                 logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
-        return query.all()
+        return query.limit(50).all()
 
     def delete(self):
         raise AttributeError(f"Delete not implemented for {self.__class__}")

src/submissions/frontend/widgets/sample_search.py

@@ -24,7 +24,7 @@ class SearchBox(QDialog):
         self.sample_type = QComboBox(self)
         self.sample_type.setObjectName("sample_type")
         self.sample_type.currentTextChanged.connect(self.update_widgets)
-        options = [cls.__mapper_args__['polymorphic_identity'] for cls in BasicSample.__subclasses__()]
+        options = ["Any"] + [cls.__mapper_args__['polymorphic_identity'] for cls in BasicSample.__subclasses__()]
         self.sample_type.addItems(options)
         self.sample_type.setEditable(False)
         self.setMinimumSize(600, 600)
@@ -34,6 +34,7 @@ class SearchBox(QDialog):
         self.layout.addWidget(self.results, 5, 0)
         self.setLayout(self.layout)
         self.update_widgets()
+        self.update_data()
 
     def update_widgets(self):
         """
@@ -43,6 +44,9 @@ class SearchBox(QDialog):
         # logger.debug(deletes)
         for item in deletes:
             item.setParent(None)
+        if self.sample_type.currentText() == "Any":
+            self.type = BasicSample
+        else:
             self.type = BasicSample.find_polymorphic_subclass(self.sample_type.currentText())
         # logger.debug(f"Sample type: {self.type}")
         searchables = self.type.get_searchables()
@@ -50,6 +54,7 @@ class SearchBox(QDialog):
         for iii, item in enumerate(searchables):
             widget = FieldSearch(parent=self, label=item['label'], field_name=item['field'])
             self.layout.addWidget(widget, start_row+iii, 0)
+            widget.search_widget.textChanged.connect(self.update_data)
 
     def parse_form(self) -> dict:
         """
@@ -65,9 +70,11 @@ class SearchBox(QDialog):
         """
         Shows dataframe of relevant samples.
         """
+        # logger.debug(f"Running update_data with sample type: {self.type}")
         fields = self.parse_form()
-        data = self.type.fuzzy_search(sample_type=self.type, **fields)
+        # logger.debug(f"Got fields: {fields}")
-        data = self.type.samples_to_df(sample_list=data)
+        sample_list_creator = self.type.fuzzy_search(sample_type=self.type, **fields)
+        data = self.type.samples_to_df(sample_list=sample_list_creator)
         # logger.debug(f"Data: {data}")
         self.results.setData(df=data)
 

src/submissions/tools/__init__.py

@@ -25,6 +25,7 @@ from __init__ import project_path
 from configparser import ConfigParser
 from tkinter import Tk  # from tkinter import Tk for Python 3.x
 from tkinter.filedialog import askdirectory
+from .error_messaging import parse_error_to_message
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -765,10 +766,10 @@ def setup_lookup(func):
     return wrapper
 
 
-class Result(BaseModel):
+class Result(BaseModel, arbitrary_types_allowed=True):
     owner: str = Field(default="", validate_default=True)
     code: int = Field(default=0)
-    msg: str
+    msg: str | Exception
     status: Literal["NoIcon", "Question", "Information", "Warning", "Critical"] = Field(default="NoIcon")
 
     @field_validator('status', mode='before')
@@ -779,6 +780,13 @@ class Result(BaseModel):
         else:
             return value.title()
 
+    @field_validator('msg')
+    @classmethod
+    def set_message(cls, value):
+        if isinstance(value, Exception):
+            value = parse_error_to_message(value=value)
+        return value
+
     def __repr__(self) -> str:
         return f"Result({self.owner})"
 
@@ -822,7 +830,7 @@ class Report(BaseModel):
 
 def rreplace(s: str, old: str, new: str) -> str:
     """
-    Removes rightmost occurence of a substring
+    Removes rightmost occurrence of a substring
 
     Args:
         s (str): input string
@@ -873,20 +881,6 @@ def remove_key_from_list_of_dicts(input: list, key: str) -> list:
     return input
 
 
-# def workbook_2_csv(worksheet: Worksheet, filename: Path):
-#     """
-#     Export an excel worksheet (workbook is not correct) to csv file.
-#
-#     Args:
-#         worksheet (Worksheet): Incoming worksheet
-#         filename (Path): Output csv filepath.
-#     """
-#     with open(filename, 'w', newline="") as f:
-#         c = csv.writer(f)
-#         for r in worksheet.rows:
-#             c.writerow([cell.value for cell in r])
-
-
 ctx = get_config(None)
 
 
@@ -909,7 +903,7 @@ def check_authorization(func):
     Decorator to check if user is authorized to access function
 
     Args:
-        func (_type_): Function to be used.
+        func (function): Function to be used.
     """
 
     def wrapper(*args, **kwargs):
@@ -918,15 +912,27 @@ def check_authorization(func):
             return func(*args, **kwargs)
         else:
             logger.error(f"User {getpass.getuser()} is not authorized for this function.")
-            return dict(code=1, message="This user does not have permission for this function.", status="warning")
+            # return dict(code=1, message="This user does not have permission for this function.", status="warning")
-
+            report = Report()
+            report.add_result(Result(owner=func.__str__(), code=1, msg="This user does not have permission for this function.", status="warning"))
+            return report
     return wrapper
 
 
 def report_result(func):
+    """
+    Decorator to display any reports returned from a function.
+
+    Args:
+        func (function): Function being decorated
+
+    Returns:
+        __type__: Output from decorated function
+
+    """
     def wrapper(*args, **kwargs):
-        logger.debug(f"Arguments: {args}")
+        # logger.debug(f"Arguments: {args}")
-        logger.debug(f"Keyword arguments: {kwargs}")
+        # logger.debug(f"Keyword arguments: {kwargs}")
         output = func(*args, **kwargs)
         match output:
             case Report():
@@ -955,3 +961,9 @@ def report_result(func):
         logger.debug(f"Returning: {output}")
         return output
     return wrapper
+
+
+@report_result
+@check_authorization
+def test_function():
+    print("Success!")

src/submissions/tools/error_messaging.py

@@ -0,0 +1,30 @@
+from sqlalchemy.exc import ArgumentError, IntegrityError as sqlalcIntegrityError
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+
+def parse_error_to_message(value: Exception):
+    """
+    Converts an except to a human-readable error message for display.
+
+    Args:
+        value (Exception): Input exception
+
+    Returns:
+        str: Output message for display
+
+    """
+    match value:
+        case sqlalcIntegrityError():
+            origin = value.orig.__str__().lower()
+            logger.error(f"Exception origin: {origin}")
+            if "unique constraint failed:" in origin:
+                field = " ".join(origin.split(".")[1:]).replace("_", " ").upper()
+                # logger.debug(field)
+                value = f"{field} doesn't have a unique value.\nIt must be changed."
+            else:
+                value = f"Got unknown integrity error: {value}"
+        case _:
+            value = f"Got generic error: {value}"
+    return value

submissions.spec

@@ -3,6 +3,7 @@
 block_cipher = None
 
 #### custom for automation of documentation building ####
+
 import sys, subprocess
 from pathlib import Path
 sys.path.append(Path(__name__).parent.joinpath('src').absolute().__str__())
@@ -17,6 +18,7 @@ print(bcolors.BOLD + "Running Sphinx subprocess to generate html docs..." + bcol
 docs_build = doc_path.joinpath("build")
 #docs_build.mkdir(exist_ok=True, parents=True)
 subprocess.run([build_path, doc_path.joinpath("source").__str__(), docs_build.__str__(), "-a"])
+
 #########################################################
 
 options = [