Bug fixes.

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

@@ -11,7 +11,7 @@ from sqlalchemy.ext.associationproxy import association_proxy
 from datetime import date
 import logging, re
 from tools import check_authorization, setup_lookup, Report, Result
-from typing import List, Literal, Generator
+from typing import List, Literal, Generator, Any
 from pandas import ExcelFile
 from pathlib import Path
 from . import Base, BaseClass, Organization
@@ -261,7 +261,7 @@ class KitType(BaseClass):
         base_dict['reagent roles'] = []
         base_dict['equipment roles'] = []
         for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
-            logger.debug(f"Value: {v}")
+            # logger.debug(f"Value: {v}")
             try:
                 assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0]
             except IndexError as e:
@@ -275,10 +275,10 @@ class KitType(BaseClass):
             except IndexError:
                 continue
             for kk, vv in assoc.to_export_dict(kit_type=self).items():
-                logger.debug(f"{kk}:{vv}")
+                # logger.debug(f"{kk}:{vv}")
                 v[kk] = vv
             base_dict['equipment roles'].append(v)
-        logger.debug(f"KT returning {base_dict}")
+        # logger.debug(f"KT returning {base_dict}")
         return base_dict
 
 
@@ -1492,6 +1492,16 @@ class SubmissionEquipmentAssociation(BaseClass):
                       processes=[process], role=self.role, nickname=self.equipment.nickname)
         return output
 
+    @classmethod
+    @setup_lookup
+    def query(cls, equipment_id:int, submission_id:int, role:str, limit:int=0, **kwargs) -> Any | List[Any]:
+        query: Query = cls.__database_session__.query(cls)
+        query = query.filter(cls.equipment_id==equipment_id)
+        query = query.filter(cls.submission_id==submission_id)
+        query = query.filter(cls.role==role)
+        return cls.execute_query(query=query, limit=limit, **kwargs)
+
+
 
 class SubmissionTypeEquipmentRoleAssociation(BaseClass):
     """

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

@@ -295,8 +295,10 @@ class BasicSubmission(BaseClass):
                     if k == 'info':
                         continue
                     if not any([item['role'] == k for item in reagents]):
+                        # expiry = date(year=1970, month=1, day=1)
+                        expiry = "NA"
                         reagents.append(
-                            dict(role=k, name="Not Applicable", lot="NA", expiry=date(year=1970, month=1, day=1),
+                            dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
                                  missing=True))
             except Exception as e:
                 logger.error(f"We got an error retrieving reagents: {e}")
@@ -507,10 +509,10 @@ class BasicSubmission(BaseClass):
                     sample, _ = sample.to_sql(submission=self)
                 return
             case "reagents":
-                logger.debug(f"Reagents coming into SQL: {value}")
+                # logger.debug(f"Reagents coming into SQL: {value}")
                 field_value = [reagent['value'].to_sql()[0] if isinstance(reagent, dict) else reagent.to_sql()[0] for
                                reagent in value]
-                logger.debug(f"Reagents coming out of SQL: {field_value}")
+                # logger.debug(f"Reagents coming out of SQL: {field_value}")
             case "submission_type":
                 field_value = SubmissionType.query(name=value)
             case "sample_count":
@@ -521,7 +523,7 @@ class BasicSubmission(BaseClass):
             case "ctx" | "csv" | "filepath" | "equipment":
                 return
             case item if item in self.jsons():
-                logger.debug(f"Setting JSON attribute.")
+                # logger.debug(f"Setting JSON attribute.")
                 existing = self.__getattribute__(key)
                 if value is None or value in ['', 'null']:
                     logger.error(f"No value given, not setting.")
@@ -617,7 +619,7 @@ class BasicSubmission(BaseClass):
         Args:
             original (bool, optional): Is this the first save. Defaults to True.
         """
-        logger.debug("Saving submission.")
+        # logger.debug("Saving submission.")
         if original:
             self.uploaded_by = getuser()
         super().save()
@@ -1177,9 +1179,12 @@ class BasicSubmission(BaseClass):
                 # logger.debug(f"Processing: {equip}")
                 _, assoc = equip.toSQL(submission=self)
                 # logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}")
-                assoc.save()
+                try:
+                    assoc.save()
+                except AttributeError as e:
+                    logger.error(f"Couldn't save association with {equip} due to {e}")
                 if equip.tips:
-                    logger.debug("We have tips in this equipment")
+                    # logger.debug("We have tips in this equipment")
                     for tips in equip.tips:
                         tassoc = tips.to_sql(submission=self)
                         tassoc.save()
@@ -1308,7 +1313,7 @@ class BacterialCulture(BasicSubmission):
         idx = df[df[0] == sample.well]
         if idx.empty:
             new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
-            logger.debug(f"Checking: {new}")
+            # logger.debug(f"Checking: {new}")
             idx = df[df[0] == new]
         # logger.debug(f"Here is the row: {idx}")
         row = idx.index.to_list()[0]
@@ -1366,7 +1371,7 @@ class Wastewater(BasicSubmission):
             dict: Updated sample dictionary
         """
         input_dict = super().custom_info_parser(input_dict)
-        logger.debug(f"Input dict: {pformat(input_dict)}")
+        # logger.debug(f"Input dict: {pformat(input_dict)}")
         if xl is not None:
             try:
                 input_dict['csv'] = xl["Copy to import file"]
@@ -1636,12 +1641,14 @@ class WastewaterArtic(BasicSubmission):
         input_dict = super().custom_info_parser(input_dict)
         egel_section = custom_fields['egel_results']
         ws = xl[egel_section['sheet']]
-        data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']) for
-                ii in range(egel_section['start_row'], egel_section['end_row'])]
+        data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']+1) for
+                ii in range(egel_section['start_row'], egel_section['end_row']+1)]
         data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
+        # logger.debug(f"Got gel control map: {data}")
         input_dict['gel_controls'] = [
             dict(sample_id=cell.value, location=f"{row_map[cell.row - 9]}{str(cell.column - 14).zfill(2)}") for cell in
             data]
+        # logger.debug(f"Got gel control info: {input_dict['gel_controls']}")
         # NOTE: Get source plate information
         source_plates_section = custom_fields['source_plates']
         ws = xl[source_plates_section['sheet']]
@@ -1854,10 +1861,10 @@ class WastewaterArtic(BasicSubmission):
         """
         input_excel = super().custom_info_writer(input_excel, info, backup)
         if isinstance(info, types.GeneratorType):
-            logger.debug(f"Unpacking info generator.")
+            # logger.debug(f"Unpacking info generator.")
             info = {k: v for k, v in info}
-        logger.debug(f"Info:\n{pformat(info)}")
-        logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
+        # logger.debug(f"Info:\n{pformat(info)}")
+        # logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
         # NOTE: check for source plate information
         if check_key_or_attr(key='source_plates', interest=info, check_none=True):
             source_plates_section = custom_fields['source_plates']
@@ -2016,7 +2023,7 @@ class WastewaterArtic(BasicSubmission):
                 img = zipped.read(input_dict['gel_image_path'])
             with tempfile.TemporaryFile(mode="wb", suffix=".jpg", delete=False) as tmp:
                 tmp.write(img)
-            logger.debug(f"Tempfile: {tmp.name}")
+            # logger.debug(f"Tempfile: {tmp.name}")
         img = InlineImage(tpl_obj, image_descriptor=tmp.name, width=Inches(5.5))  #, width=5.5)#, height=400)
         input_dict['gel_image'] = img
         return input_dict

src/submissions/backend/excel/parser.py

@@ -209,7 +209,7 @@ class InfoParser(object):
         """
         dicto = {}
         # NOTE: This loop parses generic info
-        logger.debug(f"Map: {self.map}")
+        # logger.debug(f"Map: {self.map}")
         for sheet in self.xl.sheetnames:
             ws = self.xl[sheet]
             relevant = []
@@ -590,7 +590,7 @@ class EquipmentParser(object):
         Returns:
             List[dict]: list of equipment
         """
-        logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
+        # logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
         output = []
         # logger.debug(f"Sheets: {sheets}")
         for sheet in self.xl.sheetnames:
@@ -600,17 +600,17 @@ class EquipmentParser(object):
             except (TypeError, KeyError) as e:
                 logger.error(f"Error creating relevant equipment list: {e}")
                 continue
-            logger.debug(f"Relevant equipment: {pformat(relevant)}")
+            # logger.debug(f"Relevant equipment: {pformat(relevant)}")
             previous_asset = ""
             for k, v in relevant.items():
-                logger.debug(f"Checking: {v}")
+                # logger.debug(f"Checking: {v}")
                 asset = ws.cell(v['name']['row'], v['name']['column']).value
                 if not check_not_nan(asset):
                     asset = previous_asset
                 else:
                     previous_asset = asset
                 asset = self.get_asset_number(input=asset)
-                logger.debug(f"asset: {asset}")
+                # logger.debug(f"asset: {asset}")
                 eq = Equipment.query(asset_number=asset)
                 if eq is None:
                     eq = Equipment.query(name=asset)
@@ -621,7 +621,7 @@ class EquipmentParser(object):
                              nickname=eq.nickname))
                 except AttributeError:
                     logger.error(f"Unable to add {eq} to list.")
-                logger.debug(f"Here is the output so far: {pformat(output)}")
+                # logger.debug(f"Here is the output so far: {pformat(output)}")
         return output
 
 
@@ -668,7 +668,7 @@ class TipParser(object):
             except (TypeError, KeyError) as e:
                 logger.error(f"Error creating relevant equipment list: {e}")
                 continue
-            logger.debug(f"Relevant equipment: {pformat(relevant)}")
+            # logger.debug(f"Relevant equipment: {pformat(relevant)}")
             previous_asset = ""
             for k, v in relevant.items():
                 asset = ws.cell(v['name']['row'], v['name']['column']).value
@@ -680,14 +680,14 @@ class TipParser(object):
                     asset = previous_asset
                 else:
                     previous_asset = asset
-                logger.debug(f"asset: {asset}")
+                # logger.debug(f"asset: {asset}")
                 eq = Tips.query(lot=lot, name=asset, limit=1)
                 try:
                     output.append(
                         dict(name=eq.name, role=k, lot=lot))
                 except AttributeError:
                     logger.error(f"Unable to add {eq} to PydTips list.")
-                logger.debug(f"Here is the output so far: {pformat(output)}")
+                # logger.debug(f"Here is the output so far: {pformat(output)}")
         return output
 
 

src/submissions/backend/validators/__init__.py

@@ -103,11 +103,11 @@ class RSLNamer(object):
             regex (str): string to construct pattern
             filename (str): string to be parsed
         """
-        logger.debug(f"Input string to be parsed: {filename}")
+        logger.info(f"Input string to be parsed: {filename}")
         if regex is None:
             regex = BasicSubmission.construct_regex()
         else:
-            logger.debug(f"Incoming regex: {regex}")
+            # logger.debug(f"Incoming regex: {regex}")
             try:
                 regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
             except re.error as e:

src/submissions/backend/validators/pydant.py

@@ -334,15 +334,20 @@ class PydEquipment(BaseModel, extra='ignore'):
             Tuple[Equipment, SubmissionEquipmentAssociation]: SQL objects
         """
         if isinstance(submission, str):
+            logger.info(f"Got string, querying {submission}")
             submission = BasicSubmission.query(rsl_number=submission)
         equipment = Equipment.query(asset_number=self.asset_number)
         if equipment is None:
+            logger.error("No equipment found. Returning None.")
             return
         if submission is not None:
             # NOTE: Need to make sure the same association is not added to the submission
-
-            assoc = SubmissionEquipmentAssociation.query(equipment_id=equipment.id, submission_id=submission.id,
+            try:
+                assoc = SubmissionEquipmentAssociation.query(equipment_id=equipment.id, submission_id=submission.id,
                                                          role=self.role, limit=1)
+            except TypeError as e:
+                logger.error(f"Couldn't get association due to {e}, returning...")
+                return equipment, None
             if assoc is None:
                 assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
                 process = Process.query(name=self.processes[0])
@@ -351,8 +356,10 @@ class PydEquipment(BaseModel, extra='ignore'):
                 assoc.process = process
                 assoc.role = self.role
             else:
+                logger.warning(f"Found already existing association: {assoc}")
                 assoc = None
         else:
+            logger.warning(f"No submission found")
             assoc = None
         return equipment, assoc
 
@@ -608,7 +615,7 @@ class PydSubmission(BaseModel, extra='allow'):
     @field_validator("contact")
     @classmethod
     def get_contact_from_org(cls, value, values):
-        logger.debug(f"Checking on value: {value}")
+        # logger.debug(f"Checking on value: {value}")
         match value:
             case dict():
                 if isinstance(value['value'], tuple):
@@ -621,7 +628,7 @@ class PydSubmission(BaseModel, extra='allow'):
         if check is None:
             org = Organization.query(name=values.data['submitting_lab']['value'])
             contact = org.contacts[0].name
-            logger.debug(f"Pulled: {contact}")
+            # logger.debug(f"Pulled: {contact}")
             if isinstance(contact, tuple):
                 contact = contact[0]
             return dict(value=contact, missing=True)
@@ -758,7 +765,7 @@ class PydSubmission(BaseModel, extra='allow'):
                     for tips in self.tips:
                         if tips is None:
                             continue
-                        logger.debug(f"Converting tips: {tips} to sql.")
+                        # logger.debug(f"Converting tips: {tips} to sql.")
                         try:
                             association = tips.to_sql(submission=instance)
                         except AttributeError: