Bug fixes.
This commit is contained in:
lwark
@@ -11,7 +11,7 @@ from sqlalchemy.ext.associationproxy import association_proxy
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from datetime import date
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import logging, re
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from tools import check_authorization, setup_lookup, Report, Result
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from typing import List, Literal, Generator
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from typing import List, Literal, Generator, Any
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from pandas import ExcelFile
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from pathlib import Path
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from . import Base, BaseClass, Organization
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@@ -261,7 +261,7 @@ class KitType(BaseClass):
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base_dict['reagent roles'] = []
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base_dict['equipment roles'] = []
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for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
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logger.debug(f"Value: {v}")
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# logger.debug(f"Value: {v}")
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try:
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assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0]
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except IndexError as e:
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@@ -275,10 +275,10 @@ class KitType(BaseClass):
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except IndexError:
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continue
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for kk, vv in assoc.to_export_dict(kit_type=self).items():
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logger.debug(f"{kk}:{vv}")
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# logger.debug(f"{kk}:{vv}")
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v[kk] = vv
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base_dict['equipment roles'].append(v)
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logger.debug(f"KT returning {base_dict}")
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# logger.debug(f"KT returning {base_dict}")
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return base_dict
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@@ -1492,6 +1492,16 @@ class SubmissionEquipmentAssociation(BaseClass):
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processes=[process], role=self.role, nickname=self.equipment.nickname)
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return output
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@classmethod
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@setup_lookup
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def query(cls, equipment_id:int, submission_id:int, role:str, limit:int=0, **kwargs) -> Any | List[Any]:
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query: Query = cls.__database_session__.query(cls)
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query = query.filter(cls.equipment_id==equipment_id)
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query = query.filter(cls.submission_id==submission_id)
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query = query.filter(cls.role==role)
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return cls.execute_query(query=query, limit=limit, **kwargs)
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class SubmissionTypeEquipmentRoleAssociation(BaseClass):
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"""
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@@ -295,8 +295,10 @@ class BasicSubmission(BaseClass):
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if k == 'info':
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continue
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if not any([item['role'] == k for item in reagents]):
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# expiry = date(year=1970, month=1, day=1)
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expiry = "NA"
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reagents.append(
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dict(role=k, name="Not Applicable", lot="NA", expiry=date(year=1970, month=1, day=1),
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dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
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missing=True))
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except Exception as e:
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logger.error(f"We got an error retrieving reagents: {e}")
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@@ -507,10 +509,10 @@ class BasicSubmission(BaseClass):
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sample, _ = sample.to_sql(submission=self)
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return
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case "reagents":
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logger.debug(f"Reagents coming into SQL: {value}")
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# logger.debug(f"Reagents coming into SQL: {value}")
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field_value = [reagent['value'].to_sql()[0] if isinstance(reagent, dict) else reagent.to_sql()[0] for
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reagent in value]
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logger.debug(f"Reagents coming out of SQL: {field_value}")
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# logger.debug(f"Reagents coming out of SQL: {field_value}")
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case "submission_type":
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field_value = SubmissionType.query(name=value)
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case "sample_count":
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@@ -521,7 +523,7 @@ class BasicSubmission(BaseClass):
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case "ctx" | "csv" | "filepath" | "equipment":
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return
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case item if item in self.jsons():
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logger.debug(f"Setting JSON attribute.")
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# logger.debug(f"Setting JSON attribute.")
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existing = self.__getattribute__(key)
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if value is None or value in ['', 'null']:
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logger.error(f"No value given, not setting.")
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@@ -617,7 +619,7 @@ class BasicSubmission(BaseClass):
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Args:
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original (bool, optional): Is this the first save. Defaults to True.
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"""
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logger.debug("Saving submission.")
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# logger.debug("Saving submission.")
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if original:
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self.uploaded_by = getuser()
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super().save()
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@@ -1177,9 +1179,12 @@ class BasicSubmission(BaseClass):
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# logger.debug(f"Processing: {equip}")
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_, assoc = equip.toSQL(submission=self)
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# logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}")
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assoc.save()
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try:
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assoc.save()
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except AttributeError as e:
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logger.error(f"Couldn't save association with {equip} due to {e}")
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if equip.tips:
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logger.debug("We have tips in this equipment")
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# logger.debug("We have tips in this equipment")
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for tips in equip.tips:
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tassoc = tips.to_sql(submission=self)
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tassoc.save()
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@@ -1308,7 +1313,7 @@ class BacterialCulture(BasicSubmission):
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idx = df[df[0] == sample.well]
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if idx.empty:
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new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
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logger.debug(f"Checking: {new}")
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# logger.debug(f"Checking: {new}")
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idx = df[df[0] == new]
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# logger.debug(f"Here is the row: {idx}")
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row = idx.index.to_list()[0]
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@@ -1366,7 +1371,7 @@ class Wastewater(BasicSubmission):
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dict: Updated sample dictionary
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"""
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input_dict = super().custom_info_parser(input_dict)
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logger.debug(f"Input dict: {pformat(input_dict)}")
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# logger.debug(f"Input dict: {pformat(input_dict)}")
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if xl is not None:
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try:
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input_dict['csv'] = xl["Copy to import file"]
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@@ -1636,12 +1641,14 @@ class WastewaterArtic(BasicSubmission):
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input_dict = super().custom_info_parser(input_dict)
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egel_section = custom_fields['egel_results']
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ws = xl[egel_section['sheet']]
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data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']) for
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ii in range(egel_section['start_row'], egel_section['end_row'])]
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data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']+1) for
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ii in range(egel_section['start_row'], egel_section['end_row']+1)]
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data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
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# logger.debug(f"Got gel control map: {data}")
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input_dict['gel_controls'] = [
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dict(sample_id=cell.value, location=f"{row_map[cell.row - 9]}{str(cell.column - 14).zfill(2)}") for cell in
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data]
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# logger.debug(f"Got gel control info: {input_dict['gel_controls']}")
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# NOTE: Get source plate information
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source_plates_section = custom_fields['source_plates']
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ws = xl[source_plates_section['sheet']]
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@@ -1854,10 +1861,10 @@ class WastewaterArtic(BasicSubmission):
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"""
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input_excel = super().custom_info_writer(input_excel, info, backup)
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if isinstance(info, types.GeneratorType):
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logger.debug(f"Unpacking info generator.")
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# logger.debug(f"Unpacking info generator.")
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info = {k: v for k, v in info}
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logger.debug(f"Info:\n{pformat(info)}")
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logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
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# logger.debug(f"Info:\n{pformat(info)}")
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# logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
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# NOTE: check for source plate information
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if check_key_or_attr(key='source_plates', interest=info, check_none=True):
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source_plates_section = custom_fields['source_plates']
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@@ -2016,7 +2023,7 @@ class WastewaterArtic(BasicSubmission):
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img = zipped.read(input_dict['gel_image_path'])
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with tempfile.TemporaryFile(mode="wb", suffix=".jpg", delete=False) as tmp:
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tmp.write(img)
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logger.debug(f"Tempfile: {tmp.name}")
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# logger.debug(f"Tempfile: {tmp.name}")
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img = InlineImage(tpl_obj, image_descriptor=tmp.name, width=Inches(5.5)) #, width=5.5)#, height=400)
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input_dict['gel_image'] = img
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return input_dict
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