diff --git a/CHANGELOG.md b/CHANGELOG.md
index aaaa9fc..4866c11 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,8 @@
+## 202406.04
+
+- Adding in tips to Equipment usage.
+- New WastewaterArticAssociation will track previously missed sample info.
+
## 202406.02
- Attached Contact to Submission.
diff --git a/src/submissions/backend/db/models/submissions.py b/src/submissions/backend/db/models/submissions.py
index 33daa01..06c09f8 100644
--- a/src/submissions/backend/db/models/submissions.py
+++ b/src/submissions/backend/db/models/submissions.py
@@ -8,9 +8,9 @@ from getpass import getuser
import logging, uuid, tempfile, re, yaml, base64
from zipfile import ZipFile
from tempfile import TemporaryDirectory
-from operator import attrgetter, itemgetter
+from operator import itemgetter
from pprint import pformat
-from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, Tips, TipRole, SubmissionTipsAssociation
+from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, Tips
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified
@@ -19,14 +19,14 @@ from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityErr
ArgumentError
from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
import pandas as pd
-from openpyxl import Workbook, load_workbook
+from openpyxl import Workbook
from openpyxl.worksheet.worksheet import Worksheet
from openpyxl.drawing.image import Image as OpenpyxlImage
-from tools import check_not_nan, row_map, setup_lookup, jinja_template_loading, rreplace
+from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys
from datetime import datetime, date
from typing import List, Any, Tuple, Literal
from dateutil.parser import parse
-from dateutil.parser import ParserError
+# from dateutil.parser import ParserError
from pathlib import Path
from jinja2.exceptions import TemplateNotFound
from jinja2 import Template
@@ -67,7 +67,7 @@ class BasicSubmission(BaseClass):
String(64)) #: Permanent storage of used cost centre in case organization field changed in the future.
contact = relationship("Contact", back_populates="submissions") #: client org
contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
- name="fk_BS_contact_id")) #: client lab id from _organizations
+ name="fk_BS_contact_id")) #: client lab id from _organizations
submission_sample_associations = relationship(
"SubmissionSampleAssociation",
@@ -126,7 +126,7 @@ class BasicSubmission(BaseClass):
Returns:
List[str]: List of column names
- """
+ """
output = [item.name for item in cls.__table__.columns if isinstance(item.type, JSON)]
if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission":
output += BasicSubmission.jsons()
@@ -139,7 +139,7 @@ class BasicSubmission(BaseClass):
Returns:
List[str]: List of column names
- """
+ """
output = [item.name for item in cls.__table__.columns if isinstance(item.type, TIMESTAMP)]
if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission":
output += BasicSubmission.timestamps()
@@ -198,12 +198,12 @@ class BasicSubmission(BaseClass):
Returns:
SubmissionType: SubmissionType with name equal to this polymorphic identity
- """
+ """
name = cls.__mapper_args__['polymorphic_identity']
return SubmissionType.query(name=name)
@classmethod
- def construct_info_map(cls, mode:Literal["read", "write"]) -> dict:
+ def construct_info_map(cls, mode: Literal["read", "write"]) -> dict:
"""
Method to call submission type's construct info map.
@@ -212,7 +212,7 @@ class BasicSubmission(BaseClass):
Returns:
dict: Map of info locations.
- """
+ """
return cls.get_submission_type().construct_info_map(mode=mode)
@classmethod
@@ -222,9 +222,14 @@ class BasicSubmission(BaseClass):
Returns:
dict: sample location map
- """
+ """
return cls.get_submission_type().construct_sample_map()
+ @classmethod
+ def finalize_details(cls, input_dict: dict) -> dict:
+ del input_dict['id']
+ return input_dict
+
def to_dict(self, full_data: bool = False, backup: bool = False, report: bool = False) -> dict:
"""
Constructs dictionary used in submissions summary
@@ -317,7 +322,7 @@ class BasicSubmission(BaseClass):
try:
contact = self.contact.name
except AttributeError as e:
- logger.error(f"Problem setting contact: {e}")
+ # logger.error(f"Problem setting contact: {e}")
contact = "NA"
try:
contact_phone = self.contact.phone
@@ -372,7 +377,7 @@ class BasicSubmission(BaseClass):
else:
try:
self.run_cost = assoc.constant_cost + (assoc.mutable_cost_column * cols_count_96) + (
- assoc.mutable_cost_sample * int(self.sample_count))
+ assoc.mutable_cost_sample * int(self.sample_count))
except Exception as e:
logger.error(f"Calculation error: {e}")
self.run_cost = round(self.run_cost, 2)
@@ -387,7 +392,8 @@ class BasicSubmission(BaseClass):
output_list = [assoc.to_hitpick() for assoc in self.submission_sample_associations]
return output_list
- def make_plate_map(self, plate_rows: int = 8, plate_columns=12) -> str:
+ @classmethod
+ def make_plate_map(cls, sample_list: list, plate_rows: int = 8, plate_columns=12) -> str:
"""
Constructs an html based plate map for submission details.
@@ -399,17 +405,6 @@ class BasicSubmission(BaseClass):
Returns:
str: html output string.
"""
- # logger.debug("Creating basic hitpick")
- sample_list = self.hitpick_plate()
- # logger.debug("Setting background colours")
- for sample in sample_list:
- if sample['positive']:
- sample['background_color'] = "#f10f07"
- else:
- if "colour" in sample.keys():
- sample['background_color'] = "#69d84f"
- else:
- sample['background_color'] = "#80cbc4"
output_samples = []
# logger.debug("Setting locations.")
for column in range(1, plate_columns + 1):
@@ -434,7 +429,8 @@ class BasicSubmission(BaseClass):
return [item.role for item in self.submission_equipment_associations]
@classmethod
- def submissions_to_df(cls, submission_type: str | None = None, limit: int = 0, chronologic:bool=True) -> pd.DataFrame:
+ def submissions_to_df(cls, submission_type: str | None = None, limit: int = 0,
+ chronologic: bool = True) -> pd.DataFrame:
"""
Convert all submissions to dataframe
@@ -448,7 +444,8 @@ class BasicSubmission(BaseClass):
# logger.debug(f"Querying Type: {submission_type}")
# logger.debug(f"Using limit: {limit}")
# use lookup function to create list of dicts
- subs = [item.to_dict() for item in cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)]
+ subs = [item.to_dict() for item in
+ cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)]
# logger.debug(f"Got {len(subs)} submissions.")
df = pd.DataFrame.from_records(subs)
# logger.debug(f"Column names: {df.columns}")
@@ -456,7 +453,8 @@ class BasicSubmission(BaseClass):
excluded = ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
- 'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact', 'tips']
+ 'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact',
+ 'tips']
for item in excluded:
try:
df = df.drop(item, axis=1)
@@ -1163,6 +1161,7 @@ class BasicSubmission(BaseClass):
writer = pyd.to_writer()
writer.xl.save(filename=fname.with_suffix(".xlsx"))
+
# Below are the custom submission types
class BacterialCulture(BasicSubmission):
@@ -1235,7 +1234,7 @@ class BacterialCulture(BasicSubmission):
new_lot = matched.group()
try:
pos_control_reg = \
- [reg for reg in input_dict['reagents'] if reg['role'] == "Bacterial-Positive Control"][0]
+ [reg for reg in input_dict['reagents'] if reg['role'] == "Bacterial-Positive Control"][0]
except IndexError:
logger.error(f"No positive control reagent listed")
return input_dict
@@ -1397,6 +1396,39 @@ class Wastewater(BasicSubmission):
row = idx.index.to_list()[0]
return row + 1
+ @classmethod
+ def get_details_template(cls, base_dict: dict) -> Tuple[dict, Template]:
+ """
+ Get the details jinja template for the correct class. Extends parent
+
+ Args:
+ base_dict (dict): incoming dictionary of Submission fields
+
+ Returns:
+ Tuple[dict, Template]: (Updated dictionary, Template to be rendered)
+ """
+ base_dict, template = super().get_details_template(base_dict=base_dict)
+ base_dict['excluded'] += ['origin_plate']
+ return base_dict, template
+
+ @classmethod
+ def finalize_details(cls, input_dict: dict) -> dict:
+ input_dict = super().finalize_details(input_dict)
+ dummy_samples = []
+ for item in input_dict['samples']:
+ # logger.debug(f"Sample dict: {item}")
+ thing = item
+ try:
+ thing['row'] = thing['source_row']
+ thing['column'] = thing['source_column']
+ except KeyError:
+ logger.error(f"No row or column for sample: {item['submitter_id']}")
+ continue
+ thing['tooltip'] = f"Sample Name: {thing['name']}\nWell: {thing['sample_location']}"
+ dummy_samples.append(thing)
+ input_dict['origin_plate'] = cls.make_plate_map(sample_list=dummy_samples, plate_rows=4, plate_columns=6)
+ return input_dict
+
def custom_context_events(self) -> dict:
events = super().custom_context_events()
events['Link PCR'] = self.link_pcr
@@ -1479,7 +1511,6 @@ class WastewaterArtic(BasicSubmission):
dict: Updated sample dictionary
"""
input_dict = super().custom_info_parser(input_dict)
- # workbook = load_workbook(xl.io, data_only=True)
ws = xl['Egel results']
data = [ws.cell(row=ii, column=jj) for jj in range(15, 27) for ii in range(10, 18)]
data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
@@ -1994,7 +2025,7 @@ class BasicSample(BaseClass):
return model
@classmethod
- def sql_enforcer(cls, pyd_sample:"PydSample"):
+ def sql_enforcer(cls, pyd_sample: "PydSample"):
return pyd_sample
@classmethod
@@ -2088,7 +2119,7 @@ class BasicSample(BaseClass):
disallowed = ["id"]
if kwargs == {}:
raise ValueError("Need to narrow down query or the first available instance will be returned.")
- sanitized_kwargs = {k:v for k,v in kwargs.items() if k not in disallowed}
+ sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
instance = cls.query(sample_type=sample_type, limit=1, **kwargs)
# logger.debug(f"Retrieved instance: {instance}")
if instance is None:
@@ -2100,11 +2131,11 @@ class BasicSample(BaseClass):
@classmethod
def fuzzy_search(cls,
- # submitter_id: str | None = None,
- sample_type: str | BasicSample | None = None,
- # limit: int = 0,
- **kwargs
- ) -> List[BasicSample]:
+ # submitter_id: str | None = None,
+ sample_type: str | BasicSample | None = None,
+ # limit: int = 0,
+ **kwargs
+ ) -> List[BasicSample]:
match sample_type:
case str():
model = cls.find_polymorphic_subclass(polymorphic_identity=sample_type)
@@ -2130,10 +2161,9 @@ class BasicSample(BaseClass):
def get_searchables(cls):
return [dict(label="Submitter ID", field="submitter_id")]
-
@classmethod
def samples_to_df(cls, sample_type: str | None | BasicSample = None, **kwargs):
- # def samples_to_df(cls, sample_type:str|None|BasicSample=None, searchables:dict={}):
+ # def samples_to_df(cls, sample_type:str|None|BasicSample=None, searchables:dict={}):
logger.debug(f"Checking {sample_type} with type {type(sample_type)}")
match sample_type:
case str():
@@ -2178,6 +2208,7 @@ class BasicSample(BaseClass):
if dlg.exec():
pass
+
# Below are the custom sample types
class WastewaterSample(BasicSample):
@@ -2309,6 +2340,7 @@ class BacterialCultureSample(BasicSample):
# logger.debug(f"Done converting to {self} to dict after {time()-start}")
return sample
+
# Submission to Sample Associations
class SubmissionSampleAssociation(BaseClass):
@@ -2322,7 +2354,7 @@ class SubmissionSampleAssociation(BaseClass):
submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id"), primary_key=True) #: id of associated submission
row = Column(INTEGER, primary_key=True) #: row on the 96 well plate
column = Column(INTEGER, primary_key=True) #: column on the 96 well plate
- submission_rank = Column(INTEGER, nullable=False, default=0) #: Location in sample list
+ submission_rank = Column(INTEGER, nullable=False, default=0) #: Location in sample list
# reference to the Submission object
submission = relationship(BasicSubmission,
@@ -2353,7 +2385,7 @@ class SubmissionSampleAssociation(BaseClass):
else:
self.id = self.__class__.autoincrement_id()
# logger.debug(f"Looking at kwargs: {pformat(kwargs)}")
- for k,v in kwargs.items():
+ for k, v in kwargs.items():
try:
self.__setattr__(k, v)
except AttributeError:
@@ -2405,11 +2437,19 @@ class SubmissionSampleAssociation(BaseClass):
env = jinja_template_loading()
template = env.get_template("tooltip.html")
tooltip_text = template.render(fields=sample)
+ try:
+ control = self.sample.control
+ except AttributeError:
+ control = None
+ if control is not None:
+ background = "rgb(128, 203, 196)"
+ else:
+ background = "rgb(105, 216, 79)"
try:
tooltip_text += sample['tooltip']
except KeyError:
pass
- sample.update(dict(Name=self.sample.submitter_id[:10], tooltip=tooltip_text))
+ sample.update(dict(Name=self.sample.submitter_id[:10], tooltip=tooltip_text, background_color=background))
return sample
@classmethod
@@ -2524,7 +2564,7 @@ class SubmissionSampleAssociation(BaseClass):
association_type: str = "Basic Association",
submission: BasicSubmission | str | None = None,
sample: BasicSample | str | None = None,
- id:int|None=None,
+ id: int | None = None,
**kwargs) -> SubmissionSampleAssociation:
"""
Queries for an association, if none exists creates a new one.
@@ -2601,6 +2641,11 @@ class WastewaterAssociation(SubmissionSampleAssociation):
sample = super().to_sub_dict()
sample['ct'] = f"({self.ct_n1}, {self.ct_n2})"
+ try:
+ sample['source_row'] = row_keys[self.sample.sample_location[0]]
+ sample['source_column'] = int(self.sample.sample_location[1:])
+ except (TypeError, AttributeError) as e:
+ logger.error(f"Couldn't set sources for {self.sample.rsl_number}. Looks like there isn't data.")
try:
sample['positive'] = any(["positive" in item for item in [self.n1_status, self.n2_status]])
except (TypeError, AttributeError) as e:
@@ -2615,6 +2660,18 @@ class WastewaterAssociation(SubmissionSampleAssociation):
dict: dictionary of sample id, row and column in elution plate
"""
sample = super().to_hitpick()
+ try:
+ scaler = max([self.ct_n1, self.ct_n2])
+ except TypeError:
+ scaler = 0.0
+ if scaler == 0.0:
+ scaler = 45
+ bg = (45 - scaler) * 17
+ red = min([128 + bg, 255])
+ grn = max([255 - bg, 0])
+ blu = 128
+ rgb = f"rgb({red}, {grn}, {blu})"
+ sample['background_color'] = rgb
try:
sample[
'tooltip'] += f"
- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})
- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
@@ -2682,5 +2739,3 @@ class WastewaterArticAssociation(SubmissionSampleAssociation):
except ValueError as e:
logger.error(f"Problem incrementing id: {e}")
return 1
-
-
diff --git a/src/submissions/frontend/widgets/submission_details.py b/src/submissions/frontend/widgets/submission_details.py
index 8518f9f..adb90fe 100644
--- a/src/submissions/frontend/widgets/submission_details.py
+++ b/src/submissions/frontend/widgets/submission_details.py
@@ -86,10 +86,11 @@ class SubmissionDetails(QDialog):
self.base_dict = submission.to_dict(full_data=True)
# logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
# NOTE: don't want id
- del self.base_dict['id']
+ self.base_dict = submission.finalize_details(self.base_dict)
+ # del self.base_dict['id']
# logger.debug(f"Creating barcode.")
# logger.debug(f"Making platemap...")
- self.base_dict['platemap'] = submission.make_plate_map()
+ self.base_dict['platemap'] = BasicSubmission.make_plate_map(sample_list=submission.hitpick_plate())
self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
self.webview.setHtml(self.html)
diff --git a/src/submissions/templates/wastewater_details.html b/src/submissions/templates/wastewater_details.html
new file mode 100644
index 0000000..35e1f2e
--- /dev/null
+++ b/src/submissions/templates/wastewater_details.html
@@ -0,0 +1,18 @@
+{% extends "basicsubmission_details.html" %}
+
+
+ {% block head %}
+ {{ super() }}
+ {% endblock %}
+
+
+
+ {% block body %}
+ {{ super() }}
+ {% if sub['origin_plate'] %}
+
+ 24 Well Plate:
+ {{ sub['origin_plate'] }}
+ {% endif %}
+ {% endblock %}
+