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lwark
2025-07-08 12:17:32 -05:00
parent 0472afd9a5
commit 432854e76f
12 changed files with 141 additions and 129 deletions
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25
src/submissions/backend/db/models/__init__.py
View File

@@ -18,7 +18,10 @@ from sqlalchemy.exc import ArgumentError
from typing import Any, List, ClassVar
from pathlib import Path
from sqlalchemy.orm.relationships import _RelationshipDeclared
from frontend import select_save_file
from tools import report_result, list_sort_dict
from backend.excel import writers
# NOTE: Load testing environment
if 'pytest' in sys.modules:
@@ -241,6 +244,7 @@ class BaseClass(Base):
allowed = [k for k, v in cls.__dict__.items() if isinstance(v, InstrumentedAttribute) or isinstance(v, hybrid_property)]
# and not isinstance(v.property, _RelationshipDeclared)]
sanitized_kwargs = {k: v for k, v in kwargs.items() if k in allowed}
outside_kwargs = {k: v for k, v in kwargs.items() if k not in allowed}
logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
instance = cls.query(**sanitized_kwargs)
if not instance or isinstance(instance, list):
@@ -258,6 +262,7 @@ class BaseClass(Base):
setattr(instance, k, v.to_sql())
else:
logger.error(f"Could not set {k} due to {e}")
instance._misc_info.update(outside_kwargs)
logger.info(f"Instance from query or create: {instance}, new: {new}")
return instance, new
@@ -309,10 +314,16 @@ class BaseClass(Base):
check = False
if check:
logger.debug("Got uselist")
try:
query = query.filter(attr.contains(v))
except ArgumentError:
continue
else:
logger.debug("Single item.")
try:
query = query.filter(attr == v)
except ArgumentError:
continue
if k in singles:
logger.warning(f"{k} is in singles. Returning only one value.")
limit = 1
@@ -496,7 +507,10 @@ class BaseClass(Base):
value = json.dumps(value)
except TypeError:
value = str(value)
try:
self._misc_info.update({key: value})
except AttributeError:
self._misc_info = {key: value}
return
try:
field_type = getattr(self.__class__, key)
@@ -623,6 +637,17 @@ class BaseClass(Base):
if dlg.exec():
pass
def export(self, obj, output_filepath: str|Path|None=None):
if not hasattr(self, "template_file"):
logger.error(f"Export not implemented for {self.__class__.__name__}")
return
pyd = self.to_pydantic()
if not output_filepath:
output_filepath = select_save_file(obj=obj, default_name=pyd.construct_filename(), extension="xlsx")
Writer = getattr(writers, f"{self.__class__.__name__}Writer")
writer = Writer(output_filepath=output_filepath, pydant_obj=pyd, range_dict=self.range_dict)
workbook = writer
class LogMixin(Base):
tracking_exclusion: ClassVar = ['artic_technician', 'clientsubmissionsampleassociation',

30
src/submissions/backend/db/models/submissions.py
View File

@@ -15,6 +15,8 @@ from operator import itemgetter
from pprint import pformat
from pandas import DataFrame
from sqlalchemy.ext.hybrid import hybrid_property
from frontend import select_save_file
from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin, Procedure, kittype_procedure
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func, Table, Sequence
from sqlalchemy.orm import relationship, validates, Query
@@ -158,6 +160,14 @@ class ClientSubmission(BaseClass, LogMixin):
offset = None
return cls.execute_query(query=query, limit=limit, offset=offset, **kwargs)
@property
def template_file(self):
return self.submissiontype.template_file
@property
def range_dict(self):
return self.submissiontype.info_map
@classmethod
def submissions_to_df(cls, submissiontype: str | None = None, limit: int = 0,
chronologic: bool = True, page: int = 1, page_size: int = 250) -> pd.DataFrame:
@@ -318,12 +328,12 @@ class ClientSubmission(BaseClass, LogMixin):
logger.debug(f"Sample: {sample.id}")
if sample not in run.sample:
assoc = run.add_sample(sample)
assoc.save()
# assoc.save()
run.save()
else:
logger.warning("Run cancelled.")
obj.set_data()
def edit(self, obj):
logger.debug("Edit")
@@ -352,6 +362,9 @@ class ClientSubmission(BaseClass, LogMixin):
output['expanded'] = ["clientlab", "contact", "submissiontype"]
return output
def to_pydantic(self, filepath: Path|str|None=None, **kwargs):
output = super().to_pydantic(filepath=filepath, **kwargs)
return output
class Run(BaseClass, LogMixin):
"""
@@ -1266,6 +1279,15 @@ class Run(BaseClass, LogMixin):
self.set_attribute(key='comment', value=comment)
self.save(original=False)
def export(self, obj, output_filepath: str|Path|None=None):
clientsubmission_pyd = self.clientsubmission.to_pydantic()
if not output_filepath:
output_filepath = select_save_file(obj=obj, default_name=clientsubmission_pyd.construct_filename(), extension="xlsx")
Writer = getattr(writers, "ClientSubmissionWriter")
writer = Writer(output_filepath=output_filepath, pydant_obj=pyd, range_dict=self.range_dict)
workbook = writer.
def backup(self, obj=None, fname: Path | None = None, full_backup: bool = False):
"""
Exports xlsx info files for this instance.
@@ -1890,8 +1912,8 @@ class RunSampleAssociation(BaseClass):
# id = Column(INTEGER, unique=True, nullable=False) #: id to be used for inheriting purposes
sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True) #: id of associated sample
run_id = Column(INTEGER, ForeignKey("_run.id"), primary_key=True) #: id of associated procedure
row = Column(INTEGER) #: row on the 96 well plate
column = Column(INTEGER) #: column on the 96 well plate
# row = Column(INTEGER) #: row on the 96 well plate
# column = Column(INTEGER) #: column on the 96 well plate
# misc_info = Column(JSON)
# NOTE: reference to the Submission object

11
src/submissions/backend/excel/parsers/__init__.py
View File

@@ -5,6 +5,8 @@ from __future__ import annotations
import logging, re
from pathlib import Path
from typing import Generator, Tuple, TYPE_CHECKING
from openpyxl.reader.excel import load_workbook
from pandas import DataFrame
from backend.validators import pydant
if TYPE_CHECKING:
@@ -78,8 +80,6 @@ class DefaultKEYVALUEParser(DefaultParser):
sheet="Sample List"
)]
@property
def parsed_info(self) -> Generator[Tuple, None, None]:
for item in self.range_dict:
@@ -91,7 +91,10 @@ class DefaultKEYVALUEParser(DefaultParser):
key = re.sub(r"\(.*\)", "", key)
key = key.lower().replace(":", "").strip().replace(" ", "_")
value = item['worksheet'].cell(row, item['value_column']).value
value = dict(value=value, missing=False if value else True)
missing = False if value else True
location_map = dict(row=row, key_column=item['key_column'], value_column=item['value_column'], sheet=item['sheet'])
value = dict(value=value, location=location_map, missing=missing)
logger.debug(f"Yieldings {value} for {key}")
yield key, value
@@ -126,5 +129,5 @@ class DefaultTABLEParser(DefaultParser):
def to_pydantic(self, **kwargs):
return [self._pyd_object(**output) for output in self.parsed_info]
from .clientsubmission_parser import *
from .clientsubmission_parser import ClientSubmissionSampleParser, ClientSubmissionInfoParser
from backend.excel.parsers.results_parsers.pcr_results_parser import PCRInfoParser, PCRSampleParser

2
src/submissions/backend/excel/parsers/clientsubmission_parser.py
View File

@@ -96,8 +96,6 @@ class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
# TODO: check if run with name already exists
add_run = QuestionAsker(title="Add Run?", message="We've detected a sheet corresponding to an associated procedure type.\nWould you like to add a new run?")
if add_run.accepted:
# NOTE: recruit parser.
try:
manager = getattr(procedure_managers, name)

72
src/submissions/backend/validators/pydant.py
View File

@@ -27,6 +27,7 @@ logger = logging.getLogger(f"procedure.{__name__}")
class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
_sql_object: ClassVar = None
# _misc_info: dict|None = None
@model_validator(mode="before")
@classmethod
@@ -67,6 +68,10 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
def __init__(self, **data):
# NOTE: Grab the sql model for validation purposes.
self.__class__._sql_object = getattr(models, self.__class__.__name__.replace("Pyd", ""))
# try:
# self.template_file = self.__class__._sql_object.template_file
# except AttributeError:
# pass
super().__init__(**data)
def filter_field(self, key: str) -> Any:
@@ -105,6 +110,12 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
output = {k: getattr(self, k) for k in fields}
else:
output = {k: self.filter_field(k) for k in fields}
if hasattr(self, "misc_info") and "info_placement" in self.misc_info:
for k, v in output.items():
try:
output[k]['location'] = [item['location'] for item in self.misc_info['info_placement'] if item['name'] == k]
except (TypeError, KeyError):
continue
return output
def to_sql(self):
@@ -301,6 +312,7 @@ class PydSample(PydBaseClass):
sql._misc_info["submission_rank"] = self.submission_rank
return sql
class PydTips(BaseModel):
name: str
lot: str | None = Field(default=None)
@@ -1662,7 +1674,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
class PydClientSubmission(PydBaseClass):
# sql_object: ClassVar = ClientSubmission
filepath: Path
filepath: Path | None = Field(default=None)
submissiontype: dict | None
submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
clientlab: dict | None
@@ -1673,6 +1685,39 @@ class PydClientSubmission(PydBaseClass):
contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
@field_validator("submitted_date", mode="before")
@classmethod
def enforce_submitted_date(cls, value):
match value:
case str():
value = dict(value=datetime.strptime(value, "%Y-%m-%d %H:%M:%S"), missing=False)
case date() | datetime():
value = dict(value=value, missing=False)
case _:
pass
return value
@field_validator("submitter_plate_id", mode="before")
@classmethod
def enforce_submitter_plate_id(cls, value):
if isinstance(value, str):
value = dict(value=value, missing=False)
return value
@field_validator("submission_category", mode="before")
@classmethod
def enforce_submission_category_id(cls, value):
if isinstance(value, str):
value = dict(value=value, missing=False)
return value
@field_validator("sample_count", mode="before")
@classmethod
def enforce_sample_count(cls, value):
if isinstance(value, str) or isinstance(value, int):
value = dict(value=value, missing=False)
return value
@field_validator("sample_count")
@classmethod
def enforce_integer(cls, value):
@@ -1700,7 +1745,7 @@ class PydClientSubmission(PydBaseClass):
except TypeError:
check = True
if check:
return dict(value=date.today(), missing=True)
value.update(dict(value=date.today(), missing=True))
else:
match value['value']:
case str():
@@ -1735,6 +1780,29 @@ class PydClientSubmission(PydBaseClass):
from frontend.widgets.submission_widget import ClientSubmissionFormWidget
return ClientSubmissionFormWidget(parent=parent, clientsubmission=self, samples=samples, disable=disable)
def to_sql(self):
sql = super().to_sql()
if "info_placement" not in sql._misc_info:
sql._misc_info['info_placement'] = []
info_placement = []
for k in list(self.model_fields.keys()) + list(self.model_extra.keys()):
attribute = getattr(self, k)
match k:
case "filepath":
sql._misc_info[k] = attribute.__str__()
continue
case _:
pass
logger.debug(f"Setting {k} to {attribute}")
if isinstance(attribute, dict):
if "location" in attribute:
info_placement.append(dict(name=k, location=attribute['location']))
else:
info_placement.append(dict(name=k, location=None))
max_row = max([value['location']['row'] for value in info_placement if value])
sql._misc_info['info_placement'] = info_placement
return sql
class PydResults(PydBaseClass, arbitrary_types_allowed=True):
results: dict = Field(default={})

4
src/submissions/frontend/widgets/sample_checker.py
View File

@@ -35,8 +35,8 @@ class SampleChecker(QDialog):
self.channel = QWebChannel()
self.channel.registerObject('backend', self)
# NOTE: Used to maintain javascript functions.
template = env.get_template("sample_checker.html")
template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
# template = env.get_template("sample_checker.html")
# template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
# with open(template_path.joinpath("css", "styles.css"), "r") as f:
# css = [f.read()]
try:

8
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -472,6 +472,10 @@ class SubmissionFormWidget(QWidget):
self.missing: bool = value['missing']
except (TypeError, KeyError):
self.missing: bool = True
try:
self.location: dict|None = value['location']
except (TypeError, KeyError):
self.location: dict|None = None
if self.input is not None:
layout.addWidget(self.label)
layout.addWidget(self.input)
@@ -501,7 +505,7 @@ class SubmissionFormWidget(QWidget):
value = self.input.date().toPyDate()
case _:
return None, None
return self.input.objectName(), dict(value=value, missing=self.missing)
return self.input.objectName(), dict(value=value, missing=self.missing, location=self.location)
def set_widget(self, parent: QWidget, key: str, value: dict,
submission_type: str | SubmissionType | None = None,
@@ -518,6 +522,7 @@ class SubmissionFormWidget(QWidget):
Returns:
QWidget: Form object
"""
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
if sub_obj is None:
@@ -843,6 +848,7 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
value = getattr(self, item)
info[item] = value
for k, v in info.items():
logger.debug(f"Setting pyd {k} to {v}")
self.pyd.__setattr__(k, v)
report.add_result(report)
return report

28
src/submissions/templates/bacterialculture_details.html
View File

@@ -1,28 +0,0 @@
{% extends "basicsubmission_details.html" %}
<head>
{% block head %}
{{ super() }}
{% endblock %}
</head>
<body>
{% block body %}
{{ super() }}
{% if sub['controls'] %}
<h3><u>Attached Controls:</u></h3>
{% for item in sub['controls'] %}
<p>&nbsp;&nbsp;&nbsp;<b>{{ item['name'] }}:</b> {{ item['type'] }} (Targets: {{ item['targets'] }})</p>
{% if item['kraken'] %}
<p>&nbsp;&nbsp;&nbsp;{{ item['name'] }} Top 10 Kraken Results:</p>
<p>{% for genera in item['kraken'] %}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{{ genera['name'] }}: {{ genera['kraken_count'] }} ({{ genera['kraken_percent'] }})<br>
{% endfor %}</p>
{% endif %}
{% endfor %}
{% endif %}
{% endblock %}
{% block signing_button %}
{{ super() }}
{% endblock %}
</body>

4
src/submissions/templates/equipment_details.html
View File

@@ -10,12 +10,8 @@
<h2><u>Equipment Details for {{ equipment['name'] }}</u></h2>
{{ super() }}
<p>{% for key, value in equipment.items() if key not in equipment['excluded'] %}
<!-- &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{% if permission and key in reagent['editable']%}<input type={% if key=='expiry' %}"date"{% else %}"text"{% endif %} id="{{ key }}" name="{{ key }}" value="{{ value }}">{% else %}{{ value }}{% endif %}<br>-->
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
{% endfor %}</p>
<!-- {% if permission %}-->
<!-- <button type="button" id="save_btn">Save</button>-->
<!-- {% endif %}-->
{% if equipment['submissions'] %}<h2>Submissions:</h2>
{% for submission in equipment['submissions'] %}
<p><b><a class="data-link" id="{{ submission['plate'] }}">{{ submission['plate'] }}:</a></b> <a class="data-link process" id="{{ submission['process'] }}">{{ submission['process'] }}</a></p>

2
src/submissions/templates/support/tooltip.html
View File

@@ -1,4 +1,4 @@
Sample name: {{ fields['submitter_id'] }}<br>
{% if fields['organism'] %}Organism: {{ fields['organism'] }}<br>{% endif %}
{% if fields['concentration'] %}Concentration: {{ fields['concentration'] }}<br>{% endif %}
Well: {{ fields['well'] }}<!--{{ fields['column'] }}-->
Well: {{ fields['well'] }}

37
src/submissions/templates/wastewater_details.html
View File

@@ -1,37 +0,0 @@
{% extends "basicsubmission_details.html" %}
<head>
{% block head %}
{{ super() }}
{% endblock %}
</head>
<body>
{% block body %}
{{ super() }}
{% if sub['pcr_info'] %}
{% for entry in sub['pcr_info'] %}
{% if 'comment' not in entry.keys() %}
<h3><u>qPCR Momentum Status:</u></h3>
{% else %}
<h3><u>qPCR Status:</u></h3>
{% endif %}
<p>{% for key, value in entry.items() if key != 'imported_by'%}
{% if "column" in key %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}uL<br>
{% else %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}<br>
{% endif %}
{% endfor %}</p>
{% endfor %}
{% endif %}
{% if sub['origin_plate'] %}
<br/>
<h3><u>24 Well Plate:</u></h3>
{{ sub['origin_plate'] }}
{% endif %}
{% endblock %}
{% block signing_button %}
{{ super() }}
{% endblock %}
</body>

41
src/submissions/templates/wastewaterartic_details.html
View File

@@ -1,41 +0,0 @@
{% extends "basicsubmission_details.html" %}
<head>
{% block head %}
{{ super() }}
{% endblock %}
</head>
<body>
{% block body %}
{{ super() }}
{% if sub['gel_info'] %}
<br/>
<h3><u>Gel Box:</u></h3>
{% if sub['gel_image_actual'] %}
<br/>
<img align='left' height="400px" width="600px" src="data:image/jpeg;base64,{{ sub['gel_image_actual'] | safe }}">
{% endif %}
<br/>
<table style="width:100%; border: 1px solid black; border-collapse: collapse;">
<tr>
{% for header in sub['headers'] %}
<th>{{ header }}</th>
{% endfor %}
</tr>
{% for field in sub['gel_info'] %}
<tr>
<td>{{ field['name'] }}</td>
{% for item in field['values'] %}
<td>{{ item['value'] }}</td>
{% endfor %}
</tr>
{% endfor %}
</table>
<br/>
{% endif %}
{% endblock %}
{% block signing_button %}
{{ super() }}
{% endblock %}
</body>