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added kraken data to details.

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This commit is contained in:
Landon Wark
2023-02-06 13:39:35 -06:00
parent 7fb5bb12f3
commit 963ac7d4a4
11 changed files with 177 additions and 24 deletions
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32
alembic/versions/785bb1140878_added_user_tracking.py Normal file
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@@ -0,0 +1,32 @@
"""added user tracking
Revision ID: 785bb1140878
Revises: 178203610c3b
Create Date: 2023-02-06 09:54:20.371117
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '785bb1140878'
down_revision = '178203610c3b'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_submissions', schema=None) as batch_op:
batch_op.add_column(sa.Column('uploaded_by', sa.String(length=32), nullable=True))
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_submissions', schema=None) as batch_op:
batch_op.drop_column('uploaded_by')
# ### end Alembic commands ###

2
src/submissions/__init__.py
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@@ -1,4 +1,4 @@
# __init__.py
# Version of the realpython-reader package
__version__ = "1.2.1"
__version__ = "1.2.2"

6
src/submissions/backend/db/__init__.py
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@@ -341,6 +341,12 @@ def submissions_to_df(ctx:dict, type:str|None=None) -> pd.DataFrame:
# pass to lookup function
subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, type=type)]
df = pd.DataFrame.from_records(subs)
# logger.debug(f"Pre: {df['Technician']}")
try:
df = df.drop("controls", axis=1)
except:
logger.warning(f"Couldn't drop 'controls' column from submissionsheet df.")
# logger.debug(f"Post: {df['Technician']}")
return df

26
src/submissions/backend/db/models/controls.py
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@@ -1,6 +1,11 @@
from . import Base
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey
from sqlalchemy.orm import relationship
import logging
from operator import itemgetter
import json
logger = logging.getLogger(f"submissions.{__name__}")
class ControlType(Base):
"""
@@ -35,3 +40,24 @@ class Control(Base):
submission_id = Column(INTEGER, ForeignKey("_submissions.id")) #: parent submission id
submission = relationship("BacterialCulture", back_populates="controls", foreign_keys=[submission_id]) #: parent submission
def to_sub_dict(self):
kraken = json.loads(self.kraken)
kraken_cnt_total = sum([kraken[item]['kraken_count'] for item in kraken])
new_kraken = []
for item in kraken:
kraken_percent = kraken[item]['kraken_count'] / kraken_cnt_total
new_kraken.append({'name': item, 'kraken_count':kraken[item]['kraken_count'], 'kraken_percent':"{0:.0%}".format(kraken_percent)})
new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)
if self.controltype.targets == []:
targets = ["None"]
else:
targets = self.controltype.targets
output = {
"name" : self.name,
"type" : self.controltype.name,
"targets" : " ,".join(targets),
"kraken" : new_kraken[0:5]
}
return output

13
src/submissions/backend/db/models/submissions.py
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@@ -2,6 +2,9 @@ from . import Base
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT
from sqlalchemy.orm import relationship
from datetime import datetime as dt
import logging
logger = logging.getLogger(f"submissions.{__name__}")
# table containing reagents/submission relationships
reagents_submissions = Table("_reagents_submissions", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("submission_id", INTEGER, ForeignKey("_submissions.id")))
@@ -28,6 +31,7 @@ class BasicSubmission(Base):
reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
extraction_info = Column(JSON) #: unstructured output from the extraction table logger.
run_cost = Column(FLOAT(2))
uploaded_by = Column(String(32))
__mapper_args__ = {
"polymorphic_identity": "basic_submission",
@@ -77,6 +81,7 @@ class BasicSubmission(Base):
"Technician": self.technician,
"Cost": self.run_cost,
}
logger.debug(f"{self.rsl_plate_num} technician: {output['Technician']}")
return output
@@ -107,6 +112,7 @@ class BasicSubmission(Base):
# cost = self.extraction_kit.cost_per_run
# except AttributeError:
# cost = None
output = {
"id": self.id,
"Plate Number": self.rsl_plate_num,
@@ -131,6 +137,13 @@ class BacterialCulture(BasicSubmission):
samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
# bc_sample_id = Column(INTEGER, ForeignKey("_bc_samples.id", ondelete="SET NULL", name="fk_BC_sample_id"))
__mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"}
def to_dict(self) -> dict:
output = super().to_dict()
output['controls'] = [item.to_sub_dict() for item in self.controls]
# logger.debug(f"{self.rsl_plate_num} technician: {output}")
return output
class Wastewater(BasicSubmission):

2
src/submissions/backend/excel/reports.py
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@@ -165,7 +165,7 @@ def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -
"""
df = DataFrame.from_records(input)
safe = ['name', 'submitted_date', 'genus', 'target']
logger.debug(df)
# logger.debug(df)
for column in df.columns:
if "percent" in column:
count_col = [item for item in df.columns if "count" in item][0]

20
src/submissions/frontend/__init__.py
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@@ -35,6 +35,7 @@ import numpy
from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder, ControlsDatePicker, OverwriteSubQuestion
import logging
import difflib
from getpass import getuser
from datetime import date
from frontend.visualizations.charts import create_charts
@@ -65,7 +66,7 @@ class App(QMainWindow):
self._createMenuBar()
self._createToolBar()
self._connectActions()
self.controls_getter()
self._controls_getter()
self.show()
@@ -109,10 +110,10 @@ class App(QMainWindow):
self.addReagentAction.triggered.connect(self.add_reagent)
self.generateReportAction.triggered.connect(self.generateReport)
self.addKitAction.triggered.connect(self.add_kit)
self.table_widget.control_typer.currentIndexChanged.connect(self.controls_getter)
self.table_widget.mode_typer.currentIndexChanged.connect(self.controls_getter)
self.table_widget.datepicker.start_date.dateChanged.connect(self.controls_getter)
self.table_widget.datepicker.end_date.dateChanged.connect(self.controls_getter)
self.table_widget.control_typer.currentIndexChanged.connect(self._controls_getter)
self.table_widget.mode_typer.currentIndexChanged.connect(self._controls_getter)
self.table_widget.datepicker.start_date.dateChanged.connect(self._controls_getter)
self.table_widget.datepicker.end_date.dateChanged.connect(self._controls_getter)
def importSubmission(self):
@@ -268,6 +269,7 @@ class App(QMainWindow):
# logger.debug(info)
# move samples into preliminary submission dict
info['samples'] = self.samples
info['uploaded_by'] = getuser()
# construct submission object
logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
base_submission, output = construct_submission_info(ctx=self.ctx, info_dict=info)
@@ -445,7 +447,7 @@ class App(QMainWindow):
def controls_getter(self):
def _controls_getter(self):
"""
Lookup controls from database and send to chartmaker
"""
@@ -476,14 +478,14 @@ class App(QMainWindow):
with QSignalBlocker(self.table_widget.sub_typer) as blocker:
self.table_widget.sub_typer.addItems(sub_types)
self.table_widget.sub_typer.setEnabled(True)
self.table_widget.sub_typer.currentTextChanged.connect(self.chart_maker)
self.table_widget.sub_typer.currentTextChanged.connect(self._chart_maker)
else:
self.table_widget.sub_typer.clear()
self.table_widget.sub_typer.setEnabled(False)
self.chart_maker()
self._chart_maker()
def chart_maker(self):
def _chart_maker(self):
"""
Creates plotly charts for webview
"""

52
src/submissions/frontend/custom_widgets/__init__.py
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@@ -5,14 +5,14 @@ from PyQt6.QtWidgets import (
QTextEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox,
QScrollBar, QScrollArea, QHBoxLayout,
QMessageBox
QMessageBox, QFileDialog, QToolBar
)
from PyQt6.QtCore import Qt, QDate, QAbstractTableModel, QSize
from PyQt6.QtGui import QFontMetrics
from PyQt6.QtGui import QFontMetrics, QAction
from backend.db import get_all_reagenttype_names, submissions_to_df, lookup_submission_by_id, lookup_all_sample_types, create_kit_from_yaml
from jinja2 import Environment, FileSystemLoader
from xhtml2pdf import pisa
import sys
from pathlib import Path
import logging
@@ -212,23 +212,25 @@ class SubmissionDetails(QDialog):
def __init__(self, ctx:dict, id:int) -> None:
super().__init__()
self.ctx = ctx
self.setWindowTitle("Submission Details")
# create scrollable interior
interior = QScrollArea()
interior.setParent(self)
# get submision from db
data = lookup_submission_by_id(ctx=ctx, id=id)
base_dict = data.to_dict()
self.base_dict = data.to_dict()
logger.debug(f"Base dict: {self.base_dict}")
# don't want id
del base_dict['id']
del self.base_dict['id']
# convert sub objects to dicts
base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
# retrieve jinja template
template = env.get_template("submission_details.txt")
# render using object dict
text = template.render(sub=base_dict)
text = template.render(sub=self.base_dict)
# create text field
txt_editor = QTextEdit(self)
txt_editor.setReadOnly(True)
@@ -247,7 +249,37 @@ class SubmissionDetails(QDialog):
interior.setWidget(txt_editor)
self.layout = QVBoxLayout()
self.setFixedSize(w, 900)
self.layout.addWidget(interior)
btn = QPushButton("Export PDF")
btn.setParent(self)
btn.setFixedWidth(w)
btn.clicked.connect(self.export)
# def _create_actions(self):
# self.exportAction = QAction("Export", self)
def export(self):
template = env.get_template("submission_details.html")
html = template.render(sub=self.base_dict)
# logger.debug(f"Submission details: {self.base_dict}")
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
# logger.debug(f"report output name: {fname}")
# df.to_excel(fname, engine='openpyxl')
if fname.__str__() == ".":
logger.debug("Saving pdf was cancelled.")
return
try:
with open(fname, "w+b") as f:
pisa.CreatePDF(html, dest=f)
except PermissionError as e:
logger.error(f"Error saving pdf: {e}")
msg = QMessageBox()
msg.setText("Permission Error")
msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
msg.setWindowTitle("Permission Error")
msg.exec()

2
src/submissions/frontend/visualizations/charts.py
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@@ -94,7 +94,7 @@ def generic_figure_markers(fig:Figure, modes:list=[], ytitle:str|None=None) -> F
])
)
)
logger.debug(f"Returning figure {fig}")
# logger.debug(f"Returning figure {fig}")
assert type(fig) == Figure
return fig

32
src/submissions/templates/submission_details.html Normal file
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@@ -0,0 +1,32 @@
<!doctype html>
<html>
<head>
<title>Submission Details for {{ sub['Plate Number'] }}</title>
</head>
<body>
<h2><u>Submission Details for {{ sub['Plate Number'] }}</u></h2>
{% for key, value in sub.items() if key != 'reagents' and key != 'samples' and key != 'controls' %}
{% if key=='Cost' %} <p>{{ key }}: {{ "${:,.2f}".format(value) }}</p> {% else %} <p>{{ key }}: {{ value }}</p> {% endif %}
{% endfor %}
<h3><u>Reagents:</u></h3>
{% for item in sub['reagents'] %}
<p>{{ item['type'] }}: {{ item['lot'] }} (EXP: {{ item['expiry'] }})</p>
{% endfor %}
<h3><u>Samples:</u></h3>
{% for item in sub['samples'] %}
<p>{{ item['well'] }}: {{ item['name'] }}</p>
{% endfor %}
{% if sub['controls'] %}
<h3><u>Attached Controls:</u></h3>
{% for item in sub['controls'] %}
<p><b>{{ item['name'] }}:</b> {{ item['type'] }} (Targets: {{ item['targets'] }})</p>
{% if item['kraken'] %}
<p>{{ item['name'] }} Top 5 Kraken Results</p>
{% for genera in item['kraken'] %}
<p>{{ genera['name'] }}: {{ genera['kraken_count'] }} ({{ genera['kraken_percent'] }})</p>
{% endfor %}
{% endif %}
{% endfor %}
{% endif %}
</body>
</html>

14
src/submissions/templates/submission_details.txt
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@@ -1,6 +1,6 @@
{# template for constructing submission details #}
{% for key, value in sub.items() if key != 'reagents' and key != 'samples' %}
{% for key, value in sub.items() if key != 'reagents' and key != 'samples' and key != 'controls' %}
{% if key=='Cost' %} {{ key }}: {{ "${:,.2f}".format(value) }} {% else %} {{ key }}: {{ value }} {% endif %}
{% endfor %}
Reagents:
@@ -10,4 +10,14 @@ Reagents:
Samples:
{% for item in sub['samples'] %}
{{ item['well'] }}: {{ item['name'] }}
{% endfor %}
{% endfor %}
{% if sub['controls'] %}
Attached Controls:
{% for item in sub['controls'] %}
{{ item['name'] }}: {{ item['type'] }} (Targets: {{ item['targets'] }})
{% if item['kraken'] %}
{{ item['name'] }} Top 5 Kraken Results
{% for genera in item['kraken'] %}
{{ genera['name'] }}: {{ genera['kraken_count'] }} ({{ genera['kraken_percent'] }}){% endfor %}{% endif %}
{% endfor %}
{% endif %}