added kraken data to details.

alembic/versions/785bb1140878_added_user_tracking.py

@@ -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 ###

src/submissions/__init__.py

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

src/submissions/backend/db/__init__.py

@@ -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
      
     

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

@@ -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
+

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

@@ -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):

src/submissions/backend/excel/reports.py

@@ -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]

src/submissions/frontend/__init__.py

@@ -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.control_typer.currentIndexChanged.connect(self._controls_getter)
-        self.table_widget.mode_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.start_date.dateChanged.connect(self._controls_getter)
-        self.table_widget.datepicker.end_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
         """        

src/submissions/frontend/custom_widgets/__init__.py

@@ -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]
+        self.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['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()
         
 
 

src/submissions/frontend/visualizations/charts.py

@@ -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
 

src/submissions/templates/submission_details.html

@@ -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>

src/submissions/templates/submission_details.txt

@@ -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 %}