Adding in commenting submissions and barcode creation.

CHANGELOG.md

@@ -1,5 +1,7 @@
 ## 202305.02
 
+- Added rudimentary barcode printing.
+- Added ability to comment on submissions.
 - Updated kit creation methods to keep pace with new cost calculations.
 
 ## 202305.01

TODO.md

@@ -1 +1,3 @@
+- [ ] Create a method for commenting submissions.
+- [ ] Create barcode generator, because of reasons that may or may not exist.
 - [x] Move bulk of functions from frontend.__init__ to frontend.functions as __init__ is getting bloated.

alembic.ini

@@ -55,9 +55,9 @@ version_path_separator = os  # Use os.pathsep. Default configuration used for ne
 # are written from script.py.mako
 # output_encoding = utf-8
 
-; sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
+sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
-sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230427.db
+; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230427.db
-; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\tests\test_assets\submissions_test.db
+; msqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\tests\test_assets\submissions_test.db
 
 
 [post_write_hooks]

alembic/versions/a31943b2284c_added_commenting.py

@@ -0,0 +1,33 @@
+"""added commenting
+
+Revision ID: a31943b2284c
+Revises: 83b06f3f4869
+Create Date: 2023-05-10 11:34:30.339915
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'a31943b2284c'
+down_revision = '83b06f3f4869'
+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('comment', sa.JSON(), 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('comment')
+
+    # ### end Alembic commands ###

alembic/versions/dc780c868efd_split_mutable_costs_into_96_and_24.py

@@ -1,51 +0,0 @@
-"""split mutable costs into 96 and 24
-
-Revision ID: dc780c868efd
-Revises: 83b06f3f4869
-Create Date: 2023-05-01 14:05:47.762441
-
-"""
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import sqlite
-
-# revision identifiers, used by Alembic.
-revision = 'dc780c868efd'
-down_revision = '83b06f3f4869'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_table('_alembic_tmp__kits')
-    with op.batch_alter_table('_kits', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('mutable_cost_96', sa.FLOAT(precision=2), nullable=True))
-        batch_op.add_column(sa.Column('mutable_cost_24', sa.FLOAT(precision=2), nullable=True))
-        batch_op.drop_column('mutable_cost')
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    
-    with op.batch_alter_table('_kits', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('mutable_cost', sa.FLOAT(), nullable=True))
-        batch_op.drop_column('mutable_cost_24')
-        batch_op.drop_column('mutable_cost_96')
-
-    op.create_table('_alembic_tmp__kits',
-    sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.VARCHAR(length=64), nullable=True),
-    sa.Column('used_for', sqlite.JSON(), nullable=True),
-    sa.Column('cost_per_run', sa.FLOAT(), nullable=True),
-    sa.Column('reagent_types_id', sa.INTEGER(), nullable=True),
-    sa.Column('constant_cost', sa.FLOAT(), nullable=True),
-    sa.Column('mutable_cost_96', sa.FLOAT(), nullable=True),
-    sa.Column('mutable_cost_24', sa.FLOAT(), nullable=True),
-    sa.ForeignKeyConstraint(['reagent_types_id'], ['_reagent_types.id'], ondelete='SET NULL'),
-    sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('name')
-    )
-    # ### end Alembic commands ###

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

@@ -38,6 +38,7 @@ class BasicSubmission(Base):
     extraction_info = Column(JSON) #: unstructured output from the extraction table logger.
     run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from constant and mutable kit costs at time of creation.
     uploaded_by = Column(String(32)) #: user name of person who submitted the submission to the database.
+    comment = Column(JSON)
 
     # Allows for subclassing into ex. BacterialCulture, Wastewater, etc.
     __mapper_args__ = {
@@ -93,6 +94,11 @@ class BasicSubmission(Base):
             samples = [item.to_sub_dict() for item in self.samples]
         except:
             samples = None
+        try:
+            comments = self.comment
+        except:
+            logger.error(self.comment)
+            comments = None
         output = {
             "id": self.id,
             "Plate Number": self.rsl_plate_num,
@@ -106,9 +112,11 @@ class BasicSubmission(Base):
             "Cost": self.run_cost,
             "reagents": reagents,
             "samples": samples,
-            "ext_info": ext_info
+            "ext_info": ext_info,
+            "comments": comments
         }
         # logger.debug(f"{self.rsl_plate_num} extraction: {output['Extraction Status']}")
+        # logger.debug(f"Output dict: {output}")
         return output
 
 

src/submissions/frontend/custom_widgets/sub_details.py

@@ -1,20 +1,25 @@
 '''
 Contains widgets specific to the submission summary and submission details.
 '''
+from datetime import datetime
+from PyQt6 import QtPrintSupport
 from PyQt6.QtWidgets import (
     QVBoxLayout, QDialog, QTableView,
     QTextEdit, QPushButton, QScrollArea, 
-    QMessageBox, QFileDialog, QMenu
+    QMessageBox, QFileDialog, QMenu, QLabel,
+    QDialogButtonBox, QToolBar, QMainWindow
 )
 from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
-from PyQt6.QtGui import QFontMetrics, QAction, QCursor
+from PyQt6.QtGui import QFontMetrics, QAction, QCursor, QPixmap, QPainter
-from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id
+from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num
 from jinja2 import Environment, FileSystemLoader
 from xhtml2pdf import pisa
 import sys
 from pathlib import Path
 import logging
 from .pop_ups import QuestionAsker
+from ..visualizations import make_plate_barcode
+from getpass import getuser
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -120,6 +125,22 @@ class SubmissionsSheet(QTableView):
         if dlg.exec():
             pass
 
+    def create_barcode(self) -> None:
+        index = (self.selectionModel().currentIndex())
+        value = index.sibling(index.row(),1).data()
+        logger.debug(f"Selected value: {value}")
+        dlg = BarcodeWindow(value)
+        if dlg.exec():
+            dlg.print_barcode()
+
+    def add_comment(self) -> None:
+        index = (self.selectionModel().currentIndex())
+        value = index.sibling(index.row(),1).data()
+        logger.debug(f"Selected value: {value}")
+        dlg = SubmissionComment(ctx=self.ctx, rsl=value)
+        if dlg.exec():
+            dlg.add_comment()
+
 
     def contextMenuEvent(self, event):
         """
@@ -131,10 +152,16 @@ class SubmissionsSheet(QTableView):
         self.menu = QMenu(self)
         renameAction = QAction('Delete', self)
         detailsAction = QAction('Details', self)
+        barcodeAction = QAction("Print Barcode", self)
+        commentAction = QAction("Add Comment", self)
         renameAction.triggered.connect(lambda: self.delete_item(event))
         detailsAction.triggered.connect(lambda: self.show_details())
+        barcodeAction.triggered.connect(lambda: self.create_barcode())
+        commentAction.triggered.connect(lambda: self.add_comment())
         self.menu.addAction(detailsAction)
         self.menu.addAction(renameAction)
+        self.menu.addAction(barcodeAction)
+        self.menu.addAction(commentAction)
         # add other required actions
         self.menu.popup(QCursor.pos())
 
@@ -227,3 +254,122 @@ class SubmissionDetails(QDialog):
             msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
             msg.setWindowTitle("Permission Error")
             msg.exec()
+
+class BarcodeWindow(QDialog):
+
+    def __init__(self, rsl_num:str):
+        super().__init__()
+        # set the title
+        self.setWindowTitle("Image")
+        self.layout = QVBoxLayout()
+        # setting  the geometry of window
+        self.setGeometry(0, 0, 400, 300)
+        # creating label
+        self.label = QLabel()
+        self.img = make_plate_barcode(rsl_num)
+        # logger.debug(dir(img), img.contents[0])
+        # fp = BytesIO().read()
+        # img.save(formats=['png'], fnRoot=fp)
+        # pixmap = QPixmap("C:\\Users\\lwark\\Documents\\python\\submissions\\src\\Drawing000.png")
+        self.pixmap = QPixmap()
+        # self.pixmap.loadFromData(self.img.asString("bmp"))
+        self.pixmap.loadFromData(self.img)
+        # adding image to label
+        self.label.setPixmap(self.pixmap)
+        # Optional, resize label to image size
+        # self.label.resize(self.pixmap.width(), self.pixmap.height())
+        # self.label.resize(200, 200)
+        # show all the widgets]
+        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+        self.buttonBox = QDialogButtonBox(QBtn)
+        self.buttonBox.accepted.connect(self.accept)
+        self.buttonBox.rejected.connect(self.reject)
+        self.layout.addWidget(self.label)
+        self.layout.addWidget(self.buttonBox)
+        self.setLayout(self.layout)
+        self._createActions()
+        self._createToolBar()
+        self._connectActions()
+        
+
+
+    def _createToolBar(self):
+        """
+        adds items to menu bar
+        """    
+        toolbar = QToolBar("My main toolbar")
+        # self.addToolBar(toolbar)  
+        # self.layout.setToolBar(toolbar)  
+        toolbar.addAction(self.printAction)
+        
+
+    def _createActions(self):
+        """
+        creates actions
+        """        
+        self.printAction = QAction("&Print", self)
+
+
+    def _connectActions(self):
+        """
+        connect menu and tool bar item to functions
+        """
+        self.printAction.triggered.connect(self.print_barcode)
+
+
+    def print_barcode(self):
+        printer = QtPrintSupport.QPrinter()
+        
+        dialog = QtPrintSupport.QPrintDialog(printer)
+        if dialog.exec():
+            self.handle_paint_request(printer, self.pixmap.toImage())
+
+
+    def handle_paint_request(self, printer:QtPrintSupport.QPrinter, im):
+        logger.debug(f"Hello from print handler.")
+        painter = QPainter(printer)
+        image = QPixmap.fromImage(im)
+        painter.drawPixmap(120, -20, image)
+        painter.end()
+        
+
+class SubmissionComment(QDialog):
+    """
+    a window showing text details of submission
+    """    
+    def __init__(self, ctx:dict, rsl:str) -> None:
+
+        super().__init__()
+        self.ctx = ctx
+        self.rsl = rsl
+        self.setWindowTitle(f"{self.rsl} Submission Comment")
+        # create text field
+        self.txt_editor = QTextEdit(self)
+        self.txt_editor.setReadOnly(False)
+        self.txt_editor.setText("Add Comment")
+        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+        self.buttonBox = QDialogButtonBox(QBtn)
+        self.buttonBox.accepted.connect(self.accept)
+        self.buttonBox.rejected.connect(self.reject)
+        self.layout = QVBoxLayout()
+        self.setFixedSize(400, 300)
+        self.layout.addWidget(self.txt_editor)
+        self.layout.addWidget(self.buttonBox, alignment=Qt.AlignmentFlag.AlignBottom)
+        self.setLayout(self.layout)
+        
+    def add_comment(self):
+        commenter = getuser()
+        comment = self.txt_editor.toPlainText()
+        dt = datetime.strftime(datetime.now(), "%Y-%m-d %H:%M:%S")
+        full_comment = {"name":commenter, "time": dt, "text": comment}
+        logger.debug(f"Full comment: {full_comment}")
+        sub = lookup_submission_by_rsl_num(ctx = self.ctx, rsl_num=self.rsl)
+        try:
+            sub.comment.append(full_comment)
+        except AttributeError:
+            sub.comment = [full_comment]
+        logger.debug(sub.__dict__)
+        self.ctx['database_session'].add(sub)
+        self.ctx['database_session'].commit()
+
+        

src/submissions/frontend/visualizations/__init__.py

@@ -2,3 +2,4 @@
 Contains all operations for creating charts, graphs and visual effects.
 '''
 from .control_charts import *
+from .barcode import *

src/submissions/frontend/visualizations/barcode.py

@@ -0,0 +1,8 @@
+from reportlab.graphics.barcode import createBarcodeDrawing, createBarcodeImageInMemory
+from reportlab.graphics.shapes import Drawing
+from reportlab.lib.units import mm
+
+
+def make_plate_barcode(text:str) -> Drawing:
+    # return createBarcodeDrawing('Code128', value=text, width=200, height=50, humanReadable=True)
+    return createBarcodeImageInMemory('Code128', value=text, width=100*mm, height=25*mm, humanReadable=True, format="png")

src/submissions/templates/submission_details.html

@@ -3,7 +3,7 @@
     <head>
         <title>Submission Details for {{ sub['Plate Number'] }}</title>
     </head>
-    {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info'] %}
+    {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments'] %}
     <body>
         <h2><u>Submission Details for {{ sub['Plate Number'] }}</u></h2>
         <p>{% for key, value in sub.items() if key not in excluded %}
@@ -51,7 +51,7 @@
         {% for entry in sub['ext_info'] %}
         <h3><u>Extraction Status:</u></h3>
         <p>{% for key, value in entry.items() %}
-            {% if loop.index == 1%}
+            {% if loop.index == 1 %}
                 &nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}<br>
             {% else %}
                 {% if "column" in key %}
@@ -71,7 +71,7 @@
             <h3><u>qPCR Status:</u></h3>
         {% endif %}
         <p>{% for key, value in entry.items() if key != 'imported_by'%}
-            {% if loop.index == 1%}
+            {% if loop.index == 1 %}
                 &nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}<br>
             {% else %}
                 {% if "column" in key %}
@@ -83,5 +83,15 @@
         {% endfor %}</p>
         {% endfor %}
         {% endif %}
+        {% if sub['comments'] %}
+        <h3><u>Comments:</u></h3>
+        <p>{% for entry in sub['comments'] %}
+            {% if loop.index == 1 %}
+                &nbsp;&nbsp;&nbsp;<b>{{ entry['name'] }}:</b><br> {{ entry['text'] }}<br>- {{ entry['time'] }}<br>
+            {% else %}
+                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ entry['name'] }}:</b><br> {{ entry['text'] }}<br>- {{ entry['time'] }}<br>
+            {% endif %}
+        {% endfor %}</p>
+        {% endif %}
     </body>
 </html>

src/submissions/templates/submission_details.txt

@@ -1,5 +1,5 @@
 {# template for constructing submission details #}
-{% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info'] %}
+{% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments'] %}
 {# for key, value in sub.items() if key != 'reagents' and key != 'samples' and key != 'controls' and key != 'ext_info' #}
 {% for key, value in sub.items() if key not in excluded %}
 {% if key=='Cost' %} {{ key }}: {{ "${:,.2f}".format(value) }} {% else %} {{ key }}: {{ value }} {% endif %}
@@ -30,3 +30,11 @@ qPCR Status{% endif %}
 {% for key, value in entry.items() if key != 'imported_by' %}
     {{ key|replace('_', ' ')|title() }}: {{ value }}{% endfor %}{% endfor %}
 {% endif %}
+{% if sub['comments'] %}
+Comments:
+{% for item in sub['comments'] %}
+    {{ item['name'] }}: 
+    {{ item['text'] }}
+    - {{ item['time'] }}
+{% endfor %}
+{% endif %}

src/submissions/tools/__init__.py

@@ -195,7 +195,7 @@ class RSLNamer(object):
             return
         logger.debug(f"Attempting match of {in_str}")
         regex = re.compile(r"""
-            (?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)\d(?!\d))?)|
+            (?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)R?\d(?!\d))?)|
             (?P<bacterial_culture>RSL-?\d{2}-?\d{4})
             """, flags = re.IGNORECASE | re.VERBOSE)
         m = regex.search(in_str)