diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9537f78..866c245 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/TODO.md b/TODO.md
index c075321..bdd2875 100644
--- a/TODO.md
+++ b/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.
\ No newline at end of file
diff --git a/alembic.ini b/alembic.ini
index 20ebdc4..37e6f8c 100644
--- a/alembic.ini
+++ b/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:///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
+sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
+; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230427.db
+; msqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\tests\test_assets\submissions_test.db
[post_write_hooks]
diff --git a/alembic/versions/a31943b2284c_added_commenting.py b/alembic/versions/a31943b2284c_added_commenting.py
new file mode 100644
index 0000000..59ea0da
--- /dev/null
+++ b/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 ###
diff --git a/alembic/versions/dc780c868efd_split_mutable_costs_into_96_and_24.py b/alembic/versions/dc780c868efd_split_mutable_costs_into_96_and_24.py
deleted file mode 100644
index bf56000..0000000
--- a/alembic/versions/dc780c868efd_split_mutable_costs_into_96_and_24.py
+++ /dev/null
@@ -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 ###
diff --git a/src/submissions/backend/db/models/submissions.py b/src/submissions/backend/db/models/submissions.py
index 3be1144..560bf9e 100644
--- a/src/submissions/backend/db/models/submissions.py
+++ b/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
diff --git a/src/submissions/frontend/custom_widgets/sub_details.py b/src/submissions/frontend/custom_widgets/sub_details.py
index 6ed37bf..7c0a988 100644
--- a/src/submissions/frontend/custom_widgets/sub_details.py
+++ b/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 backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id
+from PyQt6.QtGui import QFontMetrics, QAction, QCursor, QPixmap, QPainter
+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()
+
+
\ No newline at end of file
diff --git a/src/submissions/frontend/visualizations/__init__.py b/src/submissions/frontend/visualizations/__init__.py
index ef76651..da0b5f0 100644
--- a/src/submissions/frontend/visualizations/__init__.py
+++ b/src/submissions/frontend/visualizations/__init__.py
@@ -1,4 +1,5 @@
'''
Contains all operations for creating charts, graphs and visual effects.
'''
-from .control_charts import *
\ No newline at end of file
+from .control_charts import *
+from .barcode import *
\ No newline at end of file
diff --git a/src/submissions/frontend/visualizations/barcode.py b/src/submissions/frontend/visualizations/barcode.py
new file mode 100644
index 0000000..16ca96c
--- /dev/null
+++ b/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")
\ No newline at end of file
diff --git a/src/submissions/templates/submission_details.html b/src/submissions/templates/submission_details.html
index 4a9c55d..89d46dd 100644
--- a/src/submissions/templates/submission_details.html
+++ b/src/submissions/templates/submission_details.html
@@ -3,7 +3,7 @@
Submission Details for {{ sub['Plate Number'] }}
- {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info'] %}
+ {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments'] %}
Submission Details for {{ sub['Plate Number'] }}
{% for key, value in sub.items() if key not in excluded %}
@@ -51,7 +51,7 @@
{% for entry in sub['ext_info'] %}
Extraction Status:
{% for key, value in entry.items() %}
- {% if loop.index == 1%}
+ {% if loop.index == 1 %}
{{ key|replace('_', ' ')|title() }}: {{ value }}
{% else %}
{% if "column" in key %}
@@ -71,7 +71,7 @@
qPCR Status:
{% endif %}
{% for key, value in entry.items() if key != 'imported_by'%}
- {% if loop.index == 1%}
+ {% if loop.index == 1 %}
{{ key|replace('_', ' ')|title() }}: {{ value }}
{% else %}
{% if "column" in key %}
@@ -83,5 +83,15 @@
{% endfor %}
{% endfor %}
{% endif %}
+ {% if sub['comments'] %}
+ Comments:
+ {% for entry in sub['comments'] %}
+ {% if loop.index == 1 %}
+ {{ entry['name'] }}:
{{ entry['text'] }}
- {{ entry['time'] }}
+ {% else %}
+ {{ entry['name'] }}:
{{ entry['text'] }}
- {{ entry['time'] }}
+ {% endif %}
+ {% endfor %}
+ {% endif %}