Merge pull request #197 from CWRUbotix/dna

Dna

Author: benjaminwp18

src/surface/gui/README.md

@@ -9,6 +9,12 @@ Then `operator_app.py` and `pilot_app.py` inherit from App to make our two custo
 
 ## Installation
 
+Install pypdf with
+
+```bash
+pip install pypdf --break-system-packages
+```
+
 ## Usage
 
 Run the operator GUI with

src/surface/gui/gui/operator_app.py

@@ -8,6 +8,7 @@
 from gui.widgets.ip_widget import IPWidget
 from gui.widgets.logger import Logger
 from gui.widgets.tabs.carp_model_tab import CarpModelTab
+from gui.widgets.tabs.dna_tab import DNATab
 from gui.widgets.tabs.general_debug_tab import GeneralDebugTab
 from gui.widgets.tabs.photosphere_tab import PhotosphereTab
 from gui.widgets.tabs.shipwreck import ShipwreckTab
@@ -59,6 +60,7 @@ def __init__(self) -> None:
         self.tabs.addTab(PhotosphereTab(), 'Photosphere')
         self.tabs.addTab(CarpModelTab(), 'Carp Model')
         self.shipwreck_tab = ShipwreckTab()
+        self.tabs.addTab(DNATab(), 'DNA Sample')
         self.tabs.addTab(self.shipwreck_tab, SHIPWRECK_TEXT)
         self.tabs.currentChanged.connect(self.changed_tabs)
         root_layout.addWidget(self.tabs)

src/surface/gui/gui/widgets/dna.py

@@ -0,0 +1,152 @@
+import re
+from pathlib import Path
+
+from pypdf import PdfReader
+from PyQt6.QtWidgets import (
+    QFileDialog,
+    QHBoxLayout,
+    QLabel,
+    QLineEdit,
+    QPlainTextEdit,
+    QPushButton,
+    QTextEdit,
+    QVBoxLayout,
+    QWidget,
+)
+
+DNA_NEEDLES = [
+    [
+        'Bighead Carp',
+        'AACTTAAATAAACAGATTATTCCACTAACAATTGATTCTCAAATTTATTACTGAATTATTAACTAAAATCTAACTCAAGTATATTATTAAAGTAAGAGACCACCTACTTATTTATATTAAGGTATTATATTCATGATAAGATCAAGGACAATAACAGTGGGGGTGGCGCAAAATGAACTATTACTTGCATCTGGTTTGGAATCTCACGGACATGGCTACAAAATTCCACCCCCGTTACATTATAACTGGCATATGGTTAAATGATGTGAGTACATACTCCTCATTAACCCCACATGCCGAGCATTCTTTTAT',
+    ],
+    [
+        'Silver Carp',
+        'CCTGAGAAAAGAGTTGTTCCACTATAATTGGTTCTCAAATATTTCCTTGAAATATTAACTTCTATTTAATTTAACTATATTAATGTAGTAAGAAACCACCTACTGGTTTATATTAAGGTATTCTATTCATGATAAGATCAGGGACAATAATCGTGGGGGTGGCGCAGAATGAACTATTACTTGCATTTGGC',
+    ],
+    [
+        'Grass Carp',
+        'GAGTTTCTGACTTCTACCCCCTTCTTTCCTCCTACTATTAGCCTCTTCTGGTGTTGAGGCCGGAGCTGGAACAGGGTGAACAG',
+    ],
+    [
+        'Black Carp',
+        'ACACCACGTTCTTTGACCCAGCAGGCGGAGGAGACCCAATCCTATATCAACACCTGTTCTGATTCTTCGGCCACCCAGAAGTTTACATTCTTATTTTACCCGGGTTTGGGATCATTTCAC',
+    ],
+]
+
+
+class DNA(QWidget):
+    def __init__(self) -> None:
+        super().__init__()
+
+        self.root_layout = QVBoxLayout()
+        self.base_layout = QHBoxLayout()
+
+        self.input_layout = QVBoxLayout()
+        self.auto_output_layout = QVBoxLayout()
+        self.manual_output_layout = QVBoxLayout()
+
+        file_picker_layout = QHBoxLayout()
+
+        self.sample = QPlainTextEdit()
+
+        file_browse = QPushButton('Browse')
+        file_browse.clicked.connect(self.open_file_dialog)
+        self.filename = QLineEdit()
+
+        show_button = QPushButton('Search Database', None)
+
+        show_button.clicked.connect(self.display_result)
+
+        self.check_text = QTextEdit()
+
+        self.input_layout.addWidget(QLabel('Select PDF File: '))
+        file_picker_layout.addWidget(self.filename)
+        file_picker_layout.addWidget(file_browse)
+        self.input_layout.addLayout(file_picker_layout)
+
+        self.input_layout.addWidget(QLabel('Or enter sample directly: '))
+        self.input_layout.addWidget(self.sample)
+
+        self.input_layout.addWidget(show_button)
+
+        self.base_layout.addLayout(self.input_layout)
+
+        self.base_layout.addLayout(self.auto_output_layout)
+        self.base_layout.addLayout(self.manual_output_layout)
+        self.root_layout.addLayout(self.base_layout)
+        self.root_layout.addWidget(QLabel('Check DNA Samples:'))
+        self.root_layout.addWidget(self.check_text)
+
+        self.manual_result: QLabel | None = None
+        self.auto_results: list[QLabel] = []
+
+        self.setLayout(self.root_layout)
+
+    def open_file_dialog(self) -> None:
+        filename, _ = QFileDialog.getOpenFileName(
+            caption='Select a File', filter='PDF files (*.pdf)'
+        )
+        if filename:
+            path = Path(filename)
+            self.text_file = str(path)
+            self.filename.setText(self.text_file)
+
+    def find_samples(self, pdf_file: str) -> list[str]:
+        reader = PdfReader(pdf_file)
+        samples = []
+        self.check_text.setText('')
+        for page in reader.pages:
+            text = page.extract_text()
+            last_index = 0
+            while text.find('Unknown Sample', last_index) != -1:
+                current_index = text.find(
+                    'Unknown Sample', last_index
+                )  # Roughly identify location of next sample
+                sample_index = text.find('\n', current_index) + 1  # Find start of sample
+                sample_index_end = text.find(' \n', sample_index)  # Find end of sample
+                sample = text[sample_index:sample_index_end].replace('\n', '')
+                samples.append(sample)
+                self.check_sample(sample, len(samples))
+                last_index = sample_index_end
+        return samples
+
+    def check_sample(self, sample: str, sample_num: int) -> None:
+        # Check if sample has characters not corresponding to a DNA base
+        if sample.replace('A', '').replace('C', '').replace('G', '').replace('T', '') != '':
+            self.check_text.setText(
+                'Sample '
+                + str(sample_num)
+                + ' has characters other than ACGT\n\n'
+                + self.check_text.toPlainText()
+            )
+
+        # Display all samples for manual checking
+        self.check_text.setText(
+            self.check_text.toPlainText() + ('Sample ' + str(sample_num) + ': ' + sample) + '\n\n'
+        )
+
+    def display_result(self) -> None:
+        for result in self.auto_results:
+            self.auto_output_layout.removeWidget(result)
+        self.manual_output_layout.removeWidget(self.manual_result)
+
+        if self.filename.text():
+            self.auto_results = []
+            samples = self.find_samples(self.filename.text())
+            for i, sample in enumerate(samples):
+                self.auto_results.append(QLabel(str(i + 1) + ': ' + self.search(sample)))
+        if self.sample.toPlainText():
+            sample = self.sample.toPlainText()
+            sample = re.sub('[^ACGT]', '', sample)  # Remove every character except ACGT
+            self.manual_result = QLabel('Manual: ' + self.search(sample))
+
+        for result in self.auto_results:
+            self.auto_output_layout.addWidget(result)
+        self.manual_output_layout.addWidget(self.manual_result)
+
+    def search(self, sample: str) -> str:
+        for name, substr in DNA_NEEDLES:
+            if sample.find(substr) != -1:
+                return name
+
+        return 'No match'

src/surface/gui/gui/widgets/tabs/dna_tab.py

@@ -0,0 +1,12 @@
+from PyQt6.QtWidgets import QVBoxLayout, QWidget
+
+from gui.widgets.dna import DNA
+
+
+class DNATab(QWidget):
+    def __init__(self) -> None:
+        super().__init__()
+
+        root_layout = QVBoxLayout()
+        root_layout.addWidget(DNA())
+        self.setLayout(root_layout)