Merge branch 'develop' into log_mem

Author: i-jey

.gitignore

@@ -127,5 +127,8 @@ lock.py
 # config ini files
 */configs/*.ini
 
+# study config
+ulc_mm_package/study_configurations/*.toml
+
 #logging config
 /log_config

setup.py

@@ -40,6 +40,7 @@ def readme():
         "py_cameras @ git+https://github.com/czbiohub/pyCameras@master",
         "pymotors @ git+https://github.com/czbiohub/PyMotors@master",
         "stats_utils @ git+https://github.com/czbiohub-sf/[email protected]",
+        "tomli==2.0.1",
         "typer==0.4.1",
         "tqdm==4.63.0",
         "transitions==0.8.11",

ulc_mm_package/QtGUI/form_gui.py

@@ -18,18 +18,18 @@
     QDesktopWidget,
 )
 from PyQt5.QtGui import QIcon
-from PyQt5.QtCore import pyqtSignal, QDate, QTime
+from PyQt5.QtCore import pyqtSignal
 
 from ulc_mm_package.scope_constants import EXPERIMENT_METADATA_KEYS
 from ulc_mm_package.image_processing.processing_constants import TARGET_FLOWRATE
-from PyQt5.QtWidgets import QDateEdit, QTimeEdit
 from ulc_mm_package.QtGUI.gui_constants import (
     ICON_PATH,
     SITE_ENV_VAR,
     SITE_LIST,
     SAMPLE_LIST,
     TOOLBAR_OFFSET,
 )
+import ulc_mm_package.QtGUI.study_metadata_form as study_form
 
 
 class FormGUI(QDialog):
@@ -42,22 +42,20 @@ def __init__(self):
 
         self._load_ui()
 
+    def _study_select(self) -> None:
+        text = self.study_select_val.currentText()
+        if text != "":
+            self.start_btn.setText("Enter additional study metadata")
+        else:
+            self.start_btn.setText("Start")
+
     def closeEvent(self, event):
         if event.spontaneous():
             self.close_event.emit()
             event.ignore()
         else:
             event.accept()
 
-    def _validate_temperature(self):
-        text = self.sample_storage_temp.text()
-        if not text.endswith(("C", "F", "c", "f")) or not text[:-1].isdigit():
-            self.sample_storage_temp.setStyleSheet("border: 1px solid red;")
-            self.start_btn.setEnabled(False)
-        else:
-            self.sample_storage_temp.setStyleSheet("")
-            self.start_btn.setEnabled(True)
-
     def _load_ui(self):
         self.setWindowTitle("Experiment form")
 
@@ -87,35 +85,16 @@ def _load_ui(self):
 
         # Labels
         self.operator_lbl = QLabel("Operator ID")
-        self.participant_lbl = QLabel("Non-identifying participant ID")
-        self.sample_collection_date_lbl = QLabel("Sample collection date")
-        self.sample_collection_time_lbl = QLabel("Sample collection time")
-        self.sample_storage_temp_lbl = QLabel("Sample storage temperature (°C or °F)")
+        self.sample_id_lbl = QLabel("Non-identifying sample ID")
+        self.study_select_lbl = QLabel("Select study")
         self.flowcell_lbl = QLabel("Flowcell ID")
         self.notes_lbl = QLabel("Other notes")
         self.site_lbl = QLabel("Site")
         self.sample_lbl = QLabel("Sample type")
 
         # Text boxes
         self.operator_val = QLineEdit()
-        self.participant_val = QLineEdit()
-
-        # Sample collection date
-        self.sample_collection_date = QDateEdit(QDate.currentDate())
-        self.sample_collection_date.setCalendarPopup(True)
-        self.sample_collection_date.setDisplayFormat("yyyy-MMM-dd")
-
-        # Sample collection time
-        self.sample_collection_time = QTimeEdit(QTime.currentTime())
-        self.sample_collection_time.setDisplayFormat("hh:mm AP")
-        self.sample_collection_time.setCalendarPopup(True)
-
-        # Sample storage temperature
-        self.sample_storage_temp = QLineEdit()
-        self.sample_storage_temp.setPlaceholderText(
-            "Enter temperature (e.g. 25C or 77F)"
-        )
-        self.sample_storage_temp.textChanged.connect(self._validate_temperature)
+        self.sample_id_val = QLineEdit()
 
         self.flowcell_val = QLineEdit()
         self.notes_val = QPlainTextEdit()
@@ -127,9 +106,15 @@ def _load_ui(self):
         # Dropdown menus
         self.site_val = QComboBox()
         self.sample_val = QComboBox()
+        self.study_select_val = QComboBox()
+        self.study_select_val.currentTextChanged.connect(self._study_select)
 
         self.site_val.addItems(SITE_LIST)
         self.sample_val.addItems(SAMPLE_LIST)
+        self.study_select_val.addItems(
+            list(study_form.list_available_studies().keys()) + [""]
+        )
+        self.study_select_val.setCurrentIndex(-1)
 
         if SITE_ENV_VAR is not None:
             self.site_val.setEnabled(False)
@@ -139,21 +124,17 @@ def _load_ui(self):
 
         # Place widgets
         self.main_layout.addWidget(self.operator_lbl, 0, 0)
-        self.main_layout.addWidget(self.participant_lbl, 1, 0)
-        self.main_layout.addWidget(self.sample_collection_date_lbl, 2, 0)
-        self.main_layout.addWidget(self.sample_collection_time_lbl, 3, 0)
-        self.main_layout.addWidget(self.sample_storage_temp_lbl, 4, 0)
+        self.main_layout.addWidget(self.sample_id_lbl, 1, 0)
+        self.main_layout.addWidget(self.study_select_lbl, 2, 0)
         self.main_layout.addWidget(self.flowcell_lbl, 5, 0)
         self.main_layout.addWidget(self.site_lbl, 6, 0)
         self.main_layout.addWidget(self.sample_lbl, 7, 0)
         self.main_layout.addWidget(self.notes_lbl, 8, 0)
         self.main_layout.addWidget(self.exit_btn, 9, 0)
 
         self.main_layout.addWidget(self.operator_val, 0, 1)
-        self.main_layout.addWidget(self.participant_val, 1, 1)
-        self.main_layout.addWidget(self.sample_collection_date, 2, 1)
-        self.main_layout.addWidget(self.sample_collection_time, 3, 1)
-        self.main_layout.addWidget(self.sample_storage_temp, 4, 1)
+        self.main_layout.addWidget(self.sample_id_val, 1, 1)
+        self.main_layout.addWidget(self.study_select_val, 2, 1)
         self.main_layout.addWidget(self.flowcell_val, 5, 1)
         self.main_layout.addWidget(self.site_val, 6, 1)
         self.main_layout.addWidget(self.sample_val, 7, 1)
@@ -165,33 +146,24 @@ def _load_ui(self):
         self.start_btn.setDefault(True)
 
     def get_form_input(self) -> dict:
-        # Determine the sample age from the current time and the sample collection time
-        current_date = QDate.currentDate()
-        current_time = QTime.currentTime()
-
-        sample_date = self.sample_collection_date.date()
-        sample_time = self.sample_collection_time.time()
-
-        date_diff_in_hours = sample_date.daysTo(current_date) * 24
-        time_diff_in_hours = sample_time.secsTo(current_time) / 3600
-
-        sample_age_hours = round(date_diff_in_hours + time_diff_in_hours, 2)
+        study_name = self.study_select_val.currentText()
+        if study_name != "":
+            study_id = study_form.get_study_id_from_name(study_name)
+        else:
+            study_id = None
 
         form_metadata = {
             "operator_id": self.operator_val.text(),
-            "participant_id": self.participant_val.text(),
+            "sample_id": self.sample_id_val.text(),
             "flowcell_id": self.flowcell_val.text(),
-            "sample_collection_date": self.sample_collection_date.text(),
-            "sample_collection_time": self.sample_collection_time.text(),
-            "sample_age_hours": sample_age_hours,
-            "sample_storage_temp": self.sample_storage_temp.text(),
             "target_flowrate": (
                 TARGET_FLOWRATE.name.capitalize(),
                 TARGET_FLOWRATE.value,
             ),  # fixed flowrate
             "site": self.site_val.currentText(),
             "sample_type": self.sample_val.currentText(),
             "notes": self.notes_val.toPlainText(),
+            "study_id": study_id,
         }
 
         if not all(key in EXPERIMENT_METADATA_KEYS for key in form_metadata):
@@ -201,15 +173,25 @@ def get_form_input(self) -> dict:
 
     def reset_parameters(self) -> None:
         """Clear specific inputs which are expected to be unique for the next run."""
-        self.participant_val.setText("")
+        self.sample_id_val.setText("")
         self.flowcell_val.setText("")
         self.notes_val.setPlainText("")
 
+    def sf(self) -> None:
+        metadata = self.get_form_input()
+        cfg = study_form.get_cfg_from_study_id(metadata["study_id"])
+        if cfg is not None:
+            sf = study_form.StudyMetadata(cfg, gui)
+            sf.show()
+        else:
+            raise ValueError(f"Was unable to fetch {metadata['study_id']}")
+
 
 if __name__ == "__main__":
     app = QApplication(sys.argv)
     gui = FormGUI()
     gui.exit_btn.clicked.connect(gui.close)
+    gui.start_btn.clicked.connect(gui.sf)
 
     print(gui.get_form_input())
 

ulc_mm_package/QtGUI/liveview_gui.py

@@ -91,7 +91,7 @@ def closeEvent(self, event):
     def update_experiment(self, metadata: dict):
         # TODO standardize dict input
         self.operator_val.setText(f"{metadata['operator_id']}")
-        self.participant_val.setText(f"{metadata['participant_id']}")
+        self.sample_val.setText(f"{metadata['sample_id']}")
         self.flowcell_val.setText(f"{metadata['flowcell_id']}")
         self.target_flowrate_val.setText(f"{metadata['target_flowrate'][0]}")
         self.site_val.setText(f"{metadata['site']}")
@@ -560,35 +560,35 @@ def _load_metadata_ui(self):
 
         # Populate metadata tab
         self.operator_lbl = QLabel("Operator ID")
-        self.participant_lbl = QLabel("Participant ID")
+        self.sample_lbl = QLabel("Sample ID")
         self.flowcell_lbl = QLabel("Flowcell ID")
         self.target_flowrate_lbl = QLabel("Flowrate")
         self.site_lbl = QLabel("Site")
         self.notes_lbl = QLabel("Other notes")
 
         self.operator_val = QLineEdit()
-        self.participant_val = QLineEdit()
+        self.sample_val = QLineEdit()
         self.flowcell_val = QLineEdit()
         self.target_flowrate_val = QLineEdit()
         self.site_val = QLineEdit()
         self.notes_val = QPlainTextEdit()
 
         self.operator_val.setReadOnly(True)
-        self.participant_val.setReadOnly(True)
+        self.sample_val.setReadOnly(True)
         self.flowcell_val.setReadOnly(True)
         self.target_flowrate_val.setReadOnly(True)
         self.site_val.setReadOnly(True)
         self.notes_val.setReadOnly(True)
 
         self.metadata_layout.addWidget(self.operator_lbl, 1, 1)
-        self.metadata_layout.addWidget(self.participant_lbl, 2, 1)
+        self.metadata_layout.addWidget(self.sample_lbl, 2, 1)
         self.metadata_layout.addWidget(self.flowcell_lbl, 3, 1)
         self.metadata_layout.addWidget(self.target_flowrate_lbl, 4, 1)
         self.metadata_layout.addWidget(self.site_lbl, 5, 1)
         self.metadata_layout.addWidget(self.notes_lbl, 6, 1)
 
         self.metadata_layout.addWidget(self.operator_val, 1, 2)
-        self.metadata_layout.addWidget(self.participant_val, 2, 2)
+        self.metadata_layout.addWidget(self.sample_val, 2, 2)
         self.metadata_layout.addWidget(self.flowcell_val, 3, 2)
         self.metadata_layout.addWidget(self.target_flowrate_val, 4, 2)
         self.metadata_layout.addWidget(self.site_val, 5, 2)
@@ -601,7 +601,7 @@ def _load_metadata_ui(self):
 
     experiment_metadata = {
         "operator_id": "1234",
-        "participant_id": "567",
+        "sample_id": "567",
         "flowcell_id": "A2",
         "target_flowrate": ("Fast", 15),
         "site": "Uganda",

ulc_mm_package/QtGUI/oracle.py

@@ -35,6 +35,7 @@
 )
 from PyQt5.QtCore import Qt, QThread, pyqtSignal
 from PyQt5.QtGui import QIcon, QPixmap
+from PyQt5.QtWidgets import QPushButton
 
 from ulc_mm_package.scope_constants import (
     LOCKFILE,
@@ -68,6 +69,7 @@
     FAIL_MSG,
     TERMINATED_MSG,
 )
+import ulc_mm_package.QtGUI.study_metadata_form as study_form
 from ulc_mm_package.neural_nets.neural_network_constants import (
     AUTOFOCUS_MODEL_DIR,
     YOGO_MODEL_DIR,
@@ -77,7 +79,6 @@
 from ulc_mm_package.QtGUI.scope_op import ScopeOp
 from ulc_mm_package.QtGUI.form_gui import FormGUI
 from ulc_mm_package.QtGUI.liveview_gui import LiveviewGUI
-from PyQt5.QtWidgets import QPushButton
 
 
 QApplication.setAttribute(Qt.AA_EnableHighDpiScaling, True)
@@ -209,6 +210,7 @@ def _check_lock(self):
     def _set_variables(self):
         # Instantiate metadata dicts
         self.form_metadata = None
+        self.study_metadata = None
         self.experiment_metadata = {key: None for key in EXPERIMENT_METADATA_KEYS}
 
         self.liveview_window.set_infopanel_vals()
@@ -268,7 +270,7 @@ def _init_states(self):
 
     def _init_sigslots(self):
         # Connect experiment form buttons
-        self.form_window.start_btn.clicked.connect(self.save_form)
+        self.form_window.start_btn.clicked.connect(self._maybe_start_study_form)
         self.form_window.exit_btn.clicked.connect(self.form_exit_handler)
         self.form_window.close_event.connect(self.close_handler)
 
@@ -428,7 +430,7 @@ def general_pause_handler(
             (
                 "The CAP module can now be removed."
                 "\n\nPlease empty both reservoirs and reload 12 uL of fresh "
-                "diluted blood (from the same participant) into the sample reservoir. Make sure to close the lid after."
+                "diluted blood (from the same sample) into the sample reservoir. Make sure to close the lid after."
                 '\n\nAfter reloading the reservoir and closing the lid, click "OK" to resume this run.'
             ),
             buttons=Buttons.OK,
@@ -626,6 +628,26 @@ def _end_setup(self, *args):
     def _start_form(self, *args):
         self.form_window.showMaximized()
 
+    def _maybe_start_study_form(self):
+        form_metadata = self.form_window.get_form_input()
+        study_id = form_metadata["study_id"]
+        if study_id != "":
+            cfg = study_form.get_cfg_from_study_id(study_id)
+            if cfg is not None:
+                self.study_form_dialog = study_form.StudyMetadata(cfg, self.form_window)
+                self.study_form_dialog.btn_start.clicked.connect(
+                    self.get_study_metadata
+                )
+                self.study_form_dialog.showMaximized()
+            else:
+                self.save_form()
+        else:
+            self.save_form()
+
+    def get_study_metadata(self):
+        self.study_metadata = self.study_form_dialog.get_form_input()
+        self.save_form()
+
     def save_form(self):
         self.form_metadata = self.form_window.get_form_input()
         self.form_window.reset_parameters()
@@ -635,10 +657,6 @@ def save_form(self):
         for key in self.form_metadata:
             self.experiment_metadata[key] = self.form_metadata[key]
 
-        # DATA-TODO verify if user input satisfies required format
-        # -> if data fails verification, prompt user for correction using "display_message" (defined above)
-        # -> if data passes verification, call "self.next_state" to open liveview
-
         # Assign other metadata parameters
         self.experiment_metadata["scope"] = socket.gethostname()
         self.experiment_metadata["camera"] = CAMERA_SELECTION.name
@@ -688,6 +706,7 @@ def save_form(self):
             "",
             self.datetime_str,
             self.experiment_metadata,
+            self.study_metadata,
             PER_IMAGE_METADATA_KEYS,
         )