Improved previous sub finding.

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 202402.04
+
+- Addition of comments to gel box.
+
 ## 202402.01
 
 - Addition of gel box for Artic quality control.

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\Submissions_app_backups\DB_backups\submissions-new.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\Submissions_app_backups\DB_backups\submissions-demo.db
+sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\tests\test_assets\submissions-test.db
 
 
 [post_write_hooks]

alembic/versions/fabf697c721d_adding_source_plates_to_artic_submission.py

@@ -0,0 +1,48 @@
+"""adding source plates to Artic submission
+
+Revision ID: fabf697c721d
+Revises: 70426df72f80
+Create Date: 2024-03-06 11:01:34.794411
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'fabf697c721d'
+down_revision = '70426df72f80'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    # with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
+    #     batch_op.create_unique_constraint("ssa_unique", ['id'])
+
+    with op.batch_alter_table('_wastewaterartic', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('source_plates', sa.JSON(), nullable=True))
+
+    with op.batch_alter_table('_wastewaterassociation', schema=None) as batch_op:
+        batch_op.alter_column('id',
+               existing_type=sa.INTEGER(),
+               nullable=False)
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_wastewaterassociation', schema=None) as batch_op:
+        batch_op.alter_column('id',
+               existing_type=sa.INTEGER(),
+               nullable=True)
+
+    with op.batch_alter_table('_wastewaterartic', schema=None) as batch_op:
+        batch_op.drop_column('source_plates')
+
+    # with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
+    #     batch_op.drop_constraint("ssa_unique", type_='unique')
+
+    # ### end Alembic commands ###

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202402.4b"
+__version__ = "202403.1b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2024, Government of Canada"
 

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

@@ -276,7 +276,7 @@ class BasicSubmission(BaseClass):
         sample_list = self.hitpick_plate()
         # logger.debug("Setting background colours")
         for sample in sample_list:
-            if sample['positive']:
+            if sample['Positive']:
                 sample['background_color'] = "#f10f07"
             else:
                 if "colour" in sample.keys():
@@ -288,7 +288,7 @@ class BasicSubmission(BaseClass):
         for column in range(1, plate_columns+1):
             for row in range(1, plate_rows+1):
                 try:
-                    well = [item for item in sample_list if item['row'] == row and item['column']==column][0]
+                    well = [item for item in sample_list if item['Row'] == row and item['Column']==column][0]
                 except IndexError:
                     well = dict(name="", row=row, column=column, background_color="#ffffff")
                 output_samples.append(well)
@@ -429,7 +429,8 @@ class BasicSubmission(BaseClass):
                 case "reagents":
                     new_dict[key] = [PydReagent(**reagent) for reagent in value]
                 case "samples":
-                    new_dict[key] = [PydSample(**sample) for sample in dicto['samples']]
+                    # samples = {k.lower().replace(" ", "_"):v for k,v in dicto['samples'].items()}
+                    new_dict[key] = [PydSample(**{k.lower().replace(" ", "_"):v for k,v in sample.items()}) for sample in dicto['samples']]
                 case "equipment":
                     try:
                         new_dict[key] = [PydEquipment(**equipment) for equipment in dicto['equipment']]
@@ -1293,6 +1294,7 @@ class WastewaterArtic(BasicSubmission):
     pcr_info = Column(JSON) #: unstructured output from pcr table logger or user(Artic)
     gel_image = Column(String(64)) #: file name of gel image in zip file
     gel_info = Column(JSON) #: unstructured data from gel.
+    source_plates = Column(JSON) #: wastewater plates that samples come from
 
     __mapper_args__ = dict(polymorphic_identity="Wastewater Artic", 
                            polymorphic_load="inline", 
@@ -1328,12 +1330,33 @@ class WastewaterArtic(BasicSubmission):
         output['gel_info'] = self.gel_info
         output['gel_image'] = self.gel_image
         output['dna_core_submission_number'] = self.dna_core_submission_number
+        output['source_plates'] = self.source_plates
         return output
 
     @classmethod
     def get_abbreviation(cls) -> str:
         return "AR"
 
+    @classmethod
+    def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict:
+        """
+        Update submission dictionary with type specific information
+
+        Args:
+            input_dict (dict): Input sample dictionary
+            xl (pd.ExcelFile): original xl workbook, used for child classes mostly
+
+        Returns:
+            dict: Updated sample dictionary
+        """        
+        input_dict = super().parse_info(input_dict)
+        df = xl.parse("First Strand List", header=None)
+        plates = []
+        for row in [8,9,10]:
+            plates.append(dict(plate=df.iat[row-1, 2], start_sample=df.iat[row-1, 3]))
+        input_dict['source_plates'] = plates
+        return input_dict
+
     @classmethod
     def parse_samples(cls, input_dict: dict) -> dict:
         """
@@ -1364,8 +1387,11 @@ class WastewaterArtic(BasicSubmission):
 
         Returns:
             str: output name
-        """        
+        """       
+        # Remove letters. 
         processed = re.sub(r"[A-Z]", "", input_str)
+        # Remove trailing '-' if any
+        processed = processed.strip("-")
         try:
             en_num = re.search(r"\-\d{1}$", processed).group()
             processed = rreplace(processed, en_num, "")
@@ -1507,18 +1533,22 @@ class WastewaterArtic(BasicSubmission):
         worksheet = input_excel["First Strand List"]
         samples = cls.query(rsl_number=info['rsl_plate_num']['value']).submission_sample_associations
         samples = sorted(samples, key=attrgetter('column', 'row'))
-        source_plates = []
-        first_samples = []
-        for sample in samples:
-            sample = sample.sample
-            try:
-                assoc = [item.submission.rsl_plate_num for item in sample.sample_submission_associations if item.submission.submission_type_name=="Wastewater"][-1]
-            except IndexError:
-                logger.error(f"Association not found for {sample}")
-                continue
-            if assoc not in source_plates:
-                source_plates.append(assoc)
-                first_samples.append(sample.ww_processing_num)
+        try:
+            source_plates = [item['plate'] for item in info['source_plates']]
+            first_samples = [item['start_sample'] for item in info['source_plates']]
+        except:
+            source_plates = []
+            first_samples = []
+            for sample in samples:
+                sample = sample.sample
+                try:
+                    assoc = [item.submission.rsl_plate_num for item in sample.sample_submission_associations if item.submission.submission_type_name=="Wastewater"][-1]
+                except IndexError:
+                    logger.error(f"Association not found for {sample}")
+                    continue
+                if assoc not in source_plates:
+                    source_plates.append(assoc)
+                    first_samples.append(sample.ww_processing_num)
         # Pad list to length of 3
         source_plates += ['None'] * (3 - len(source_plates))
         first_samples += [''] * (3 - len(first_samples))
@@ -1573,7 +1603,7 @@ class WastewaterArtic(BasicSubmission):
             Tuple[dict, Template]: (Updated dictionary, Template to be rendered)
         """        
         base_dict, template = super().get_details_template(base_dict=base_dict)
-        base_dict['excluded'] += ['gel_info', 'gel_image', 'headers', "dna_core_submission_number"]
+        base_dict['excluded'] += ['gel_info', 'gel_image', 'headers', "dna_core_submission_number", "source_plates"]
         base_dict['DNA Core ID'] = base_dict['dna_core_submission_number']
         check = 'gel_info' in base_dict.keys() and base_dict['gel_info'] != None
         if check:
@@ -1598,20 +1628,20 @@ class WastewaterArtic(BasicSubmission):
             List[dict]: Updated dictionaries
         """       
         logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
-        if backup:
-            output = []
-            for assoc in self.submission_sample_associations:
-                dicto = assoc.to_sub_dict()
-                old_sub = assoc.sample.get_previous_ww_submission(current_artic_submission=self)
-                try:
-                    dicto['plate_name'] = old_sub.rsl_plate_num
-                except AttributeError:
-                    dicto['plate_name'] = ""
-                old_assoc = WastewaterAssociation.query(submission=old_sub, sample=assoc.sample, limit=1)
-                dicto['well'] = f"{row_map[old_assoc.row]}{old_assoc.column}"
-                output.append(dicto)
-        else:
-            output = super().adjust_to_dict_samples(backup=False)
+        # if backup:
+        output = []
+        for assoc in self.submission_sample_associations:
+            dicto = assoc.to_sub_dict()
+            old_sub = assoc.sample.get_previous_ww_submission(current_artic_submission=self)
+            try:
+                dicto['plate_name'] = old_sub.rsl_plate_num
+            except AttributeError:
+                dicto['plate_name'] = ""
+            old_assoc = WastewaterAssociation.query(submission=old_sub, sample=assoc.sample, limit=1)
+            dicto['well'] = f"{row_map[old_assoc.row]}{old_assoc.column}"
+            output.append(dicto)
+        # else:
+        #     output = super().adjust_to_dict_samples(backup=False)
         return output
 
     def custom_context_events(self) -> dict:
@@ -1637,9 +1667,15 @@ class WastewaterArtic(BasicSubmission):
         fname = select_open_file(obj=obj, file_extension="jpg")
         dlg = GelBox(parent=obj, img_path=fname)
         if dlg.exec():
-            self.dna_core_submission_number, img_path, output = dlg.parse_form()
+            self.dna_core_submission_number, img_path, output, comment = dlg.parse_form()
             self.gel_image = img_path.name
             self.gel_info = output
+            dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
+            com = dict(text=comment, name=getuser(), time=dt)
+            if self.comment is not None:
+                self.comment.append(com)
+            else:
+                self.comment = [com]
             logger.debug(pformat(self.gel_info))
             with ZipFile(self.__directory_path__.joinpath("submission_imgs.zip"), 'a') as zipf:
                 # Add a file located at the source_path to the destination within the zip
@@ -1703,7 +1739,7 @@ class BasicSample(BaseClass):
         except AttributeError:
             return f"<Sample({self.submitter_id})"
     
-    def to_sub_dict(self) -> dict:
+    def to_sub_dict(self, full_data:bool=False) -> dict:
         """
         gui friendly dictionary, extends parent method.
 
@@ -1712,8 +1748,10 @@ class BasicSample(BaseClass):
         """
         # logger.debug(f"Converting {self} to dict.")
         sample = {}
-        sample['submitter_id'] = self.submitter_id
-        sample['sample_type'] = self.sample_type
+        sample['Submitter ID'] = self.submitter_id
+        sample['Sample Type'] = self.sample_type
+        if full_data:
+            sample['submissions'] = [item.to_sub_dict() for item in self.sample_submission_associations]
         return sample
 
     def set_attribute(self, name:str, value):
@@ -1797,6 +1835,41 @@ class BasicSample(BaseClass):
         """        
         return input_dict
     
+    @classmethod
+    def get_details_template(cls, base_dict:dict) -> Tuple[dict, Template]:
+        """
+        Get the details jinja template for the correct class
+
+        Args:
+            base_dict (dict): incoming dictionary of Submission fields
+
+        Returns:
+            Tuple(dict, Template): (Updated dictionary, Template to be rendered)
+        """        
+        base_dict['excluded'] = ['submissions', 'excluded']
+        env = jinja_template_loading()
+        temp_name = f"{cls.__name__.lower()}_details.html"
+        logger.debug(f"Returning template: {temp_name}")
+        try:
+            template = env.get_template(temp_name)
+        except TemplateNotFound as e:
+            logger.error(f"Couldn't find template {e}")
+            template = env.get_template("basicsample_details.html")
+        return base_dict, template
+
+    def show_details(self, obj):
+        """
+        Creates Widget for showing sample details.
+
+        Args:
+            obj (_type_): parent widget
+        """        
+        logger.debug("Hello from details")
+        from frontend.widgets.sample_details import SampleDetails
+        dlg = SampleDetails(parent=obj, samp=self)
+        if dlg.exec():
+            pass
+
     @classmethod
     @setup_lookup
     def query(cls, 
@@ -1896,18 +1969,18 @@ class WastewaterSample(BasicSample):
                            polymorphic_load="inline", 
                            inherit_condition=(id == BasicSample.id))
 
-    def to_sub_dict(self) -> dict:
+    def to_sub_dict(self, full_data:bool=False) -> dict:
         """
         gui friendly dictionary, extends parent method.
 
         Returns:
             dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
         """
-        sample = super().to_sub_dict()
-        sample['ww_processing_num'] = self.ww_processing_num
-        sample['sample_location'] = self.sample_location
-        sample['received_date'] = self.received_date
-        sample['collection_date'] = self.collection_date
+        sample = super().to_sub_dict(full_data=full_data)
+        sample['WW Processing Number'] = self.ww_processing_num
+        sample['Sample Location'] = self.sample_location
+        sample['Received Date'] = self.received_date
+        sample['Collection Date'] = self.collection_date
         return sample
         
     @classmethod
@@ -1944,9 +2017,14 @@ class WastewaterSample(BasicSample):
     
     def get_previous_ww_submission(self, current_artic_submission:WastewaterArtic):
         # assocs = [assoc for assoc in self.sample_submission_associations if assoc.submission.submission_type_name=="Wastewater"]
-        subs = self.submissions[:self.submissions.index(current_artic_submission)]
-        subs = [sub for sub in subs if sub.submission_type_name=="Wastewater"]
-        logger.debug(f"Submissions up to current artic submission: {subs}")
+        # subs = self.submissions[:self.submissions.index(current_artic_submission)]
+        try:
+            plates = [item['plate'] for item in current_artic_submission.source_plates]
+        except TypeError as e:
+            logger.error(f"source_plates must not be present")
+            plates = [item.rsl_plate_num for item in self.submissions[:self.submissions.index(current_artic_submission)]]
+        subs = [sub for sub in self.submissions if sub.rsl_plate_num in plates]
+        logger.debug(f"Submissions: {subs}")
         try:
             return subs[-1]
         except IndexError:
@@ -1964,17 +2042,17 @@ class BacterialCultureSample(BasicSample):
                            polymorphic_load="inline", 
                            inherit_condition=(id == BasicSample.id))
 
-    def to_sub_dict(self) -> dict:
+    def to_sub_dict(self, full_data:bool=False) -> dict:
         """
         gui friendly dictionary, extends parent method.
 
         Returns:
             dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
         """
-        sample = super().to_sub_dict()
-        sample['name'] = self.submitter_id
-        sample['organism'] = self.organism
-        sample['concentration'] = self.concentration
+        sample = super().to_sub_dict(full_data=full_data)
+        sample['Name'] = self.submitter_id
+        sample['Organism'] = self.organism
+        sample['Concentration'] = self.concentration
         if self.control != None:
             sample['colour'] = [0,128,0]
             sample['tooltip'] = f"Control: {self.control.controltype.name} - {self.control.controltype.targets}"
@@ -2038,16 +2116,16 @@ class SubmissionSampleAssociation(BaseClass):
         # Get sample info
         # logger.debug(f"Running {self.__repr__()}")
         sample = self.sample.to_sub_dict()
-        sample['name'] = self.sample.submitter_id
-        sample['row'] = self.row
-        sample['column'] = self.column
+        sample['Name'] = self.sample.submitter_id
+        sample['Row'] = self.row
+        sample['Column'] = self.column
         try:
-            sample['well'] = f"{row_map[self.row]}{self.column}"
+            sample['Well'] = f"{row_map[self.row]}{self.column}"
         except KeyError as e:
             logger.error(f"Unable to find row {self.row} in row_map.")
-            sample['well'] = None
-        sample['plate_name'] = self.submission.rsl_plate_num
-        sample['positive'] = False
+            sample['Well'] = None
+        sample['Plate Name'] = self.submission.rsl_plate_num
+        sample['Positive'] = False
         return sample
     
     def to_hitpick(self) -> dict|None:

src/submissions/backend/validators/pydant.py

@@ -225,6 +225,7 @@ class PydEquipment(BaseModel, extra='ignore'):
     @classmethod
     def make_empty_list(cls, value):
         # logger.debug(f"Pydantic value: {value}")
+        value = convert_nans_to_nones(value)
         if value == None:
             value = ['']
         if len(value)==0:

src/submissions/frontend/widgets/gel_checker.py

@@ -2,7 +2,8 @@
 Gel box for artic quality control
 """
 from PyQt6.QtWidgets import (QWidget, QDialog, QGridLayout,
-                             QLabel, QLineEdit, QDialogButtonBox
+                             QLabel, QLineEdit, QDialogButtonBox,
+                             QTextEdit
                              )
 import numpy as np
 import pyqtgraph as pg
@@ -44,7 +45,8 @@ class GelBox(QDialog):
         # creating image view object
         self.imv = pg.ImageView()
         img = np.array(Image.open(self.img_path).rotate(-90).transpose(Image.FLIP_LEFT_RIGHT))
-        self.imv.setImage(img)#, xvals=np.linspace(1., 3., data.shape[0]))
+        self.imv.setImage(img, scale=None)#, xvals=np.linspace(1., 3., data.shape[0]))
+        
         layout = QGridLayout()
         layout.addWidget(QLabel("DNA Core Submission Number"),0,1)
         self.core_number = QLineEdit()
@@ -59,7 +61,7 @@ class GelBox(QDialog):
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
-        layout.addWidget(self.buttonBox, 22, 5, 1, 1)#, alignment=Qt.AlignmentFlag.AlignTop)
+        layout.addWidget(self.buttonBox, 23, 1, 1, 1)#, alignment=Qt.AlignmentFlag.AlignTop)
         self.setLayout(layout)
 
     def parse_form(self) -> Tuple[str, str|Path, list]:
@@ -70,14 +72,14 @@ class GelBox(QDialog):
             Tuple[str, str|Path, list]: output values
         """        
         dna_core_submission_number = self.core_number.text()
-        return dna_core_submission_number, self.img_path, self.form.parse_form()
+        values, comment = self.form.parse_form()
+        return dna_core_submission_number, self.img_path, values, comment
         
 class ControlsForm(QWidget):
 
     def __init__(self, parent) -> None:
         super().__init__(parent)
         self.layout = QGridLayout()
-        
         columns = []
         rows = []
         for iii, item in enumerate(["Negative Control Key", "Description", "Results - 65 C", "Results - 63 C", "Results - Spike"]):
@@ -98,6 +100,11 @@ class ControlsForm(QWidget):
                 widge.setText("Neg")
                 widge.setObjectName(f"{rows[iii]} : {columns[jjj]}")
                 self.layout.addWidget(widge, iii+1, jjj+2, 1, 1)
+        self.layout.addWidget(QLabel("Comments:"), 0,5,1,1)
+        self.comment_field = QTextEdit(self)
+        self.comment_field.setFixedHeight(50)
+        self.layout.addWidget(self.comment_field, 1,5,4,1)
+        
         self.setLayout(self.layout)
 
     def parse_form(self) -> List[dict]:
@@ -118,4 +125,4 @@ class ControlsForm(QWidget):
             if label[0] not in [item['name'] for item in output]:
                 output.append(dicto)
         logger.debug(pformat(output))
-        return output
+        return output, self.comment_field.toPlainText()

src/submissions/frontend/widgets/submission_details.py

@@ -1,8 +1,10 @@
 from PyQt6.QtWidgets import (QDialog, QScrollArea, QPushButton, QVBoxLayout, QMessageBox,
                              QDialogButtonBox, QTextEdit)
 from PyQt6.QtWebEngineWidgets import QWebEngineView
-from PyQt6.QtCore import Qt
-from backend.db.models import BasicSubmission
+from PyQt6.QtWebChannel import QWebChannel
+from PyQt6.QtCore import Qt, pyqtSlot
+
+from backend.db.models import BasicSubmission, BasicSample
 from tools import check_if_app
 from .functions import select_save_file
 from io import BytesIO
@@ -31,7 +33,7 @@ class SubmissionDetails(QDialog):
             self.app = parent.parent().parent().parent().parent().parent().parent()
         except AttributeError:
             self.app = None
-        self.setWindowTitle("Submission Details")
+        self.setWindowTitle(f"Submission Details - {sub.rsl_plate_num}")
         # create scrollable interior
         interior = QScrollArea()
         interior.setParent(self)
@@ -46,19 +48,34 @@ class SubmissionDetails(QDialog):
         self.base_dict['platemap'] = sub.make_plate_map()
         self.base_dict, self.template = sub.get_details_template(base_dict=self.base_dict)
         self.html = self.template.render(sub=self.base_dict)
-        webview = QWebEngineView()
-        webview.setMinimumSize(900, 500)
-        webview.setMaximumSize(900, 500)
-        webview.setHtml(self.html)
+        self.webview = QWebEngineView(parent=self)
+        self.webview.setMinimumSize(900, 500)
+        self.webview.setMaximumSize(900, 500)
+        self.webview.setHtml(self.html)
         self.layout = QVBoxLayout()
         interior.resize(900, 500)
-        interior.setWidget(webview)
+        interior.setWidget(self.webview)
         self.setFixedSize(900, 500)
         # button to export a pdf version
         btn = QPushButton("Export PDF")
         btn.setParent(self)
         btn.setFixedWidth(900)
         btn.clicked.connect(self.export)
+        # setup channel
+        self.channel = QWebChannel()
+        self.channel.registerObject('backend', self)
+        self.webview.page().setWebChannel(self.channel)
+
+    @pyqtSlot(str)
+    def sample_details(self, sample):
+        # print(f"{string} is in row {row}, column {column}")
+        # self.webview.setHtml(f"<html><body><br><br>{sample}</body></html>")
+        sample = BasicSample.query(submitter_id=sample)
+        base_dict = sample.to_sub_dict(full_data=True)
+        base_dict, template = sample.get_details_template(base_dict=base_dict)
+        html = template.render(sample=base_dict)
+        self.webview.setHtml(html)
+        # sample.show_details(obj=self)
 
     def export(self):
         """
@@ -130,4 +147,4 @@ class SubmissionComment(QDialog):
         full_comment = [{"name":commenter, "time": dt, "text": comment}]
         logger.debug(f"Full comment: {full_comment}")
         return full_comment
-        
+

src/submissions/frontend/widgets/submission_table.py

@@ -103,6 +103,7 @@ class SubmissionsSheet(QTableView):
         Args:
             event (_type_): the item of interest
         """        
+        # logger.debug(event().__dict__)
         id = self.selectionModel().currentIndex()
         id = id.sibling(id.row(),0).data()
         submission = BasicSubmission.query(id=id)

src/submissions/templates/basicsample_details.html

@@ -0,0 +1,54 @@
+<!doctype html>
+<html>
+    <head>
+        {% block head %}
+        <style>
+            /* Tooltip container */
+            .tooltip {
+              position: relative;
+              display: inline-block;
+              border-bottom: 1px dotted black; /* If you want dots under the hoverable text */
+            }
+            
+            /* Tooltip text */
+            .tooltip .tooltiptext {
+              visibility: hidden;
+              width: 120px;
+              background-color: black;
+              color: #fff;
+              text-align: center;
+              padding: 5px 0;
+              border-radius: 6px;
+             
+              /* Position the tooltip text - see examples below! */
+              position: absolute;
+              z-index: 1;
+              bottom: 100%;
+              left: 50%;
+              margin-left: -60px;
+            }
+            
+            /* Show the tooltip text when you mouse over the tooltip container */
+            .tooltip:hover .tooltiptext {
+              visibility: visible;
+              font-size: large;
+            }
+        </style>
+        <title>Sample Details for {{ sample['Submitter ID'] }}</title>
+        <script src="qrc:///qtwebchannel/qwebchannel.js"></script>
+        {% endblock %}
+    </head>
+    <body>
+        {% block body %}
+        <h2><u>Sample Details for {{ sample['Submitter ID'] }}</u></h2>
+        <p>{% for key, value in sample.items() if key not in sample['excluded'] %}
+            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key }}: </b>{{ value }}<br>
+        {% endfor %}</p>
+        {% if sample['submissions'] %}<h2>Submissions:</h2>
+            {% for submission in sample['submissions'] %}
+            <p>{{ submission['Plate Name'] }}: {{ submission['Well'] }}</p>
+            {% endfor %}
+        {% endif %}
+        {% endblock %}
+    </body>
+</html>

src/submissions/templates/basicsubmission_details.html

@@ -35,6 +35,7 @@
             }
         </style>
         <title>Submission Details for {{ sub['Plate Number'] }}</title>
+        <script src="qrc:///qtwebchannel/qwebchannel.js"></script>
         {% endblock %}
     </head>
     <body>
@@ -57,7 +58,7 @@
         {% if sub['samples'] %}
         <h3><u>Samples:</u></h3>
         <p>{% for item in sub['samples'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['well'] }}:</b> {% if item['organism'] %} {{ item['name'] }} - ({{ item['organism']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}){% else %} {{ item['name']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}{% endif %}<br>
+            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['Well'] }}:</b> {% if item['Organism'] %} {{ item['Name'] }} - ({{ item['Organism']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}){% else %} {{ item['Name']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}{% endif %}<br>
         {% endfor %}</p>
         {% endif %}
         {% if sub['controls'] %}
@@ -116,4 +117,15 @@
         {% endif %}
         {% endblock %}
     </body>
+    <script>
+        var backend;
+        new QWebChannel(qt.webChannelTransport, function (channel) {
+            backend = channel.objects.backend;
+        });
+        {% for sample in sub['samples'] %}
+        document.getElementById("{{sample['Submitter ID']}}").addEventListener("dblclick", function(){
+            backend.sample_details("{{ sample['Submitter ID'] }}");
+        });
+        {% endfor %}
+    </script>
 </html>

src/submissions/templates/plate_map.html

@@ -1,15 +1,15 @@
         <div class="gallery" style="display: grid;grid-template-columns: repeat({{ PLATE_COLUMNS }}, 7.5vw);grid-template-rows: repeat({{ PLATE_ROWS }}, 7.5vw);grid-gap: 2px;">
             {% for sample in samples %}
-                <div class="well" style="background-color: {{sample['background_color']}};
+                <div class="well" id="{{sample['Submitter ID']}}" style="background-color: {{sample['background_color']}};
                 border: 1px solid #000;
                 padding: 20px;
-                grid-column-start: {{sample['column']}};
-                grid-column-end: {{sample['column']}};
-                grid-row-start: {{sample['row']}};
-                grid-row-end: {{sample['row']}};
+                grid-column-start: {{sample['Column']}};
+                grid-column-end: {{sample['Column']}};
+                grid-row-start: {{sample['Row']}};
+                grid-row-end: {{sample['Row']}};
                 display: flex;
                 ">
-                    <div class="tooltip" style="font-size: 0.5em; text-align: center; word-wrap: break-word;">{{ sample['name'] }}
+                    <div class="tooltip" style="font-size: 0.5em; text-align: center; word-wrap: break-word;">{{ sample['Name'] }}
                         <span class="tooltiptext">{{ sample['tooltip'] }}</span>
                     </div>
                 </div>

src/submissions/templates/tooltip.html

@@ -1,4 +1,4 @@
-Sample name: {{ fields['submitter_id'] }}<br>
-{% if fields['organism'] %}Organism: {{ fields['organism'] }}<br>{% endif %}
-{% if fields['concentration'] %}Concentration: {{ fields['concentration'] }}<br>{% endif %}
-Well: {{ fields['well'] }}<!--{{ fields['column'] }}-->
+Sample name: {{ fields['Submitter ID'] }}<br>
+{% if fields['Organism'] %}Organism: {{ fields['Organism'] }}<br>{% endif %}
+{% if fields['Concentration'] %}Concentration: {{ fields['Concentration'] }}<br>{% endif %}
+Well: {{ fields['Well'] }}<!--{{ fields['column'] }}-->

src/submissions/tools.py

@@ -116,37 +116,7 @@ def check_regex_match(pattern:str, check:str) -> bool:
     except TypeError:
         return False
     
-class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):
-
-    def doRollover(self):
-        """
-        Override base class method to make the new log file group writable.
-        """
-        # Rotate the file first.
-        handlers.RotatingFileHandler.doRollover(self)
-        # Add group write to the current permissions.
-        currMode = os.stat(self.baseFilename).st_mode
-        os.chmod(self.baseFilename, currMode | stat.S_IWGRP)
-
-    def _open(self):
-        prevumask=os.umask(0o002)
-        rtv=handlers.RotatingFileHandler._open(self)
-        os.umask(prevumask)
-        return rtv
-
-class StreamToLogger(object):
-    """
-    Fake file-like stream object that redirects writes to a logger instance.
-    """
-
-    def __init__(self, logger, log_level=logging.INFO):
-        self.logger = logger
-        self.log_level = log_level
-        self.linebuf = ''
-
-    def write(self, buf):
-        for line in buf.rstrip().splitlines():
-            self.logger.log(self.log_level, line.rstrip())
+# Settings
 
 class Settings(BaseSettings):
     """
@@ -303,6 +273,26 @@ def get_config(settings_path: Path|str|None=None) -> Settings:
         settings = yaml.load(stream, Loader=yaml.Loader)
     return Settings(**settings)
 
+# Logging formatters
+
+class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):
+
+    def doRollover(self):
+        """
+        Override base class method to make the new log file group writable.
+        """
+        # Rotate the file first.
+        handlers.RotatingFileHandler.doRollover(self)
+        # Add group write to the current permissions.
+        currMode = os.stat(self.baseFilename).st_mode
+        os.chmod(self.baseFilename, currMode | stat.S_IWGRP)
+
+    def _open(self):
+        prevumask=os.umask(0o002)
+        rtv=handlers.RotatingFileHandler._open(self)
+        os.umask(prevumask)
+        return rtv
+
 class CustomFormatter(logging.Formatter):
 
     grey = "\x1b[38;20m"
@@ -326,6 +316,20 @@ class CustomFormatter(logging.Formatter):
         formatter = logging.Formatter(log_fmt)
         return formatter.format(record)
 
+class StreamToLogger(object):
+    """
+    Fake file-like stream object that redirects writes to a logger instance.
+    """
+
+    def __init__(self, logger, log_level=logging.INFO):
+        self.logger = logger
+        self.log_level = log_level
+        self.linebuf = ''
+
+    def write(self, buf):
+        for line in buf.rstrip().splitlines():
+            self.logger.log(self.log_level, line.rstrip())
+
 def setup_logger(verbosity:int=3):
     """
     Set logger levels using settings.