Various bug fixes

TODO.md

@@ -1,3 +1,4 @@
+- [x] Fix cropping of gel image.
 - [ ] Create Tips ... *sigh*.
 - [x] Create platemap image from html for export to pdf.
 - [x] Move plate map maker to submission.

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

@@ -9,7 +9,7 @@ from tempfile import TemporaryDirectory
 from reportlab.graphics.barcode import createBarcodeImageInMemory
 from reportlab.graphics.shapes import Drawing
 from reportlab.lib.units import mm
-from operator import attrgetter
+from operator import attrgetter, itemgetter
 from pprint import pformat
 from . import Reagent, SubmissionType, KitType, Organization
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
@@ -1349,11 +1349,13 @@ class WastewaterArtic(BasicSubmission):
         Returns:
             dict: Updated sample dictionary
         """        
+        from backend.validators import RSLNamer
         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]))
+            plate_name = RSLNamer(df.iat[row-1, 2]).parsed_name
+            plates.append(dict(plate=plate_name, start_sample=df.iat[row-1, 3]))
         input_dict['source_plates'] = plates
         return input_dict
 
@@ -1373,6 +1375,16 @@ class WastewaterArtic(BasicSubmission):
         # Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
         # at the end, this has to be done here. No moving to sqlalchemy object :(
         input_dict['submitter_id'] = re.sub(r"\s\(.+\)\s?$", "", str(input_dict['submitter_id'])).strip()
+        try: 
+            input_dict['ww_processing_num'] = input_dict['sample_name_(lims)']
+            del input_dict['sample_name_(lims)']
+        except KeyError:
+            logger.error(f"Unable to set ww_processing_num for sample {input_dict['submitter_id']}")
+        try: 
+            input_dict['ww_full_sample_id'] = input_dict['sample_name_(ww)']
+            del input_dict['sample_name_(ww)']
+        except KeyError:
+            logger.error(f"Unable to set ww_processing_num for sample {input_dict['submitter_id']}")
         if "ENC" in input_dict['submitter_id']:
             input_dict['submitter_id'] = cls.en_adapter(input_str=input_dict['submitter_id'])
         return input_dict
@@ -1642,6 +1654,7 @@ class WastewaterArtic(BasicSubmission):
             output.append(dicto)
         # else:
         #     output = super().adjust_to_dict_samples(backup=False)
+        
         return output
 
     def custom_context_events(self) -> dict:
@@ -1751,7 +1764,7 @@ class BasicSample(BaseClass):
         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]
+            sample['submissions'] = sorted([item.to_sub_dict() for item in self.sample_submission_associations], key=itemgetter('submitted_date'))
         return sample
 
     def set_attribute(self, name:str, value):
@@ -1857,19 +1870,6 @@ class BasicSample(BaseClass):
             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, 
@@ -2126,6 +2126,7 @@ class SubmissionSampleAssociation(BaseClass):
             sample['Well'] = None
         sample['Plate Name'] = self.submission.rsl_plate_num
         sample['Positive'] = False
+        sample['submitted_date'] = self.submission.submitted_date
         return sample
     
     def to_hitpick(self) -> dict|None:

src/submissions/frontend/widgets/gel_checker.py

@@ -44,9 +44,11 @@ class GelBox(QDialog):
         pg.setConfigOptions(antialias=True)
         # creating image view object
         self.imv = pg.ImageView()
-        img = np.array(Image.open(self.img_path).rotate(-90).transpose(Image.FLIP_LEFT_RIGHT))
+        # Create image.
-        self.imv.setImage(img, scale=None)#, xvals=np.linspace(1., 3., data.shape[0]))
+        # For some reason, ImageView wants to flip the image, so we have to rotate and flip the array first.
-        
+        # Using the Image.rotate function results in cropped image.
+        img = np.flip(np.rot90(np.array(Image.open(self.img_path)),1),0)
+        self.imv.setImage(img)
         layout = QGridLayout()
         layout.addWidget(QLabel("DNA Core Submission Number"),0,1)
         self.core_number = QLineEdit()

src/submissions/frontend/widgets/submission_details.py

@@ -37,21 +37,21 @@ class SubmissionDetails(QDialog):
         # create scrollable interior
         interior = QScrollArea()
         interior.setParent(self)
-        self.base_dict = sub.to_dict(full_data=True)
+        # self.base_dict = sub.to_dict(full_data=True)
-        logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
+        # logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
-        # don't want id
+        # # don't want id
-        del self.base_dict['id']
+        # del self.base_dict['id']
-        logger.debug(f"Creating barcode.")
+        # logger.debug(f"Creating barcode.")
-        if not check_if_app():
+        # if not check_if_app():
-            self.base_dict['barcode'] = base64.b64encode(sub.make_plate_barcode(width=120, height=30)).decode('utf-8')
+        #     self.base_dict['barcode'] = base64.b64encode(sub.make_plate_barcode(width=120, height=30)).decode('utf-8')
-        logger.debug(f"Making platemap...")
+        # logger.debug(f"Making platemap...")
-        self.base_dict['platemap'] = sub.make_plate_map()
+        # self.base_dict['platemap'] = sub.make_plate_map()
-        self.base_dict, self.template = sub.get_details_template(base_dict=self.base_dict)
+        # self.base_dict, self.template = sub.get_details_template(base_dict=self.base_dict)
-        self.html = self.template.render(sub=self.base_dict)
+        # self.html = self.template.render(sub=self.base_dict)
         self.webview = QWebEngineView(parent=self)
         self.webview.setMinimumSize(900, 500)
         self.webview.setMaximumSize(900, 500)
-        self.webview.setHtml(self.html)
+        # self.webview.setHtml(self.html)
         self.layout = QVBoxLayout()
         interior.resize(900, 500)
         interior.setWidget(self.webview)
@@ -64,18 +64,46 @@ class SubmissionDetails(QDialog):
         # setup channel
         self.channel = QWebChannel()
         self.channel.registerObject('backend', self)
+        self.submission_details(submission=sub)
         self.webview.page().setWebChannel(self.channel)
 
     @pyqtSlot(str)
-    def sample_details(self, sample):
+    def sample_details(self, sample:str):
-        # print(f"{string} is in row {row}, column {column}")
+        """
-        # self.webview.setHtml(f"<html><body><br><br>{sample}</body></html>")
+        Changes details view to summary of Sample
+
+        Args:
+            sample (str): Submitter Id of the sample.
+        """        
         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)
+        
+    @pyqtSlot(str)
+    def submission_details(self, submission:str|BasicSubmission):
+        """
+        Sets details view to summary of Submission.
+
+        Args:
+            submission (str | BasicSubmission): Submission of interest.
+        """        
+        logger.debug(f"Details for: {submission}")
+        if isinstance(submission, str):
+            submission = BasicSubmission.query(rsl_number=submission)
+        self.base_dict = submission.to_dict(full_data=True)
+        logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
+        # don't want id
+        del self.base_dict['id']
+        logger.debug(f"Creating barcode.")
+        if not check_if_app():
+            self.base_dict['barcode'] = base64.b64encode(submission.make_plate_barcode(width=120, height=30)).decode('utf-8')
+        logger.debug(f"Making platemap...")
+        self.base_dict['platemap'] = submission.make_plate_map()
+        self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
+        self.html = self.template.render(sub=self.base_dict)
+        self.webview.setHtml(self.html)
 
     def export(self):
         """

src/submissions/frontend/widgets/submission_widget.py

@@ -395,7 +395,7 @@ class SubmissionFormWidget(QWidget):
 
     def __init__(self, parent: QWidget, **kwargs) -> None:
         super().__init__(parent)
-        self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment', 'equipment']
+        self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment', 'equipment', 'source_plates']
         self.recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
         layout = QVBoxLayout()
         for k, v in kwargs.items():

src/submissions/templates/basicsample_details.html

@@ -46,9 +46,20 @@
         {% endfor %}</p>
         {% if sample['submissions'] %}<h2>Submissions:</h2>
             {% for submission in sample['submissions'] %}
-            <p>{{ submission['Plate Name'] }}: {{ submission['Well'] }}</p>
+            <p id="{{ submission['Plate Name'] }}"><b>{{ submission['Plate Name'] }}:</b> {{ submission['Well'] }}</p>
             {% endfor %}
         {% endif %}
         {% endblock %}
     </body>
+    <script>
+      var backend;
+      new QWebChannel(qt.webChannelTransport, function (channel) {
+          backend = channel.objects.backend;
+      });
+      {% for submission in sample['submissions'] %}
+      document.getElementById("{{ submission['Plate Name'] }}").addEventListener("dblclick", function(){
+          backend.submission_details("{{ submission['Plate Name'] }}");
+      });
+      {% endfor %}
+  </script>
 </html>