Various bugfixes, new template sub-docs

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

@@ -1499,7 +1499,7 @@ class Process(BaseClass):
     @setup_lookup
     def query(cls,
               name: str | None = None,
-              id: int = 1,
+              id: int | None = None,
               limit: int = 0) -> Process | List[Process]:
         """
         Lookup Processes
@@ -1514,7 +1514,7 @@ class Process(BaseClass):
         query = cls.__database_session__.query(cls)
         match name:
             case str():
-                # logger.debug(f"Lookup Process with name str {name}")
+                logger.debug(f"Lookup Process with name str {name}")
                 query = query.filter(cls.name == name)
                 limit = 1
             case _:

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

@@ -31,6 +31,8 @@ from dateutil.parser import parse
 from pathlib import Path
 from jinja2.exceptions import TemplateNotFound
 from jinja2 import Template
+from docxtpl import InlineImage
+from io import BytesIO
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -730,7 +732,7 @@ class BasicSubmission(BaseClass):
         return input_excel
 
     @classmethod
-    def custom_docx_writer(cls, input_dict):
+    def custom_docx_writer(cls, input_dict:dict, tpl_obj=None):
 
         return input_dict
 
@@ -1493,7 +1495,7 @@ class Wastewater(BasicSubmission):
         # self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
 
     @classmethod
-    def custom_docx_writer(cls, input_dict):
+    def custom_docx_writer(cls, input_dict:dict, tpl_obj=None):
         from backend.excel.writer import DocxWriter
         input_dict = super().custom_docx_writer(input_dict)
         well_24 = []
@@ -1551,7 +1553,7 @@ class WastewaterArtic(BasicSubmission):
         if report:
             return output
         output['gel_info'] = self.gel_info
-        output['gel_image'] = self.gel_image
+        output['gel_image_path'] = self.gel_image
         output['dna_core_submission_number'] = self.dna_core_submission_number
         output['source_plates'] = self.source_plates
         output['artic_date'] = self.artic_date or self.submitted_date
@@ -1856,7 +1858,7 @@ class WastewaterArtic(BasicSubmission):
         """
         base_dict, template = super().get_details_template(base_dict=base_dict)
         base_dict['excluded'] += ['gel_info', 'gel_image', 'headers', "dna_core_submission_number", "source_plates",
-                                  "gel_controls"]
+                                  "gel_controls, gel_image_path"]
         base_dict['DNA Core ID'] = base_dict['dna_core_submission_number']
         # check = 'gel_info' in base_dict.keys() and base_dict['gel_info'] is not None
         if check_key_or_attr(key='gel_info', interest=base_dict, check_none=True):
@@ -1865,9 +1867,9 @@ class WastewaterArtic(BasicSubmission):
             base_dict['headers'] += headers
             # logger.debug(f"Gel info: {pformat(base_dict['headers'])}")
         # check = 'gel_image' in base_dict.keys() and base_dict['gel_image'] is not None
-        if check_key_or_attr(key='gel_image', interest=base_dict, check_none=True):
+        if check_key_or_attr(key='gel_image_path', interest=base_dict, check_none=True):
             with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
-                base_dict['gel_image'] = base64.b64encode(zipped.read(base_dict['gel_image'])).decode('utf-8')
+                base_dict['gel_image'] = base64.b64encode(zipped.read(base_dict['gel_image_path'])).decode('utf-8')
         return base_dict, template
 
     # def adjust_to_dict_samples(self, backup: bool = False) -> List[dict]:
@@ -1935,6 +1937,20 @@ class WastewaterArtic(BasicSubmission):
                 zipf.write(img_path, self.gel_image)
             self.save()
 
+    @classmethod
+    def custom_docx_writer(cls, input_dict:dict, tpl_obj=None):
+        input_dict = super().custom_docx_writer(input_dict)
+        if check_key_or_attr(key='gel_image_path', interest=input_dict, check_none=True):
+            with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
+                img = zipped.read(input_dict['gel_image_path'])
+            with tempfile.TemporaryFile(mode="wb", suffix=".jpg", delete=False) as tmp:
+                tmp.write(img)
+            logger.debug(f"Tempfile: {tmp.name}")
+        img = InlineImage(tpl_obj, image_descriptor=tmp.name)#, width=5.5)#, height=400)
+        input_dict['gel_image'] = img
+        return input_dict
+
+
 
 # Sample Classes
 

src/submissions/backend/excel/writer.py

@@ -477,7 +477,7 @@ class DocxWriter(object):
             base_dict['excluded'] += ["platemap"]
         except KeyError:
             base_dict['excluded'] = ["platemap"]
-        base_dict = self.sub_obj.custom_docx_writer(base_dict)
+        base_dict = self.sub_obj.custom_docx_writer(base_dict, tpl_obj=self.template)
         # logger.debug(f"Base dict: {pformat(base_dict)}")
         self.template.render({"sub": base_dict})
 

src/submissions/backend/validators/pydant.py

@@ -304,7 +304,10 @@ class PydEquipment(BaseModel, extra='ignore'):
             value = ['']
         if len(value) == 0:
             value = ['']
+        try:
             value = [item.strip() for item in value]
+        except AttributeError:
+            pass
         return value
 
     def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Equipment, SubmissionEquipmentAssociation]:

src/submissions/frontend/widgets/equipment_usage.py

@@ -59,7 +59,10 @@ class EquipmentUsage(QDialog):
                 case _:
                     pass
         logger.debug(f"parsed output of Equsage form: {pformat(output)}")
+        try:
             return [item.strip() for item in output if item is not None]
+        except AttributeError:
+            return [item for item in output if item is not None]
 
     class LabelRow(QWidget):
 
@@ -131,8 +134,8 @@ class RoleComboBox(QWidget):
         """
         Changes what tips are available when process is changed
         """        
-        process = self.process.currentText()
+        process = self.process.currentText().strip()
-        logger.debug(f"Checking process: {process}")
+        logger.debug(f"Checking process: {process} for equipment {self.role.name}")
         process = Process.query(name=process)
         if process.tip_roles:
             for iii, tip_role in enumerate(process.tip_roles):

src/submissions/frontend/widgets/gel_checker.py

@@ -54,9 +54,11 @@ class GelBox(QDialog):
         layout = QGridLayout()
         layout.addWidget(QLabel("DNA Core Submission Number"),0,1)
         self.core_number = QLineEdit()
+        self.core_number.setText(self.submission.dna_core_submission_number)
         layout.addWidget(self.core_number, 0,2)
         layout.addWidget(QLabel("Gel Barcode"),0,3)
         self.gel_barcode = QLineEdit()
+        self.gel_barcode.setText(self.submission.gel_barcode)
         layout.addWidget(self.gel_barcode, 0, 4)
         # setting this layout to the widget
         # plot window goes on right side, spanning 3 rows

src/submissions/frontend/widgets/submission_details.py

@@ -10,7 +10,6 @@ from backend.db.models import BasicSubmission, BasicSample
 from tools import is_power_user, html_to_pdf
 from .functions import select_save_file
 from io import BytesIO
-from tempfile import TemporaryFile, TemporaryDirectory
 from pathlib import Path
 import logging, base64
 from getpass import getuser
@@ -43,7 +42,7 @@ class SubmissionDetails(QDialog):
         self.layout = QVBoxLayout()
         self.setFixedSize(900, 500)
         # NOTE: button to export a pdf version
-        btn = QPushButton("Export PDF")
+        btn = QPushButton("Export DOCX")
         btn.setFixedWidth(875)
         btn.clicked.connect(self.export)
         self.layout.addWidget(btn)
@@ -103,8 +102,6 @@ class SubmissionDetails(QDialog):
         logger.debug(f"Submission_details: {pformat(self.base_dict)}")
         self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user(), css=css)
         self.webview.setHtml(self.html)
-        with open("test.html", "w") as f:
-            f.write(self.html)
         self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
 
     @pyqtSlot(str)