Returned to pdf exports from details.

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

@@ -1042,7 +1042,7 @@ class BasicSubmission(BaseClass):
     #     return [item.to_sub_dict() for item in self.submission_sample_associations]
 
     @classmethod
-    def get_details_template(cls, base_dict: dict) -> Tuple[dict, Template]:
+    def get_details_template(cls, base_dict: dict) -> Template:
         """
         Get the details jinja template for the correct class
 
@@ -1357,13 +1357,13 @@ class BasicSubmission(BaseClass):
         if fname.name == "":
             # logger.debug(f"export cancelled.")
             return
-        if full_backup:
-            backup = self.to_dict(full_data=True)
-            try:
-                with open(self.__backup_path__.joinpath(fname.with_suffix(".yml")), "w") as f:
-                    yaml.dump(backup, f)
-            except KeyError as e:
-                logger.error(f"Problem saving yml backup file: {e}")
+        # if full_backup:
+        #     backup = self.to_dict(full_data=True)
+        #     try:
+        #         with open(self.__backup_path__.joinpath(fname.with_suffix(".yml")), "w") as f:
+        #             yaml.dump(backup, f)
+        #     except KeyError as e:
+        #         logger.error(f"Problem saving yml backup file: {e}")
         writer = pyd.to_writer()
         writer.xl.save(filename=fname.with_suffix(".xlsx"))
 
@@ -1632,6 +1632,8 @@ class Wastewater(BasicSubmission):
             dict: Updated information
         """
         input_dict = super().finalize_details(input_dict)
+        # NOTE: Currently this is preserving the generator items, can we come up with a better way?
+        input_dict['samples'] = [sample for sample in input_dict['samples']]
         dummy_samples = []
         for item in input_dict['samples']:
             # logger.debug(f"Sample dict: {item}")
@@ -1681,12 +1683,10 @@ class Wastewater(BasicSubmission):
         for sample in self.samples:
             # logger.debug(f"Running update on: {sample}")
             try:
-                # sample_dict = [item for item in parser.samples if item['sample'] == sample.rsl_number][0]
                 sample_dict = next(item for item in parser.samples if item['sample'] == sample.rsl_number)
             except StopIteration:
                 continue
             self.update_subsampassoc(sample=sample, input_dict=sample_dict)
-        # 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: dict, tpl_obj=None) -> dict:
@@ -1703,6 +1703,7 @@ class Wastewater(BasicSubmission):
         from backend.excel.writer import DocxWriter
         input_dict = super().custom_docx_writer(input_dict)
         well_24 = []
+        input_dict['samples'] = [item for item in input_dict['samples']]
         samples_copy = deepcopy(input_dict['samples'])
         for sample in sorted(samples_copy, key=itemgetter('column', 'row')):
             try:

src/submissions/backend/excel/writer.py

@@ -519,6 +519,7 @@ class DocxWriter(object):
         Args:
             base_dict (dict): dictionary of info to be written to template.
         """
+        logger.debug(f"Incoming base dict: {pformat(base_dict)}")
         self.sub_obj = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=base_dict['submission_type'])
         env = jinja_template_loading()
         temp_name = f"{base_dict['submission_type'].replace(' ', '').lower()}_subdocument.docx"
@@ -528,8 +529,8 @@ class DocxWriter(object):
         if subdocument.exists():
             main_template = self.create_merged_template(main_template, subdocument)
         self.template = DocxTemplate(main_template)
-        base_dict['platemap'] = self.create_plate_map(base_dict['samples'], rows=8, columns=12)
-        # logger.debug(pformat(base_dict['plate_map']))
+        base_dict['platemap'] = [item for item in self.create_plate_map(base_dict['samples'], rows=8, columns=12)]
+        # logger.debug(pformat(base_dict['platemap']))
         try:
             base_dict['excluded'] += ["platemap"]
         except KeyError:

src/submissions/backend/validators/pydant.py

@@ -739,11 +739,22 @@ class PydSubmission(BaseModel, extra='allow'):
                 pass
         else:
             # logger.debug("Extracting 'value' from attributes")
-            output = {k: (getattr(self, k) if not isinstance(getattr(self, k), dict) else getattr(self, k)['value']) for
-                      k in fields}
-
+            output = {k: self.filter_field(k) for k in fields}
         return output
 
+    def filter_field(self, key:str):
+        item = getattr(self, key)
+        # logger.debug(f"Attempting deconstruction of {key}: {item} with type {type(item)}")
+        match item:
+            case dict():
+                try:
+                    item = item['value']
+                except KeyError:
+                    logger.error(f"Couldn't get dict value: {item}")
+            case _:
+                pass
+        return item
+
     def find_missing(self) -> Tuple[dict, dict]:
         """
         Retrieves info and reagents marked as missing.

src/submissions/frontend/widgets/submission_details.py

@@ -1,12 +1,13 @@
 """
 Webview to show submission and sample details.
 """
-from PyQt6.QtGui import QColor
+from PyQt6.QtGui import QColor, QPageSize, QPageLayout
+from PyQt6.QtPrintSupport import QPrinter
 from PyQt6.QtWidgets import (QDialog, QPushButton, QVBoxLayout,
                              QDialogButtonBox, QTextEdit, QGridLayout)
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWebChannel import QWebChannel
-from PyQt6.QtCore import Qt, pyqtSlot
+from PyQt6.QtCore import Qt, pyqtSlot, QMarginsF
 from jinja2 import TemplateNotFound
 
 from backend.db.models import BasicSubmission, BasicSample, Reagent, KitType
@@ -43,7 +44,7 @@ class SubmissionDetails(QDialog):
         self.layout = QGridLayout()
         # self.setFixedSize(900, 500)
         # NOTE: button to export a pdf version
-        self.btn = QPushButton("Export DOCX")
+        self.btn = QPushButton("Export PDF")
         self.btn.setFixedWidth(775)
         self.btn.clicked.connect(self.export)
         self.back = QPushButton("Back")
@@ -151,7 +152,8 @@ class SubmissionDetails(QDialog):
         self.base_dict = submission.finalize_details(self.base_dict)
         # logger.debug(f"Creating barcode.")
         # logger.debug(f"Making platemap...")
-        self.base_dict['platemap'] = BasicSubmission.make_plate_map(sample_list=submission.hitpick_plate())
+        self.base_dict['platemap'] = submission.make_plate_map(sample_list=submission.hitpick_plate())
+        self.base_dict['excluded'] = submission.get_default_info("details_ignore")
         self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
         template_path = Path(self.template.environment.loader.__getattribute__("searchpath")[0])
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
@@ -159,11 +161,10 @@ class SubmissionDetails(QDialog):
         # logger.debug(f"Submission_details: {pformat(self.base_dict)}")
         # logger.debug(f"User is power user: {is_power_user()}")
         self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user(), css=css)
-        with open("test.html", "w") as f:
-            f.write(self.html)
+        # with open("test.html", "w") as f:
+        #     f.write(self.html)
         self.webview.setHtml(self.html)
 
-
     @pyqtSlot(str)
     def sign_off(self, submission: str | BasicSubmission):
         # logger.debug(f"Signing off on {submission} - ({getuser()})")
@@ -177,18 +178,12 @@ class SubmissionDetails(QDialog):
         """
         Renders submission to html, then creates and saves .pdf file to user selected file.
         """
-        export_plate = BasicSubmission.query(rsl_plate_num=self.export_plate)
-        base_dict = export_plate.to_dict(full_data=True)
-        base_dict['excluded'] = export_plate.get_default_info('details_ignore')
-        logger.debug(f"base dict: {pformat(base_dict)}")
-        writer = DocxWriter(base_dict=base_dict)
-        fname = select_save_file(obj=self, default_name=base_dict['plate_number'], extension="docx")
-        writer.save(fname)
-        # try:
-        #     html_to_pdf(html=self.html, output_file=fname)
-        # except PermissionError as e:
-        #     logger.error(f"Error saving pdf: {e}")
-
+        fname = select_save_file(obj=self, default_name=self.export_plate, extension="pdf")
+        page_layout = QPageLayout()
+        page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
+        page_layout.setOrientation(QPageLayout.Orientation.Portrait)
+        page_layout.setMargins(QMarginsF(25, 25, 25, 25))
+        self.webview.page().printToPdf(fname.with_suffix(".pdf").__str__(), page_layout)
 
 class SubmissionComment(QDialog):
     """