New docx templates

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

@@ -4,6 +4,7 @@ Models for the main submission and sample types.
 from __future__ import annotations
 
 import sys
+from copy import deepcopy
 from getpass import getuser
 import logging, uuid, tempfile, re, yaml, base64
 from zipfile import ZipFile
@@ -728,6 +729,11 @@ class BasicSubmission(BaseClass):
         logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} autofill")
         return input_excel
 
+    @classmethod
+    def custom_docx_writer(cls, input_dict):
+
+        return input_dict
+
     @classmethod
     def enforce_name(cls, instr: str, data: dict | None = {}) -> str:
         """
@@ -1439,7 +1445,7 @@ class Wastewater(BasicSubmission):
         dummy_samples = []
         for item in input_dict['samples']:
             # logger.debug(f"Sample dict: {item}")
-            thing = item
+            thing = deepcopy(item)
             try:
                 thing['row'] = thing['source_row']
                 thing['column'] = thing['source_column']
@@ -1486,6 +1492,28 @@ class Wastewater(BasicSubmission):
             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):
+        from backend.excel.writer import DocxWriter
+        input_dict = super().custom_docx_writer(input_dict)
+        well_24 = []
+        samples_copy = deepcopy(input_dict['samples'])
+        for sample in sorted(samples_copy, key=itemgetter('column', 'row')):
+        # for sample in input_dict['samples']:
+            try:
+                row = sample['source_row']
+            except KeyError:
+                continue
+            try:
+                column = sample['source_column']
+            except KeyError:
+                continue
+            copy = dict(submitter_id=sample['submitter_id'], row=row, column=column)
+            well_24.append(copy)
+        input_dict['origin_plate'] = DocxWriter.create_plate_map(sample_list=well_24, rows=4, columns=6)
+        return input_dict
+
+
 
 class WastewaterArtic(BasicSubmission):
     """

src/submissions/backend/excel/writer.py

@@ -1,10 +1,11 @@
 import logging
 from copy import copy
+from operator import itemgetter
 from pathlib import Path
 # from pathlib import Path
 from pprint import pformat
 from typing import List
-
+from collections import OrderedDict
 from jinja2 import TemplateNotFound
 from openpyxl import load_workbook, Workbook
 from backend.db.models import SubmissionType, KitType, BasicSubmission
@@ -13,6 +14,7 @@ from io import BytesIO
 from collections import OrderedDict
 from tools import jinja_template_loading
 from docxtpl import DocxTemplate
+from docx import Document
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -460,14 +462,65 @@ class TipWriter(object):
 class DocxWriter(object):
 
     def __init__(self, base_dict: 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()}_document.docx"
+        temp_name = f"{base_dict['submission_type'].replace(' ', '').lower()}_subdocument.docx"
-        path = Path(env.loader.__getattribute__("searchpath")[0]).joinpath(temp_name)
+        path = Path(env.loader.__getattribute__("searchpath")[0])
-        template = DocxTemplate(path)
+        main_template = path.joinpath("basicsubmission_document.docx")
+        subdocument = path.joinpath(temp_name)
+        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']))
         try:
-            template.render(base_dict)
+            base_dict['excluded'] += ["platemap"]
-        except FileNotFoundError:
+        except KeyError:
-            template = DocxTemplate(
+            base_dict['excluded'] = ["platemap"]
-                Path(env.loader.__getattribute__("searchpath")[0]).joinpath("basicsubmission_document.docx"))
+        base_dict = self.sub_obj.custom_docx_writer(base_dict)
-            template.render({"sub": base_dict})
+        # logger.debug(f"Base dict: {pformat(base_dict)}")
-        template.save("test.docx")
+        self.template.render({"sub": base_dict})
+
+    @classmethod
+    def create_plate_map(self, sample_list: List[dict], rows: int = 0, columns: int = 0) -> List[list]:
+        sample_list = sorted(sample_list, key=itemgetter('column', 'row'))
+        if rows == 0:
+            rows = max([sample['row'] for sample in sample_list])
+        if columns == 0:
+            columns = max([sample['column'] for sample in sample_list])
+        output = []
+        for row in range(0, rows):
+            contents = [''] * columns
+            for column in range(0, columns):
+                try:
+                    ooi = [item for item in sample_list if item['row']==row+1 and item['column']==column+1][0]
+                except IndexError:
+                    continue
+                contents[column] = ooi['submitter_id']
+            # contents = [sample['submitter_id'] for sample in sample_list if sample['row'] == row + 1]
+            # contents = [f"{sample['row']},{sample['column']}" for sample in sample_list if sample['row'] == row + 1]
+            if len(contents) < columns:
+                contents += [''] * (columns - len(contents))
+            if not contents:
+                contents = [''] * columns
+            output.append(contents)
+        return output
+
+    def create_merged_template(self, *args):
+        merged_document = Document()
+        output = BytesIO()
+        for index, file in enumerate(args):
+            sub_doc = Document(file)
+            # Don't add a page break if you've reached the last file.
+            # if index < len(args) - 1:
+            #     sub_doc.add_page_break()
+            for element in sub_doc.element.body:
+                merged_document.element.body.append(element)
+        merged_document.save(output)
+        return output
+
+
+    def save(self, filename: Path | str):
+        if isinstance(filename, str):
+            filename = Path(filename)
+        self.template.save(filename)

src/submissions/backend/validators/pydant.py

@@ -327,17 +327,17 @@ class PydEquipment(BaseModel, extra='ignore'):
             process = Process.query(name=self.processes[0])
             if process is None:
                 logger.error(f"Found unknown process: {process}.")
-                from frontend.widgets.pop_ups import QuestionAsker
+                # from frontend.widgets.pop_ups import QuestionAsker
-                dlg = QuestionAsker(title="Add Process?",
+                # dlg = QuestionAsker(title="Add Process?",
-                                    message=f"Unable to find {self.processes[0]} in the database.\nWould you like to add it?")
+                #                     message=f"Unable to find {self.processes[0]} in the database.\nWould you like to add it?")
-                if dlg.exec():
+                # if dlg.exec():
-                    kit = submission.extraction_kit
+                #     kit = submission.extraction_kit
-                    submission_type = submission.submission_type
+                #     submission_type = submission.submission_type
-                    process = Process(name=self.processes[0])
+                #     process = Process(name=self.processes[0])
-                    process.kit_types.append(kit)
+                #     process.kit_types.append(kit)
-                    process.submission_types.append(submission_type)
+                #     process.submission_types.append(submission_type)
-                    process.equipment.append(equipment)
+                #     process.equipment.append(equipment)
-                    process.save()
+                #     process.save()
             assoc.process = process
             assoc.role = self.role
         else:
@@ -727,7 +727,7 @@ class PydSubmission(BaseModel, extra='allow'):
                         if equip is None:
                             continue
                         equip, association = equip.toSQL(submission=instance)
-                        if association is not None:
+                        if association is not None and association not in instance.submission_equipment_associations:
                             # association.save()
                             # logger.debug(
                             #     f"Equipment association SQL object to be added to submission: {association.__dict__}")
@@ -738,7 +738,7 @@ class PydSubmission(BaseModel, extra='allow'):
                             continue
                         logger.debug(f"Converting tips: {tips} to sql.")
                         association = tips.to_sql(submission=instance)
-                        if association is not None:
+                        if association is not None and association not in instance.submission_tips_associations:
                             # association.save()
                             instance.submission_tips_associations.append(association)
                 case item if item in instance.jsons():

src/submissions/frontend/widgets/equipment_usage.py

@@ -59,7 +59,7 @@ class EquipmentUsage(QDialog):
                 case _:
                     pass
         logger.debug(f"parsed output of Equsage form: {pformat(output)}")
-        return [item for item in output if item is not None]
+        return [item.strip() for item in output if item is not None]
 
     class LabelRow(QWidget):
 
@@ -165,7 +165,7 @@ class RoleComboBox(QWidget):
         try:
             return PydEquipment(
                 name=eq.name,
-                processes=[self.process.currentText()],
+                processes=[self.process.currentText().strip()],
                 role=self.role.name,
                 asset_number=eq.asset_number,
                 nickname=eq.nickname,

src/submissions/frontend/widgets/submission_details.py

@@ -1,3 +1,5 @@
+from PyQt6.QtGui import QPageSize
+from PyQt6.QtPrintSupport import QPrinter
 from PyQt6.QtWidgets import (QDialog, QPushButton, QVBoxLayout, QMessageBox,
                              QDialogButtonBox, QTextEdit)
 from PyQt6.QtWebEngineWidgets import QWebEngineView
@@ -17,6 +19,8 @@ from pprint import pformat
 from html2image import Html2Image
 from PIL import Image
 from typing import List
+from backend.excel.writer import DocxWriter
+
 
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -90,13 +94,17 @@ class SubmissionDetails(QDialog):
         # del self.base_dict['id']
         # 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, 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:
+            css = f.read()
         logger.debug(f"Submission_details: {pformat(self.base_dict)}")
-        self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
+        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:
+        with open("test.html", "w") as f:
-        #     f.write(self.html)
+            f.write(self.html)
         self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
 
     @pyqtSlot(str)
@@ -112,31 +120,32 @@ class SubmissionDetails(QDialog):
         """
         Renders submission to html, then creates and saves .pdf file to user selected file.
         """
-        logger.debug(f"Base dict: {pformat(self.base_dict)}")
+        writer = DocxWriter(base_dict=self.base_dict)
         fname = select_save_file(obj=self, default_name=self.base_dict['plate_number'], extension="docx")
-        image_io = BytesIO()
+        writer.save(fname)
-        temp_dir = Path(TemporaryDirectory().name)
+        # image_io = BytesIO()
-        hti = Html2Image(output_path=temp_dir, size=(2400, 1500))
+        # temp_dir = Path(TemporaryDirectory().name)
-        temp_file = Path(TemporaryFile(dir=temp_dir, suffix=".png").name)
+        # hti = Html2Image(output_path=temp_dir, size=(2400, 1500))
-        screenshot = hti.screenshot(self.base_dict['platemap'], save_as=temp_file.name)
+        # temp_file = Path(TemporaryFile(dir=temp_dir, suffix=".png").name)
-        export_map = Image.open(screenshot[0])
+        # screenshot = hti.screenshot(self.base_dict['platemap'], save_as=temp_file.name)
-        export_map = export_map.convert('RGB')
+        # export_map = Image.open(screenshot[0])
+        # export_map = export_map.convert('RGB')
+        # try:
+        #     export_map.save(image_io, 'JPEG')
+        # except AttributeError:
+        #     logger.error(f"No plate map found")
+        # self.base_dict['export_map'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
+        # del self.base_dict['platemap']
+        # self.html2 = self.template.render(sub=self.base_dict)
         try:
-            export_map.save(image_io, 'JPEG')
+            html_to_pdf(html=self.html, output_file=fname)
-        except AttributeError:
-            logger.error(f"No plate map found")
-        self.base_dict['export_map'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
-        del self.base_dict['platemap']
-        self.html2 = self.template.render(sub=self.base_dict)
-        try:
-            html_to_pdf(html=self.html2, output_file=fname)
         except PermissionError as e:
             logger.error(f"Error saving pdf: {e}")
-            msg = QMessageBox()
+        #     msg = QMessageBox()
-            msg.setText("Permission Error")
+        #     msg.setText("Permission Error")
-            msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
+        #     msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
-            msg.setWindowTitle("Permission Error")
+        #     msg.setWindowTitle("Permission Error")
-            msg.exec()
+        #     msg.exec()
 
 
 class SubmissionComment(QDialog):

src/submissions/frontend/widgets/submission_widget.py

@@ -312,6 +312,7 @@ class SubmissionFormWidget(QWidget):
                 if dlg.exec():
                     # NOTE: Do not add duplicate reagents.
                     result = None
+
                 else:
                     self.app.ctx.database_session.rollback()
                     report.add_result(Result(msg="Overwrite cancelled", status="Information"))

src/submissions/templates/basicsubmission_details.html

@@ -2,38 +2,11 @@
 <html>
     <head>
         {% block head %}
+        {% if css %}
         <style>
-            /* Tooltip container */
+            {{ css }}
-            .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>
+        {% endif %}
         <title>Submission Details for {{ sub['Plate Number'] }}</title>
         <script src="qrc:///qtwebchannel/qwebchannel.js"></script>
         {% endblock %}

src/submissions/templates/css/styles.css

@@ -0,0 +1,29 @@
+/* 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;
+}

src/submissions/tools.py

@@ -658,11 +658,13 @@ def html_to_pdf(html, output_file: Path | str):
     logger.debug(f"Printing PDF to {output_file}")
     document = QWebEngineView()
     document.setHtml(html)
+    # document.show()
     printer = QPrinter(QPrinter.PrinterMode.HighResolution)
     printer.setOutputFormat(QPrinter.OutputFormat.PdfFormat)
     printer.setOutputFileName(output_file.absolute().__str__())
     printer.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
     document.print(printer)
+    # document.close()
     # HTML(string=html).write_pdf(output_file)
     # new_parser = HtmlToDocx()
     # docx = new_parser.parse_html_string(html)