Added html links for equipment/processes/tips.

CHANGELOG.md

@@ -1,3 +1,7 @@
+# 202504.04
+
+- Added html links for equipment/processes/tips.
+
 # 202504.03
 
 - Split Concentration controls on the chart so they are individually selectable.

TODO.md

@@ -1,3 +1,6 @@
+- [ ] transfer details template rendering fully into sql objects
+- [x] Add in connecting links for tips.
+- [x] Add in connecting links for equipment/processes. 
 - [ ] move functions from widgets.functions to... app?
 - [x] Apply below fix to all other date-based queries.
 - [x] Fix Control graph chart bug that excludes today's controls.
@@ -12,7 +15,6 @@
 - [x] Upgrade to generators when returning lists.
 - [x] Revamp frontend.widgets.controls_chart to include visualizations?
 - [x] Convert Parsers to using openpyxl.
-  - The hardest part of this is going to be the sample parsing. I'm onto using the cell formulas in the plate map to suss out the location in the lookup table, but it could get a little recursive up in here.
 - [ ] Create a default info return function.
 - [x] Parse comment from excel sheet.
 - [x] Make reporting better. 

src/submissions/backend/db/__init__.py

@@ -55,9 +55,10 @@ def update_log(mapper, connection, target):
             continue
         added = [str(item) for item in hist.added]
         # NOTE: Attributes left out to save space
-        if attr.key in ['artic_technician', 'submission_sample_associations', 'submission_reagent_associations',
+        # if attr.key in ['artic_technician', 'submission_sample_associations', 'submission_reagent_associations',
-                        'submission_equipment_associations', 'submission_tips_associations', 'contact_id', 'gel_info',
+        #                 'submission_equipment_associations', 'submission_tips_associations', 'contact_id', 'gel_info',
-                        'gel_controls', 'source_plates']:
+        #                 'gel_controls', 'source_plates']:
+        if attr.key in LogMixin.tracking_exclusion:
             continue
         deleted = [str(item) for item in hist.deleted]
         change = dict(field=attr.key, added=added, deleted=deleted)

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

@@ -9,7 +9,7 @@ from sqlalchemy import Column, INTEGER, String, JSON
 from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session, InstrumentedAttribute, ColumnProperty
 from sqlalchemy.ext.declarative import declared_attr
 from sqlalchemy.exc import ArgumentError
-from typing import Any, List
+from typing import Any, List, ClassVar
 from pathlib import Path
 from sqlalchemy.orm.relationships import _RelationshipDeclared
 from tools import report_result, list_sort_dict
@@ -25,6 +25,12 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 
 class LogMixin(Base):
+
+    tracking_exclusion: ClassVar = ['artic_technician', 'submission_sample_associations',
+                                    'submission_reagent_associations', 'submission_equipment_associations',
+                                    'submission_tips_associations', 'contact_id', 'gel_info', 'gel_controls',
+                                    'source_plates']
+
     __abstract__ = True
 
     @property

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

@@ -4,12 +4,15 @@ All kit and reagent related models
 from __future__ import annotations
 import json, zipfile, yaml, logging, re, sys
 from pprint import pformat
+
+from jinja2 import Template, TemplateNotFound
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.ext.associationproxy import association_proxy
 from sqlalchemy.ext.hybrid import hybrid_property
 from datetime import date, datetime, timedelta
-from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, yaml_regex_creator, timezone
+from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, yaml_regex_creator, timezone, \
+    jinja_template_loading
 from typing import List, Literal, Generator, Any, Tuple
 from pandas import ExcelFile
 from pathlib import Path
@@ -2065,6 +2068,53 @@ class Equipment(BaseClass, LogMixin):
             output.append(equipment[choice])
         return output
 
+    def to_sub_dict(self, full_data: bool = False, **kwargs) -> dict:
+        """
+        dictionary containing values necessary for gui
+
+        Args:
+            full_data (bool, optional): Whether to include submissions in data for details. Defaults to False.
+
+        Returns:
+            dict: representation of the equipment's attributes
+        """
+        if self.nickname:
+            nickname = self.nickname
+        else:
+            nickname = self.name
+        output = dict(
+            name=self.name,
+            nickname=nickname,
+            asset_number=self.asset_number
+        )
+        if full_data:
+            subs = []
+            output['submissions'] = [dict(plate=item.submission.rsl_plate_num, process=item.process.name)
+                                     if item.process else dict(plate=item.submission.rsl_plate_num, process="NA")
+                                     for item in self.equipment_submission_associations]
+            output['excluded'] = ['missing', 'submissions', 'excluded', 'editable']
+        return output
+
+    @classproperty
+    def details_template(cls) -> 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)
+        """
+        env = jinja_template_loading()
+        temp_name = f"{cls.__name__.lower()}_details.html"
+        try:
+            template = env.get_template(temp_name)
+        except TemplateNotFound as e:
+            logger.error(f"Couldn't find template {e}")
+            template = env.get_template("equipment_details.html")
+        return template
+
 
 class EquipmentRole(BaseClass):
     """
@@ -2219,6 +2269,10 @@ class SubmissionEquipmentAssociation(BaseClass):
         self.equipment = equipment
         self.role = role
 
+    @property
+    def process(self):
+        return Process.query(id=self.process_id)
+
     def to_sub_dict(self) -> dict:
         """
         This SubmissionEquipmentAssociation as a dictionary
@@ -2433,6 +2487,44 @@ class Process(BaseClass):
             tip_roles=tip_roles
         )
 
+    def to_sub_dict(self, full_data: bool = False, **kwargs) -> dict:
+        """
+        dictionary containing values necessary for gui
+
+        Args:
+            full_data (bool, optional): Whether to include submissions in data for details. Defaults to False.
+
+        Returns:
+            dict: representation of the equipment's attributes
+        """
+        output = dict(
+            name=self.name,
+        )
+        if full_data:
+            output['submissions'] = [dict(plate=sub.submission.rsl_plate_num, equipment=sub.equipment.name) for sub in self.submissions]
+            output['excluded'] = ['missing', 'submissions', 'excluded', 'editable']
+        return output
+
+    @classproperty
+    def details_template(cls) -> 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)
+        """
+        env = jinja_template_loading()
+        temp_name = f"{cls.__name__.lower()}_details.html"
+        try:
+            template = env.get_template(temp_name)
+        except TemplateNotFound as e:
+            logger.error(f"Couldn't find template {e}")
+            template = env.get_template("process_details.html")
+        return template
+
 
 class TipRole(BaseClass):
     """
@@ -2576,6 +2668,45 @@ class Tips(BaseClass, LogMixin):
             name=self.name
         )
 
+    def to_sub_dict(self, full_data: bool = False, **kwargs) -> dict:
+        """
+        dictionary containing values necessary for gui
+
+        Args:
+            full_data (bool, optional): Whether to include submissions in data for details. Defaults to False.
+
+        Returns:
+            dict: representation of the equipment's attributes
+        """
+        output = dict(
+            name=self.name,
+            lot=self.lot,
+        )
+        if full_data:
+            output['submissions'] = [dict(plate=item.submission.rsl_plate_num, role=item.role_name)
+                                     for item in self.tips_submission_associations]
+            output['excluded'] = ['missing', 'submissions', 'excluded', 'editable']
+        return output
+
+    @classproperty
+    def details_template(cls) -> 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)
+        """
+        env = jinja_template_loading()
+        temp_name = f"{cls.__name__.lower()}_details.html"
+        try:
+            template = env.get_template(temp_name)
+        except TemplateNotFound as e:
+            logger.error(f"Couldn't find template {e}")
+            template = env.get_template("tips_details.html")
+        return template
 
 class SubmissionTypeTipRoleAssociation(BaseClass):
     """

src/submissions/frontend/visualizations/__init__.py

@@ -133,8 +133,8 @@ class CustomFigure(Figure):
         else:
             html += "<h1>No data was retrieved for the given parameters.</h1>"
         html += '</body></html>'
-        with open("test.html", "w", encoding="utf-8") as f:
+        # with open("test.html", "w", encoding="utf-8") as f:
-            f.write(html)
+        #     f.write(html)
         return html
 
 

src/submissions/frontend/widgets/submission_details.py

@@ -7,7 +7,7 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWebChannel import QWebChannel
 from PyQt6.QtCore import Qt, pyqtSlot
 from jinja2 import TemplateNotFound
-from backend.db.models import BasicSubmission, BasicSample, Reagent, KitType
+from backend.db.models import BasicSubmission, BasicSample, Reagent, KitType, Equipment, Process, Tips
 from tools import is_power_user, jinja_template_loading, timezone, get_application_from_parent
 from .functions import select_save_file, save_pdf
 from pathlib import Path
@@ -84,6 +84,48 @@ class SubmissionDetails(QDialog):
         else:
             self.back.setEnabled(True)
 
+    @pyqtSlot(str)
+    def equipment_details(self, equipment: str | Equipment):
+        logger.debug(f"Equipment details")
+        if isinstance(equipment, str):
+            equipment = Equipment.query(name=equipment)
+        base_dict = equipment.to_sub_dict(full_data=True)
+        template = equipment.details_template
+        template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
+        with open(template_path.joinpath("css", "styles.css"), "r") as f:
+            css = f.read()
+        html = template.render(equipment=base_dict, css=css)
+        self.webview.setHtml(html)
+        self.setWindowTitle(f"Equipment Details - {equipment.name}")
+
+    @pyqtSlot(str)
+    def process_details(self, process: str | Process):
+        logger.debug(f"Equipment details")
+        if isinstance(process, str):
+            process = Process.query(name=process)
+        base_dict = process.to_sub_dict(full_data=True)
+        template = process.details_template
+        template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
+        with open(template_path.joinpath("css", "styles.css"), "r") as f:
+            css = f.read()
+        html = template.render(process=base_dict, css=css)
+        self.webview.setHtml(html)
+        self.setWindowTitle(f"Process Details - {process.name}")
+
+    @pyqtSlot(str)
+    def tips_details(self, tips: str | Tips):
+        logger.debug(f"Equipment details: {tips}")
+        if isinstance(tips, str):
+            tips = Tips.query(lot=tips)
+        base_dict = tips.to_sub_dict(full_data=True)
+        template = tips.details_template
+        template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
+        with open(template_path.joinpath("css", "styles.css"), "r") as f:
+            css = f.read()
+        html = template.render(tips=base_dict, css=css)
+        self.webview.setHtml(html)
+        self.setWindowTitle(f"Process Details - {tips.name}")
+
     @pyqtSlot(str)
     def sample_details(self, sample: str | BasicSample):
         """
@@ -103,8 +145,8 @@ class SubmissionDetails(QDialog):
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
             css = f.read()
         html = template.render(sample=base_dict, css=css)
-        with open(f"{sample.submitter_id}.html", 'w') as f:
+        # with open(f"{sample.submitter_id}.html", 'w') as f:
-            f.write(html)
+        #     f.write(html)
         self.webview.setHtml(html)
         self.setWindowTitle(f"Sample Details - {sample.submitter_id}")
 

src/submissions/templates/basicsubmission_details.html

@@ -20,19 +20,19 @@
         {% if sub['reagents'] %}
         <h3><u>Reagents:</u></h3>
         <p>{% for item in sub['reagents'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}</b>: <a class="data-link reagent" id="{{ item['lot'] }}">{{ item['lot'] }} (EXP: {{ item['expiry'] }})</a><br>
+            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}:</b> <a class="data-link reagent" id="{{ item['lot'] }}">{{ item['lot'] }} (EXP: {{ item['expiry'] }})</a><br>
         {% endfor %}</p>
         {% endif %}
         {% if sub['equipment'] %}
         <h3><u>Equipment:</u></h3>
         <p>{% for item in sub['equipment'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}:</b> {{ item['name'] }} ({{ item['asset_number'] }}): {{ item['processes'][0]|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}<br>
+            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}:</b> <a class="data-link equipment" id="{{ item['name'] }}"> {{ item['name'] }} ({{ item['asset_number'] }})</a>: <a class="data-link process" id="{{ item['processes'][0]|replace('\n\t', '') }}">{{ item['processes'][0]|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}</a><br>
         {% endfor %}</p>
         {% endif %}
         {% if sub['tips'] %}
         <h3><u>Tips:</u></h3>
         <p>{% for item in sub['tips'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}:</b> {{ item['name'] }} ({{ item['lot'] }})<br>
+            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}:</b> <a class="data-link tips" id="{{ item['lot'] }}">{{ item['name'] }} ({{ item['lot'] }})</a><br>
         {% endfor %}</p>
         {% endif %}
         {% if sub['samples'] %}
@@ -99,6 +99,33 @@
           })
         }
 
+        var equipmentSelection = document.getElementsByClassName('equipment');
+
+        for(let i = 0; i < equipmentSelection.length; i++) {
+          equipmentSelection[i].addEventListener("click", function() {
+            console.log(equipmentSelection[i].id);
+            backend.equipment_details(equipmentSelection[i].id);
+          })
+        }
+
+        var processSelection = document.getElementsByClassName('process');
+
+        for(let i = 0; i < processSelection.length; i++) {
+          processSelection[i].addEventListener("click", function() {
+            console.log(processSelection[i].id);
+            backend.process_details(processSelection[i].id);
+          })
+        }
+
+        var tipsSelection = document.getElementsByClassName('tips');
+
+        for(let i = 0; i < tipsSelection.length; i++) {
+          tipsSelection[i].addEventListener("click", function() {
+            console.log(tipsSelection[i].id);
+            backend.tips_details(tipsSelection[i].id);
+          })
+        }
+
         document.getElementById("sign_btn").addEventListener("click", function(){
             backend.sign_off("{{ sub['plate_number'] }}");
         });

src/submissions/templates/equipment_details.html

@@ -0,0 +1,50 @@
+{% extends "details.html" %}
+<head>
+    {% block head %}
+    {{ super() }}
+    <title>Equipment Details for {{ equipment['name'] }}</title>
+    {% endblock %}
+</head>
+<body>
+    {% block body %}
+    <h2><u>Equipment Details for {{ equipment['name'] }}</u></h2>
+    {{ super() }}
+    <p>{% for key, value in equipment.items() if key not in equipment['excluded'] %}
+<!--        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{% if permission and key in reagent['editable']%}<input type={% if key=='expiry' %}"date"{% else %}"text"{% endif %} id="{{ key }}" name="{{ key }}" value="{{ value }}">{% else %}{{ value }}{% endif %}<br>-->
+        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
+    {% endfor %}</p>
+<!--    {% if permission %}-->
+<!--        <button type="button" id="save_btn">Save</button>-->
+<!--    {% endif %}-->
+    {% if equipment['submissions'] %}<h2>Submissions:</h2>
+        {% for submission in equipment['submissions'] %}
+        <p><b><a class="data-link" id="{{ submission['plate'] }}">{{ submission['plate'] }}:</a></b> <a class="data-link process" id="{{ submission['process'] }}">{{ submission['process'] }}</a></p>
+        {% endfor %}
+    {% endif %}
+    {% endblock %}
+</body>
+<script>
+  {% block script %}
+  {{ super() }}
+
+  var processSelection = document.getElementsByClassName('process');
+
+        for(let i = 0; i < processSelection.length; i++) {
+          processSelection[i].addEventListener("click", function() {
+            console.log(processSelection[i].id);
+            backend.process_details(processSelection[i].id);
+          })
+        }
+
+  {% for submission in equipment['submissions'] %}
+  document.getElementById("{{ submission }}").addEventListener("click", function(){
+      backend.submission_details("{{ submission }}");
+  });
+  {% endfor %}
+
+  document.addEventListener('DOMContentLoaded', function() {
+          backend.activate_export(false);
+      }, false);
+  {% endblock %}
+</script>
+</html>

src/submissions/templates/process_details.html

@@ -0,0 +1,49 @@
+{% extends "details.html" %}
+<head>
+    {% block head %}
+    {{ super() }}
+    <title>Process Details for {{ process['name'] }}</title>
+    {% endblock %}
+</head>
+<body>
+    {% block body %}
+    <h2><u>Process Details for {{ process['name'] }}</u></h2>
+    {{ super() }}
+    <p>{% for key, value in process.items() if key not in process['excluded'] %}
+<!--        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{% if permission and key in reagent['editable']%}<input type={% if key=='expiry' %}"date"{% else %}"text"{% endif %} id="{{ key }}" name="{{ key }}" value="{{ value }}">{% else %}{{ value }}{% endif %}<br>-->
+        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
+    {% endfor %}</p>
+<!--    {% if permission %}-->
+<!--        <button type="button" id="save_btn">Save</button>-->
+<!--    {% endif %}-->
+    {% if process['submissions'] %}<h2>Submissions:</h2>
+        {% for submission in process['submissions'] %}
+        <p><b><a class="data-link" id="{{ submission['plate'] }}">{{ submission['plate'] }}:</a></b><a class="data-link equipment" id="{{ submission['equipment'] }}">{{ submission['equipment'] }}</a></p>
+        {% endfor %}
+    {% endif %}
+    {% endblock %}
+</body>
+<script>
+  {% block script %}
+  {{ super() }}
+
+  var equipmentSelection = document.getElementsByClassName('equipment');
+
+        for(let i = 0; i < equipmentSelection.length; i++) {
+          equipmentSelection[i].addEventListener("click", function() {
+            console.log(equipmentSelection[i].id);
+            backend.equipment_details(equipmentSelection[i].id);
+          })
+        }
+
+  {% for submission in process['submissions'] %}
+  document.getElementById("{{ submission['plate'] }}").addEventListener("click", function(){
+      backend.submission_details("{{ submission['plate'] }}");
+  });
+  {% endfor %}
+  document.addEventListener('DOMContentLoaded', function() {
+          backend.activate_export(false);
+      }, false);
+  {% endblock %}
+</script>
+</html>

src/submissions/templates/tips_details.html

@@ -0,0 +1,50 @@
+{% extends "details.html" %}
+<head>
+    {% block head %}
+    {{ super() }}
+    <title>Tips Details for {{ tips['name'] }}</title>
+    {% endblock %}
+</head>
+<body>
+    {% block body %}
+    <h2><u>Tips Details for {{ tips['name'] }}</u></h2>
+    {{ super() }}
+    <p>{% for key, value in tips.items() if key not in tips['excluded'] %}
+<!--        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{% if permission and key in reagent['editable']%}<input type={% if key=='expiry' %}"date"{% else %}"text"{% endif %} id="{{ key }}" name="{{ key }}" value="{{ value }}">{% else %}{{ value }}{% endif %}<br>-->
+        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
+    {% endfor %}</p>
+<!--    {% if permission %}-->
+<!--        <button type="button" id="save_btn">Save</button>-->
+<!--    {% endif %}-->
+    {% if tips['submissions'] %}<h2>Submissions:</h2>
+        {% for submission in tips['submissions'] %}
+        <p><b><a class="data-link" id="{{ submission['plate'] }}">{{ submission['plate'] }}:</a></b> <a class="data-link process" id="{{ submission['role'] }}">{{ submission['role'] }}</a></p>
+        {% endfor %}
+    {% endif %}
+    {% endblock %}
+</body>
+<script>
+  {% block script %}
+  {{ super() }}
+
+  var processSelection = document.getElementsByClassName('process');
+
+        for(let i = 0; i < processSelection.length; i++) {
+          processSelection[i].addEventListener("click", function() {
+            console.log(processSelection[i].id);
+            backend.process_details(processSelection[i].id);
+          })
+        }
+
+  {% for submission in tips['submissions'] %}
+  document.getElementById("{{ submission }}").addEventListener("click", function(){
+      backend.submission_details("{{ submission }}");
+  });
+  {% endfor %}
+
+  document.addEventListener('DOMContentLoaded', function() {
+          backend.activate_export(false);
+      }, false);
+  {% endblock %}
+</script>
+</html>

submissions.spec

@@ -16,7 +16,8 @@ api_path = project_path.joinpath(".venv", "Scripts", "sphinx-apidoc").absolute()
 subprocess.run([api_path, "-o", doc_path.joinpath("source").__str__(), project_path.joinpath("src", "submissions").__str__(), "-f"])
 print(bcolors.BOLD + "Running Sphinx subprocess to generate html docs..." + bcolors.ENDC)
 docs_build = doc_path.joinpath("build")
-#docs_build.mkdir(exist_ok=True, parents=True)
+if not docs_build.exists():
+    docs_build.mkdir(exist_ok=True, parents=True)
 subprocess.run([build_path, doc_path.joinpath("source").__str__(), docs_build.__str__(), "-a"])
 
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