landon/Submissions-App
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Addition of procedure parser in import.

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This commit is contained in:
lwark
2025-06-17 15:09:51 -05:00
parent 0233bc3ac2
commit d8c3f3bbb2
31 changed files with 688 additions and 304 deletions
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37
src/submissions/templates/clientsubmission_details.html Normal file
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@@ -0,0 +1,37 @@
{% extends "details.html"%}
<head>
{% block head %}
{{ super() }}
<title>ClientSubmission Details for {{ clientsubmission['name'] }}</title>
{% endblock %}
</head>
<body>
{% block body %}
<h2><u>Submission Details for {{ clientsubmission['name'] }}</u></h2>
{{ super() }}
<p>{% for key, value in clientsubmission.items() if key not in clientsubmission['excluded'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title | replace("Id", "ID") }}: </b>{% if key=='cost' %}{% if clientsubmission['cost'] %} {{ "${:,.2f}".format(value) }}{% endif %}{% else %}{{ value }}{% endif %}<br>
{% endfor %}
</p>
{% if clientsubmission['sample'] %}
<button type="button" class="collapsible"><h3><u>Client Submitted Samples:</u></h3></button>
<div class="nested">
<p>{% for sample in clientsubmission['sample'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<a class="data-link sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
{% endfor %}</p>
</div>
{% endif %}
{% if clientsubmission['run'] %}
<button type="button" class="collapsible"><h3><u>Runs:</u></h3></button>
<div class="nested">
{% for run in clientsubmission['run'] %}
{% with run=run, child=True %}
{% include "run_details.html" %}
{% endwith %}
{% endfor %}
</div>
{% endif %}
{% endblock %}
</body>

33
src/submissions/templates/css/styles.css
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@@ -146,3 +146,36 @@ ul.no-bullets {
background-color: pink;
}
/* */
.nested {
margin-left: 50px;
padding: 0 18px;
display: none;
overflow: hidden;
background-color: #f1f1f1;
}
/* Style the button that is used to open and close the collapsible content */
.collapsible {
background-color: #eee;
color: #444;
cursor: pointer;
padding: 18px;
width: 100%;
border: none;
text-align: left;
outline: none;
font-size: 15px;
}
/* Add a background color to the button if it is clicked on (add the .active class with JS), and when you move the mouse over it (hover) */
.active, .collapsible:hover {
background-color: #ccc;
}
.unused {
color: red;
text-decoration-line: line-through;
text-decoration-color: red;
}

30
src/submissions/templates/details.html
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@@ -1,4 +1,4 @@
<!DOCTYPE html>
{% if not child %}
<html lang="en">
<head>
{% block head %}
@@ -14,17 +14,41 @@
{% endblock %}
</head>
<body>
{% endif %}
{% block body %}
<!--<button type="button" id="back_btn">Back</button>-->
{% endblock %}
{% block signing_button %}{% endblock %}
{% if not child %}
</body>
{% endif %}
{% block script %}
{% if not child %}
<script>
var coll = document.getElementsByClassName("collapsible");
var i;
for (i = 0; i < coll.length; i++) {
coll[i].addEventListener("click", function() {
this.classList.toggle("active");
var content = this.nextElementSibling;
if (content.style.display === "block") {
content.style.display = "none";
} else {
content.style.display = "block";
}
});
}
</script>
{% endif %}
{% for j in js%}
<script>
{{ j }}
</script>
{% endfor %}
{% endblock %}
</html>
{% if not child %}
</html>
{% endif %}

15
src/submissions/templates/procedure_creation.html
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@@ -28,13 +28,24 @@
<br><hr><br>
{% for key, value in procedure['reagentrole'].items() %}
<label for="{{ key }}">{{ key }}:</label><br>
<select class="reagentrole dropdown" id="{{ key }}" name="{{ reagentrole }}"><br>
<datalist class="reagentrole dropdown" id="{{ key }}" name="{{ reagentrole }}"><br>
{% for reagent in value %}
<option value="{{ reagent }}">{{ reagent }}</option>
{% endfor %}
</select>
</datalist>
{% endfor %}
{% endif %}
{% if proceduretype['equipment'] %}
<br><hr><br>
{% for equipmentrole in proceduretype['equipment'] %}
<label for="{{ equipmentrole['name'] }}">{{ equipmentrole['name'] }}:</label><br>
<select class="equipmentrole dropdown" id="{{ equipmentrole['name'] }}" name="{{ equipmentrole['name'] }}"><br>
{% for equipment in equipmentrole['equipment'] %}
<option value="{{ equipment['name'] }}">{{ equipment['name'] }}</option>
{% endfor %}
</select>
{% endfor %}
{% endif%}
</form>
</div>
<div class="right">

29
src/submissions/templates/procedure_details.html
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@@ -1,4 +1,5 @@
{% extends "details.html" %}
{% if not child %}
<head>
{% block head %}
@@ -7,9 +8,31 @@
{% endblock %}
</head>
<body>
{% endif %}
{% block body %}
<h2><u>Procedure Details for {{ procedure['name'] }}</u></h2>
{{ super() }}
<p>{% for key, value in procedure.items() if key not in procedure['excluded'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title | replace("Pcr", "PCR") }}: {{ value }}</b><br>
{% endfor %}</p>
{% if procedure['results'] %}
<button type="button" class="collapsible"><h3><u>Results:</u></h3></button>
<div class="nested">
{% for result in procedure['results'] %}
<p>{% for k, v in result['result'].items() %}
<b>{{ key | replace("_", " ") | title | replace("Rsl", "RSL") }}:</b> {{ value }}<br>
{% endfor %}</p>
{% endfor %}
</div>
{% endif %}
{% if procedure['sample'] %}
<button type="button" class="collapsible"><h3><u>Procedure Samples:</u></h3></button>
<div class="nested">
<p>{% for sample in procedure['sample'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<a class="{% if sample['active'] %}data-link {% else %}unused {% endif %}sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
{% endfor %}</p>
</div>
{% endif %}
{% endblock %}
</body>
</body>

176
src/submissions/templates/run_details.html
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@@ -1,135 +1,59 @@
{% extends "details.html" %}
<html>
<head>
{% block head %}
{{ super() }}
<title>Submission Details for {{ sub['plate_number'] }}</title>
{% endblock %}
</head>
<body>
{% block body %}
<h2><u>Submission Details for {{ sub['plate_number'] }}</u></h2>&nbsp;&nbsp;&nbsp;{% if sub['barcode'] %}<img align='right' height="30px" width="120px" src="data:image/jpeg;base64,{{ sub['barcode'] | safe }}">{% endif %}
{{ super() }}
<p>{% for key, value in sub.items() if key not in sub['excluded'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title | replace("Pcr", "PCR") }}: </b>{% if key=='cost' %}{% if sub['cost'] %} {{ "${:,.2f}".format(value) }}{% endif %}{% else %}{{ value }}{% endif %}<br>
{% endfor %}
{% if sub['custom'] %}{% for key, value in sub['custom'].items() %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
{% endfor %}{% endif %}</p>
{% 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>
{% 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> <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> <a class="data-link tips" id="{{ item['lot'] }}">{{ item['name'] }} ({{ item['lot'] }})</a><br>
{% endfor %}</p>
{% endif %}
{% if sub['samples'] %}
<h3><u>Samples:</u></h3>
<p>{% for item in sub['samples'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['well'] }}:</b><a class="data-link sample" id="{{ item['submitter_id'] }}">{% if item['organism'] %} {{ item['name'] }} - ({{ item['organism']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}){% else %} {{ item['name']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}{% endif %}</a><br>
{% endfor %}</p>
{% endif %}
<head>
{% block head %}
{{ super() }}
<title>Run Details for {{ run['rsl_plate_number'] }}</title>
{% endblock %}
</head>
<body>
{% if sub['ext_info'] %}
{% for entry in sub['ext_info'] %}
<h3><u>Extraction Status:</u></h3>
<p>{% for key, value in entry.items() %}
{% if "column" in key %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}uL<br>
{% else %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}<br>
{% endif %}
{% endfor %}</p>
{% endfor %}
{% endif %}
{% block body %}
<h2><u>Run Details for {{ run['rsl_plate_number'] }}</u></h2>
{{ super() }}
<p>{% for key, value in run.items() if key not in run['excluded'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title | replace("Rsl", "RSL") }}:</b> {{ value }}<br>
{% endfor %}</p>
{% if run['sample'] %}
<button type="button" class="collapsible"><h3><u>Run Samples:</u></h3></button>
<p>{% for sample in run['sample'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<a class="{% if sample['active'] %}data-link {% else %}unused {% endif %}sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
{% endfor %}</p>
{% endif %}
{% if run['procedure'] %}
<button type="button" class="collapsible"><h3><u>Procedures:</u></h3></button>
<div class="nested">
{% for procedure in run['procedure'] %}
{% with procedure=procedure, child=True %}
{% include "procedure_details.html" %}
{% endwith %}
{% endfor %}
</div>
{% endif %}
{% endblock %}
{% block signing_button %}
<button type="button" id="sign_btn" {% if run['permission'] and not run['signed_by'] %}{% else %}hidden{% endif %}>Sign Off</button>
{% endblock %}
<br>
{% if sub['comment'] %}
<h3><u>Comments:</u></h3>
<p>{% for entry in sub['comment'] %}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ entry['name'] }}:</b><br> {{ entry['text'] }}<br>- {{ entry['time'] }}<br>
{% endfor %}</p>
{% endif %}
{% if sub['platemap'] %}
<h3><u>Plate map:</u></h3>
{{ sub['platemap'] }}
{% endif %}
{% if sub['export_map'] %}
<h3><u>Plate map:</u></h3>
<img height="600px" width="1300px" src="data:image/jpeg;base64,{{ sub['export_map'] | safe }}">
{% endif %}
{% endblock %}
{% block signing_button %}
<button type="button" id="sign_btn" {% if permission and not sub['signed_by'] %}{% else %}hidden{% endif %}>Sign Off</button>
{% endblock %}
<br>
<br>
<br>
</body>
</body>
{% block script %}
{{ super() }}
<script>
var sampleSelection = document.getElementsByClassName('sample');
{% block script %}
{{ super() }}
<script>
var sampleSelection = document.getElementsByClassName('sample');
for(let i = 0; i < sampleSelection.length; i++) {
sampleSelection[i].addEventListener("click", function() {
console.log(sampleSelection[i].id);
backend.sample_details(sampleSelection[i].id);
})
}
for(let i = 0; i < sampleSelection.length; i++) {
sampleSelection[i].addEventListener("click", function() {
console.log(sampleSelection[i].id);
backend.sample_details(sampleSelection[i].id);
})
}
var reagentSelection = document.getElementsByClassName('reagent');
document.getElementById("sign_btn").addEventListener("click", function(){
backend.sign_off("{{ run['rsl_plate_num'] }}");
});
</script>
{% endblock %}
for(let i = 0; i < reagentSelection.length; i++) {
reagentSelection[i].addEventListener("click", function() {
console.log(reagentSelection[i].id);
backend.reagent_details(reagentSelection[i].id, "{{ sub['extraction_kit'] }}");
})
}
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'] }}");
});
</script>
{% endblock %}
</html>

4
src/submissions/templates/sample_checker.html
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@@ -10,8 +10,8 @@
<h2><u>Sample Checker</u></h2>
<br>
{% if rsl_plate_num %}
<label for="rsl_plate_num">RSL Plate Number:</label><br>
<input type="text" id="rsl_plate_num" name="sample_id" value="{{ rsl_plate_num }}" size="40">
<label for="rsl_plate_number">RSL Plate Number:</label><br>
<input type="text" id="rsl_plate_number" name="sample_id" value="{{ rsl_plate_number }}" size="40">
{% endif %}
<br>