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EVA-3275: Improvements to validation report #9

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merged 2 commits into from
Sep 7, 2023
Merged

EVA-3275: Improvements to validation report #9

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9bc5978
update tests
apriltuesday Aug 22, 2023
7daaa89
various updates to validation report
apriltuesday Aug 31, 2023
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3 changes: 1 addition & 2 deletions .github/workflows/tests.yml
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Expand Up @@ -12,15 +12,14 @@ jobs:
strategy:
matrix:
python-version: [3.9]
nextflow-version: [21.10.5]

steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies ${{ matrix.nextflow-version }}
- name: Install dependencies and build docker image
run: |
python -m pip install --upgrade pip
pip install flake8 pytest
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -127,3 +127,6 @@ dmypy.json

# Pyre type checker
.pyre/

# PyCharm
.idea/
4 changes: 2 additions & 2 deletions cli/docker_validator.py
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Expand Up @@ -163,11 +163,11 @@ def verify_container_is_running(self):
return False

def verify_container_is_stopped(self):
container_stop_cmd_ouptut = run_command_with_output(
container_stop_cmd_output = run_command_with_output(
"check if container is stopped",
f"{self.docker_path} ps -a"
)
if container_stop_cmd_ouptut is not None and self.container_name in container_stop_cmd_ouptut:
if container_stop_cmd_output is not None and self.container_name in container_stop_cmd_output:
logger.info(f"Container ({self.container_name}) is in stop state")
return True
else:
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124 changes: 68 additions & 56 deletions cli/jinja_templates/file_validation.html
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@@ -1,61 +1,73 @@

{% macro file_validation_report(validation_results, file_name) -%}
<ul>
{% for check_type, check_per_file in validation_results.items() %}
{% set result = check_per_file.get(file_name, {}) %}
{% if check_type == "assembly_check" %}
{% set nb_match = result.get("match", 0) %}
{% set nb_total = result.get("total", 0) %}
{% set match_percentage = nb_match / nb_total * 100 %}
{% if result.get("nb_mismatch", 0) > 0 %}
{% set icon = "&#10060;" %}
{% set row_class = "fail collapsible" %}
{% else %}
{% set icon = "&#10004;" %}
{% set row_class = "pass" %}
{% endif %}
<li class='{{ row_class }}'>{{ icon }} Assembly check: {{ nb_match }}/{{ nb_total }} ({{ match_percentage|round(2) }}%)</li>
{% set mismatch_list = result.get("mismatch_list") %}
{% if mismatch_list %}
<div class='error-list'>
<ul>
{% for error in mismatch_list %}
<li><strong>{{ check_type }} error:</strong> {{ error }}</li>
{% endfor %}
</ul>
</div>
{% endif %}
{% elif check_type == "vcf_check" %}
{% set critical_count = result.get("critical_count", 0) %}
{% set error_count = result.get("error_count", 0) %}
{% set warning_count = result.get("warning_count", 0) %}
{% if critical_count > 0 %}
{% set icon = "&#10060;" %}
{% set row_class = "fail collapsible" %}
{% elif error_count > 0 %}
{% set icon = "&#10060;" %}
{% set row_class = "warn collapsible" %}
{% else %}
{% set icon = "&#10004;" %}
{% set row_class = "pass" %}
{% endif %}
<li class='{{ row_class }}'>{{ icon }} VCF check: {{ critical_count }} critical errors {{ error_count }} non critical error {{ warning_count }} warning </li>
{% set critical_list = result.get("critical_list") %}
{% set error_list = result.get("error_list") %}
{% for check_type, check_per_file in validation_results.items() %}
{% set result = check_per_file.get(file_name, {}) %}
{% if check_type == "assembly_check" %}
{% set nb_match = result.get("match", 0) %}
{% set nb_total = result.get("total", 0) %}
{% set match_percentage = nb_match / nb_total * 100 %}
{% if result.get("nb_mismatch", 0) > 0 %}
{% set icon = "&#10060;" %}
{% set row_class = "report-section fail collapsible" %}
{% else %}
{% set icon = "&#10004;" %}
{% set row_class = "report-section pass" %}
{% endif %}
<div class='{{ row_class }}'>{{ icon }} Assembly check: {{ nb_match }}/{{ nb_total }} ({{ match_percentage|round(2) }}%)</div>
{% set mismatch_list = result.get("mismatch_list") %}
{% if mismatch_list %}
<div class="error-list">
<div class="error-description">First 10 errors per category are below. <strong>Full report:</strong> {{ result.get('report_path', '') }}</div>
<table>
<tr>
<th>Category</th><th>Error</th>
</tr>
{% for error in mismatch_list[:10] %}
<tr>
<td><strong>mismatch error</strong></td><td> {{ error }}</td>
</tr>
{% endfor %}
</table>
</div>
{% endif %}
{% elif check_type == "vcf_check" %}
{% set critical_count = result.get("critical_count", 0) %}
{% set error_count = result.get("error_count", 0) %}
{% set warning_count = result.get("warning_count", 0) %}
{% if critical_count > 0 %}
{% set icon = "&#10060;" %}
{% set row_class = "report-section fail collapsible" %}
{% elif error_count > 0 %}
{% set icon = "&#10060;" %}
{% set row_class = "report-section warn collapsible" %}
{% else %}
{% set icon = "&#10004;" %}
{% set row_class = "report-section pass" %}
{% endif %}
<div class='{{ row_class }}'>{{ icon }} VCF check: {{ critical_count }} critical errors, {{ error_count }} non-critical errors, {{ warning_count }} warnings </div>
{% set critical_list = result.get("critical_list") %}
{% set error_list = result.get("error_list") %}

{% if critical_list or error_list %}
<div class='error-list'>
<ul>
{% for error in critical_list %}
<li><strong>{{ check_type }} error:</strong> {{ error }}</li>
{% endfor %}
{% for error in error_list %}
<li><strong>{{ check_type }} error:</strong> {{ error }}</li>
{% endfor %}
</ul>
</div>
{% endif %}
{% if critical_list or error_list%}
<div class="error-list">
<div class="error-description">First 10 errors per category are below. <strong>Full report:</strong> {{ result.get('report_path', '') }}</div>
<table>
<tr>
<th>Category</th><th>Error</th>
</tr>
{% for error in critical_list[:10] %}
<tr>
<td><strong>critical error</strong></td><td> {{ error }}</td>
</tr>
{% endfor %}
{% for error in error_list[:10] %}
<tr>
<td><strong>non-critical error</strong></td><td> {{ error }}</td>
</tr>
{% endfor %}
</table>
</div>
{% endif %}
{% endfor %}
</ul>
{% endif %}
{% endfor %}
{%- endmacro %}
80 changes: 65 additions & 15 deletions cli/jinja_templates/html_report.html
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Expand Up @@ -7,36 +7,86 @@
<meta charset="UTF-8">
<title>Validation Report</title>
<style>
table { border-collapse: collapse; }
body { font-family: Verdana, sans-serif; }

.logo { float: left; padding: 20px; }
.title { padding: 8px; }
header { overflow: auto; }
header::after { clear: both; }

section { padding: 20px 20px 10px 40px; }
.description { padding-bottom: 10px}
.error-description { padding: 10px 0px 10px}

.report-section { padding: 12px; border: 1px solid white; }
.active, .collapsible:hover, .fail { background-color: #e6a3ae; }

table { border-collapse: collapse; padding: 10px; }
th, td { border: 1px solid black; padding: 8px; text-align: left; }
th { background-color: lightgrey; }
tr.fail { background-color: #FFB6C1; }
tr.pass { background-color: #90EE90; }
.fail { background-color: #FFB6C1; }
.pass { background-color: #90EE90; }
.error-list { display: none; }
</style>
</head>
<body>
<img src="data:image/png;base64,{{ logo_data }}" width="100" height="100">
<h1>Validation Report</h1>
<h2>Metadata validation results</h2>
{{ metadata_validation_report(validation_results) }}

{% for file_name in file_names %}
<h2>Validation results for file {{ file_name }}</h2>
{{ file_validation_report(validation_results, file_name) }}
{% endfor %}
<header>
<div class="logo">
<img src="data:image/png;base64,{{ logo_data }}" width="100" height="100" alt="EVA logo">
</div>
<div class="title">
{% if project_title %}
<h1>Validation Report: {{ project_title }}</h1>
{% else %}
<h1>Validation Report</h1>
{% endif %}
Generated at {{ validation_date }}
</div>
</header>

<section>
<h2>Metadata validation results</h2>
<div class="description">
Ensures that required fields are present and values are formatted correctly.
For requirements, please refer to the <a href="https://www.ebi.ac.uk/eva/?Submit-Data">EVA website</a>.
</div>
{{ metadata_validation_report(validation_results) }}
</section>

<section>
<h2>VCF validation results</h2>
<div class="description">
Checks whether each file is compliant with the <a href="http://samtools.github.io/hts-specs/VCFv4.3.pdf">VCF specification</a>.
Also checks whether the variants' reference alleles match against the reference assembly.
</div>
{% for file_name in file_names %}
<h3>{{ file_name }}</h3>
{{ file_validation_report(validation_results, file_name) }}
{% endfor %}
</section>

<h2>Sample name concordance check</h2>
{{ sample_name_check_report(validation_results)}}
<section>
<h2>Sample name concordance check</h2>
<div class="description">
Checks whether information in the metadata is concordant with that contained in the VCF files, in particular sample names.
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Suggested change
Checks whether information in the metadata is concordant with that contained in the VCF files, in particular sample names.
Checks whether information in the metadata (ex: Sample names) is concordant with that contained in the VCF files.

</div>
{{ sample_name_check_report(validation_results)}}
</section>

<script>
let collapsibles = document.querySelectorAll('.collapsible');
for (let collapsible of collapsibles) {
collapsible.addEventListener('click', function() {
this.classList.toggle('active');
let content = this.nextElementSibling;
if (content.style.display === 'block') { content.style.display = 'none'; }
else { content.style.display = 'block'; }
if (content.style.display === 'block') {
content.style.display = 'none';
}
else {
content.style.display = 'block';
content.scrollIntoView({block: 'nearest'});
}
});
}
</script>
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27 changes: 17 additions & 10 deletions cli/jinja_templates/metadata_validation.html
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@@ -1,21 +1,28 @@

{% macro metadata_validation_report(validation_results) -%}
{% set json_errors = validation_results.get('metadata_check', {}).get('json_errors', []) %}
{% set results = validation_results.get('metadata_check', {}) %}
{% set json_errors = results.get('json_errors', []) %}
{% if json_errors %}
{% set icon = "&#10060;" %}
{% set row_class = "fail collapsible" %}
{% set row_class = "report-section fail collapsible" %}
{% else %}
{% set icon = "&#10004;" %}
{% set row_class = "pass" %}
{% set row_class = "report-section pass" %}
{% endif %}
<li class='{{ row_class }}'>{{ icon }} Metadata validation check </li>
<div class='{{ row_class }}'>{{ icon }} Metadata validation check </div>
{% if json_errors %}
<div class='error-list'>
<ul>
{% for error in json_errors %}
<li><strong> {{ error.get('property') }} : {{ error.get('description') }} </strong></li>
{% endfor %}
</ul>
<div class="error-list">
<div class="error-description"><strong>Full report:</strong> {{ results.get('report_path', '') }}</div>
<table>
<tr>
<th>Property</th><th>Error</th>
</tr>
{% for error in json_errors %}
<tr>
<td><strong>{{ error.get('property') }}</strong></td><td> {{ error.get('description') }}</td>
</tr>
{% endfor %}
</table>
</div>
{% endif %}
{%- endmacro %}
26 changes: 18 additions & 8 deletions cli/jinja_templates/sample_name_check.html
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Expand Up @@ -4,18 +4,28 @@
{% for analysis, results_for_analysis in results.get('results_per_analysis', {}).items() %}
{% if results_for_analysis.get('difference') %}
{% set icon = "&#10060;" %}
{% set row_class = "fail collapsible" %}
{% set row_class = "report-section fail collapsible" %}
{% else %}
{% set icon = "&#10004;" %}
{% set row_class = "pass" %}
{% set row_class = "report-section pass" %}
{% endif %}
<li class='{{ row_class }}'>{{ icon }} {{ analysis }}: Sample names concordance check </li>
<div class='{{ row_class }}'>{{ icon }} {{ analysis }}: Sample names concordance check </div>
{% if results_for_analysis.get('difference') %}
<div class='error-list'>
<ul>
<li><strong> List of samples described in the metadata but not in the VCF files:</strong> {{ results_for_analysis.get('more_metadata_submitted_files')|join(", ") }}</li>
<li><strong> List of samples used in the VCF files but not described in the metadata:</strong> {{ results_for_analysis.get('more_submitted_files_metadata')|join(", ") }}</li>
</ul>
<div class="error-list">
<div class="error-description">First 10 errors per category are below. <strong>Full report:</strong> {{ results.get('report_path', '') }}</div>
<table>
<tr>
<th>Category</th><th>Error</th>
</tr>
<tr>
<td><strong>Samples described in the metadata but not in the VCF files</strong></td>
<td>{{ results_for_analysis.get('more_metadata_submitted_files')[:10]|join(", ") }}</td>
</tr>
<tr>
<td><strong>Samples in the VCF files but not described in the metadata</strong></td>
<td>{{ results_for_analysis.get('more_submitted_files_metadata')[:10]|join(", ") }}</td>
</tr>
</table>
</div>
{% endif %}
{% endfor %}
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13 changes: 7 additions & 6 deletions cli/report.py
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@@ -1,8 +1,7 @@
import base64
import os.path
from pprint import pprint

from jinja2 import Template, Environment, FileSystemLoader
from jinja2 import Environment, FileSystemLoader
from minify_html import minify_html

current_dir = os.path.dirname(__file__)
Expand All @@ -14,17 +13,19 @@ def get_logo_data():
return logo_data


def generate_html_report(validation_results):
def generate_html_report(validation_results, validation_date, project_title=None):
file_names = sorted(set([file_name
for check in validation_results if check in ["vcf_check", "assembly_check"]
for file_name in validation_results[check]
]))
for check in validation_results if check in ["vcf_check", "assembly_check"]
for file_name in validation_results[check]
]))

template = Environment(
loader=FileSystemLoader(os.path.join(current_dir, 'jinja_templates'))
).get_template('html_report.html')
rendered_template = template.render(
logo_data=get_logo_data(),
project_title=project_title,
validation_date=validation_date,
file_names=file_names,
validation_results=validation_results,
)
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