EVA-3525 update validation report

bin/eva-sub-cli.py

@@ -70,9 +70,6 @@ def get_version():
                                                                   'upload to the EVA')
     credential_group.add_argument("--username", help="Username used for connecting to the ENA webin account")
     credential_group.add_argument("--password", help="Password used for connecting to the ENA webin account")
-    argparser.add_argument("--resume", default=False, action='store_true',
-                           help="Resume the process execution from where it left of. This is currently only supported "
-                                "for the upload part of the SUBMIT task.")
 
     args = argparser.parse_args()
 

eva_sub_cli/jinja_templates/fasta_check.html

@@ -1,18 +1,19 @@
 
 {% macro fasta_check_report(validation_results, file_name) -%}
     {% set results_for_fasta = validation_results['fasta_check'][file_name] %}
-
+    {% set expand_icon = "" %}
     <!-- All INSDC check results -->
     {% if results_for_fasta.get('all_insdc') %}
         {% set icon = "&#10004;" %}
         {% set row_class = "report-section pass" %}
         {% set text = "All sequences are INSDC accessioned" %}
     {% else %}
+        {% set expand_icon = "&#9654;" %}
         {% set icon = "&#10060;" %}
         {% set row_class = "report-section fail collapsible" %}
         {% set text = "Some sequences are not INSDC accessioned" %}
     {% endif %}
-    <div class='{{ row_class }}'>{{ icon }} {{ text }} </div>
+    <div class='{{ row_class }}'><span class="expand_icon">{{ expand_icon }}</span> {{ icon }} {{ text }} </div>
     {% if not results_for_fasta.get('all_insdc') %}
         <div class="error-list">
             <div class="error-description">First 10 sequences not in INSDC. <strong>Full report:</strong> {{ results_for_fasta.get('report_path', '') }}</div>
@@ -35,22 +36,25 @@
         {% if 'metadata_assembly_compatible' in results_for_fasta %}
             <!-- found assembly in metadata, so definitely know the analysis -->
             {% set analysis_text = results_for_fasta.get('associated_analyses')|join(", ") %}
+            {% set expand_icon = "" %}
             {% if results_for_fasta.get('metadata_assembly_compatible') %}
                 {% set icon = "&#10004;" %}
                 {% set row_class = "report-section pass" %}
                 {% set text = analysis_text + ": Assembly accession in metadata is compatible" %}
             {% else %}
+                {% set expand_icon = "&#9654;" %}
                 {% set icon = "&#10060;" %}
                 {% set row_class = "report-section fail collapsible" %}
                 {% set text = analysis_text + ": Assembly accession in metadata is not compatible" %}
             {% endif %}
         {% else %}
             <!-- has possible assemblies but no metadata assembly -->
+            {% set expand_icon = "&#9654;" %}
             {% set icon = "&#10060;" %}
             {% set row_class = "report-section fail collapsible" %}
             {% set text = "No assembly accession found in metadata" %}
         {% endif %}
-        <div class='{{ row_class }}'>{{ icon }} {{ text }} </div>
+        <div class='{{ row_class }}'><span class="expand_icon">{{ expand_icon }}</span> {{ icon }} {{ text }} </div>
         {% if 'metadata_assembly_compatible' not in results_for_fasta or not results_for_fasta['metadata_assembly_compatible'] %}
             <div class="error-list">
                 <div class="error-description"><strong>Full report:</strong> {{ results_for_fasta.get('report_path', '') }}</div>

eva_sub_cli/jinja_templates/file_validation.html

@@ -13,18 +13,20 @@
 {% macro vcf_check(vcf_check_result) %}
     {% set critical_count = vcf_check_result.get("critical_count", 0) %}
     {% set error_count = vcf_check_result.get("error_count", 0) %}
-    {% set warning_count = vcf_check_result.get("warning_count", 0) %}
+    {% set expand_icon = "" %}
     {% if critical_count > 0 %}
+        {% set expand_icon = "▶" %}
         {% set icon = "❌" %}
         {% set row_class = "report-section fail collapsible" %}
     {% elif error_count > 0 %}
+        {% set expand_icon = "▶" %}
         {% set icon = "❌" %}
         {% set row_class = "report-section warn collapsible" %}
     {% else %}
         {% set icon = "✔" %}
         {% 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>
+    <div class='{{ row_class }}'><span class="expand_icon">{{ expand_icon }}</span> {{ icon }} VCF check: {{ critical_count }} critical errors, {{ error_count }} non-critical errors </div>
     {% set critical_list = vcf_check_result.get("critical_list") %}
     {% set error_list = vcf_check_result.get("error_list") %}
 
@@ -54,14 +56,16 @@
     {% set nb_match = assembly_check_result.get("match", 0) %}
     {% set nb_total = assembly_check_result.get("total", 0) %}
     {% set match_percentage = nb_match / nb_total * 100 if nb_total else 0 %}
+    {% set expand_icon = "" %}
     {% if assembly_check_result.get("nb_mismatch", 0) > 0 %}
+        {% set expand_icon = "&#9654;" %}
         {% 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>
+    <div class='{{ row_class }}'><span class="expand_icon">{{ expand_icon }}</span> {{ icon }} Assembly check: {{ nb_match }}/{{ nb_total }} ({{ match_percentage|round(2) }}%)</div>
     {% set mismatch_list = assembly_check_result.get("mismatch_list") %}
     {% set error_list = assembly_check_result.get("error_list") %}
     {% if mismatch_list or error_list %}

eva_sub_cli/jinja_templates/html_report.html

@@ -1,4 +1,5 @@
 <!DOCTYPE html>
+{% from 'project_details.html' import project_details_report %}
 {% from 'file_validation.html' import file_validation_report %}
 {% from 'sample_name_check.html' import sample_name_check_report %}
 {% from 'fasta_check.html' import fasta_check_report %}
@@ -20,15 +21,17 @@
         .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; }
+        .report-section { padding: 12px; border: 1px solid white; margin-bottom: 5px}
+        .active, .collapsible:hover.fail { background-color: #e6a3ae; }
+        .active, .collapsible:hover.info { background-color: #c0c0c0; }
 
-        table { border-collapse: collapse; padding: 10px; }
+        table { border-collapse: collapse; padding: 10px; margin-bottom: 20px}
         th, td { border: 1px solid black;  padding: 8px;  text-align: left; }
         th {  background-color: lightgrey;  }
         .fail { background-color: #FFB6C1; }
         .pass { background-color: #90EE90; }
-        .error-list { display: none; }
+        .info { background-color: #dadada; }
+        .error-list, .no-show { display: none; }
     </style>
 </head>
 <body>
@@ -38,28 +41,31 @@
     <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 }}
+        <h1>Validation Report</h1>
     </div>
 </header>
 
+<section>
+    <h2>Project Summary</h2>
+    <div class="description">
+        General details about the project
+    </div>
+    {{ project_details_report(project_title, validation_date, submission_dir, vcf_fasta_analysis_mapping) }}
+</section>
+
 <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>.
+        For requirements, please refer to the <a href="https://www.ebi.ac.uk/eva/?Submit-Data" target=”_blank”>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>.
+        Checks whether each file is compliant with the <a href="http://samtools.github.io/hts-specs/VCFv4.3.pdf" target=”_blank”>VCF specification</a>.
         Also checks whether the variants' reference alleles match against the reference assembly.
     </div>
     {% for file_name in vcf_files %}
@@ -93,6 +99,14 @@ <h3>{{ file_name }}</h3>
     for (let collapsible of collapsibles) {
         collapsible.addEventListener('click', function() {
             this.classList.toggle('active');
+
+             let icon = this.querySelector('.expand_icon');
+             if (this.classList.contains('active')) {
+                 icon.innerHTML = '&#9660;';
+             } else {
+                 icon.innerHTML = '&#9654;';
+             }
+
             let content = this.nextElementSibling;
             if (content.style.display === 'block') {
                 content.style.display = 'none';

eva_sub_cli/jinja_templates/metadata_validation.html

@@ -3,13 +3,14 @@
     {% set results = validation_results.get('metadata_check', {}) %}
     {% set spreadsheet_errors = results.get('spreadsheet_errors', []) %}
     {% if spreadsheet_errors %}
+        {% set expand_icon = "▶" %}
         {% set icon = "❌" %}
         {% set row_class = "report-section fail collapsible" %}
     {% else %}
         {% set icon = "✔" %}
         {% set row_class = "report-section pass" %}
     {% endif %}
-    <div class='{{ row_class }}'>{{ icon }} Metadata validation check </div>
+    <div class='{{ row_class }}'><span class="expand_icon">{{ expand_icon }}</span> {{ icon }} Metadata validation check </div>
     {% if spreadsheet_errors %}
         <div class="error-list">
             <div class="error-description"><strong>Full report:</strong> {{ results.get('spreadsheet_report_path', '') }}</div>

eva_sub_cli/jinja_templates/project_details.html

@@ -0,0 +1,35 @@
+{% macro project_details_report(project_title, validation_date, submission_dir, vcf_fasta_analysis_mapping) -%}
+    <div class="report-section info">
+          {% if project_title %}
+             <p><b>Project Title:</b> {{ project_title }}</p>
+         {% else %}
+             <p><b>Project Title:</b> Not Found</p>
+         {% endif %}
+        <p><b>Validation Date:</b> {{ validation_date }}</p>
+        <p><b>Submission Directory:</b> {{ submission_dir }}</p>
+    </div>
+
+    {% if vcf_fasta_analysis_mapping %}
+        {% set row_class = "report-section info collapsible" %}
+        {% set expand_icon = "&#9654;" %}
+        <div class='{{ row_class }}'><span class="expand_icon">{{ expand_icon }}</span> Files mapping</div>
+            <div class="no-show">
+                <table>
+                    <tr>
+                        <th><strong>VCF File</strong></th>
+                        <th><strong>Fasta File</strong></th>
+                        <th><strong>Analysis</strong></th>
+                    </tr>
+                    {% for mapping in vcf_fasta_analysis_mapping %}
+                    <tr>
+                        <td>{{ mapping.vcf_file }}</td>
+                        <td>{{ mapping.fasta_file }}</td>
+                        <td>{{ mapping.analysis }}</td>
+                    </tr>
+                    {% endfor %}
+                </table>
+            </div>
+        </div>
+    {% endif %}
+
+{%- endmacro %}

eva_sub_cli/jinja_templates/sample_name_check.html

@@ -3,13 +3,16 @@
     {% set results = validation_results.get('sample_check', {}) %}
     {% for analysis, results_for_analysis in results.get('results_per_analysis', {}).items() %}
         {% if results_for_analysis.get('difference') %}
+            {% set expand_icon = "▶" %}
             {% set icon = "❌" %}
             {% set row_class = "report-section fail collapsible" %}
+            {% set text = "Sample names in metadata do not match with those in VCF files" %}
         {% else %}
             {% set icon = "✔" %}
             {% set row_class = "report-section pass" %}
+            {% set text = "Sample names in metadata match with those in VCF files" %}
         {% endif %}
-        <div class='{{ row_class }}'>{{ icon }} {{ analysis }}: Sample names concordance check </div>
+        <div class='{{ row_class }}'><span class="expand_icon">{{ expand_icon }}</span> {{ icon }} {{ analysis }}: {{ text }} </div>
         {% if results_for_analysis.get('difference') %}
             <div class="error-list">
                 <div class="error-description">First 10 errors per category are below. <strong>Full report:</strong> {{ results.get('report_path', '') }}</div>