EVA-3581 Add option to see all errors of all categories for a sample (#…

…41) * add option to see all errors of all categories for a sample
EBIvariation · Jun 17, 2024 · 690610e · 690610e
1 parent 0233459
commit 690610e
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Showing 10 changed files with 61 additions and 12 deletions.
diff --git a/bin/xlsx2json.py b/bin/xlsx2json.py
@@ -20,7 +20,7 @@
 ANALYSIS_ALIAS_KEY = 'Analysis Alias'
 SAMPLE_NAME_IN_VCF_KEY = 'Sample Name in VCF'
 SAMPLE_ACCESSION_KEY = 'Sample Accession'
-SAMPLE_NAME_KEY = 'Sample Name'
+SAMPLE_NAME_KEY = 'BioSample Name'
 SCIENTIFIC_NAME_KEY = 'Scientific Name'
 SPECIES = 'species'
 

diff --git a/eva_sub_cli/etc/EVA_Submission_template.xlsx b/eva_sub_cli/etc/EVA_Submission_template.xlsx
diff --git a/eva_sub_cli/etc/spreadsheet2json_conf.yaml b/eva_sub_cli/etc/spreadsheet2json_conf.yaml
@@ -71,7 +71,7 @@ Sample:
     Sample Name in VCF: sampleInVCF
   optional:
     Sample Accession: bioSampleAccession
-    Sample Name: bioSampleName
+    BioSample Name: bioSampleName
     Title: title
     Description: description
     Unique Name: uniqueName
@@ -114,7 +114,7 @@ Sample:
     serovar: serovar
   cast:
     Sample ID: string
-    Sample Name: string
+    BioSample Name: string
 
 
 Files:

diff --git a/eva_sub_cli/jinja_templates/html_report.html b/eva_sub_cli/jinja_templates/html_report.html
@@ -117,6 +117,18 @@ <h3>{{ file_name }}</h3>
             }
         });
     }
+
+    function toggleSampleAllErrorsList(id) {
+        var element = document.getElementById(id);
+        var link = document.querySelector(`a[onclick="toggleSampleAllErrorsList('${id}'); return false;"]`);
+        if (element.style.display === "none" || element.style.display === "") {
+            element.style.display = "block";
+            link.innerHTML = "Hide All Errors for Category";
+        } else {
+            element.style.display = "none";
+            link.innerHTML = "Show All Errors for Category";
+        }
+    }
 </script>
 </body>
 </html>
diff --git a/eva_sub_cli/jinja_templates/sample_name_check.html b/eva_sub_cli/jinja_templates/sample_name_check.html
@@ -1,6 +1,10 @@
 
 {% macro sample_name_check_report(validation_results) -%}
     {% set results = validation_results.get('sample_check', {}) %}
+    {% macro format_error(error) %}
+        {{ error | replace(' ', '•') }}
+    {% endmacro %}
+
     {% for analysis, results_for_analysis in results.get('results_per_analysis', {}).items() %}
         {% if results_for_analysis.get('difference') %}
             {% set expand_icon = "&#9654;" %}
@@ -12,23 +16,44 @@
             {% set row_class = "report-section pass" %}
             {% set text = "Sample names in metadata match with those in VCF files" %}
         {% endif %}
-        <div class='{{ row_class }}'><span class="expand_icon">{{ expand_icon }}</span> {{ icon }} {{ analysis }}: {{ text }} </div>
+        <div class='{{ row_class }}'><span class="expand_icon">{{ expand_icon }}</span> {{ icon }} <b>{{ analysis }}</b>: {{ 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>
                 <table>
                     <tr>
-                        <th>Category</th><th>Error</th>
+                        <th>Category</th><th>First 5 Errors For Category</th><th>Link To View All Errors</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>
+                        <td>{{ results_for_analysis.get('more_metadata_submitted_files')[:5]|join(", ") }}</td>
+                        <td> <a href="#" onclick="toggleSampleAllErrorsList('metadata-{{ loop.index0 }}'); return false;">Show All Errors For Category</a></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>
+                        <td>{{ results_for_analysis.get('more_submitted_files_metadata')[:5]|join(", ") }}</td>
+                        <td> <a href="#" onclick="toggleSampleAllErrorsList('vcf-{{ loop.index0 }}'); return false;">Show All Errors For Category</a></td>
                     </tr>
                 </table>
+
+                <div id="metadata-{{ loop.index0 }}" class="description no-show">
+                    <div class="error-description"><strong>All Errors For Category - Samples described in the metadata but not in the VCF files:</strong></div>
+                    <ol>
+                        {% for error in results_for_analysis.get('more_metadata_submitted_files') %}
+                            <li>{{ format_error(error) }}</li>
+                        {% endfor %}
+                    </ol>
+                    <a href="#" onclick="toggleSampleAllErrorsList('metadata-{{ loop.index0 }}'); return false;">Hide</a>
+                </div>
+
+                <div id="vcf-{{ loop.index0 }}" class="description no-show">
+                    <div class="error-description"><strong>All Errors For Category - Samples in the VCF files but not described in the metadata:</strong></div>
+                    <ol>
+                        {% for error in results_for_analysis.get('more_submitted_files_metadata') %}
+                            <li>{{ format_error(error) }}</li>
+                        {% endfor %}
+                    </ol>
+                    <a href="#" onclick="toggleSampleAllErrorsList('vcf-{{ loop.index0 }}'); return false;">Hide</a>
+                </div>
             </div>
         {% endif %}
     {% endfor %}

diff --git a/eva_sub_cli/validators/docker_validator.py b/eva_sub_cli/validators/docker_validator.py
@@ -12,7 +12,7 @@
 logger = logging_config.get_logger(__name__)
 
 container_image = 'ebivariation/eva-sub-cli'
-container_tag = 'v0.0.1.dev7'
+container_tag = 'v0.0.1.dev8'
 container_validation_dir = '/opt/vcf_validation'
 container_validation_output_dir = 'vcf_validation_output'
 

diff --git a/tests/resources/EVA_Submission_test.xlsx b/tests/resources/EVA_Submission_test.xlsx
diff --git a/tests/resources/EVA_Submission_test_fails.xlsx b/tests/resources/EVA_Submission_test_fails.xlsx
diff --git a/tests/resources/validation_reports/expected_report.html b/tests/resources/validation_reports/expected_report.html
diff --git a/tests/test_report.py b/tests/test_report.py
@@ -59,9 +59,21 @@
         'results_per_analysis': {
             'Analysis A': {
                 'difference': True,
-                'more_metadata_submitted_files': ['Sample1'],
+                'more_metadata_submitted_files': [' SampleA1', 'SampleA2 ','SampleA3', 'SampleA4', 'SampleA5', 'SampleA6', 'SampleA7','SampleA8', 'SampleA9', 'SampleA10'],
                 'more_per_submitted_files_metadata': {},
-                'more_submitted_files_metadata': ['1Sample']
+                'more_submitted_files_metadata': ['A1Sample ', ' A2Sample', 'A3Sample', 'A4Sample', 'A5Sample', 'A6Sample', 'A7Sample', 'A8Sample', 'A9Sample', 'A10Sample']
+            },
+            'Analysis B': {
+                'difference': False,
+                'more_metadata_submitted_files': [],
+                'more_per_submitted_files_metadata': {},
+                'more_submitted_files_metadata': []
+            },
+            'Analysis C': {
+                'difference': True,
+                'more_metadata_submitted_files': ['SampleC1 ', ' SampleC2', 'SampleC3', 'SampleC4'],
+                'more_per_submitted_files_metadata': {},
+                'more_submitted_files_metadata': ['C1Sample ', ' C2Sample', 'C3Sample', 'C4Sample']
             }
         }
     },