Address comments from review

EBIvariation · Sep 9, 2024 · aecf386 · aecf386
1 parent 45e6d68
commit aecf386
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Showing 7 changed files with 20 additions and 28 deletions.
diff --git a/eva_sub_cli/jinja_templates/html_report.html b/eva_sub_cli/jinja_templates/html_report.html
@@ -4,7 +4,7 @@
 {% from 'sample_name_check.html' import sample_name_check_report %}
 {% from 'fasta_check.html' import fasta_check_report %}
 {% from 'metadata_validation.html' import metadata_validation_report %}
-{% from 'shallow_validation.html' import shallow_validation_report %}
+{% from 'shallow_validation.html' import optional_shallow_validation_report %}
 
 <html lang="EN">
 <head>
@@ -47,9 +47,7 @@ <h6>eva-sub-cli v{{cli_version}}</h6>
     </div>
 </header>
 
-<section>
-    {{ shallow_validation_report(validation_results) }}
-</section>
+{{ optional_shallow_validation_report(validation_results) }}
 
 <section>
     <h2>Project Summary</h2>

diff --git a/eva_sub_cli/jinja_templates/shallow_validation.html b/eva_sub_cli/jinja_templates/shallow_validation.html
@@ -1,17 +1,18 @@
 
-{% macro shallow_validation_report(validation_results) -%}
+{% macro optional_shallow_validation_report(validation_results) -%}
     {% set results = validation_results.get('shallow_validation', {}) %}
 
     {% if results.get('required') %}
+    <section>
         <div class="report-section fail collapsible"> <span class="expand_icon">&#9654;</span>
             &#10060; <b>You requested to run the shallow validation, please run full validation before submitting the data</b>
         </div>
         <div class="no-show">
         <table>
             <tr>
                 <th><strong>VCF File</strong></th>
-                <th><strong>Records validated in VCF</strong></th>
-                <th><strong>Records validated in Fasta</strong></th>
+                <th><strong>Variant lines validated in VCF</strong></th>
+                <th><strong>Entries used in Fasta</strong></th>
             </tr>
             {% for vcf_file in results.get('metrics') %}
                 <tr>
@@ -22,6 +23,7 @@
                 {% endfor %}
             </table>
         </div>
+    </section>
     {% endif %}
 
 {%- endmacro %}
diff --git a/eva_sub_cli/validators/docker_validator.py b/eva_sub_cli/validators/docker_validator.py
@@ -37,24 +37,15 @@ def _validation_file_path_for(file_path):
         return f'{container_validation_dir}/{file_path}'
 
     def get_docker_validation_cmd(self):
-        if self.metadata_xlsx and not self.metadata_json:
-            docker_cmd = ''.join([
-                f"{self.docker_path} exec {self.container_name} nextflow run eva_sub_cli/nextflow/validation.nf ",
-                f"--base_dir {container_validation_dir} ",
-                f"--vcf_files_mapping {self.mapping_file} ",
-                f"--metadata_xlsx {self.metadata_xlsx} ",
-                f"--shallow_validation true " if self.shallow_validation else "",
-                f"--output_dir {container_validation_output_dir}"
-            ])
-        else:
-            docker_cmd = ''.join([
-                f"{self.docker_path} exec {self.container_name} nextflow run eva_sub_cli/nextflow/validation.nf ",
-                f"--base_dir {container_validation_dir} ",
-                f"--vcf_files_mapping {self.mapping_file} ",
-                f"--metadata_json {self.metadata_json} ",
-                f"--shallow_validation true " if self.shallow_validation else "",
-                f"--output_dir {container_validation_output_dir}"
-            ])
+        docker_cmd = ''.join([
+            f"{self.docker_path} exec {self.container_name} nextflow run eva_sub_cli/nextflow/validation.nf ",
+            f"--base_dir {container_validation_dir} ",
+            f"--vcf_files_mapping {self.mapping_file} ",
+            f"--metadata_xlsx {self.metadata_xlsx} " if self.metadata_xlsx and not self.metadata_json
+                                                     else f"--metadata_json {self.metadata_json} ",
+            f"--shallow_validation true " if self.shallow_validation else "",
+            f"--output_dir {container_validation_output_dir}"
+        ])
         return docker_cmd
 
     def run_docker_validator(self):

diff --git a/eva_sub_cli/validators/validator.py b/eva_sub_cli/validators/validator.py
@@ -167,6 +167,7 @@ def verify_ready_for_submission_to_eva(self):
             )),
             self.results.get('sample_check', {}).get('overall_differences', True) is False,
             len(self.results.get('metadata_check', {}).get('spreadsheet_errors', [])) == 0,
+            len(self.results.get('metadata_check', {}).get('json_errors', [])) == 0,
             any((
                 self.results['shallow_validation']['requested'] is False,
                 self.results['shallow_validation'].get('required', True) is False

diff --git a/tests/resources/validation_reports/expected_report_metadata_json.html b/tests/resources/validation_reports/expected_report_metadata_json.html
diff --git a/tests/resources/validation_reports/expected_report_metadata_xlsx.html b/tests/resources/validation_reports/expected_report_metadata_xlsx.html
diff --git a/tests/resources/validation_reports/expected_shallow_metadata_xlsx_report.html b/tests/resources/validation_reports/expected_shallow_metadata_xlsx_report.html