eva-sub-cli 0.4.10__tar.gz → 0.4.11__tar.gz

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/.github/workflows/trigger-eva-sub-cli-integration-tests.yml

@@ -2,7 +2,7 @@ name: Trigger Eva Sub Cli Integration Tests
 
 on:
   push:
-    branches: [main, test-trigger-integration-tests]
+    branches: [main]
 
 jobs:
   trigger-integration-tests:
@@ -11,6 +11,6 @@ jobs:
       - name: Trigger eva sub cli integration tests
         uses: peter-evans/repository-dispatch@v2
         with:
-          token: ${{ secrets.TRIGGER_INTEGRATION_TESTS }}
+          token: ${{ secrets.WORKFLOW_ACCESS_TOKEN }}
           repository: EBIvariation/eva-integration-tests
           event-type: trigger-eva-sub-cli-tests

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eva_sub_cli
-Version: 0.4.10
+Version: 0.4.11
 Summary: EBI EVA - validation and submission command line tool
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
@@ -24,6 +24,7 @@ Requires-Dist: jinja2==3.*,>=3.0.0
 Requires-Dist: jsonschema==4.*
 Requires-Dist: openpyxl==3.*
 Requires-Dist: pyyaml==6.*
+Requires-Dist: pysam==0.*,>=0.23.3
 Requires-Dist: requests==2.*
 Requires-Dist: packaging==24.*
 Requires-Dist: setuptools-scm

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/docker/Dockerfile

@@ -1,6 +1,6 @@
 FROM python:3.10
 
-ENV vcf_validator_version=0.10.0
+ENV vcf_validator_version=0.10.2
 ENV NXF_VER=22.10.6
 
 WORKDIR /opt

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.4.10'
-__version_tuple__ = version_tuple = (0, 4, 10)
+__version__ = version = '0.4.11'
+__version_tuple__ = version_tuple = (0, 4, 11)

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/etc/eva_schema.json

@@ -168,6 +168,14 @@
             "type": "string",
             "description": "Reference against which the analysis was performed. ENA or NCBI accession (starting with GCA) accepted."
           },
+          "evidenceType": {
+            "type": "string",
+            "description": "The type of evidence (allele frequencies or genotypes) provided in the VCF files of the analysis",
+            "enum": [
+              "genotype",
+              "allele_frequency"
+            ]
+          },
           "referenceFasta": {
             "type": "string",
             "description": "The path to the reference in fasta format that was used to create the VCF. (This is a local path)"
@@ -366,7 +374,7 @@
     "projectAccession": {
       "type": "string",
       "description": "ENA project accession",
-      "pattern": "^PRJ(EB|NA)\\d+$"
+      "pattern": "^PRJ(E|D|N)[A-Z][0-9]+$"
     }
   }
 }

eva_sub_cli-0.4.11/eva_sub_cli/executables/evidence_type_checker.py

@@ -0,0 +1,51 @@
+import argparse
+
+import yaml
+from ebi_eva_common_pyutils.logger import logging_config
+
+from eva_sub_cli.file_utils import detect_vcf_evidence_type
+from eva_sub_cli.metadata import EvaMetadataJson
+
+logger = logging_config.get_logger(__name__)
+
+
+def check_evidence_type(metadata_json, output_yaml):
+    metadata = EvaMetadataJson(metadata_json)
+    results_per_analysis_alias = {}
+
+    for analysis_alias, vcf_file_set in metadata.files_per_analysis.items():
+        results_per_analysis_alias[analysis_alias] = {
+            'evidence_type': None,
+            'errors': None
+        }
+        vcf_files = list(vcf_file_set)
+        evidence_types_for_vcf_files = [detect_vcf_evidence_type(vcf_file) for vcf_file in vcf_files]
+
+        if len(set(evidence_types_for_vcf_files)) == 1 and None not in evidence_types_for_vcf_files:
+            results_per_analysis_alias[analysis_alias]['evidence_type'] = set(evidence_types_for_vcf_files).pop()
+        elif None in evidence_types_for_vcf_files:
+            indices = [i for i, x in enumerate(evidence_types_for_vcf_files) if x is None]
+            results_per_analysis_alias[analysis_alias][
+                'errors'] = f'VCF file evidence type could not be determined: {", ".join([vcf_files[i] for i in indices])}'
+        else:
+            results_per_analysis_alias[analysis_alias][
+                'errors'] = f'Multiple evidence types found: {", ".join(set(evidence_types_for_vcf_files))}'
+
+    write_result_yaml(output_yaml, results_per_analysis_alias)
+
+
+def write_result_yaml(output_yaml, results_per_analysis_alias):
+    with open(output_yaml, 'w') as open_yaml:
+        yaml.safe_dump(data=results_per_analysis_alias, stream=open_yaml, default_flow_style=False)
+
+
+def main():
+    arg_parser = argparse.ArgumentParser(description='Check the evidence type in the VCF files for all analysis')
+    arg_parser.add_argument('--metadata_json', required=True, dest='metadata_json',
+                            help='EVA metadata json file')
+    arg_parser.add_argument('--output_yaml', required=True, dest='output_yaml',
+                            help='Path to the location of the results')
+
+    args = arg_parser.parse_args()
+    logging_config.add_stdout_handler()
+    check_evidence_type(args.metadata_json, args.output_yaml)

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/executables/samples_checker.py

@@ -5,7 +5,7 @@ from ebi_eva_common_pyutils.logger import logging_config
 
 import yaml
 
-from eva_sub_cli.file_utils import open_gzip_if_required
+from eva_sub_cli.file_utils import open_gzip_if_required, detect_vcf_evidence_type
 from eva_sub_cli.metadata import EvaMetadataJson
 
 logger = logging_config.get_logger(__name__)
@@ -64,20 +64,41 @@ def compare_all_analysis(metadata, files_per_analysis):
             file_path: get_samples_from_vcf(file_path)
             for file_path in files_per_analysis.get(analysis_alias, [])
         }
-        (
-            has_difference, more_per_submitted_files_metadata,
-            more_submitted_files_metadata, more_metadata_submitted_files
-        ) = compare_names_in_files_and_samples(sample_name_in_analysis, sample_name_per_file)
-        overall_differences = overall_differences or has_difference
-        results_per_analysis_alias[analysis_alias] = {
-            'difference': has_difference,
-            'more_per_submitted_files_metadata': more_per_submitted_files_metadata,
-            'more_submitted_files_metadata': more_submitted_files_metadata,
-            'more_metadata_submitted_files': more_metadata_submitted_files
-        }
+
+        if need_to_check_samples(sample_name_per_file):
+            (
+                has_difference, more_per_submitted_files_metadata,
+                more_submitted_files_metadata, more_metadata_submitted_files
+            ) = compare_names_in_files_and_samples(sample_name_in_analysis, sample_name_per_file)
+            overall_differences = overall_differences or has_difference
+            results_per_analysis_alias[analysis_alias] = {
+                'difference': has_difference,
+                'more_per_submitted_files_metadata': more_per_submitted_files_metadata,
+                'more_submitted_files_metadata': more_submitted_files_metadata,
+                'more_metadata_submitted_files': more_metadata_submitted_files
+            }
+        else:
+            results_per_analysis_alias[analysis_alias] = {
+                'difference': False,
+                'more_per_submitted_files_metadata': [],
+                'more_submitted_files_metadata': [],
+                'more_metadata_submitted_files': []
+            }
+
+
     return overall_differences, results_per_analysis_alias
 
 
+def need_to_check_samples(sample_name_per_file):
+    no_samples_in_vcf = all(len(v) == 0 for v in sample_name_per_file.values())
+    if no_samples_in_vcf:
+        evidence_types_for_vcf_files = [detect_vcf_evidence_type(vcf_file) for vcf_file in sample_name_per_file.keys()]
+        if set(evidence_types_for_vcf_files) == {'allele_frequency'}:
+            return False
+
+    return True
+
+
 def associate_vcf_path_with_analysis(metadata, vcf_files):
     """
     Match the files names associated with analysis provided in the metadata with the file path given on the command

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/file_utils.py

@@ -5,6 +5,11 @@ import shutil
 import time
 from itertools import groupby
 
+import pysam
+from ebi_eva_common_pyutils.logger import logging_config
+
+logger = logging_config.get_logger(__name__)
+
 
 def resolve_single_file_path(file_path):
     files = glob.glob(file_path)
@@ -23,12 +28,86 @@ def is_submission_dir_writable(submission_dir):
         return False
     return True
 
+
 def is_vcf_file(file_path):
     if file_path:
         file_path = file_path.strip().lower()
         return file_path.endswith('.vcf') or file_path.endswith('.vcf.gz')
     return False
 
+
+def detect_vcf_evidence_type(vcf_file):
+    """
+    Detect the type of evidence (genotype aggregation) provided in the VCF file by checking the first 10 data lines
+    The evidence type is determined to be "genotype" (meaning genotype are all present) if a GT field can be found in
+    all the samples. It is determined to be "allele_frequency" if it is not "genotype" and an AF field or AN and AC fields are found
+    in every line checked.
+    Otherwise, it returns None meaning that the evidence type could not be determined.
+    """
+
+    try:
+        samples, af_in_info, gt_in_format = _assess_vcf_evidence_type_with_pysam(vcf_file)
+    except Exception:
+        logger.error(f"Pysam Failed to open and read {vcf_file}")
+        try:
+            samples, af_in_info, gt_in_format = _assess_vcf_evidence_type_manual(vcf_file)
+        except Exception:
+            logger.error(f"Manual parsing Failed to open or read {vcf_file}")
+            return None
+    if len(samples) > 0 and gt_in_format:
+        return 'genotype'
+    elif len(samples) == 0 and af_in_info:
+        return 'allele_frequency'
+    else:
+        logger.error(f'Aggregation type could not be detected for {vcf_file}')
+        return None
+
+
+def _assess_vcf_evidence_type_with_pysam(vcf_file):
+    with pysam.VariantFile(vcf_file, 'r') as vcf_in:
+        samples = list(vcf_in.header.samples)
+        # check that the first 10 lines have genotypes for all the samples present and if they have allele frequency
+        nb_line_checked = 0
+        max_line_check = 10
+        gt_in_format = True
+        af_in_info = True
+        for vcf_rec in vcf_in:
+            gt_in_format = gt_in_format and all('GT' in vcf_rec.samples.get(sample, {}) for sample in samples)
+            af_in_info = af_in_info and ('AF' in vcf_rec.info or ('AC' in vcf_rec.info and 'AN' in vcf_rec.info))
+            nb_line_checked += 1
+            if nb_line_checked >= max_line_check:
+                break
+        return samples, af_in_info, gt_in_format
+
+
+def _assess_vcf_evidence_type_manual(vcf_file):
+    try:
+        if vcf_file.endswith('.gz'):
+            open_file = gzip.open(vcf_file, 'rt')
+        else:
+            open_file = open(vcf_file, 'r')
+
+        nb_line_checked = 0
+        max_line_check = 10
+        gt_in_format = True
+        af_in_info = True
+        samples = []
+        for line in open_file:
+            sp_line = line.strip().split('\t')
+            if line.startswith('#CHROM'):
+                if len(sp_line) > 9:
+                    samples = sp_line[9:]
+            if not line.startswith('#'):
+                gt_in_format = gt_in_format and len(sp_line) > 8 and 'GT' in sp_line[8]
+                af_in_info = af_in_info and (
+                        sp_line[7].find('AF=') or (sp_line[7].find('AC=') and sp_line[7].find('AN=')))
+            if nb_line_checked >= max_line_check:
+                break
+        return samples, af_in_info, gt_in_format
+    finally:
+        open_file.close()
+
+
 def backup_file_or_directory(file_name, max_backups=None):
     """
     Rename a file or directory by adding a '.1' at the end. If the '.1' file exists it move it to a '.2' and so on.
@@ -83,7 +162,6 @@ class DirLockError(Exception):
 
 
 class DirLock(object):
-
     _SPIN_PERIOD_SECONDS = 0.05
 
     def __init__(self, dirname, timeout=3):
@@ -119,4 +197,4 @@ class DirLock(object):
         return self
 
     def __exit__(self, type_, value, traceback):
-        self.release()
+        self.release()

eva_sub_cli-0.4.11/eva_sub_cli/jinja_templates/html/project_details.html

@@ -0,0 +1,65 @@
+{% macro project_details_report(validation_results, project_title, validation_date, submission_dir, consent_statement_required, 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>
+        {% if consent_statement_required %}
+        <br>
+        <p><b>Note for human genotype data:</b></p> <p>You will need to provide a signed copy of our <a href="https://docs.google.com/document/d/1UaRmimAe919IZYIH55mDXMe-4sHsRVqaP4moqx2IYE4" target="_blank">Consent Statement</a> via email to <a href="mailto:eva-helpdesk@ebi.ac.uk">eva-helpdesk@ebi.ac.uk</a> after submission.
+            Your submission will only be processed after receiving the consent statement. For more info, please see our <a href="https://www.ebi.ac.uk/eva/?Help#submissionPanel&link=consent-statement-for-human-genotype-data" target="_blank">help</a> section.</p>
+        {% endif %}
+    </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 %}
+
+
+    {% set evidence_type_check_results = validation_results.get('evidence_type_check', {}) %}
+    {% set evidence_check_type_pass = evidence_type_check_results.get('pass', true) %}
+    {% if not evidence_check_type_pass %}
+        <div class="report-section fail collapsible"><span class="expand_icon">&#9654;</span>&#10060; Evidence Type Check Failures </div>
+         <div class="error-list">
+            <table>
+                <tr>
+                    <th>Analysis Alias</th><th>Errors</th>
+                </tr>
+                    {% for alias, alias_result in evidence_type_check_results.items() if alias != 'pass' %}
+                        {% if alias_result.evidence_type is none and alias_result.errors %}
+                             <tr>
+                                <td><strong>{{ alias }} </strong></td>
+                                <td>{{ alias_result.errors }}</td>
+                            </tr>
+                        {% endif %}
+                    {% endfor %}
+            </table>
+        </div>
+    {% endif %}
+
+
+
+{%- endmacro %}

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/jinja_templates/html/report.html

@@ -54,7 +54,7 @@
     <div class="description">
         General details about the project
     </div>
-    {{ project_details_report(project_title, validation_date, submission_dir, vcf_fasta_analysis_mapping) }}
+    {{ project_details_report(validation_results, project_title, validation_date, submission_dir, consent_statement_required, vcf_fasta_analysis_mapping) }}
 </section>
 
 <section>

eva_sub_cli-0.4.11/eva_sub_cli/jinja_templates/text/project_details.txt

@@ -0,0 +1,37 @@
+{% macro project_details_report(validation_results, project_title, validation_date, submission_dir, consent_statement_required, vcf_fasta_analysis_mapping) -%}
+
+{% if project_title %}
+	Project Title: {{ project_title }}
+{% else %}
+	Project Title: Not Found
+{% endif %}
+	Validation Date: {{ validation_date }}
+	Submission Directory: {{ submission_dir }}
+{% if consent_statement_required %}
+    Note for human genotype data:
+        You will need to provide a signed copy of our Consent Statement (https://docs.google.com/document/d/1UaRmimAe919IZYIH55mDXMe-4sHsRVqaP4moqx2IYE4) via email to eva-helpdesk@ebi.ac.uk after submission.
+        Your submission will only be processed after receiving the consent statement.For more info, please see our help section (https://www.ebi.ac.uk/eva/?Help#submissionPanel&link=consent-statement-for-human-genotype-data).
+{% endif %}
+
+{% if vcf_fasta_analysis_mapping %}
+	Files mapping:
+	{% for mapping in vcf_fasta_analysis_mapping %}
+		---
+		VCF File: {{ mapping.vcf_file }}
+		Fasta File: {{ mapping.fasta_file }}
+		Analysis: {{ mapping.analysis }}
+	{% endfor %}
+{% endif %}
+
+{% set evidence_type_check_results = validation_results.get('evidence_type_check', {}) %}
+{% set evidence_check_type_pass = evidence_type_check_results.get('pass', true) %}
+{% if not evidence_check_type_pass %}
+    Evidence Type Check Failures:
+    {% for alias, alias_result in evidence_type_check_results.items() if alias != 'pass' %}
+        {% if alias_result.evidence_type is none and alias_result.errors %}
+            {{ alias }}: {{ alias_result.errors }}
+        {% endif %}
+    {% endfor %}
+{% endif %}
+
+{%- endmacro %}

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/jinja_templates/text/report.txt

@@ -15,7 +15,7 @@ eva-sub-cli v{{cli_version}}
 PROJECT SUMMARY
 General details about the project
 
-{{ project_details_report(project_title, validation_date, submission_dir, vcf_fasta_analysis_mapping) }}
+{{ project_details_report(validation_results, project_title, validation_date, submission_dir, consent_statement_required, vcf_fasta_analysis_mapping) }}
 
 -
 

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/metadata.py

@@ -49,6 +49,10 @@ class EvaMetadataJson(AppLogger):
         if self.resolved_files:
             del self.resolved_files
 
+    def set_analyses(self, analysis_list):
+        assert isinstance(analysis_list, list)
+        self.content['analysis'] = analysis_list
+
     @cached_property
     def samples_per_analysis(self):
         """Returns mapping of analysis alias to sample names, based on metadata."""

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/nextflow/validation.nf

@@ -28,6 +28,7 @@ params.executable = [
 // python scripts - installed as part of eva-sub-cli
 params.python_scripts = [
     "samples_checker": "samples_checker.py",
+    "evidence_type_checker": "evidence_type_checker.py",
     "fasta_checker": "check_fasta_insdc.py",
     "xlsx2json": "xlsx2json.py",
     "semantic_checker": "check_metadata_semantics.py",
@@ -99,6 +100,7 @@ workflow {
         metadata_json_validation(metadata_json)
         metadata_semantic_check(metadata_json)
         sample_name_concordance(metadata_json, vcf_files.collect())
+        evidence_type_check(metadata_json)
         insdc_checker(metadata_json, fasta_to_vcfs)
     }
 }
@@ -265,6 +267,25 @@ process sample_name_concordance {
 }
 
 
+process evidence_type_check {
+    publishDir output_dir,
+            overwrite: true,
+            mode: "copy"
+
+    input:
+    path(metadata_json)
+
+    output:
+    path "evidence_type_checker.yml", emit: evidence_type_checker_yml
+    path "evidence_type_checker.log", emit: evidence_type_checker_log
+
+    script:
+    """
+    $params.python_scripts.evidence_type_checker --metadata_json $metadata_json --output_yaml evidence_type_checker.yml > evidence_type_checker.log 2>&1
+    """
+}
+
+
 process insdc_checker {
     publishDir output_dir,
             overwrite: true,

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/report.py

@@ -16,12 +16,13 @@ def get_logo_data():
 
 
 def generate_report(validation_results, validation_date, submission_dir, vcf_fasta_analysis_mapping, project_title,
-                    subdir, template_file):
+                    consent_statement_required, subdir, template_file):
+    results_for_report = {k: v for k, v in validation_results.items() if k != 'ready_for_submission_to_eva'}
     vcf_files = 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 results_for_report if check in ["vcf_check", "assembly_check"]
+                            for file_name in results_for_report[check]
                             ]))
-    fasta_files = sorted([file_name for file_name in validation_results['fasta_check']])
+    fasta_files = sorted([file_name for file_name in results_for_report['fasta_check']])
     template = Environment(
         loader=FileSystemLoader(os.path.join(current_dir, 'jinja_templates', subdir))
     ).get_template(template_file)
@@ -33,17 +34,20 @@ def generate_report(validation_results, validation_date, submission_dir, vcf_fas
         vcf_files=vcf_files,
         fasta_files=fasta_files,
         submission_dir=submission_dir,
+        consent_statement_required=consent_statement_required,
         vcf_fasta_analysis_mapping=vcf_fasta_analysis_mapping,
-        validation_results=validation_results
+        validation_results=results_for_report
     )
     return re.sub('\s+\n', '\n', rendered_template)
 
 
-def generate_html_report(validation_results, validation_date, submission_dir, vcf_fasta_analysis_mapping, project_title):
-    return generate_report(validation_results, validation_date, submission_dir, vcf_fasta_analysis_mapping, project_title,
-                           subdir='html', template_file='report.html')
+def generate_html_report(validation_results, validation_date, submission_dir, vcf_fasta_analysis_mapping, project_title,
+                         consent_statement_required):
+    return generate_report(validation_results, validation_date, submission_dir, vcf_fasta_analysis_mapping,
+                           project_title, consent_statement_required, subdir='html', template_file='report.html')
 
 
-def generate_text_report(validation_results, validation_date, submission_dir, vcf_fasta_analysis_mapping, project_title):
-    return generate_report(validation_results, validation_date, submission_dir, vcf_fasta_analysis_mapping, project_title,
-                           subdir='text', template_file='report.txt')
+def generate_text_report(validation_results, validation_date, submission_dir, vcf_fasta_analysis_mapping, project_title,
+                         consent_statement_required):
+    return generate_report(validation_results, validation_date, submission_dir, vcf_fasta_analysis_mapping,
+                           project_title, consent_statement_required, subdir='text', template_file='report.txt')

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/semantic_metadata.py

@@ -57,6 +57,7 @@ class SemanticMetadataChecker(AppLogger):
         self.check_existing_biosamples()
         self.check_all_analysis_run_accessions()
         self.check_analysis_alias_coherence()
+        self.check_all_analysis_contain_samples()
 
     def check_all_project_accessions(self):
         """Check that ENA project accessions exist and are public."""
@@ -288,3 +289,15 @@ class SemanticMetadataChecker(AppLogger):
                     property=json_path,
                     description=f'{",".join(list2_list1)} present in {list2_desc} not in {list1_desc}'
                 )
+
+    def check_all_analysis_contain_samples(self):
+        sample_analysis_aliases_set = set()
+        for sample in self.metadata.get(SAMPLE_KEY, []):
+            for analysis_alias in sample.get(ANALYSIS_ALIAS_KEY, []):
+                sample_analysis_aliases_set.add(analysis_alias)
+
+        for idx, analysis in enumerate(self.metadata.get(ANALYSIS_KEY, [])):
+            analysis_alias = analysis.get(ANALYSIS_ALIAS_KEY)
+            if analysis_alias and analysis_alias not in sample_analysis_aliases_set:
+                json_path = f'/{ANALYSIS_KEY}/{idx}'
+                self.add_error(property=json_path, description=f'No sample found for the analysis. Should have at the least one sample.')

{eva_sub_cli-0.4.10 → eva_sub_cli-0.4.11}/eva_sub_cli/validators/docker_validator.py

@@ -12,7 +12,7 @@ from eva_sub_cli.validators.validator import Validator
 logger = logging_config.get_logger(__name__)
 
 default_container_image = 'ebivariation/eva-sub-cli'
-default_container_tag = 'v0.0.4.dev0'
+default_container_tag = 'v0.0.5'
 container_validation_dir = '/opt/vcf_validation'
 container_validation_output_dir = 'vcf_validation_output'