eva-sub-cli 0.5.2__tar.gz → 0.5.3__tar.gz

{eva_sub_cli-0.5.2/eva_sub_cli.egg-info → eva_sub_cli-0.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eva_sub_cli
-Version: 0.5.2
+Version: 0.5.3
 Summary: EBI EVA - validation and submission command line tool
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console

{eva_sub_cli-0.5.2 → eva_sub_cli-0.5.3}/docker/Dockerfile

@@ -6,7 +6,9 @@ ENV NXF_VER=23.10.0
 WORKDIR /opt
 
 # Install JAVA and Node
-RUN apt update && apt install -y default-jdk nodejs npm
+RUN apt update && apt install -y default-jdk build-essential \
+    && curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
+    && apt install -y nodejs
 
 # Install VCF validator
 RUN curl -LJo /usr/local/bin/vcf_validator  https://github.com/EBIvariation/vcf-validator/releases/download/v${vcf_validator_version}/vcf_validator_linux \

{eva_sub_cli-0.5.2 → eva_sub_cli-0.5.3}/eva_sub_cli/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.5.2'
-__version_tuple__ = version_tuple = (0, 5, 2)
+__version__ = version = '0.5.3'
+__version_tuple__ = version_tuple = (0, 5, 3)
 
-__commit_id__ = commit_id = 'g31e734672'
+__commit_id__ = commit_id = 'gc81081e35'

{eva_sub_cli-0.5.2 → eva_sub_cli-0.5.3}/eva_sub_cli/executables/check_fasta_insdc.py

@@ -132,11 +132,11 @@ def get_analyses_and_reference_genome_from_metadata(vcf_files_for_fasta, json_fi
         else:
             all_analyses.add(analysis_aliases[0])
     # Get (single) assembly associated with these analyses
-    assemblies = [metadata.get_reference_assembly_for_analysis(analysis) for analysis in all_analyses]
+    assemblies = {metadata.get_reference_assembly_for_analysis(analysis) for analysis in all_analyses}
     if len(assemblies) != 1:
         logger.error(f'Could not determine assembly accession to check against fasta file, out of: {assemblies}')
         return all_analyses, None
-    return all_analyses, assemblies[0]
+    return all_analyses, assemblies.pop()
 
 
 def check_assembly_in_metadata(assembly_in_metadata):

{eva_sub_cli-0.5.2 → eva_sub_cli-0.5.3}/eva_sub_cli/validators/docker_validator.py

@@ -9,7 +9,7 @@ from retry import retry
 from eva_sub_cli.validators.validator import Validator, ALL_VALIDATION_TASKS
 
 default_container_image = 'ebivariation/eva-sub-cli'
-default_container_tag = 'v0.0.9'
+default_container_tag = 'v0.0.10'
 container_validation_dir = '/opt/vcf_validation'
 container_validation_output_dir = 'vcf_validation_output'
 

{eva_sub_cli-0.5.2 → eva_sub_cli-0.5.3/eva_sub_cli.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eva_sub_cli
-Version: 0.5.2
+Version: 0.5.3
 Summary: EBI EVA - validation and submission command line tool
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console

{eva_sub_cli-0.5.2 → eva_sub_cli-0.5.3}/tests/test_check_fasta_insdc.py

@@ -23,6 +23,22 @@ class TestFastaChecker(TestCase):
         assert analyses == {'VD1'}
         assert reference == 'GCA_000001405.27'
 
+    def test_get_analysis_and_reference_genome_from_metadata_multiple_analyses(self):
+        """Test that multiple analyses with the same referenceGenome return that single assembly."""
+        working_dir = os.path.join(self.resource_dir, 'sample_checker')
+        metadata_json = os.path.join(working_dir, 'metadata.json')
+        vcf_file1 = os.path.join(working_dir, 'example1.vcf.gz')  # VD1
+        vcf_file2 = os.path.join(working_dir, 'example2.vcf')     # VD2
+        vcf_file3 = os.path.join(working_dir, 'example3.vcf')     # VD3
+        os.chdir(working_dir)
+
+        # Multiple VCF files from different analyses, all with same referenceGenome
+        analyses, reference = get_analyses_and_reference_genome_from_metadata(
+            [vcf_file1, vcf_file2, vcf_file3], metadata_json
+        )
+        assert analyses == {'VD1', 'VD2', 'VD3'}
+        assert reference == 'GCA_000001405.27'
+
     def test_get_analysis_and_reference_genome_from_metadata_absolute_paths(self):
         working_dir = os.path.join(self.resource_dir, 'sample_checker')
         metadata_json = os.path.join(working_dir, 'metadata.json')