eva-sub-cli 0.4.11__tar.gz → 0.4.13__tar.gz

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eva_sub_cli
-Version: 0.4.11
+Version: 0.4.13
 Summary: EBI EVA - validation and submission command line tool
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
@@ -19,7 +19,7 @@ Classifier: License :: OSI Approved :: Apache Software License
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: ebi_eva_common_pyutils==0.*,>=0.7.3
+Requires-Dist: ebi_eva_common_pyutils==0.*,>=0.7.4
 Requires-Dist: jinja2==3.*,>=3.0.0
 Requires-Dist: jsonschema==4.*
 Requires-Dist: openpyxl==3.*

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli/_version.py

@@ -1,7 +1,14 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -9,13 +16,19 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
 
-__version__ = version = '0.4.11'
-__version_tuple__ = version_tuple = (0, 4, 11)
+__version__ = version = '0.4.13'
+__version_tuple__ = version_tuple = (0, 4, 13)
+
+__commit_id__ = commit_id = 'gc6e52eaa9'

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli/etc/eva_schema.json

@@ -330,7 +330,7 @@
                 "$ref": "eva-biosamples.json"
               },
               {
-                "$ref": "https://www.ebi.ac.uk/biosamples/schema/store/registry/schemas/ERC000011"
+                "$ref": "https://www.ebi.ac.uk/biosamples/schema-store/registry/schemas/ERC000011"
               },
               {
                 "$ref": "https://www.ebi.ac.uk/biosamples/schemas/certification/plant-miappe.json"

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli/etc/spreadsheet2json_conf.yaml

@@ -81,6 +81,8 @@ Sample:
   required:
     Analysis Alias: analysisAlias
     Sample Name in VCF: sampleInVCF
+  # Sample property names taken from ERC000011 where present
+  # See https://www.ebi.ac.uk/biosamples/schema-store/registry/schemas/ERC000011
   optional:
     Sample Accession: bioSampleAccession
     BioSample Name: bioSampleName
@@ -91,37 +93,37 @@ Sample:
     Subject: subject
     Derived From: derivedFrom
     Taxonomy ID: taxId
-    Scientific Name: scientificName
+    Scientific Name: scientific name
     Common Name: commonName
-    mating_type: matingType
+    mating_type: mating_type
     sex: sex
     population: population
-    cell_type: cellType
-    dev_stage: devStage
+    cell_type: cell_type
+    dev_stage: dev_stage
     germline: germline
-    tissue_lib: tissueLib
-    tissue_type: tissueType
-    bio_material: BioMaterial
-    culture_collection: cultureCollection
-    specimen_voucher: specimenVoucher
-    collected_by: collectedBy
-    collection_date: collectionDate
-    geographic location (country and/or sea): geographicLocationCountrySea
-    geographic location (region and locality): geographicLocationRegion
+    tissue_lib: tissue_lib
+    tissue_type: tissue_type
+    bio_material: bio_material
+    culture_collection: culture_collection
+    specimen_voucher: specimen_voucher
+    collected_by: collected_by
+    collection_date: collection date
+    geographic location (country and/or sea): geographic location (country and/or sea)
+    geographic location (region and locality): geographic location (region and locality)
     host: host
-    identified_by: identifiedBy
-    isolation_source: isolationSource
-    lat_lon: latLon
-    lab_host: LabHost
-    environmental_sample: environmentalSample
+    identified_by: identified_by
+    isolation_source: isolation_source
+    lat_lon: lat_lon
+    lab_host: lab_host
+    environmental_sample: environmental_sample
     cultivar: cultivar
     ecotype: ecotype
     isolate: isolate
     strain: strain
-    sub_species: subSpecies
+    sub_species: sub_species
     variety: variety
-    sub_strain: subStrain
-    cell_line: cellType
+    sub_strain: sub_strain
+    cell_line: cell_line
     serotype: serotype
     serovar: serovar
   cast:

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli/executables/evidence_type_checker.py

@@ -3,22 +3,30 @@ 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.file_utils import detect_vcf_evidence_type, associate_vcf_path_with_analysis
 from eva_sub_cli.metadata import EvaMetadataJson
 
 logger = logging_config.get_logger(__name__)
 
 
-def check_evidence_type(metadata_json, output_yaml):
+def check_evidence_type(metadata_json, vcf_files, output_yaml):
     metadata = EvaMetadataJson(metadata_json)
+    file_path_per_analysis = associate_vcf_path_with_analysis(metadata, vcf_files)
+
     results_per_analysis_alias = {}
 
-    for analysis_alias, vcf_file_set in metadata.files_per_analysis.items():
+    all_analysis_alias = set(metadata.files_per_analysis) | set(file_path_per_analysis)
+    for analysis_alias in all_analysis_alias:
         results_per_analysis_alias[analysis_alias] = {
             'evidence_type': None,
             'errors': None
         }
-        vcf_files = list(vcf_file_set)
+        vcf_files = list(file_path_per_analysis.get(analysis_alias, []))
+
+        if not vcf_files:
+            results_per_analysis_alias[analysis_alias]['errors'] = f'No VCF file found for the analysis'
+            continue
+
         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:
@@ -43,9 +51,11 @@ 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('--vcf_files', dest='vcf_files', nargs='+',
+                            help='Path to the vcf files to compare to the metadata')
     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)
+    check_evidence_type(args.metadata_json, args.vcf_files, args.output_yaml)

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/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, detect_vcf_evidence_type
+from eva_sub_cli.file_utils import open_gzip_if_required, detect_vcf_evidence_type, associate_vcf_path_with_analysis
 from eva_sub_cli.metadata import EvaMetadataJson
 
 logger = logging_config.get_logger(__name__)
@@ -99,32 +99,6 @@ def need_to_check_samples(sample_name_per_file):
     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
-    line.
-    :param vcf_files the list of full path to the vcf files
-    :param files_per_analysis: dictionary of the analysis and their associated VCF file names
-    :returns dictionary of analysis and their associated vcf file path
-    """
-    result_files_per_analysis = dict()
-    for analysis in metadata.files_per_analysis:
-        result_files_per_analysis[analysis] = []
-    for vcf_file in vcf_files:
-        analysis_aliases = metadata.get_analysis_for_vcf_file(vcf_file)
-        if len(analysis_aliases) == 1:
-            result_files_per_analysis[analysis_aliases[0]].append(vcf_file)
-        elif len(analysis_aliases) == 0:
-            logger.error(f'No analysis found for vcf {vcf_file}')
-            if 'No analysis' not in result_files_per_analysis:
-                result_files_per_analysis['No analysis'] = []
-            result_files_per_analysis['No analysis'].append(vcf_file)
-        else:
-            logger.error(f'More than one analysis were match to vcf {vcf_file}')
-
-    return result_files_per_analysis
-
-
 def write_result_yaml(output_yaml, overall_differences, results_per_analysis_alias):
     with open(output_yaml, 'w') as open_yaml:
         yaml.safe_dump(data={

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli/executables/xlsx2json.py

@@ -9,6 +9,8 @@ from ebi_eva_common_pyutils.logger import logging_config
 from openpyxl.reader.excel import load_workbook
 from openpyxl.workbook import Workbook
 
+from eva_sub_cli.orchestrator import get_sub_cli_version, get_sub_cli_github_tags
+
 WORKSHEETS_KEY_NAME = 'worksheets'
 REQUIRED_HEADERS_KEY_NAME = 'required'
 OPTIONAL_HEADERS_KEY_NAME = 'optional'
@@ -249,7 +251,8 @@ class XlsxParser:
         # If the file could not be loaded at all, return without generating JSON.
         if not self.file_loaded:
             return
-        json_data = {}
+        # Include which version of the EVA schema we are using
+        json_data = {'$schema': self.get_json_schema_link()}
         for title in self.xlsx_conf[WORKSHEETS_KEY_NAME]:
             self.active_worksheet = title
             if title == PROJECT:
@@ -270,6 +273,14 @@ class XlsxParser:
         with open(output_json_file, 'w') as open_file:
             json.dump(json_data, open_file, cls=DateTimeEncoder)
 
+    def get_json_schema_link(self):
+        sub_cli_version = get_sub_cli_version()
+        sub_cli_tags = get_sub_cli_github_tags()
+        if sub_cli_version in sub_cli_tags:
+            return f'https://raw.githubusercontent.com/EBIvariation/eva-sub-cli/refs/tags/v{sub_cli_version}/eva_sub_cli/etc/eva_schema.json'
+        else:
+            return 'https://raw.githubusercontent.com/EBIvariation/eva-sub-cli/main/eva_sub_cli/etc/eva_schema.json'
+
     def translate_header(self, title, header):
         if header in self.xlsx_conf[title].get(REQUIRED_HEADERS_KEY_NAME, {}):
             return self.xlsx_conf[title][REQUIRED_HEADERS_KEY_NAME][header]

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli/file_utils.py

@@ -35,6 +35,30 @@ def is_vcf_file(file_path):
         return file_path.endswith('.vcf') or file_path.endswith('.vcf.gz')
     return False
 
+def associate_vcf_path_with_analysis(metadata, vcf_files):
+    """
+    Match the files names associated with analysis provided in the metadata with the given file path
+
+    :param vcf_files the list of full path to the vcf files
+    :param files_per_analysis: dictionary of the analysis and their associated VCF file names
+    :returns dictionary of analysis and their associated vcf file path
+    """
+    result_files_per_analysis = dict()
+    for analysis in metadata.files_per_analysis:
+        result_files_per_analysis[analysis] = []
+    for vcf_file in vcf_files:
+        analysis_aliases = metadata.get_analysis_for_vcf_file(vcf_file)
+        if len(analysis_aliases) == 1:
+            result_files_per_analysis[analysis_aliases[0]].append(vcf_file)
+        elif len(analysis_aliases) == 0:
+            logger.error(f'No analysis found for vcf {vcf_file}')
+            if 'No analysis' not in result_files_per_analysis:
+                result_files_per_analysis['No analysis'] = []
+            result_files_per_analysis['No analysis'].append(vcf_file)
+        else:
+            logger.error(f'More than one analysis were match to vcf {vcf_file}')
+
+    return result_files_per_analysis
 
 def detect_vcf_evidence_type(vcf_file):
     """

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli/nextflow/validation.nf

@@ -100,7 +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)
+        evidence_type_check(metadata_json, vcf_files.collect())
         insdc_checker(metadata_json, fasta_to_vcfs)
     }
 }
@@ -274,6 +274,7 @@ process evidence_type_check {
 
     input:
     path(metadata_json)
+    path(vcf_files)
 
     output:
     path "evidence_type_checker.yml", emit: evidence_type_checker_yml
@@ -281,7 +282,7 @@ process evidence_type_check {
 
     script:
     """
-    $params.python_scripts.evidence_type_checker --metadata_json $metadata_json --output_yaml evidence_type_checker.yml > evidence_type_checker.log 2>&1
+    $params.python_scripts.evidence_type_checker --metadata_json $metadata_json --vcf_files $vcf_files --output_yaml evidence_type_checker.yml > evidence_type_checker.log 2>&1
     """
 }
 

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli/orchestrator.py

@@ -130,7 +130,10 @@ def get_project_and_vcf_fasta_mapping_from_metadata_json(metadata_json, mapping_
 
 def get_sub_cli_version():
     if version.parse(eva_sub_cli.__version__).is_devrelease:
-        major, minor, patch = map(int, version.parse(eva_sub_cli.__version__).base_version.split('.'))
+        version_values = [int(v) for v in version.parse(eva_sub_cli.__version__).base_version.split('.')]
+        major = version_values[0]
+        minor = version_values[1] if len(version_values) > 1 else 0
+        patch = version_values[2] if len(version_values) > 2 else 0
         if patch > 0:
             patch -= 1
         elif minor > 0:
@@ -160,7 +163,7 @@ def get_metadata_xlsx_template_link():
     sub_cli_version = get_sub_cli_version()
     sub_cli_tags = get_sub_cli_github_tags()
     if sub_cli_version in sub_cli_tags:
-        return f'https://raw.githubusercontent.com/EBIvariation/eva-sub-cli/v{sub_cli_version}/eva-sub-cli/eva_sub_cli/etc/EVA_Submission_template.xlsx'
+        return f'https://raw.githubusercontent.com/EBIvariation/eva-sub-cli/refs/tags/v{sub_cli_version}/eva_sub_cli/etc/EVA_Submission_template.xlsx'
     else:
         return 'https://raw.githubusercontent.com/EBIvariation/eva-sub-cli/main/eva_sub_cli/etc/EVA_Submission_template.xlsx'
 

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/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 = 'v0.0.5'
+default_container_tag = 'v0.0.6'
 container_validation_dir = '/opt/vcf_validation'
 container_validation_output_dir = 'vcf_validation_output'
 

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eva_sub_cli
-Version: 0.4.11
+Version: 0.4.13
 Summary: EBI EVA - validation and submission command line tool
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
@@ -19,7 +19,7 @@ Classifier: License :: OSI Approved :: Apache Software License
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: ebi_eva_common_pyutils==0.*,>=0.7.3
+Requires-Dist: ebi_eva_common_pyutils==0.*,>=0.7.4
 Requires-Dist: jinja2==3.*,>=3.0.0
 Requires-Dist: jsonschema==4.*
 Requires-Dist: openpyxl==3.*

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/eva_sub_cli.egg-info/requires.txt

@@ -1,4 +1,4 @@
-ebi_eva_common_pyutils==0.*,>=0.7.3
+ebi_eva_common_pyutils==0.*,>=0.7.4
 jinja2==3.*,>=3.0.0
 jsonschema==4.*
 openpyxl==3.*

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/requirements.txt

@@ -1,4 +1,4 @@
-ebi_eva_common_pyutils >= 0.7.3, == 0.*
+ebi_eva_common_pyutils >= 0.7.4, == 0.*
 jinja2 >= 3.0.0, == 3.*
 jsonschema == 4.*
 openpyxl == 3.*

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/tests/build_and_test_docker_locally.py

@@ -141,13 +141,14 @@ class TestDockerValidator(TestCase):
         expected_metadata_val = 'Validation passed successfully.'
         expected_semantic_val = {'description': 'SAME123 does not exist or is private',
                                  'property': '/sample/0/bioSampleAccession'}
+        expected_evidence_type_val = {'AA': {'evidence_type': 'genotype', 'errors': None}}
         expected_metadata_files_json = [
             {'analysisAlias': 'AA', 'fileName': 'input_passed.vcf', 'fileType': 'vcf',
              'md5': '96a80c9368cc3c37095c86fbe6044fb2', 'fileSize': 45050}
         ]
 
         self.assert_validation_results(self.validator, expected_sample_checker, expected_metadata_files_json,
-                                       expected_metadata_val, expected_semantic_val)
+                                       expected_metadata_val, expected_semantic_val, expected_evidence_type_val)
 
     def test_validate_with_xlsx(self):
         self.xlsx_validator.validate()
@@ -156,13 +157,14 @@ class TestDockerValidator(TestCase):
         expected_metadata_val = 'Validation passed successfully.'
         expected_semantic_val = {'description': 'SAME123 does not exist or is private',
                                  'property': '/sample/0/bioSampleAccession'}
+        expected_evidence_type_val = {'AA': {'evidence_type': 'genotype', 'errors': None}}
         expected_metadata_files_json = [
             {'analysisAlias': 'AA', 'fileName': 'input_passed.vcf',
              'md5': '96a80c9368cc3c37095c86fbe6044fb2', 'fileSize': 45050}
         ]
 
         self.assert_validation_results(self.xlsx_validator, expected_sample_checker, expected_metadata_files_json,
-                                       expected_metadata_val, expected_semantic_val)
+                                       expected_metadata_val, expected_semantic_val, expected_evidence_type_val)
 
     def get_submission_json_metadata(self):
         return {
@@ -230,7 +232,7 @@ class TestDockerValidator(TestCase):
         return docker_cmd
 
     def assert_validation_results(self, validator, expected_sample_checker, expected_metadata_files_json,
-                                  expected_metadata_val, expected_semantic_val):
+                                  expected_metadata_val, expected_semantic_val, expected_evidence_type_val):
         vcf_format_dir = os.path.join(validator.output_dir, 'vcf_format')
         self.assertTrue(os.path.exists(vcf_format_dir))
 
@@ -260,7 +262,10 @@ class TestDockerValidator(TestCase):
             self.assertEqual('[info] Percentage of matches: 100%\n', assembly_check_logs[5])
 
         # Assert Samples concordance
-        self.assert_sample_checker(validator._sample_check_yaml, expected_sample_checker)
+        self.assert_yaml_file(validator._sample_check_yaml, expected_sample_checker)
+
+        # assert evidence type check
+        self.assert_yaml_file(validator._evidence_type_check_yaml, expected_evidence_type_val)
 
         with open(validator.metadata_json_post_validation) as open_file:
             json_data = json.load(open_file)
@@ -278,10 +283,10 @@ class TestDockerValidator(TestCase):
             semantic_output = yaml.safe_load(open_yaml)
             assert semantic_output[0] == expected_semantic_val
 
-    def assert_sample_checker(self, sample_checker_file, expected_checker):
-        self.assertTrue(os.path.isfile(sample_checker_file))
-        with open(sample_checker_file) as open_yaml:
-            self.assert_same_dict_and_unordered_list(yaml.safe_load(open_yaml), expected_checker)
+    def assert_yaml_file(self, yaml_file, expected_data):
+        self.assertTrue(os.path.isfile(yaml_file))
+        with open(yaml_file) as open_yaml:
+            self.assert_same_dict_and_unordered_list(yaml.safe_load(open_yaml), expected_data)
 
     def assert_same_dict_and_unordered_list(self, o1, o2):
         if isinstance(o1, dict) and isinstance(o2, dict):

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/tests/test_check_fasta_insdc.py

@@ -132,5 +132,5 @@ class TestFastaChecker(TestCase):
     @pytest.mark.integration
     def test_get_containing_assemblies(self):
         results = get_containing_assemblies('6ac8f815bf8e845bb3031b73f812c012')
-        assert len(results) == 14
+        assert len(results) == 15
         assert 'GCA_000001405.29' in results

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/tests/test_docker_validator.py

@@ -158,7 +158,7 @@ class TestDockerValidator(TestCase):
             {'analysisAlias': 'AA', 'fileName': 'input_passed.vcf', 'fileType': 'vcf',
              'md5': '96a80c9368cc3c37095c86fbe6044fb2', 'fileSize': 45050}
         ]
-        expected_metadata_val = 'must match pattern "^PRJ(EB|NA)\\d+$"'
+        expected_metadata_val = 'must match pattern "^PRJ(E|D|N)[A-Z][0-9]+$"'
         expected_semantic_val = {'description': 'SAME123 does not exist or is private',
                                           'property': '/sample/0/bioSampleAccession'}
 

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/tests/test_evidence_type_checker.py

@@ -21,7 +21,12 @@ class TestEvidenceTypeChecker(TestCase):
         metadata_json = os.path.join(working_dir, 'metadata.json')
         # Change to working_dir so filenames in metadata.json are resolvable
         os.chdir(working_dir)
-        self.run_and_assert_evidence_type_check(metadata_json)
+        vcf_files = [
+            os.path.join(working_dir, file_name)
+            for file_name in ['example1.vcf.gz', 'example2.vcf', 'example3.vcf']
+        ]
+
+        self.run_and_assert_evidence_type_check(metadata_json, vcf_files)
 
     def test_evidence_check_absolute_paths(self):
         working_dir = os.path.join(self.resource_dir, 'sample_checker')
@@ -39,18 +44,17 @@ class TestEvidenceTypeChecker(TestCase):
         updated_metadata = os.path.join(working_dir, 'updated_metadata.json')
         metadata.write(updated_metadata)
 
-        self.run_and_assert_evidence_type_check(updated_metadata)
+        self.run_and_assert_evidence_type_check(updated_metadata, vcf_files)
 
         if os.path.exists(updated_metadata):
             os.remove(updated_metadata)
 
-    def run_and_assert_evidence_type_check(self, metadata_json):
-        check_evidence_type(metadata_json, self.output_yaml)
-        failing_vcf = os.path.join(self.resource_dir,'sample_checker','example1.vcf.gz.tbi')
+    def run_and_assert_evidence_type_check(self, metadata_json, vcf_files):
+        check_evidence_type(metadata_json, vcf_files, self.output_yaml)
         expected_results = {
             'VD1': {
-                'errors': f'VCF file evidence type could not be determined: {failing_vcf}',
-                'evidence_type': None
+                'evidence_type': 'genotype',
+                'errors': None
             },
             'VD2': {
                 'evidence_type': 'genotype',

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/tests/test_orchestrator.py

@@ -306,7 +306,7 @@ class TestOrchestrator(unittest.TestCase):
                 patch('eva_sub_cli.orchestrator.get_sub_cli_github_tags') as sub_cli_tags:
             sub_cli_version.return_value = '1.1.6'
             sub_cli_tags.return_value = ['1.1.6']
-            assert get_metadata_xlsx_template_link() == 'https://raw.githubusercontent.com/EBIvariation/eva-sub-cli/v1.1.6/eva-sub-cli/eva_sub_cli/etc/EVA_Submission_template.xlsx'
+            assert get_metadata_xlsx_template_link() == 'https://raw.githubusercontent.com/EBIvariation/eva-sub-cli/refs/tags/v1.1.6/eva_sub_cli/etc/EVA_Submission_template.xlsx'
 
             sub_cli_version.return_value = '1.1.5'
             sub_cli_tags.return_value = ['1.1.6']

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/tests/test_submit.py

@@ -79,8 +79,10 @@ class TestSubmit(unittest.TestCase):
         assert is_submission_dir_writable(self.test_sub_dir)
         assert not os.path.exists(self.config_file)
         sub_config = WritableConfig(self.config_file, version='version1.0')
+        sub_config.set('metadata_json', value=os.path.join(self.resource_dir, 'EVA_Submission_test.json'))
         sub_config.set(READY_FOR_SUBMISSION_TO_EVA, value=True)
         sub_config.write()
+        self.submitter = StudySubmitter(submission_dir=self.test_sub_dir, submission_config=sub_config)
 
         test_submission_ws_client = SubmissionWSClient()
 

{eva_sub_cli-0.4.11 → eva_sub_cli-0.4.13}/tests/test_xlsx2json.py

@@ -55,7 +55,8 @@ class TestXlsReader(TestCase):
         with open(output_json) as open_file:
             json_data = json.load(open_file)
             # assert json file is created with expected data
-            assert sorted(json_data.keys()) == ['analysis', 'files', 'project', 'sample', 'submitterDetails']
+            assert sorted(json_data.keys()) == ['$schema', 'analysis', 'files', 'project', 'sample', 'submitterDetails']
+            json_data.pop('$schema', None)
             self.assertEqual(self.get_expected_json(), json_data)
 
         # assert json schema
@@ -94,7 +95,7 @@ class TestXlsReader(TestCase):
         assert os.path.exists(output_json)
         with open(output_json) as open_file:
             json_data = json.load(open_file)
-            assert sorted(json_data.keys()) == ['analysis', 'files', 'project', 'sample', 'submitterDetails']
+            assert sorted(json_data.keys()) == ['$schema', 'analysis', 'files', 'project', 'sample', 'submitterDetails']
             # required field taxId is missing
             assert 'taxId' not in json_data['project']
             # novel sample is missing scientific name in characteristics and sample name
@@ -220,19 +221,19 @@ class TestXlsReader(TestCase):
                             "taxId": [
                                 {"text": "9447"}
                             ],
-                            "scientificName": [
+                            "scientific name": [
                                 {"text": "Lemur catta"}
                             ],
                             "sex": [
                                 {"text": "Female"}
                             ],
-                            "tissueType": [
+                            "tissue_type": [
                                 {"text": "skin"}
                             ],
                             "species": [
                                 {"text": "Lemur catta"}
                             ],
-                            'collectionDate': [
+                            'collection date': [
                                 {'text': '2021-03-12'}
                             ]
                         }