eva-sub-cli 0.6.7__tar.gz → 0.7.0__tar.gz

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/.github/workflows/trigger-eva-sub-cli-integration-tests.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Trigger eva sub cli integration tests
-        uses: peter-evans/repository-dispatch@v2
+        uses: peter-evans/repository-dispatch@v4
         with:
           token: ${{ secrets.WORKFLOW_ACCESS_TOKEN }}
           repository: EBIvariation/eva-integration-tests

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eva_sub_cli
-Version: 0.6.7
+Version: 0.7.0
 Summary: EBI EVA - validation and submission command line tool
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/docs/common_metadata_errors.md

@@ -71,7 +71,7 @@ The submitted project or sample accession cannot be found in ENA or is not publi
 
 **Resolution**
 
-EVA cannot access or validate private objects. Make sure the project or sample has been released publicly before submitting it to EVA for validation.
+EVA cannot add to, validate, or access private objects. Make sure the project or sample has been released publicly before submitting it to EVA for validation.
 
 ## 5. BioSamples issued by NCBI : geographic location/collection date issue 
 

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/docs/how_to_submit.md

@@ -71,7 +71,6 @@ This can be useful if you want to avoid re-running long-running validations that
 Note that all validation tasks must pass in order to submit. The report will aggregate the results of previous runs and new ones.
 The possible tasks are:
 * [`vcf_check`](validation_overview.md#vcf-checks) - includes syntax validation and other checks on VCF files
-${CODE_ROOT}/env/bin/upload_to_gcloud.py --input-file evidence.json.gz --destination-folder pharmacogenomics
 * [`assembly_check`](validation_overview.md#assembly-checks) - includes all checks involving the FASTA file
 * [`metadata_check`](validation_overview.md#metadata-check) - includes syntactic and semantic checks on metadata
 * [`sample_check`](validation_overview.md#sample-name-concordance-check) - includes sample coherence checks between VCF files and metadata

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/docs/input_file_overview.md

@@ -87,6 +87,17 @@ One important column to note is the Hold Date, which is the date until which the
 release the data automatically after this date. If it is missing, the default value is three days after the date of
 submission.
 
+### Statements
+
+This sheet contains statements that the submitter must agree to before submitting data. Please read each
+statement carefully and confirm your agreement before submitting.
+
+Additional information about the Access and Benefit-Sharing statement is available in our
+[submission FAQs](https://www.ebi.ac.uk/eva/?Help#submissionPanel&link=confirm-data-shared-openly).
+
+NOTE: To use your Webin account, you must also log in to your account and do a one time confirmation of the Access and
+Benefit-Sharing acknowledgement there. [Webin login](https://www.ebi.ac.uk/ena/submit/webin/login) => Manage Account => Tick the box => Save.
+
 ### Analysis
 
 For EVA, an analysis is a grouping of samples and data files. This sheet allows us to link VCF files to a project and

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/eva_sub_cli/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.6.7'
-__version_tuple__ = version_tuple = (0, 6, 7)
+__version__ = version = '0.7.0'
+__version_tuple__ = version_tuple = (0, 7, 0)
 
-__commit_id__ = commit_id = 'g1607240b0'
+__commit_id__ = commit_id = 'g3d76f3cd1'

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/eva_sub_cli/etc/eva_schema.json

@@ -63,6 +63,25 @@
         }
       }
     },
+    "statements": {
+      "type": "array",
+      "description": "Submitter acknowledgements of various EVA data statements",
+      "items": {
+        "type": "object",
+        "required": ["acknowledgement", "statement"],
+        "additionalProperties": false,
+        "properties": {
+          "acknowledgement": {
+            "type": "boolean",
+            "description": "Whether the submitter confirmed this statement"
+          },
+          "statement": {
+            "type": "string",
+            "description": "Full text of the statement as presented to the submitter"
+          }
+        }
+      }
+    },
     "project": {
       "type": "object",
       "if": {

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/eva_sub_cli/etc/spreadsheet2json_conf.yaml

@@ -11,6 +11,7 @@
 # List of worksheets to be parsed.
 worksheets:
   Submitter Details: submitterDetails
+  Statements: statements
   Project: project
   Analysis: analysis
   Sample: sample
@@ -26,6 +27,14 @@ Submitter Details:
   optional:
     Address: address
 
+Statements:
+  header_row: 2
+  required:
+    Acknowledgement: acknowledgement
+    Statement: statement
+  cast:
+    Acknowledgement: boolean
+
 # List of field for Projects
 Project:
   header_row: 3

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/eva_sub_cli/executables/xlsx2json.py

@@ -22,6 +22,8 @@ SAMPLE_ACCESSION_KEY = 'Sample Accession'
 SAMPLE_NAME_KEY = 'BioSample Name'
 SCIENTIFIC_NAME_KEY = 'Scientific Name'
 SPECIES = 'species'
+STATEMENTS = 'Statements'
+STATEMENTS_ACK_HEADER = 'Acknowledgement'
 
 logger = logging_config.get_logger(__name__)
 
@@ -72,7 +74,9 @@ class XlsxParser:
         if self.worksheets is None:
             self.valid_worksheets()
         if worksheet not in self.worksheets:
-            self.add_error(f'Tried to access an invalid worksheet {worksheet}', sheet=worksheet)
+            self.add_error(f'Could not find expected worksheet {worksheet}. Download the latest unmodified '
+                           f'template from https://raw.githubusercontent.com/EBIvariation/eva-sub-cli/main/eva_sub_cli/'
+                           f'etc/EVA_Submission_template.xlsx', sheet=worksheet)
             return
 
         self._active_worksheet = worksheet
@@ -182,6 +186,21 @@ class XlsxParser:
 
         return rows
 
+    def get_data_acknowledgement_json_data(self):
+        json_key = self.xlsx_conf[WORKSHEETS_KEY_NAME][STATEMENTS]
+        ack_json_key = self.xlsx_conf[STATEMENTS][REQUIRED_HEADERS_KEY_NAME][STATEMENTS_ACK_HEADER]
+
+        acknowledgements = []
+        for row in self.get_rows():
+            row.pop('row_num')
+            json_value = {self.translate_header(STATEMENTS, k): v
+                          for k, v in row.items() if v is not None}
+            # An unchecked/blank checkbox should record as an explicit False
+            json_value.setdefault(ack_json_key, False)
+            acknowledgements.append(json_value)
+
+        return {json_key: acknowledgements}
+
     def get_project_json_data(self):
         json_key = self.xlsx_conf[WORKSHEETS_KEY_NAME][PROJECT]
 
@@ -269,6 +288,8 @@ class XlsxParser:
             elif title == SAMPLE:
                 sample_data = self.get_sample_json_data()
                 json_data.update(sample_data)
+            elif title == STATEMENTS:
+                json_data.update(self.get_data_acknowledgement_json_data())
             else:
                 json_data[self.xlsx_conf[WORKSHEETS_KEY_NAME][title]] = []
                 for row in self.get_rows():

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/eva_sub_cli/semantic_metadata.py

@@ -1,4 +1,5 @@
 import json
+import re
 from collections import Counter
 from copy import deepcopy
 from datetime import datetime, timedelta
@@ -13,6 +14,7 @@ from retry import retry
 from eva_sub_cli.date_utils import check_date
 
 PROJECT_KEY = 'project'
+STATEMENTS_KEY = 'statements'
 ANALYSIS_KEY = 'analysis'
 SAMPLE_KEY = 'sample'
 FILES_KEY = 'files'
@@ -33,6 +35,11 @@ HOLD_DATE_KEY = 'holdDate'
 # Samples created before this date are not required to have collection date or geographic location
 threshold_2023 = datetime(2023, 1, 1)
 
+DATA_ACCESS_STATEMENT = """To the best of my knowledge, the data being submitted are not subject to any 
+       restrictions that prohibit their open sharing and are submitted in compliance with applicable national and 
+       international access and benefit-sharing obligations, in accordance with the EMBL-EBI Terms of Use
+       (https://www.ebi.ac.uk/about/terms-of-use/)."""
+
 
 def cast_list(l, type_to_cast=str):
     for e in l:
@@ -64,6 +71,20 @@ class SemanticMetadataChecker(AppLogger):
         self.check_all_analysis_contain_samples()
         self.check_all_samples_have_sample_in_vcf()
         self.check_hold_date()
+        self.check_statements()
+
+    @staticmethod
+    def _normalize(text):
+        return re.sub(r'\s+', ' ', text).strip().lower()
+
+    def check_statements(self):
+        if STATEMENTS_KEY in self.metadata:
+            for entry in self.metadata[STATEMENTS_KEY]:
+                if (self._normalize(entry.get('statement') or '') == self._normalize(DATA_ACCESS_STATEMENT)
+                        and entry.get('acknowledgement')):
+                    return
+
+        self.add_error(f'/{STATEMENTS_KEY}', 'Data Access & Sharing statement not acknowledged')
 
     def check_hold_date(self):
         """Check that holdDate is no later than 2 years from today."""
@@ -337,8 +358,8 @@ class SemanticMetadataChecker(AppLogger):
             json_path = f'/{SAMPLE_KEY}/{idx}/{SAMPLE_IN_VCF_KEY}'
             analysis_aliases = sample.get(ANALYSIS_ALIAS_KEY, [])
             if any([self.evidence_type_results.get(analysis_alias, {}).get('evidence_type') != 'allele_frequency' for
-                        analysis_alias in analysis_aliases]):
+                    analysis_alias in analysis_aliases]):
                 # SampleInVCF is required
                 if sample.get(SAMPLE_IN_VCF_KEY) is None or sample.get(SAMPLE_IN_VCF_KEY) == '':
-                    self.add_error(json_path, f'{SAMPLE_IN_VCF_KEY} must be provided when Genotypes are present in the VCF file')
-
+                    self.add_error(json_path,
+                                   f'{SAMPLE_IN_VCF_KEY} must be provided when Genotypes are present in the VCF file')

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/eva_sub_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eva_sub_cli
-Version: 0.6.7
+Version: 0.7.0
 Summary: EBI EVA - validation and submission command line tool
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/eva_sub_cli.egg-info/SOURCES.txt

@@ -117,6 +117,7 @@ tests/resources/EVA_Submission_test_with_non_vcf_files.json
 tests/resources/EVA_Submission_test_with_non_vcf_files.xlsx
 tests/resources/EVA_Submission_test_with_project_accession.json
 tests/resources/EVA_Submission_test_with_project_accession.xlsx
+tests/resources/EVA_Submission_test_without_data_acknowledgement_sheet.xlsx
 tests/resources/metadata_with_filename.json
 tests/resources/assembly_check/invalid.vcf.assembly_check.log
 tests/resources/assembly_check/invalid.vcf.text_assembly_report.txt

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/eva_sub_cli.egg-info/scm_file_list.json

@@ -90,6 +90,7 @@
     "tests/resources/EVA_Submission_test_with_non_vcf_files.xlsx",
     "tests/resources/EVA_Submission_test_with_project_accession.json",
     "tests/resources/EVA_Submission_test_with_project_accession.xlsx",
+    "tests/resources/EVA_Submission_test_without_data_acknowledgement_sheet.xlsx",
     "tests/resources/assembly_check/invalid.vcf.assembly_check.log",
     "tests/resources/assembly_check/invalid.vcf.text_assembly_report.txt",
     "tests/resources/assembly_reports/input_passed.txt",

eva_sub_cli-0.7.0/eva_sub_cli.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.7.0",
+  "distance": 0,
+  "node": "g3d76f3cd1a4055b493e3dc7426ee900cb648d91b",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-10-19"
+}

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/tests/test_orchestrator.py

@@ -33,7 +33,7 @@ class TestOrchestrator(unittest.TestCase):
     mapping_file = os.path.join(test_sub_dir, 'vcf_mapping_file.csv')
     metadata_json = os.path.join(test_sub_dir, 'sub_metadata.json')
     metadata_xlsx = os.path.join(test_sub_dir, 'sub_metadata.xlsx')
-    metadata_xlsx_version = '3.0.1'
+    metadata_xlsx_version = '3.1.0'
     metadata_xlsx_with_project_accession = os.path.join(test_sub_dir, 'EVA_Submission_test_with_project_accession.xlsx')
     metadata_xlsx_version_v2 = '2.0.1'
     metadata_xlsx_v2 = os.path.join(test_sub_dir, 'EVA_Submission_test_V2.xlsx')

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/tests/test_semantic_metadata.py

@@ -1,12 +1,12 @@
 from datetime import datetime, timedelta
 from unittest import TestCase
 from unittest.mock import patch
-from requests import HTTPError, Response
 
 import pytest
 from ebi_eva_common_pyutils.biosamples_communicators import NoAuthHALCommunicator
+from requests import HTTPError, Response
 
-from eva_sub_cli.semantic_metadata import SemanticMetadataChecker
+from eva_sub_cli.semantic_metadata import SemanticMetadataChecker, DATA_ACCESS_STATEMENT
 
 metadata = {
     "sample": [
@@ -105,7 +105,8 @@ class TestSemanticMetadata(TestCase):
             m_ena_download.side_effect = [True, True, HTTPError('problem downloading', response=Response())]
             checker.check_all_project_accessions()
             self.assertEqual(checker.errors, [
-                {'property': '/project/childProjects/1', 'description': 'Project PRJEBNA does not exist in ENA or is private'}
+                {'property': '/project/childProjects/1',
+                 'description': 'Project PRJEBNA does not exist in ENA or is private'}
             ])
 
     def test_check_all_taxonomy_codes(self):
@@ -205,7 +206,7 @@ class TestSemanticMetadata(TestCase):
                 'description': 'Analysis alias alias1 is present 2 times in the Analysis Sheet'
             }
         ]
-)
+                         )
 
     def test_check_all_scientific_names(self):
         metadata = {
@@ -270,7 +271,8 @@ class TestSemanticMetadata(TestCase):
     def test_check_existing_biosamples_with_checklist(self):
         checker = SemanticMetadataChecker(metadata, {})
         with patch.object(SemanticMetadataChecker, '_get_biosample',
-                          side_effect=[valid_sample, ValueError, invalid_sample1, invalid_sample2, old_invalid_sample, old_invalid_sample2]) as m_get_sample:
+                          side_effect=[valid_sample, ValueError, invalid_sample1, invalid_sample2, old_invalid_sample,
+                                       old_invalid_sample2]) as m_get_sample:
             checker.check_existing_biosamples()
             self.assertEqual(
                 checker.errors[0],
@@ -286,7 +288,7 @@ class TestSemanticMetadata(TestCase):
                 'Error validating existing sample SAME00003: geographic location (country and~1or sea) must be equal to one of the allowed values:'))
 
             self.assertEqual(checker.errors[3]['description'],
-                "Error validating existing sample SAME00004: must have required property 'geographic location (country and/or sea)'")
+                             "Error validating existing sample SAME00004: must have required property 'geographic location (country and/or sea)'")
 
             # error message lists long regex for collection date
             self.assertTrue(checker.errors[4]['description'].startswith(
@@ -296,13 +298,17 @@ class TestSemanticMetadata(TestCase):
     def test_check_existing_biosamples(self):
         checker = SemanticMetadataChecker(metadata, {}, sample_checklist=None)
         with patch.object(NoAuthHALCommunicator, 'follows_link',
-                          side_effect=[valid_sample, ValueError, invalid_sample1, invalid_sample2, old_invalid_sample, old_invalid_sample2]) as m_follows_link:
+                          side_effect=[valid_sample, ValueError, invalid_sample1, invalid_sample2, old_invalid_sample,
+                                       old_invalid_sample2]) as m_follows_link:
             checker.check_existing_biosamples()
             self.assertEqual(checker.errors, [
-                {'description': 'SAME00002 does not exist or is private','property': '/sample/1/bioSampleAccession'},
-                {'description': 'Existing sample SAME00003 does not have a valid collection date', 'property': '/sample/2/bioSampleAccession'},
-                {'description': 'Existing sample SAME00004 does not have a valid collection date', 'property': '/sample/3/bioSampleAccession'},
-                {'description': 'Existing sample SAME00004 does not have a valid geographic location', 'property': '/sample/3/bioSampleAccession'}])
+                {'description': 'SAME00002 does not exist or is private', 'property': '/sample/1/bioSampleAccession'},
+                {'description': 'Existing sample SAME00003 does not have a valid collection date',
+                 'property': '/sample/2/bioSampleAccession'},
+                {'description': 'Existing sample SAME00004 does not have a valid collection date',
+                 'property': '/sample/3/bioSampleAccession'},
+                {'description': 'Existing sample SAME00004 does not have a valid geographic location',
+                 'property': '/sample/3/bioSampleAccession'}])
 
     @pytest.mark.skip(reason='Contact BioSample API')
     def test_check_existing_real_biosamples(self):
@@ -363,7 +369,8 @@ class TestSemanticMetadata(TestCase):
 
         checker.check_all_analysis_run_accessions()
         assert checker.errors == [
-            {'property': '/analysis/1/runAccessions', 'description': 'Run SRR00000000001 does not exist in ENA or is private'}]
+            {'property': '/analysis/1/runAccessions',
+             'description': 'Run SRR00000000001 does not exist in ENA or is private'}]
 
     def test_check_all_analysis_contain_samples(self):
         # all analysis contain samples
@@ -464,4 +471,31 @@ class TestSemanticMetadata(TestCase):
         metadata = {"project": {}, "sample": [], "analysis": [], "files": []}
         checker = SemanticMetadataChecker(metadata, {})
         checker.check_hold_date()
-        self.assertEqual(checker.errors, [])
+        self.assertEqual(checker.errors, [])
+
+    def test_check_statementss(self):
+        # statement present and acknowledged
+        metadata = {"statements": [{
+            "acknowledgement": True,
+            "statement": DATA_ACCESS_STATEMENT
+        }]}
+        checker = SemanticMetadataChecker(metadata, {})
+        checker.check_statements()
+        self.assertEqual(checker.errors, [])
+
+        # statement present but not acknowledged
+        metadata = {"statements": [{
+            "acknowledgement": False,
+            "statement": DATA_ACCESS_STATEMENT
+        }]}
+        checker = SemanticMetadataChecker(metadata, {})
+        checker.check_statements()
+        self.assertEqual(checker.errors, [{'description': 'Data Access & Sharing statement not acknowledged',
+                                           'property': '/statements'}])
+
+        # no data present for acknowledgement
+        metadata = {"statements": []}
+        checker = SemanticMetadataChecker(metadata, {})
+        checker.check_statements()
+        self.assertEqual(checker.errors, [{'description': 'Data Access & Sharing statement not acknowledged',
+                                           'property': '/statements'}])

{eva_sub_cli-0.6.7 → eva_sub_cli-0.7.0}/tests/test_xlsx2json.py

@@ -7,7 +7,8 @@ import jsonschema
 import yaml
 
 from eva_sub_cli import ETC_DIR
-from eva_sub_cli.executables.xlsx2json import XlsxParser, create_xls_template_from_yaml
+from eva_sub_cli.executables.xlsx2json import XlsxParser, create_xls_template_from_yaml, STATEMENTS
+from eva_sub_cli.semantic_metadata import STATEMENTS_KEY, SemanticMetadataChecker, DATA_ACCESS_STATEMENT
 
 
 class TestXlsReader(TestCase):
@@ -24,7 +25,9 @@ class TestXlsReader(TestCase):
             os.path.join(self.resource_dir, 'EVA_Submission_test_errors.yml'),
             os.path.join(self.resource_dir, 'EVA_Submission_test_errors_v2.yml'),
             os.path.join(self.resource_dir, 'EVA_Submission_test_with_project_accession.yml'),
-            os.path.join(self.resource_dir, 'EVA_Submission_test_with_project_accession_output.json')
+            os.path.join(self.resource_dir, 'EVA_Submission_test_with_project_accession_output.json'),
+            os.path.join(self.resource_dir, 'EVA_Submission_test_output_without_data_acknowledgement_sheet.json'),
+            os.path.join(self.resource_dir, 'EVA_Submission_test_errors_without_data_acknowledgement_sheet.yml')
         ]
         for f in files_from_tests:
             if os.path.exists(f):
@@ -59,7 +62,7 @@ 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()) == ['analysis', 'files', 'project', 'sample', 'statements', 'submitterDetails']
             self.assertEqual(self.get_expected_json(), json_data)
 
         # assert json schema
@@ -87,7 +90,7 @@ 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()) == ['analysis', 'files', 'project', 'sample', 'statements', 'submitterDetails']
             self.assertEqual(self.get_expected_json(), json_data)
 
         # assert json schema
@@ -115,7 +118,7 @@ class TestXlsReader(TestCase):
             json_data = json.load(open_file)
             # assert json file is created with expected data
             assert sorted(json_data.keys()) == ['analysis', 'files', 'project', 'sample', 'submitterDetails']
-            self.assertEqual(self.get_expected_json(), json_data)
+            self.assertEqual(self.get_expected_json_v2(), json_data)
 
         # assert json schema
         with open(self.eva_schema) as eva_schema_file:
@@ -123,6 +126,41 @@ class TestXlsReader(TestCase):
 
         jsonschema.validate(json_data, eva_json_schema)
 
+    def test_conversion_2_json_with_old_worksheet(self) -> None:
+        xls_filename = os.path.join(self.resource_dir, 'EVA_Submission_test_without_data_acknowledgement_sheet.xlsx')
+        self.parser = XlsxParser(xls_filename, self.conf_filename)
+        output_json = os.path.join(self.resource_dir, 'EVA_Submission_test_output_without_data_acknowledgement_sheet.json')
+        errors_yaml = os.path.join(self.resource_dir, 'EVA_Submission_test_errors_without_data_acknowledgement_sheet.yml')
+        self.parser.json(output_json)
+        self.parser.save_errors(errors_yaml)
+
+        # confirm the error - expected sheet not found
+        with open(errors_yaml) as open_file:
+            errors_data = yaml.safe_load(open_file)
+            assert errors_data == [{'column': '', 'description': 'Could not find expected worksheet Statements. Download the latest unmodified '
+                           f'template from https://raw.githubusercontent.com/EBIvariation/eva-sub-cli/main/eva_sub_cli/'
+                           f'etc/EVA_Submission_template.xlsx', 'row': '', 'sheet': 'Statements'}]
+
+        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', 'statements', 'submitterDetails']
+            expected_json_data = self.get_expected_json()
+            expected_json_data['statements'] = []
+            self.assertEqual(expected_json_data, json_data)
+
+    def test_template_statement_matches_data_access_statement_constant(self):
+        template_xlsx = os.path.join(ETC_DIR, 'EVA_Submission_template.xlsx')
+        conf_filename = os.path.join(ETC_DIR, 'spreadsheet2json_conf.yaml')
+        parser = XlsxParser(template_xlsx, conf_filename)
+        parser.active_worksheet = STATEMENTS
+        acknowledgements = parser.get_data_acknowledgement_json_data()[STATEMENTS_KEY]
+        template_statement = acknowledgements[0]['statement']
+        self.assertEqual(
+            SemanticMetadataChecker._normalize(template_statement),
+            SemanticMetadataChecker._normalize(DATA_ACCESS_STATEMENT)
+        )
+
     def test_conversion_2_json_with_project_accession(self) -> None:
         xls_filename = os.path.join(self.resource_dir, 'EVA_Submission_test_with_project_accession.xlsx')
         self.parser = XlsxParser(xls_filename, self.conf_filename)
@@ -139,7 +177,7 @@ 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()) == ['analysis', 'files', 'project', 'sample', 'statements', 'submitterDetails']
             # get expected json and remove other fields apart from project accession for comparison
             expected_json = self.get_expected_json()
             expected_json['project'] = {'projectAccession': 'PRJEB12345'}
@@ -167,7 +205,7 @@ 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()) == ['analysis', 'files', 'project', 'sample', 'statements', 'submitterDetails']
             expected_json = self.get_expected_json()
             expected_json['analysis'][0]['links'] = ['BioProject:PRJNA1435562']
             self.assertEqual(expected_json, json_data)
@@ -201,7 +239,7 @@ 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()) == ['analysis', 'files', 'project', 'sample', 'statements', 'submitterDetails']
             # required field taxId is missing
             assert 'taxId' not in json_data['project']
             # novel sample is missing scientific name in characteristics and sample name
@@ -255,6 +293,16 @@ class TestXlsReader(TestCase):
         return "A" * length
 
     def get_expected_json(self):
+        json_data = self.get_expected_json_v2()
+        json_data["statements"] = [
+            {
+                "acknowledgement": True,
+                "statement": "To the best of my knowledge, the data being submitted are not subject to any restrictions that prohibit their open sharing and are submitted in compliance with applicable national and international access and benefit-sharing obligations, in accordance with the EMBL-EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/)."
+            }
+        ]
+        return json_data
+
+    def get_expected_json_v2(self):
         return {
             "submitterDetails": [
                 {

eva_sub_cli-0.6.7/eva_sub_cli.egg-info/scm_version.json

@@ -1,8 +0,0 @@
-{
-  "tag": "0.6.7",
-  "distance": 0,
-  "node": "g1607240b058c895aca1cb3c1f740225162f02634",
-  "dirty": false,
-  "branch": "HEAD",
-  "node_date": "2026-09-09"
-}