eva-sub-cli 0.6.4__tar.gz → 0.6.5__tar.gz

{eva_sub_cli-0.6.4 → eva_sub_cli-0.6.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eva_sub_cli
-Version: 0.6.4
+Version: 0.6.5
 Summary: EBI EVA - validation and submission command line tool
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console

{eva_sub_cli-0.6.4 → eva_sub_cli-0.6.5}/eva_sub_cli/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.6.4'
-__version_tuple__ = version_tuple = (0, 6, 4)
+__version__ = version = '0.6.5'
+__version_tuple__ = version_tuple = (0, 6, 5)
 
-__commit_id__ = commit_id = 'g1a3c8a4d1'
+__commit_id__ = commit_id = 'ge5181ff56'

{eva_sub_cli-0.6.4 → eva_sub_cli-0.6.5}/eva_sub_cli/call_home.py

@@ -1,4 +1,5 @@
 import os
+import threading
 import traceback
 import uuid
 from datetime import datetime, timezone
@@ -67,6 +68,7 @@ class CallHomeClient:
         self.run_id = _get_or_create_run_id(submission_dir)
         self.executor = executor
         self.tasks = tasks
+        self._threads = []
 
     def _build_payload(self, event_type, **kwargs):
         now = datetime.now(timezone.utc)
@@ -90,12 +92,22 @@ class CallHomeClient:
         return payload
 
     def _send_event(self, event_type, **kwargs):
+        payload = self._build_payload(event_type, **kwargs)
+        thread = threading.Thread(target=self._post_event, args=(event_type, payload))
+        thread.start()
+        self._threads.append(thread)
+
+    def _post_event(self, event_type, payload):
         try:
-            payload = self._build_payload(event_type, **kwargs)
-            requests.post(_get_call_home_url(), json=payload, timeout=5)
+            requests.post(_get_call_home_url(), json=payload, timeout=60)
         except Exception:
             logger.debug('Failed to send %s call-home event', event_type)
 
+    def wait_for_pending_events(self, timeout=None):
+        for thread in self._threads:
+            thread.join(timeout)
+        self._threads = []
+
     def send_start(self):
         self._send_event(EVENT_START)
 

{eva_sub_cli-0.6.4 → eva_sub_cli-0.6.5}/eva_sub_cli/nextflow/validation.nf

@@ -180,7 +180,6 @@ process check_vcf_valid {
     """
     trap 'if [[ \$? == 1 ]]; then exit 0; fi' EXIT
 
-    rm -rf ${output_dir}/vcf_format
     mkdir -p vcf_format
     $params.executable.vcf_validator -i $vcf -r text -o vcf_format --require-evidence > vcf_format/${vcf}.vcf_format.log 2>&1
     """
@@ -210,7 +209,6 @@ process check_vcf_reference {
     """
     trap 'if [[ \$? == 1 || \$? == 139 ]]; then exit 0; fi' EXIT
 
-    rm -rf ${output_dir}/assembly_check
     mkdir -p assembly_check
     $params.executable.vcf_assembly_checker -i $vcf -f $fasta $report_opt -r summary,text  -o assembly_check --require-genbank > assembly_check/${vcf}.assembly_check.log 2>&1
     """

{eva_sub_cli-0.6.4 → eva_sub_cli-0.6.5}/eva_sub_cli/validators/native_validator.py

@@ -1,8 +1,6 @@
 import os
 import subprocess
 
-from ebi_eva_common_pyutils.logger import logging_config
-
 from eva_sub_cli.validators.validator import Validator, ALL_VALIDATION_TASKS
 
 

{eva_sub_cli-0.6.4 → eva_sub_cli-0.6.5}/eva_sub_cli/validators/validator.py

@@ -134,6 +134,11 @@ class Validator(AppLogger):
     def set_up_output_dir(self):
         if not os.path.exists(self.output_dir):
             os.makedirs(self.output_dir, exist_ok=True)
+        # Clean up VCF check and assembly check output from previous runs
+        if VCF_CHECK in self.tasks:
+            shutil.rmtree(os.path.join(self.output_dir, 'vcf_format'), ignore_errors=True)
+        if ASSEMBLY_CHECK in self.tasks:
+            shutil.rmtree(os.path.join(self.output_dir, 'assembly_check'), ignore_errors=True)
 
     def clean_up_output_dir(self):
         # Move intermediate validation outputs into a subdir except metadata.json

{eva_sub_cli-0.6.4 → eva_sub_cli-0.6.5}/eva_sub_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eva_sub_cli
-Version: 0.6.4
+Version: 0.6.5
 Summary: EBI EVA - validation and submission command line tool
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console

{eva_sub_cli-0.6.4 → eva_sub_cli-0.6.5}/eva_sub_cli.egg-info/scm_file_list.json

@@ -1,157 +1,157 @@
 {
   "files": [
-    "README.md",
-    "setup.cfg",
-    "LICENSE",
+    "requirements.txt",
     "setup.py",
     "pyproject.toml",
-    "requirements.txt",
-    ".gitignore",
+    "setup.cfg",
+    "LICENSE",
+    "README.md",
     "pytest.ini",
-    "conda/meta.yaml",
-    "conda/build.sh",
-    "docs/README.md",
-    "docs/validation_overview.md",
-    "docs/installation.md",
-    "docs/input_file_overview.md",
-    "docs/how_to_submit.md",
-    "docs/_config.yml",
-    "docs/common_vcf_errors.md",
-    "docs/using_nextflow.md",
-    "docker/Dockerfile",
-    "tests/test_format_metadata.py",
+    ".gitignore",
+    ".github/workflows/publish_docs.yml",
+    ".github/workflows/tests.yml",
+    ".github/workflows/integration-tests.yml",
+    ".github/workflows/trigger-eva-sub-cli-integration-tests.yml",
+    ".github/workflows/publish.yml",
+    "tests/test_docker_validator.py",
+    "tests/test_auth.py",
     "tests/test_file_utils.py",
-    "tests/test_check_fasta_insdc.py",
-    "tests/test_submit.py",
     "tests/test_validator.py",
-    "tests/test_evidence_type_checker.py",
-    "tests/test_xlsx2json.py",
-    "tests/test_utils.py",
-    "tests/test_call_home.py",
-    "tests/test_auth.py",
-    "tests/ignore_test_nextflow_validation.yml",
-    "tests/test_semantic_metadata.py",
-    "tests/test_samples_checker.py",
-    "tests/test_validaton_results_parsers.py",
-    "tests/test_report.py",
-    "tests/test_docker_validator.py",
     "tests/build_and_test_docker_locally.py",
+    "tests/ignore_test_nextflow_validation.yml",
+    "tests/test_call_home.py",
+    "tests/test_submit.py",
+    "tests/test_check_fasta_insdc.py",
+    "tests/test_trim_down.py",
     "tests/test_native_validator_sample_in_vcf.py",
+    "tests/test_evidence_type_checker.py",
+    "tests/test_metadata.py",
+    "tests/test_samples_checker.py",
     "tests/test_orchestrator.py",
+    "tests/test_report.py",
+    "tests/test_xlsx2json.py",
     "tests/test_cli.py",
-    "tests/test_trim_down.py",
-    "tests/test_metadata.py",
-    "tests/resources/EVA_Submission_test_with_project_accession.json",
-    "tests/resources/EVA_Submission_test_with_non_vcf_files.json",
+    "tests/test_utils.py",
+    "tests/test_format_metadata.py",
+    "tests/test_validaton_results_parsers.py",
+    "tests/test_semantic_metadata.py",
+    "tests/resources/metadata_with_filename.json",
+    "tests/resources/EVA_Submission_Docker_Test.xlsx",
     "tests/resources/EVA_Submission_test.xlsx",
-    "tests/resources/EVA_Submission_test_fails.xlsx",
-    "tests/resources/EVA_Submission_test_version_missing.xlsx",
     "tests/resources/EVA_Submission_test_V2.xlsx",
-    "tests/resources/EVA_Submission_Docker_Test.xlsx",
-    "tests/resources/EVA_Submission_test_with_project_accession.xlsx",
     "tests/resources/EVA_Submission_test_with_links.xlsx",
+    "tests/resources/EVA_Submission_test_with_project_accession.json",
+    "tests/resources/EVA_Submission_test_fails.xlsx",
+    "tests/resources/EVA_Submission_test_with_project_accession.xlsx",
+    "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.json",
-    "tests/resources/metadata_with_filename.json",
+    "tests/resources/EVA_Submission_test_version_missing.xlsx",
     "tests/resources/EVA_Submission_test_with_asm_report.json",
-    "tests/resources/sample_checker/metadata.json",
-    "tests/resources/sample_checker/example1.vcf.gz",
-    "tests/resources/sample_checker/example3.vcf",
-    "tests/resources/sample_checker/example2.vcf",
-    "tests/resources/sample_checker/evidence_type.yaml",
-    "tests/resources/assembly_reports/input_passed.txt",
-    "tests/resources/assembly_check/invalid.vcf.text_assembly_report.txt",
-    "tests/resources/assembly_check/invalid.vcf.assembly_check.log",
-    "tests/resources/sample_in_vcf_check/allele_freq.vcf",
-    "tests/resources/sample_in_vcf_check/metadata_af_with_sample_in_vcf.json",
-    "tests/resources/sample_in_vcf_check/genotype.vcf",
-    "tests/resources/sample_in_vcf_check/metadata_af_no_sample_in_vcf.json",
-    "tests/resources/sample_in_vcf_check/metadata_genotype_no_sample_in_vcf.json",
-    "tests/resources/sample_in_vcf_check/fake_fasta.fa",
-    "tests/resources/sample_in_vcf_check/metadata_genotype_with_sample_in_vcf.json",
-    "tests/resources/vcf_files/example2.vcf.gz.tbi",
-    "tests/resources/vcf_files/example2.vcf.gz",
-    "tests/resources/vcf_files/input_passed.vcf",
-    "tests/resources/fasta_files/Saccharomyces_cerevisiae_I.fa",
-    "tests/resources/fasta_files/multi_seq.fa",
-    "tests/resources/fasta_files/input_passed.fa",
-    "tests/resources/validation_reports/expected_shallow_metadata_xlsx_report.html",
-    "tests/resources/validation_reports/expected_report_metadata_json_process_not_run.txt",
+    "tests/resources/EVA_Submission_test.json",
     "tests/resources/validation_reports/expected_metadata_xlsx_report.txt",
+    "tests/resources/validation_reports/expected_metadata_json_report.html",
+    "tests/resources/validation_reports/expected_shallow_metadata_xlsx_report.html",
+    "tests/resources/validation_reports/expected_metadata_xlsx_report.html",
     "tests/resources/validation_reports/expected_metadata_json_report.txt",
     "tests/resources/validation_reports/expected_report_metadata_json_process_not_run.html",
     "tests/resources/validation_reports/expected_shallow_metadata_xlsx_report.txt",
-    "tests/resources/validation_reports/expected_metadata_json_report.html",
-    "tests/resources/validation_reports/expected_metadata_xlsx_report.html",
+    "tests/resources/validation_reports/expected_report_metadata_json_process_not_run.txt",
     "tests/resources/validation_reports/validation_output/metadata.json",
+    "tests/resources/validation_reports/validation_output/assembly_check/input_passed.vcf.text_assembly_report.1680102476700.txt",
     "tests/resources/validation_reports/validation_output/assembly_check/input_passed.vcf.valid_assembly_report.1680102476700.txt",
     "tests/resources/validation_reports/validation_output/assembly_check/input_passed.vcf.assembly_check.log",
-    "tests/resources/validation_reports/validation_output/assembly_check/input_passed.vcf.text_assembly_report.1680102476700.txt",
-    "tests/resources/validation_reports/validation_output/other_validations/sample_checker.yml",
+    "tests/resources/validation_reports/validation_output/other_validations/input_passed_trim_down.yml",
     "tests/resources/validation_reports/validation_output/other_validations/metadata_semantic_check.yml",
+    "tests/resources/validation_reports/validation_output/other_validations/metadata_validation.txt",
+    "tests/resources/validation_reports/validation_output/other_validations/sample_checker.yml",
     "tests/resources/validation_reports/validation_output/other_validations/file_info.txt",
     "tests/resources/validation_reports/validation_output/other_validations/metadata_conversion_errors.yml",
     "tests/resources/validation_reports/validation_output/other_validations/input_passed.fa_check.yml",
-    "tests/resources/validation_reports/validation_output/other_validations/input_passed_trim_down.yml",
-    "tests/resources/validation_reports/validation_output/other_validations/metadata_validation.txt",
     "tests/resources/validation_reports/validation_output/other_validations/evidence_type_checker.yml",
     "tests/resources/validation_reports/validation_output/vcf_format/input_passed.vcf.vcf_format.log",
-    "tests/resources/validation_reports/validation_output/vcf_format/input_passed.vcf.errors.1680102476854.txt",
     "tests/resources/validation_reports/validation_output/vcf_format/input_passed.vcf.errors.1680102476854.db",
-    "eva_sub_cli/__init__.py",
-    "eva_sub_cli/exceptions.py",
-    "eva_sub_cli/report.py",
-    "eva_sub_cli/submission_ws.py",
-    "eva_sub_cli/utils.py",
+    "tests/resources/validation_reports/validation_output/vcf_format/input_passed.vcf.errors.1680102476854.txt",
+    "tests/resources/assembly_check/invalid.vcf.assembly_check.log",
+    "tests/resources/assembly_check/invalid.vcf.text_assembly_report.txt",
+    "tests/resources/vcf_files/example2.vcf.gz.tbi",
+    "tests/resources/vcf_files/example2.vcf.gz",
+    "tests/resources/vcf_files/input_passed.vcf",
+    "tests/resources/sample_in_vcf_check/metadata_genotype_with_sample_in_vcf.json",
+    "tests/resources/sample_in_vcf_check/genotype.vcf",
+    "tests/resources/sample_in_vcf_check/metadata_af_with_sample_in_vcf.json",
+    "tests/resources/sample_in_vcf_check/fake_fasta.fa",
+    "tests/resources/sample_in_vcf_check/metadata_af_no_sample_in_vcf.json",
+    "tests/resources/sample_in_vcf_check/allele_freq.vcf",
+    "tests/resources/sample_in_vcf_check/metadata_genotype_no_sample_in_vcf.json",
+    "tests/resources/fasta_files/Saccharomyces_cerevisiae_I.fa",
+    "tests/resources/fasta_files/input_passed.fa",
+    "tests/resources/fasta_files/multi_seq.fa",
+    "tests/resources/sample_checker/evidence_type.yaml",
+    "tests/resources/sample_checker/example1.vcf.gz",
+    "tests/resources/sample_checker/example3.vcf",
+    "tests/resources/sample_checker/metadata.json",
+    "tests/resources/sample_checker/example2.vcf",
+    "tests/resources/assembly_reports/input_passed.txt",
+    "eva_sub_cli/date_utils.py",
     "eva_sub_cli/submit.py",
-    "eva_sub_cli/semantic_metadata.py",
-    "eva_sub_cli/call_home.py",
+    "eva_sub_cli/report.py",
+    "eva_sub_cli/file_utils.py",
     "eva_sub_cli/auth.py",
+    "eva_sub_cli/__init__.py",
+    "eva_sub_cli/submission_ws.py",
+    "eva_sub_cli/exceptions.py",
     "eva_sub_cli/metadata.py",
-    "eva_sub_cli/date_utils.py",
+    "eva_sub_cli/semantic_metadata.py",
     "eva_sub_cli/orchestrator.py",
-    "eva_sub_cli/file_utils.py",
+    "eva_sub_cli/call_home.py",
+    "eva_sub_cli/utils.py",
     "eva_sub_cli/nextflow/validation.nf",
+    "eva_sub_cli/etc/EVA_Submission_template.xlsx",
     "eva_sub_cli/etc/eva_schema.json",
-    "eva_sub_cli/etc/eva_logo.png",
+    "eva_sub_cli/etc/EVA_Submission_Example.xlsx",
     "eva_sub_cli/etc/call_home_payload_schema.json",
     "eva_sub_cli/etc/spreadsheet2json_conf.yaml",
     "eva_sub_cli/etc/spreadsheet2json_conf_V2.yaml",
-    "eva_sub_cli/etc/EVA_Submission_Example.xlsx",
-    "eva_sub_cli/etc/EVA_Submission_template.xlsx",
+    "eva_sub_cli/etc/eva_logo.png",
     "eva_sub_cli/etc/eva-biosamples.json",
-    "eva_sub_cli/executables/check_metadata_semantics.py",
-    "eva_sub_cli/executables/__init__.py",
-    "eva_sub_cli/executables/samples_checker.py",
-    "eva_sub_cli/executables/format_metadata.py",
-    "eva_sub_cli/executables/xlsx2json.py",
-    "eva_sub_cli/executables/evidence_type_checker.py",
-    "eva_sub_cli/executables/trim_down.py",
-    "eva_sub_cli/executables/cli.py",
-    "eva_sub_cli/executables/check_fasta_insdc.py",
-    "eva_sub_cli/jinja_templates/text/shallow_validation.txt",
-    "eva_sub_cli/jinja_templates/text/project_details.txt",
+    "eva_sub_cli/validators/validation_results_parsers.py",
+    "eva_sub_cli/validators/docker_validator.py",
+    "eva_sub_cli/validators/__init__.py",
+    "eva_sub_cli/validators/validator.py",
+    "eva_sub_cli/validators/native_validator.py",
     "eva_sub_cli/jinja_templates/text/file_validation.txt",
-    "eva_sub_cli/jinja_templates/text/metadata_validation.txt",
-    "eva_sub_cli/jinja_templates/text/fasta_check.txt",
     "eva_sub_cli/jinja_templates/text/report.txt",
+    "eva_sub_cli/jinja_templates/text/fasta_check.txt",
+    "eva_sub_cli/jinja_templates/text/project_details.txt",
     "eva_sub_cli/jinja_templates/text/sample_name_check.txt",
-    "eva_sub_cli/jinja_templates/html/sample_name_check.html",
-    "eva_sub_cli/jinja_templates/html/shallow_validation.html",
-    "eva_sub_cli/jinja_templates/html/fasta_check.html",
+    "eva_sub_cli/jinja_templates/text/metadata_validation.txt",
+    "eva_sub_cli/jinja_templates/text/shallow_validation.txt",
     "eva_sub_cli/jinja_templates/html/file_validation.html",
     "eva_sub_cli/jinja_templates/html/project_details.html",
+    "eva_sub_cli/jinja_templates/html/sample_name_check.html",
+    "eva_sub_cli/jinja_templates/html/fasta_check.html",
     "eva_sub_cli/jinja_templates/html/metadata_validation.html",
     "eva_sub_cli/jinja_templates/html/report.html",
-    "eva_sub_cli/validators/validation_results_parsers.py",
-    "eva_sub_cli/validators/validator.py",
-    "eva_sub_cli/validators/__init__.py",
-    "eva_sub_cli/validators/native_validator.py",
-    "eva_sub_cli/validators/docker_validator.py",
-    ".github/workflows/trigger-eva-sub-cli-integration-tests.yml",
-    ".github/workflows/integration-tests.yml",
-    ".github/workflows/tests.yml",
-    ".github/workflows/publish_docs.yml",
-    ".github/workflows/publish.yml"
+    "eva_sub_cli/jinja_templates/html/shallow_validation.html",
+    "eva_sub_cli/executables/evidence_type_checker.py",
+    "eva_sub_cli/executables/trim_down.py",
+    "eva_sub_cli/executables/samples_checker.py",
+    "eva_sub_cli/executables/__init__.py",
+    "eva_sub_cli/executables/check_metadata_semantics.py",
+    "eva_sub_cli/executables/cli.py",
+    "eva_sub_cli/executables/format_metadata.py",
+    "eva_sub_cli/executables/check_fasta_insdc.py",
+    "eva_sub_cli/executables/xlsx2json.py",
+    "docker/Dockerfile",
+    "docs/how_to_submit.md",
+    "docs/using_nextflow.md",
+    "docs/validation_overview.md",
+    "docs/_config.yml",
+    "docs/common_vcf_errors.md",
+    "docs/input_file_overview.md",
+    "docs/installation.md",
+    "docs/README.md",
+    "conda/meta.yaml",
+    "conda/build.sh"
   ]
 }

eva_sub_cli-0.6.5/eva_sub_cli.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.6.5",
+  "distance": 0,
+  "node": "ge5181ff5686631adf32275df62f9ceb4fb733e23",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-07-30"
+}

{eva_sub_cli-0.6.4 → eva_sub_cli-0.6.5}/tests/test_call_home.py

@@ -154,16 +154,19 @@ class TestCallHomeClient(TestCase):
         client = self._create_client()
         # Should not raise
         client.send_start()
+        client.wait_for_pending_events()
 
     @patch('eva_sub_cli.call_home.requests.post', side_effect=Timeout('timed out'))
     def test_timeout_swallowed(self, mock_post):
         client = self._create_client()
         client.send_end()
+        client.wait_for_pending_events()
 
     @patch('eva_sub_cli.call_home.requests.post', side_effect=Exception('unexpected error'))
     def test_generic_exception_swallowed(self, mock_post):
         client = self._create_client()
         client.send_failure()
+        client.wait_for_pending_events()
 
     @patch('eva_sub_cli.call_home.requests.post')
     def test_send_all_event_types(self, mock_post):
@@ -176,6 +179,7 @@ class TestCallHomeClient(TestCase):
         client.send_start()
         client.send_validation_completed(common_validation_results)
         client.send_end()
+        client.wait_for_pending_events()
         self.assertEqual(mock_post.call_count, 3)
 
         for call in mock_post.call_args_list:
@@ -187,6 +191,7 @@ class TestCallHomeClient(TestCase):
     def test_send_failure_event(self, mock_post):
         client = self._create_client()
         client.send_failure()
+        client.wait_for_pending_events()
         payload = mock_post.call_args.kwargs['json']
         self.assertEqual(payload['eventType'], EVENT_FAILURE)
         self.assertNotIn('exceptionMessage', payload)
@@ -199,6 +204,7 @@ class TestCallHomeClient(TestCase):
             raise ValueError('something went wrong')
         except ValueError as e:
             client.send_failure(exception=e)
+        client.wait_for_pending_events()
         payload = mock_post.call_args.kwargs['json']
         self.assertEqual(payload['eventType'], EVENT_FAILURE)
         self.assertEqual(payload['exceptionMessage'], 'something went wrong')

eva_sub_cli-0.6.4/eva_sub_cli.egg-info/scm_version.json

@@ -1,8 +0,0 @@
-{
-  "tag": "0.6.4",
-  "distance": 0,
-  "node": "g1a3c8a4d15c9861684ab5714f0f8398b98ad4560",
-  "dirty": false,
-  "branch": "HEAD",
-  "node_date": "2026-07-08"
-}