grz-cli 1.2.0__tar.gz → 1.3.1__tar.gz

{grz_cli-1.2.0 → grz_cli-1.3.1}/CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## [1.3.1](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.3.0...grz-cli-v1.3.1) (2025-10-13)
+
+
+### Bug Fixes
+
+* **grz-cli,grz-common:** check validation progress logs before encrypt ([#411](https://github.com/BfArM-MVH/grz-tools/issues/411)) ([a33b342](https://github.com/BfArM-MVH/grz-tools/commit/a33b342da6f32a59c57acfa067584ac7798f9764))
+
+## [1.3.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.2.0...grz-cli-v1.3.0) (2025-10-07)
+
+
+### Features
+
+* **grzctl,grz-cli:** bump required dependencies ([#402](https://github.com/BfArM-MVH/grz-tools/issues/402)) ([9b7e6f6](https://github.com/BfArM-MVH/grz-tools/commit/9b7e6f6e97c603efb335c0e339a3bc08ea2b2da8))
+
 ## [1.2.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.1.2...grz-cli-v1.2.0) (2025-08-19)
 
 

{grz_cli-1.2.0 → grz_cli-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: grz-cli
-Version: 1.2.0
+Version: 1.3.1
 Summary: Tool for validation, encryption and upload of MV submissions to GDCs.
 Project-URL: Homepage, https://github.com/BfArM-MVH/grz-tools
 Project-URL: Repository, https://github.com/BfArM-MVH/grz-tools
@@ -17,7 +17,7 @@ Requires-Dist: boto3<2,>=1.36
 Requires-Dist: click<9,>=8.2
 Requires-Dist: crypt4gh<2,>=1.7
 Requires-Dist: grz-common<2,>=1.3.0
-Requires-Dist: grz-pydantic-models<3,>=2.2.1
+Requires-Dist: grz-pydantic-models<3,>=2.3
 Requires-Dist: jsonschema<5,>=4.23.0
 Requires-Dist: platformdirs<5,>=4.3.6
 Requires-Dist: pydantic-settings<2.10,>=2.9.0

{grz_cli-1.2.0 → grz_cli-1.3.1}/pyproject.toml

@@ -22,7 +22,7 @@ dependencies = [
     "pydantic >=2.9.2,<2.10",
     "pydantic-settings >=2.9.0,<2.10",
     "platformdirs >=4.3.6,<5",
-    "grz-pydantic-models >=2.2.1,<3",
+    "grz-pydantic-models >=2.3,<3",
     "pysam ==0.23.*",
     "rich ==13.*",
     "requests >=2.32.3,<3",

grz_cli-1.3.1/src/grz_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.3.1"

{grz_cli-1.2.0 → grz_cli-1.3.1}/src/grz_cli/commands/encrypt.py

@@ -18,7 +18,13 @@ log = logging.getLogger(__name__)
 @submission_dir
 @config_file
 @force
-def encrypt(submission_dir, config_file, force):
+@click.option(
+    "--check-validation-logs/--no-check-validation-logs",
+    "check_validation_logs",
+    default=True,
+    help="Check validation logs before encrypting.",
+)
+def encrypt(submission_dir, config_file, force, check_validation_logs):
     """
     Encrypt a submission.
 
@@ -45,7 +51,12 @@ def encrypt(submission_dir, config_file, force):
         with NamedTemporaryFile("w") as f:
             f.write(pubkey)
             f.flush()
-            worker_inst.encrypt(f.name, submitter_private_key_path=submitter_privkey_path, force=force)
+            worker_inst.encrypt(
+                f.name,
+                submitter_private_key_path=submitter_privkey_path,
+                force=force,
+                check_validation_logs=check_validation_logs,
+            )
     else:
         # This case cannot occur here, but an explicit check is needed for type-checking.
         if config.keys.grz_public_key_path is None:
@@ -54,6 +65,7 @@ def encrypt(submission_dir, config_file, force):
             config.keys.grz_public_key_path,
             submitter_private_key_path=submitter_privkey_path,
             force=force,
+            check_validation_logs=check_validation_logs,
         )
 
     log.info("Encryption successful!")

{grz_cli-1.2.0 → grz_cli-1.3.1}/src/grz_cli/commands/submit.py

@@ -30,6 +30,6 @@ def submit(ctx, submission_dir, config_file, threads, force):
     """
     click.echo("Starting submission process...")
     ctx.invoke(validate, submission_dir=submission_dir, config_file=config_file, force=force)
-    ctx.invoke(encrypt, submission_dir=submission_dir, config_file=config_file, force=force)
+    ctx.invoke(encrypt, submission_dir=submission_dir, config_file=config_file, force=force, check_validation_logs=True)
     ctx.invoke(upload, submission_dir=submission_dir, config_file=config_file, threads=threads)
     click.echo("Submission finished!")

grz_cli-1.2.0/src/grz_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.2.0"