grz-cli 0.7.0__tar.gz → 1.0.0__tar.gz

grz_cli-1.0.0/CHANGELOG.md

@@ -0,0 +1,31 @@
+# Changelog
+
+## [1.0.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v0.7.0...grz-cli-v1.0.0) (2025-06-30)
+
+
+### ⚠ BREAKING CHANGES
+
+* **grz-cli,grzctl:** require GRZ and LE Id in config during validate ([#226](https://github.com/BfArM-MVH/grz-tools/issues/226))
+* **grz-cli:** remove support for old configuration format ([#221](https://github.com/BfArM-MVH/grz-tools/issues/221))
+
+### Features
+
+* **grz-cli,grzctl:** require GRZ and LE Id in config during validate ([#226](https://github.com/BfArM-MVH/grz-tools/issues/226)) ([7043d9b](https://github.com/BfArM-MVH/grz-tools/commit/7043d9b3d66fcbd66bc102d9d0608467293ff7e1))
+
+
+### Bug Fixes
+
+* **grz-cli,grz-common:** Require click >=8.2 ([#214](https://github.com/BfArM-MVH/grz-tools/issues/214)) ([bc6f839](https://github.com/BfArM-MVH/grz-tools/commit/bc6f839efa3a7b88025af66199b7eea06ac688ef))
+* **grz-cli:** add missing validate parameter to submit command ([#235](https://github.com/BfArM-MVH/grz-tools/issues/235)) ([854e704](https://github.com/BfArM-MVH/grz-tools/commit/854e7046fc9bacf6a6aa71d8d6a0b4ea4b5d6d65))
+
+
+### Miscellaneous Chores
+
+* **grz-cli:** remove support for old configuration format ([#221](https://github.com/BfArM-MVH/grz-tools/issues/221)) ([49aeaae](https://github.com/BfArM-MVH/grz-tools/commit/49aeaae693a09a42505fe2606f1db8d85c1a4d21))
+
+## [0.7.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v0.6.1...grz-cli-v0.7.0) (2025-06-11)
+
+
+### Features
+
+* migrate to monorepo configuration ([36c7360](https://github.com/BfArM-MVH/grz-tools/commit/36c736044ce09473cc664b4471117465c5cab9a3))

{grz_cli-0.7.0 → grz_cli-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: grz-cli
-Version: 0.7.0
+Version: 1.0.0
 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
@@ -14,10 +14,10 @@ Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.12
 Requires-Dist: boto3<2,>=1.36
-Requires-Dist: click<9,>=8.1.7
+Requires-Dist: click<9,>=8.2
 Requires-Dist: crypt4gh<2,>=1.7
-Requires-Dist: grz-common
-Requires-Dist: grz-pydantic-models>=1.3.0
+Requires-Dist: grz-common>=1.0.0
+Requires-Dist: grz-pydantic-models>=2.0.0
 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-0.7.0 → grz_cli-1.0.0}/pyproject.toml

@@ -14,7 +14,7 @@ authors = [
 dynamic = ["version"]
 dependencies = [
     "boto3 >=1.36,<2",
-    "click >=8.1.7,<9",
+    "click >=8.2,<9",
     "crypt4gh >=1.7,<2",
     "jsonschema >=4.23.0,<5",
     "pyyaml >=6.0.2,<7",
@@ -22,11 +22,11 @@ dependencies = [
     "pydantic >=2.9.2,<2.10",
     "pydantic-settings >=2.9.0,<2.10",
     "platformdirs >=4.3.6,<5",
-    "grz-pydantic-models >=1.3.0",
+    "grz-pydantic-models >=2.0.0",
     "pysam ==0.23.*",
     "rich ==13.*",
     "requests >=2.32.3,<3",
-    "grz-common",
+    "grz-common >=1.0.0",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",
@@ -35,8 +35,12 @@ classifiers = [
 requires-python = ">=3.12"
 keywords = ["GRZ", "GDC", "S3"]
 
+[dependency-groups]
+dev = ["tox", "tox-uv"]
+
 [tool.uv.sources]
-grz-common = { workspace = true }
+grz-common = { path = "../grz-common", editable = true }
+grz-pydantic-models = { path = "../grz-pydantic-models", editable = true }
 
 [project.urls]
 Homepage = "https://github.com/BfArM-MVH/grz-tools"

grz_cli-1.0.0/src/grz_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.0.0"

{grz_cli-0.7.0 → grz_cli-1.0.0}/src/grz_cli/cli.py

@@ -41,7 +41,7 @@ def build_cli():
     @click.version_option(
         version=version("grz-cli"),
         prog_name="grz-cli",
-        message=f"%(prog)s v%(version)s (metadata schema versions: {', '.join(grz_pydantic_models.submission.metadata.get_supported_versions())})",
+        message=f"%(prog)s v%(version)s (currently accepted metadata schema versions: {', '.join(grz_pydantic_models.submission.metadata.get_accepted_versions())})",
     )
     @click.option("--log-file", metavar="FILE", type=str, help="Path to log file")
     @click.option(

{grz_cli-0.7.0 → grz_cli-1.0.0}/src/grz_cli/commands/submit.py

@@ -29,7 +29,7 @@ def submit(ctx, submission_dir, config_file, threads, force):
     3. Upload the encrypted submission
     """
     click.echo("Starting submission process...")
-    ctx.invoke(validate, submission_dir=submission_dir, force=force)
+    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(upload, submission_dir=submission_dir, config_file=config_file, threads=threads)
     click.echo("Submission finished!")

{grz_cli-0.7.0 → grz_cli-1.0.0}/src/grz_cli/commands/upload.py

@@ -39,6 +39,6 @@ def upload(
         threads=threads,
     )
     # output the generated submission ID
-    print(worker_inst.upload(config.s3))
+    click.echo(worker_inst.upload(config.s3))
 
     log.info("Upload finished!")

{grz_cli-0.7.0 → grz_cli-1.0.0}/src/grz_cli/commands/validate.py

@@ -4,7 +4,8 @@ import logging
 from pathlib import Path
 
 import click
-from grz_common.cli import force, submission_dir
+from grz_cli.models.config import ValidateConfig
+from grz_common.cli import config_file, force, submission_dir
 from grz_common.workers.worker import Worker
 
 log = logging.getLogger(__name__)
@@ -12,14 +13,17 @@ log = logging.getLogger(__name__)
 
 @click.command()
 @submission_dir
+@config_file
 @force
-def validate(submission_dir, force):
+def validate(submission_dir, config_file, force):
     """
     Validate the submission.
 
     This validates the submission by checking its checksums, as well as performing basic sanity checks on the supplied metadata.
     Must be executed before calling `encrypt` and `upload`.
     """
+    config = ValidateConfig.from_path(config_file)
+
     log.info("Starting validation...")
 
     submission_dir = Path(submission_dir)
@@ -30,6 +34,6 @@ def validate(submission_dir, force):
         log_dir=submission_dir / "logs",
         encrypted_files_dir=submission_dir / "encrypted_files",
     )
-    worker_inst.validate(force=force)
+    worker_inst.validate(identifiers=config.identifiers, force=force)
 
     log.info("Validation finished!")

grz_cli-1.0.0/src/grz_cli/models/config.py

@@ -0,0 +1,19 @@
+import logging
+
+from grz_common.models.identifiers import IdentifiersConfigModel
+from grz_common.models.keys import KeyConfigModel
+from grz_common.models.s3 import S3ConfigModel
+
+log = logging.getLogger(__name__)
+
+
+class UploadConfig(S3ConfigModel):
+    pass
+
+
+class EncryptConfig(KeyConfigModel):
+    pass
+
+
+class ValidateConfig(IdentifiersConfigModel):
+    pass