grz-cli 0.6.0__tar.gz → 0.6.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (61) hide show
  1. {grz_cli-0.6.0/src/grz_cli.egg-info → grz_cli-0.6.1}/PKG-INFO +1 -1
  2. grz_cli-0.6.1/src/grz_cli/__init__.py +1 -0
  3. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/workers/worker.py +5 -3
  4. {grz_cli-0.6.0 → grz_cli-0.6.1/src/grz_cli.egg-info}/PKG-INFO +1 -1
  5. grz_cli-0.6.0/src/grz_cli/__init__.py +0 -1
  6. {grz_cli-0.6.0 → grz_cli-0.6.1}/LICENSE +0 -0
  7. {grz_cli-0.6.0 → grz_cli-0.6.1}/MANIFEST.in +0 -0
  8. {grz_cli-0.6.0 → grz_cli-0.6.1}/README.md +0 -0
  9. {grz_cli-0.6.0 → grz_cli-0.6.1}/pyproject.toml +0 -0
  10. {grz_cli-0.6.0 → grz_cli-0.6.1}/setup.cfg +0 -0
  11. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/__init__.py +0 -0
  12. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/cli.py +0 -0
  13. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/__init__.py +0 -0
  14. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/archive.py +0 -0
  15. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/clean.py +0 -0
  16. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/common.py +0 -0
  17. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/consent.py +0 -0
  18. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/decrypt.py +0 -0
  19. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/download.py +0 -0
  20. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/encrypt.py +0 -0
  21. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/list_submissions.py +0 -0
  22. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/pruefbericht.py +0 -0
  23. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/submit.py +0 -0
  24. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/upload.py +0 -0
  25. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/commands/validate.py +0 -0
  26. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/constants.py +0 -0
  27. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/logging_setup.py +0 -0
  28. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/models/__init__.py +0 -0
  29. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/models/config.py +0 -0
  30. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/progress/__init__.py +0 -0
  31. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/progress/progress_logging.py +0 -0
  32. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/progress/states.py +0 -0
  33. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/py.typed +0 -0
  34. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/transfer.py +0 -0
  35. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/utils/__init__.py +0 -0
  36. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/utils/checksums.py +0 -0
  37. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/utils/config.py +0 -0
  38. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/utils/crypt.py +0 -0
  39. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/utils/io.py +0 -0
  40. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/utils/paths.py +0 -0
  41. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/validation/__init__.py +0 -0
  42. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/validation/bam.py +0 -0
  43. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/validation/fastq.py +0 -0
  44. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/workers/__init__.py +0 -0
  45. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/workers/download.py +0 -0
  46. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/workers/submission.py +0 -0
  47. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/workers/upload.py +0 -0
  48. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli.egg-info/SOURCES.txt +0 -0
  49. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli.egg-info/dependency_links.txt +0 -0
  50. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli.egg-info/entry_points.txt +0 -0
  51. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli.egg-info/requires.txt +0 -0
  52. {grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli.egg-info/top_level.txt +0 -0
  53. {grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_bam_validation.py +0 -0
  54. {grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_cli.py +0 -0
  55. {grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_download.py +0 -0
  56. {grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_fastq_validation.py +0 -0
  57. {grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_file_operations.py +0 -0
  58. {grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_file_progress_logging.py +0 -0
  59. {grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_parser.py +0 -0
  60. {grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_read_multiple_json.py +0 -0
  61. {grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_upload.py +0 -0
{grz_cli-0.6.0/src/grz_cli.egg-info → grz_cli-0.6.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.4
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  Name: grz-cli
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- Version: 0.6.0
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+ Version: 0.6.1
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  Summary: Tool for validation, encryption and upload of MV submissions to GDCs.
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  Author-email: Koray Kirli <koraykirli@gmail.com>, Mathias Lesche <mathias.lesche@tu-dresden.de>, "Florian R. Hölzlwimmer" <git.ich@frhoelzlwimmer.de>, Till Hartmann <till.hartmann@bih-charite.de>, Thomas Sell <thomas.sell@bih-charite.de>
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  License-Expression: MIT
grz_cli-0.6.1/src/grz_cli/__init__.py ADDED
@@ -0,0 +1 @@
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+ __version__ = "0.6.1"
{grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/workers/worker.py RENAMED
@@ -185,7 +185,7 @@ class Worker:
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  """
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  from .upload import S3BotoUploadWorker
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- upload_worker = S3BotoUploadWorker(config, status_file_path=self.progress_file_upload)
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+ upload_worker = S3BotoUploadWorker(config, status_file_path=self.progress_file_upload, threads=self._threads)
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  encrypted_submission = self.parse_encrypted_submission()
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@@ -199,7 +199,7 @@ class Worker:
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  """
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  from .upload import S3BotoUploadWorker
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- upload_worker = S3BotoUploadWorker(config, status_file_path=self.progress_file_upload)
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+ upload_worker = S3BotoUploadWorker(config, status_file_path=self.progress_file_upload, threads=self._threads)
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  encrypted_submission = self.parse_encrypted_submission()
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@@ -213,7 +213,9 @@ class Worker:
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  # delete the log file
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  self.progress_file_download.unlink()
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- download_worker = S3BotoDownloadWorker(config, status_file_path=self.progress_file_download)
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+ download_worker = S3BotoDownloadWorker(
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+ config, status_file_path=self.progress_file_download, threads=self._threads
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+ )
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  self.__log.info("Preparing output directories...")
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  download_worker.prepare_download(self.metadata_dir, self.encrypted_files_dir, self.log_dir)
{grz_cli-0.6.0 → grz_cli-0.6.1/src/grz_cli.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
2
2
  Name: grz-cli
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- Version: 0.6.0
3
+ Version: 0.6.1
4
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  Summary: Tool for validation, encryption and upload of MV submissions to GDCs.
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  Author-email: Koray Kirli <koraykirli@gmail.com>, Mathias Lesche <mathias.lesche@tu-dresden.de>, "Florian R. Hölzlwimmer" <git.ich@frhoelzlwimmer.de>, Till Hartmann <till.hartmann@bih-charite.de>, Thomas Sell <thomas.sell@bih-charite.de>
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  License-Expression: MIT
grz_cli-0.6.0/src/grz_cli/__init__.py DELETED
@@ -1 +0,0 @@
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- __version__ = "0.6.0"
{grz_cli-0.6.0 → grz_cli-0.6.1}/LICENSE RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/MANIFEST.in RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/README.md RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/pyproject.toml RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/setup.cfg RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/src/__init__.py RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/cli.py RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/py.typed RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/transfer.py RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/src/grz_cli/utils/io.py RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_cli.py RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_download.py RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_parser.py RENAMED
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{grz_cli-0.6.0 → grz_cli-0.6.1}/tests/test_upload.py RENAMED
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