geoseeq 0.6.13.dev1__tar.gz → 0.6.13.dev2__tar.gz

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  1. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/PKG-INFO +1 -1
  2. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/main.py +1 -1
  3. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/id_constructors/from_ids.py +3 -0
  4. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/knex.py +3 -3
  5. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq.egg-info/PKG-INFO +1 -1
  6. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/pyproject.toml +1 -1
  7. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/LICENSE +0 -0
  8. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/README.md +0 -0
  9. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/__init__.py +0 -0
  10. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/app.py +0 -0
  11. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/blob_constructors.py +0 -0
  12. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/bulk_creators.py +0 -0
  13. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/__init__.py +0 -0
  14. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/constants.py +0 -0
  15. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/copy.py +0 -0
  16. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/detail.py +0 -0
  17. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/download.py +0 -0
  18. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/fastq_utils.py +0 -0
  19. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/get_eula.py +0 -0
  20. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/manage.py +0 -0
  21. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/progress_bar.py +0 -0
  22. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/project.py +0 -0
  23. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/raw.py +0 -0
  24. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/run.py +0 -0
  25. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/search.py +0 -0
  26. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/shared_params/__init__.py +0 -0
  27. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/shared_params/common_state.py +0 -0
  28. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/shared_params/config.py +0 -0
  29. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/shared_params/id_handlers.py +0 -0
  30. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/shared_params/obj_getters.py +0 -0
  31. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/shared_params/opts_and_args.py +0 -0
  32. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/upload/__init__.py +0 -0
  33. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/upload/upload.py +0 -0
  34. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/upload/upload_advanced.py +0 -0
  35. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/upload/upload_reads.py +0 -0
  36. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/user.py +0 -0
  37. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/utils.py +0 -0
  38. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/cli/view.py +0 -0
  39. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/constants.py +0 -0
  40. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/contrib/__init__.py +0 -0
  41. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/contrib/ncbi/__init__.py +0 -0
  42. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/contrib/ncbi/api.py +0 -0
  43. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/contrib/ncbi/bioproject.py +0 -0
  44. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/contrib/ncbi/cli.py +0 -0
  45. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/contrib/ncbi/setup_logging.py +0 -0
  46. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/file_system_cache.py +0 -0
  47. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/id_constructors/__init__.py +0 -0
  48. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/id_constructors/from_blobs.py +0 -0
  49. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/id_constructors/from_names.py +0 -0
  50. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/id_constructors/from_uuids.py +0 -0
  51. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/id_constructors/resolvers.py +0 -0
  52. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/id_constructors/utils.py +0 -0
  53. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/organization.py +0 -0
  54. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/pipeline.py +0 -0
  55. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/plotting/__init__.py +0 -0
  56. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/plotting/constants.py +0 -0
  57. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/plotting/highcharts.py +0 -0
  58. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/plotting/map/__init__.py +0 -0
  59. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/plotting/map/base_layer.py +0 -0
  60. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/plotting/map/map.py +0 -0
  61. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/plotting/map/overlay.py +0 -0
  62. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/plotting/selectable.py +0 -0
  63. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/project.py +0 -0
  64. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/remote_object.py +0 -0
  65. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/__init__.py +0 -0
  66. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/bioinfo.py +0 -0
  67. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/file_chunker.py +0 -0
  68. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/file_download.py +0 -0
  69. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/file_upload.py +0 -0
  70. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/result_file.py +0 -0
  71. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/result_folder.py +0 -0
  72. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/resumable_download_tracker.py +0 -0
  73. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/resumable_upload_tracker.py +0 -0
  74. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/result/utils.py +0 -0
  75. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/sample.py +0 -0
  76. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/search.py +0 -0
  77. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/upload_download_manager.py +0 -0
  78. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/user.py +0 -0
  79. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/utils.py +0 -0
  80. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/vc/__init__.py +0 -0
  81. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/vc/checksum.py +0 -0
  82. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/vc/cli.py +0 -0
  83. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/vc/clone.py +0 -0
  84. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/vc/constants.py +0 -0
  85. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/vc/vc_cache.py +0 -0
  86. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/vc/vc_dir.py +0 -0
  87. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/vc/vc_sample.py +0 -0
  88. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/vc/vc_stub.py +0 -0
  89. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq/work_orders.py +0 -0
  90. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq.egg-info/SOURCES.txt +0 -0
  91. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq.egg-info/dependency_links.txt +0 -0
  92. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq.egg-info/entry_points.txt +0 -0
  93. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq.egg-info/requires.txt +0 -0
  94. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/geoseeq.egg-info/top_level.txt +0 -0
  95. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/setup.cfg +0 -0
  96. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/setup.py +0 -0
  97. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/tests/__init__.py +0 -0
  98. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/tests/test_api_client.py +0 -0
  99. {geoseeq-0.6.13.dev1 → geoseeq-0.6.13.dev2}/tests/test_plotting.py +0 -0
@@ -1,6 +1,6 @@
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1
  Metadata-Version: 2.2
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2
  Name: geoseeq
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- Version: 0.6.13.dev1
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+ Version: 0.6.13.dev2
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  Summary: GeoSeeq command line tools and python API
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  Author: David C. Danko
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  Author-email: "David C. Danko" <dcdanko@biotia.io>
@@ -54,7 +54,7 @@ def version():
54
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  Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
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55
  Run `geoseeq eula show` to view the EULA.
56
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  """
57
- click.echo('0.6.13dev1') # remember to update pyproject.toml
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+ click.echo('0.6.13dev2') # remember to update pyproject.toml
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58
 
59
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  @main.group('advanced')
@@ -1,4 +1,5 @@
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  from geoseeq import GeoseeqNotFoundError
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+ import logging
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  from .from_uuids import (
3
4
  org_from_uuid,
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  project_from_uuid,
@@ -24,6 +25,8 @@ from .from_names import (
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  from .utils import is_grn_or_uuid, is_name
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  from geoseeq.knex import with_knex
26
27
 
28
+ logger = logging.getLogger("geoseeq_api") # Same name as calling module
29
+
27
30
 
28
31
  def _generic_from_id(knex, id, from_uuid_func, from_name_func):
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  """Return the object which the id points to."""
@@ -225,17 +225,17 @@ def with_knex(func):
225
225
  logger.info(f"Checking for knex in args: {args}, kwargs: {kwargs}")
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  any_knex = any([isinstance(arg, Knex) for arg in args])
227
227
  if any_knex:
228
- logger.info("knex found in args")
228
+ logger.info("knex found in args args: {args}, kwargs: {kwargs}")
229
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  return func(*args, **kwargs)
230
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  else:
231
- logger.info("knex not found in args")
231
+ logger.info("knex not found in args args: {args}, kwargs: {kwargs}")
232
232
  varnames = [
233
233
  varname for varname in func.__code__.co_varnames
234
234
  if varname != "knex"
235
235
  ]
236
236
  kwargs.update(zip(varnames, args))
237
237
  if "knex" not in kwargs:
238
- logger.info("knex not found in kwargs")
238
+ logger.info("knex not found in kwargs args: {args}, kwargs: {kwargs}")
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239
  profile = kwargs.pop("profile", "")
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  kwargs['knex'] = Knex.load_profile(profile=profile)
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  # reorder kwargs to match the function signature
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.2
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2
  Name: geoseeq
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- Version: 0.6.13.dev1
3
+ Version: 0.6.13.dev2
4
4
  Summary: GeoSeeq command line tools and python API
5
5
  Author: David C. Danko
6
6
  Author-email: "David C. Danko" <dcdanko@biotia.io>
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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4
 
5
5
  [project]
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  name = "geoseeq"
7
- version = "0.6.13dev1"
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+ version = "0.6.13dev2"
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  authors = [
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  { name="David C. Danko", email="dcdanko@biotia.io" },
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  ]
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