dcicutils 8.8.0.1b13__tar.gz → 8.8.0.1b15__tar.gz

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Files changed (75) hide show
  1. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/PKG-INFO +1 -1
  2. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/data_readers.py +6 -1
  3. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/structured_data.py +15 -20
  4. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/pyproject.toml +1 -1
  5. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/LICENSE.txt +0 -0
  6. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/README.rst +0 -0
  7. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/__init__.py +0 -0
  8. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/base.py +0 -0
  9. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/beanstalk_utils.py +0 -0
  10. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/bundle_utils.py +0 -0
  11. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/captured_output.py +0 -0
  12. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/cloudformation_utils.py +0 -0
  13. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/codebuild_utils.py +0 -0
  14. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/command_utils.py +0 -0
  15. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/common.py +0 -0
  16. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/contribution_scripts.py +0 -0
  17. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/contribution_utils.py +0 -0
  18. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/creds_utils.py +0 -0
  19. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/data_utils.py +0 -0
  20. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/datetime_utils.py +0 -0
  21. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/deployment_utils.py +0 -0
  22. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/diff_utils.py +0 -0
  23. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/docker_utils.py +0 -0
  24. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ecr_scripts.py +0 -0
  25. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ecr_utils.py +0 -0
  26. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ecs_utils.py +0 -0
  27. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_base.py +0 -0
  28. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_manager.py +0 -0
  29. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_scripts.py +0 -0
  30. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_utils.py +0 -0
  31. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_utils_legacy.py +0 -0
  32. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/es_utils.py +0 -0
  33. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/exceptions.py +0 -0
  34. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ff_mocks.py +0 -0
  35. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ff_utils.py +0 -0
  36. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/file_utils.py +0 -0
  37. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/function_cache_decorator.py +0 -0
  38. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/glacier_utils.py +0 -0
  39. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/jh_utils.py +0 -0
  40. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/kibana/dashboards.json +0 -0
  41. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/kibana/readme.md +0 -0
  42. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/lang_utils.py +0 -0
  43. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/c4-infrastructure.jsonc +0 -0
  44. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/c4-python-infrastructure.jsonc +0 -0
  45. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-common-server.jsonc +0 -0
  46. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-common.jsonc +0 -0
  47. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-gpl-pipeline.jsonc +0 -0
  48. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-pipeline.jsonc +0 -0
  49. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_utils.py +0 -0
  50. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/log_utils.py +0 -0
  51. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/misc_utils.py +0 -0
  52. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/obfuscation_utils.py +0 -0
  53. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/opensearch_utils.py +0 -0
  54. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/portal_object_utils.py +0 -0
  55. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/portal_utils.py +0 -0
  56. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/project_utils.py +0 -0
  57. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/qa_checkers.py +0 -0
  58. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/qa_utils.py +0 -0
  59. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/redis_tools.py +0 -0
  60. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/redis_utils.py +0 -0
  61. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/s3_utils.py +0 -0
  62. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/schema_utils.py +0 -0
  63. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/scripts/publish_to_pypi.py +0 -0
  64. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/scripts/run_license_checker.py +0 -0
  65. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/scripts/view_portal_object.py +0 -0
  66. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/secrets_utils.py +0 -0
  67. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/sheet_utils.py +0 -0
  68. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/snapshot_utils.py +0 -0
  69. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ssl_certificate_utils.py +0 -0
  70. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/task_utils.py +0 -0
  71. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/tmpfile_utils.py +0 -0
  72. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/trace_utils.py +0 -0
  73. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/validation_utils.py +0 -0
  74. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/variant_utils.py +0 -0
  75. {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/zip_utils.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: dcicutils
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- Version: 8.8.0.1b13
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+ Version: 8.8.0.1b15
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  Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
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  Home-page: https://github.com/4dn-dcic/utils
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  License: MIT
@@ -168,7 +168,12 @@ class Excel:
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  def open(self) -> None:
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  if self._workbook is None:
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- self._workbook = openpyxl.load_workbook(self._file, data_only=True)
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+ import warnings
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+ with warnings.catch_warnings():
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+ # Without this warning suppression thing, for some spreadsheets we get this stdout warning:
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+ # UserWarning: data validation extension is not supported and will be removed
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+ warnings.filterwarnings("ignore", category=UserWarning)
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+ self._workbook = openpyxl.load_workbook(self._file, data_only=True)
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  self.sheet_names = [sheet_name for sheet_name in self._workbook.sheetnames
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  if not self.is_hidden_sheet(self._workbook[sheet_name])]
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@@ -7,7 +7,6 @@ from pyramid.router import Router
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  import re
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  import sys
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  import time
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- from tqdm import tqdm
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  from typing import Any, Callable, List, Optional, Tuple, Type, Union
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  from webtest.app import TestApp
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  from dcicutils.common import OrchestratedApp
@@ -70,10 +69,9 @@ class StructuredDataSet:
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  order: Optional[List[str]] = None, prune: bool = True,
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  ref_lookup_strategy: Optional[Callable] = None,
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  ref_lookup_nocache: bool = False,
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- progress: bool = False,
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+ progress: Optional[Callable] = None,
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  debug_sleep: Optional[str] = None) -> None:
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- progress = False
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- self._progress = progress
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+ self._progress = progress if callable(progress) else None
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  self._data = {}
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  self._portal = Portal(portal, data=self._data, schemas=schemas,
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  ref_lookup_strategy=ref_lookup_strategy,
@@ -93,20 +91,15 @@ class StructuredDataSet:
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  self._debug_sleep = None
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  self._load_file(file) if file else None
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- def _progress_add(self, amount: Union[int, Callable]) -> None:
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- if self._progress is not False and self._progress is not None:
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- if callable(amount):
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- amount = amount()
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- if not isinstance(amount, int):
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- return
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- if self._progress is True:
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- if amount > 0:
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- self._progress = tqdm(total=amount)
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- elif isinstance(self._progress, tqdm):
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- if amount > 0:
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- self._progress.total += amount
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- elif amount < 0:
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- self._progress.update(-amount)
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+ def _progress_update(self, nrows: Union[int, Callable],
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+ nrefs_resolved: Optional[int] = None,
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+ nrefs_unresolved: Optional[int] = None,
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+ nlookups: Optional[int] = None) -> None:
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+ if self._progress:
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+ if callable(nrows):
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+ nrows = nrows()
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+ if isinstance(nrows, int) and nrows != 0:
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+ self._progress(nrows, nrefs_resolved, nrefs_unresolved, nlookups)
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  @property
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  def data(self) -> dict:
@@ -259,7 +252,8 @@ class StructuredDataSet:
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  for row in excel.sheet_reader(sheet_name):
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  nrows += 1
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  return nrows
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- self._progress_add(calculate_total_rows_to_process)
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+ if self._progress:
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+ self._progress_update(calculate_total_rows_to_process)
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  excel = Excel(file) # Order the sheet names by any specified ordering (e.g. ala snovault.loadxl).
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  order = {Schema.type_name(key): index for index, key in enumerate(self._order)} if self._order else {}
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  for sheet_name in sorted(excel.sheet_names, key=lambda key: order.get(Schema.type_name(key), sys.maxsize)):
@@ -301,7 +295,8 @@ class StructuredDataSet:
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  if self._autoadd_properties:
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  self._add_properties(structured_row, self._autoadd_properties, schema)
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  self._add(type_name, structured_row)
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- self._progress_add(-1)
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+ if self._progress:
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+ self._progress_update(-1, len(self._resolved_refs), len(self.ref_errors), self.ref_lookup_count)
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  self._note_warning(reader.warnings, "reader")
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  if schema:
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  self._note_error(schema._unresolved_refs, "ref")
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "dcicutils"
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- version = "8.8.0.1b13" # TODO: To become 8.8.1
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+ version = "8.8.0.1b15" # TODO: To become 8.8.1
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  description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
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  authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
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  license = "MIT"