dcicutils 8.8.0.1b13__tar.gz → 8.8.0.1b15__tar.gz
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- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/PKG-INFO +1 -1
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/data_readers.py +6 -1
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/structured_data.py +15 -20
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/pyproject.toml +1 -1
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/LICENSE.txt +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/README.rst +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/__init__.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/base.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/beanstalk_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/bundle_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/captured_output.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/cloudformation_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/codebuild_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/command_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/common.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/contribution_scripts.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/contribution_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/creds_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/data_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/datetime_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/deployment_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/diff_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/docker_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ecr_scripts.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ecr_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ecs_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_base.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_manager.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_scripts.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/env_utils_legacy.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/es_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/exceptions.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ff_mocks.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ff_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/file_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/function_cache_decorator.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/glacier_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/jh_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/kibana/dashboards.json +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/kibana/readme.md +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/lang_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/c4-infrastructure.jsonc +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/c4-python-infrastructure.jsonc +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-common-server.jsonc +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-common.jsonc +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-gpl-pipeline.jsonc +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-pipeline.jsonc +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/log_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/misc_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/obfuscation_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/opensearch_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/portal_object_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/portal_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/project_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/qa_checkers.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/qa_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/redis_tools.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/redis_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/s3_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/schema_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/scripts/publish_to_pypi.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/scripts/run_license_checker.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/scripts/view_portal_object.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/secrets_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/sheet_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/snapshot_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/ssl_certificate_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/task_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/tmpfile_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/trace_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/validation_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/variant_utils.py +0 -0
- {dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/zip_utils.py +0 -0
@@ -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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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
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@@ -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:
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progress: Optional[Callable] = None,
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debug_sleep: Optional[str] = None) -> None:
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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,
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@@ -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
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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:
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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.
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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)):
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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.
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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")
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@@ -1,6 +1,6 @@
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[tool.poetry]
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name = "dcicutils"
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version = "8.8.0.
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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"
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{dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/c4-infrastructure.jsonc
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{dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-common.jsonc
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{dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-gpl-pipeline.jsonc
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{dcicutils-8.8.0.1b13 → dcicutils-8.8.0.1b15}/dcicutils/license_policies/park-lab-pipeline.jsonc
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