2025-08-30T23:29:16,234 Created temporary directory: /tmp/pip-build-tracker-b3ethesf 2025-08-30T23:29:16,235 Initialized build tracking at /tmp/pip-build-tracker-b3ethesf 2025-08-30T23:29:16,236 Created build tracker: /tmp/pip-build-tracker-b3ethesf 2025-08-30T23:29:16,236 Entered build tracker: /tmp/pip-build-tracker-b3ethesf 2025-08-30T23:29:16,237 Created temporary directory: /tmp/pip-wheel-ei3afggc 2025-08-30T23:29:16,241 Created temporary directory: /tmp/pip-ephem-wheel-cache-jm6e9qsn 2025-08-30T23:29:16,293 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-08-30T23:29:16,296 2 location(s) to search for versions of nmdc-runtime: 2025-08-30T23:29:16,296 * https://pypi.org/simple/nmdc-runtime/ 2025-08-30T23:29:16,296 * https://www.piwheels.org/simple/nmdc-runtime/ 2025-08-30T23:29:16,296 Fetching project page and analyzing links: https://pypi.org/simple/nmdc-runtime/ 2025-08-30T23:29:16,297 Getting page https://pypi.org/simple/nmdc-runtime/ 2025-08-30T23:29:16,299 Found index url https://pypi.org/simple/ 2025-08-30T23:29:16,594 Fetched page https://pypi.org/simple/nmdc-runtime/ as application/vnd.pypi.simple.v1+json 2025-08-30T23:29:16,614 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/ba/44/acaca01a3fdf26351a427b58ca793a2702c1157d5125d3101029e99d0ab0/nmdc_runtime-0.1.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.8) 2025-08-30T23:29:16,615 Found link https://files.pythonhosted.org/packages/3d/56/9ddca8b74ed798352aca6ba02e98c7bfbf232ccb237660b2488f7da8a39e/nmdc_runtime-0.1.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.8), version: 0.1.0 2025-08-30T23:29:16,615 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/38/59/cb99a0e180d0de57a68cdd118ed305b68d97561a7a82da80d48992236382/nmdc_runtime-0.1.1-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) 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https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-1.0.12-py3-none-any.whl#sha256=87d81eb829ad73563e0fa371336f03d59417e00c9dcc12d943738fa67c0287fc (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-08-30T23:29:16,894 Skipping link: No binaries permitted for nmdc-runtime: https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-1.0.11-py3-none-any.whl#sha256=b48456c6ad565bcca33642f19ca745d5e57105419ae1dc96efb9f51b349e7fbd (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-08-30T23:29:16,895 Skipping link: No binaries permitted for nmdc-runtime: https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-1.0.10-py3-none-any.whl#sha256=9575befdcc66f9de5c0c08719aa4e5986f3b8d6ec2ad11a8a8f0595ceb4b17bf (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-08-30T23:29:16,895 Skipping link: No binaries permitted for nmdc-runtime: 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https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-1.0.6-py3-none-any.whl#sha256=e15ec359d56e12a347909b6f8a8e95dfd0bc3c62eeef86496220cfdd29338c4b (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-08-30T23:29:16,897 Skipping link: No binaries permitted for nmdc-runtime: https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-1.0.5-py3-none-any.whl#sha256=56e0d62bd48bfa043e59ef94e033c8f09581b0449928cc4ac9ec1f6052ff0a39 (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-08-30T23:29:16,898 Skipping link: No binaries permitted for nmdc-runtime: https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-1.0.4-py3-none-any.whl#sha256=5e175512550dc24c2d30b9075bb2914cafdb2c653aa60975cde6c63a2829d542 (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-08-30T23:29:16,898 Skipping link: No binaries permitted for nmdc-runtime: https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-0.1.6-py3-none-any.whl#sha256=5a8149e8f3e41c8fd242361d7a5918eb005bfd8e8c5639321d4ecbfe917a1292 (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.8) 2025-08-30T23:29:16,899 Skipping link: No binaries permitted for nmdc-runtime: https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-0.1.3-py3-none-any.whl#sha256=67c7cf263830bd4c4c62dff28d0073f938ecb1055f487f43a15f935ef54e461d (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.8) 2025-08-30T23:29:16,900 Skipping link: No binaries permitted for nmdc-runtime: https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-0.1.1-py3-none-any.whl#sha256=f960697437ecf9bf8309e94fbb729ae1440468a7de29b264a61fb6de39368762 (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.8) 2025-08-30T23:29:16,900 Skipping link: No binaries permitted for nmdc-runtime: https://archive1.piwheels.org/simple/nmdc-runtime/nmdc_runtime-0.1.0-py3-none-any.whl#sha256=7a67f7282667a4265a04bf134156531046957b197da284d9550cf19e96541943 (from https://www.piwheels.org/simple/nmdc-runtime/) (requires-python:>=3.8) 2025-08-30T23:29:16,901 Skipping link: not a file: https://www.piwheels.org/simple/nmdc-runtime/ 2025-08-30T23:29:16,902 Skipping link: not a file: https://pypi.org/simple/nmdc-runtime/ 2025-08-30T23:29:16,927 Given no hashes to check 1 links for project 'nmdc-runtime': discarding no candidates 2025-08-30T23:29:16,929 Collecting nmdc-runtime==2.9.0 2025-08-30T23:29:16,932 Created temporary directory: /tmp/pip-unpack-8b242ze_ 2025-08-30T23:29:17,303 Downloading nmdc_runtime-2.9.0.tar.gz (20.4 MB) 2025-08-30T23:29:25,018 Added nmdc-runtime==2.9.0 from https://files.pythonhosted.org/packages/6c/03/6ba8c1dfb1378ba58efb72f7917e92fa3b23381082fc49ceef93f735106b/nmdc_runtime-2.9.0.tar.gz to build tracker '/tmp/pip-build-tracker-b3ethesf' 2025-08-30T23:29:25,020 Running setup.py (path:/tmp/pip-wheel-ei3afggc/nmdc-runtime_09e64a076b0343db823c388d73e9a6c9/setup.py) egg_info for package nmdc-runtime 2025-08-30T23:29:25,021 Created temporary directory: /tmp/pip-pip-egg-info-g748fhh3 2025-08-30T23:29:25,022 Preparing metadata (setup.py): started 2025-08-30T23:29:25,023 Running command python setup.py egg_info 2025-08-30T23:29:25,614 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-08-30T23:29:25,614 !! 2025-08-30T23:29:25,615 ******************************************************************************** 2025-08-30T23:29:25,615 Requirements should be satisfied by a PEP 517 installer. 2025-08-30T23:29:25,616 If you are using pip, you can try `pip install --use-pep517`. 2025-08-30T23:29:25,617 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-08-30T23:29:25,617 or your builds will no longer be supported. 2025-08-30T23:29:25,618 ******************************************************************************** 2025-08-30T23:29:25,619 !! 2025-08-30T23:29:25,619 dist.fetch_build_eggs(dist.setup_requires) 2025-08-30T23:29:28,640 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-30T23:29:28,640 !! 2025-08-30T23:29:28,641 ******************************************************************************** 2025-08-30T23:29:28,642 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-30T23:29:28,643 License :: OSI Approved :: Apache Software License 2025-08-30T23:29:28,645 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-30T23:29:28,645 ******************************************************************************** 2025-08-30T23:29:28,646 !! 2025-08-30T23:29:28,647 self._finalize_license_expression() 2025-08-30T23:29:28,673 running egg_info 2025-08-30T23:29:28,706 creating /tmp/pip-pip-egg-info-g748fhh3/nmdc_runtime.egg-info 2025-08-30T23:29:28,707 writing /tmp/pip-pip-egg-info-g748fhh3/nmdc_runtime.egg-info/PKG-INFO 2025-08-30T23:29:28,711 writing dependency_links to /tmp/pip-pip-egg-info-g748fhh3/nmdc_runtime.egg-info/dependency_links.txt 2025-08-30T23:29:28,713 writing entry points to /tmp/pip-pip-egg-info-g748fhh3/nmdc_runtime.egg-info/entry_points.txt 2025-08-30T23:29:28,714 writing top-level names to /tmp/pip-pip-egg-info-g748fhh3/nmdc_runtime.egg-info/top_level.txt 2025-08-30T23:29:28,716 writing manifest file '/tmp/pip-pip-egg-info-g748fhh3/nmdc_runtime.egg-info/SOURCES.txt' 2025-08-30T23:29:28,935 listing git files failed - pretending there aren't any 2025-08-30T23:29:28,950 reading manifest file '/tmp/pip-pip-egg-info-g748fhh3/nmdc_runtime.egg-info/SOURCES.txt' 2025-08-30T23:29:28,952 adding license file 'LICENSE' 2025-08-30T23:29:28,958 writing manifest file '/tmp/pip-pip-egg-info-g748fhh3/nmdc_runtime.egg-info/SOURCES.txt' 2025-08-30T23:29:29,069 Preparing metadata (setup.py): finished with status 'done' 2025-08-30T23:29:29,074 Source in /tmp/pip-wheel-ei3afggc/nmdc-runtime_09e64a076b0343db823c388d73e9a6c9 has version 2.9.0, which satisfies requirement nmdc-runtime==2.9.0 from https://files.pythonhosted.org/packages/6c/03/6ba8c1dfb1378ba58efb72f7917e92fa3b23381082fc49ceef93f735106b/nmdc_runtime-2.9.0.tar.gz 2025-08-30T23:29:29,075 Removed nmdc-runtime==2.9.0 from https://files.pythonhosted.org/packages/6c/03/6ba8c1dfb1378ba58efb72f7917e92fa3b23381082fc49ceef93f735106b/nmdc_runtime-2.9.0.tar.gz from build tracker '/tmp/pip-build-tracker-b3ethesf' 2025-08-30T23:29:29,081 Created temporary directory: /tmp/pip-unpack-mvrryudr 2025-08-30T23:29:29,083 Created temporary directory: /tmp/pip-unpack-vktbuxai 2025-08-30T23:29:29,083 Building wheels for collected packages: nmdc-runtime 2025-08-30T23:29:29,087 Created temporary directory: /tmp/pip-wheel-9jnxyg07 2025-08-30T23:29:29,088 DEPRECATION: Building 'nmdc-runtime' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'nmdc-runtime'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-08-30T23:29:29,090 Building wheel for nmdc-runtime (setup.py): started 2025-08-30T23:29:29,091 Destination directory: /tmp/pip-wheel-9jnxyg07 2025-08-30T23:29:29,092 Running command python setup.py bdist_wheel 2025-08-30T23:29:29,647 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-08-30T23:29:29,647 !! 2025-08-30T23:29:29,648 ******************************************************************************** 2025-08-30T23:29:29,649 Requirements should be satisfied by a PEP 517 installer. 2025-08-30T23:29:29,649 If you are using pip, you can try `pip install --use-pep517`. 2025-08-30T23:29:29,650 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-08-30T23:29:29,651 or your builds will no longer be supported. 2025-08-30T23:29:29,652 ******************************************************************************** 2025-08-30T23:29:29,653 !! 2025-08-30T23:29:29,653 dist.fetch_build_eggs(dist.setup_requires) 2025-08-30T23:29:30,266 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-30T23:29:30,267 !! 2025-08-30T23:29:30,268 ******************************************************************************** 2025-08-30T23:29:30,269 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-30T23:29:30,270 License :: OSI Approved :: Apache Software License 2025-08-30T23:29:30,271 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-30T23:29:30,271 ******************************************************************************** 2025-08-30T23:29:30,273 !! 2025-08-30T23:29:30,273 self._finalize_license_expression() 2025-08-30T23:29:30,274 running bdist_wheel 2025-08-30T23:29:30,420 running build 2025-08-30T23:29:30,421 running build_py 2025-08-30T23:29:30,454 creating build/lib/nmdc_runtime 2025-08-30T23:29:30,456 copying nmdc_runtime/__init__.py -> build/lib/nmdc_runtime 2025-08-30T23:29:30,458 copying nmdc_runtime/mongo_util.py -> build/lib/nmdc_runtime 2025-08-30T23:29:30,460 copying nmdc_runtime/containers.py -> build/lib/nmdc_runtime 2025-08-30T23:29:30,462 copying nmdc_runtime/config.py -> build/lib/nmdc_runtime 2025-08-30T23:29:30,463 copying nmdc_runtime/util.py -> build/lib/nmdc_runtime 2025-08-30T23:29:30,466 copying nmdc_runtime/main.py -> build/lib/nmdc_runtime 2025-08-30T23:29:30,468 creating build/lib/nmdc_runtime/domain 2025-08-30T23:29:30,469 copying nmdc_runtime/domain/__init__.py -> build/lib/nmdc_runtime/domain 2025-08-30T23:29:30,472 creating build/lib/nmdc_runtime/lib 2025-08-30T23:29:30,473 copying nmdc_runtime/lib/extract_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-08-30T23:29:30,475 copying nmdc_runtime/lib/__init__.py -> build/lib/nmdc_runtime/lib 2025-08-30T23:29:30,477 copying nmdc_runtime/lib/nmdc_dataframes.py -> build/lib/nmdc_runtime/lib 2025-08-30T23:29:30,480 copying nmdc_runtime/lib/load_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-08-30T23:29:30,482 copying nmdc_runtime/lib/transform_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-08-30T23:29:30,485 copying nmdc_runtime/lib/nmdc_etl_class.py -> build/lib/nmdc_runtime/lib 2025-08-30T23:29:30,488 creating build/lib/nmdc_runtime/infrastructure 2025-08-30T23:29:30,489 copying nmdc_runtime/infrastructure/__init__.py -> build/lib/nmdc_runtime/infrastructure 2025-08-30T23:29:30,491 creating build/lib/nmdc_runtime/core 2025-08-30T23:29:30,492 copying nmdc_runtime/core/__init__.py -> build/lib/nmdc_runtime/core 2025-08-30T23:29:30,494 creating build/lib/nmdc_runtime/client 2025-08-30T23:29:30,495 copying nmdc_runtime/client/__init__.py -> build/lib/nmdc_runtime/client 2025-08-30T23:29:30,498 creating build/lib/nmdc_runtime/minter 2025-08-30T23:29:30,499 copying nmdc_runtime/minter/bootstrap.py -> build/lib/nmdc_runtime/minter 2025-08-30T23:29:30,501 copying nmdc_runtime/minter/__init__.py -> build/lib/nmdc_runtime/minter 2025-08-30T23:29:30,503 copying nmdc_runtime/minter/config.py -> build/lib/nmdc_runtime/minter 2025-08-30T23:29:30,505 creating build/lib/nmdc_runtime/site 2025-08-30T23:29:30,506 copying nmdc_runtime/site/resources.py -> build/lib/nmdc_runtime/site 2025-08-30T23:29:30,509 copying nmdc_runtime/site/__init__.py -> build/lib/nmdc_runtime/site 2025-08-30T23:29:30,511 copying nmdc_runtime/site/ops.py -> build/lib/nmdc_runtime/site 2025-08-30T23:29:30,514 copying nmdc_runtime/site/repository.py -> build/lib/nmdc_runtime/site 2025-08-30T23:29:30,518 copying nmdc_runtime/site/graphs.py -> build/lib/nmdc_runtime/site 2025-08-30T23:29:30,521 copying nmdc_runtime/site/util.py -> build/lib/nmdc_runtime/site 2025-08-30T23:29:30,523 creating build/lib/nmdc_runtime/domain/users 2025-08-30T23:29:30,524 copying nmdc_runtime/domain/users/__init__.py -> build/lib/nmdc_runtime/domain/users 2025-08-30T23:29:30,526 copying nmdc_runtime/domain/users/queriesInterface.py -> build/lib/nmdc_runtime/domain/users 2025-08-30T23:29:30,528 copying nmdc_runtime/domain/users/userService.py -> build/lib/nmdc_runtime/domain/users 2025-08-30T23:29:30,530 copying nmdc_runtime/domain/users/userSchema.py -> build/lib/nmdc_runtime/domain/users 2025-08-30T23:29:30,533 creating build/lib/nmdc_runtime/infrastructure/database 2025-08-30T23:29:30,534 copying nmdc_runtime/infrastructure/database/__init__.py -> build/lib/nmdc_runtime/infrastructure/database 2025-08-30T23:29:30,536 copying nmdc_runtime/infrastructure/database/db.py -> build/lib/nmdc_runtime/infrastructure/database 2025-08-30T23:29:30,539 creating build/lib/nmdc_runtime/infrastructure/database/models 2025-08-30T23:29:30,540 copying nmdc_runtime/infrastructure/database/models/__init__.py -> build/lib/nmdc_runtime/infrastructure/database/models 2025-08-30T23:29:30,542 copying nmdc_runtime/infrastructure/database/models/user.py -> build/lib/nmdc_runtime/infrastructure/database/models 2025-08-30T23:29:30,544 creating build/lib/nmdc_runtime/core/exceptions 2025-08-30T23:29:30,545 copying nmdc_runtime/core/exceptions/token.py -> build/lib/nmdc_runtime/core/exceptions 2025-08-30T23:29:30,548 copying nmdc_runtime/core/exceptions/base.py -> build/lib/nmdc_runtime/core/exceptions 2025-08-30T23:29:30,550 copying nmdc_runtime/core/exceptions/__init__.py -> build/lib/nmdc_runtime/core/exceptions 2025-08-30T23:29:30,552 creating build/lib/nmdc_runtime/core/db 2025-08-30T23:29:30,554 copying nmdc_runtime/core/db/__init__.py -> build/lib/nmdc_runtime/core/db 2025-08-30T23:29:30,556 copying nmdc_runtime/core/db/Database.py -> build/lib/nmdc_runtime/core/db 2025-08-30T23:29:30,558 creating build/lib/nmdc_runtime/minter/domain 2025-08-30T23:29:30,559 copying nmdc_runtime/minter/domain/__init__.py -> build/lib/nmdc_runtime/minter/domain 2025-08-30T23:29:30,561 copying nmdc_runtime/minter/domain/model.py -> build/lib/nmdc_runtime/minter/domain 2025-08-30T23:29:30,563 creating build/lib/nmdc_runtime/minter/adapters 2025-08-30T23:29:30,564 copying nmdc_runtime/minter/adapters/__init__.py -> build/lib/nmdc_runtime/minter/adapters 2025-08-30T23:29:30,566 copying nmdc_runtime/minter/adapters/repository.py -> build/lib/nmdc_runtime/minter/adapters 2025-08-30T23:29:30,569 creating build/lib/nmdc_runtime/minter/entrypoints 2025-08-30T23:29:30,570 copying nmdc_runtime/minter/entrypoints/__init__.py -> build/lib/nmdc_runtime/minter/entrypoints 2025-08-30T23:29:30,572 copying nmdc_runtime/minter/entrypoints/fastapi_app.py -> build/lib/nmdc_runtime/minter/entrypoints 2025-08-30T23:29:30,574 creating build/lib/nmdc_runtime/site/changesheets 2025-08-30T23:29:30,575 copying nmdc_runtime/site/changesheets/base.py -> build/lib/nmdc_runtime/site/changesheets 2025-08-30T23:29:30,577 copying nmdc_runtime/site/changesheets/__init__.py -> build/lib/nmdc_runtime/site/changesheets 2025-08-30T23:29:30,579 creating build/lib/nmdc_runtime/site/validation 2025-08-30T23:29:30,580 copying nmdc_runtime/site/validation/emsl.py -> build/lib/nmdc_runtime/site/validation 2025-08-30T23:29:30,583 copying nmdc_runtime/site/validation/__init__.py -> build/lib/nmdc_runtime/site/validation 2025-08-30T23:29:30,584 copying nmdc_runtime/site/validation/jgi.py -> build/lib/nmdc_runtime/site/validation 2025-08-30T23:29:30,587 copying nmdc_runtime/site/validation/gold.py -> build/lib/nmdc_runtime/site/validation 2025-08-30T23:29:30,589 copying nmdc_runtime/site/validation/util.py -> build/lib/nmdc_runtime/site/validation 2025-08-30T23:29:30,592 creating build/lib/nmdc_runtime/site/export 2025-08-30T23:29:30,593 copying nmdc_runtime/site/export/__init__.py -> build/lib/nmdc_runtime/site/export 2025-08-30T23:29:30,595 copying nmdc_runtime/site/export/ncbi_xml_utils.py -> build/lib/nmdc_runtime/site/export 2025-08-30T23:29:30,597 copying nmdc_runtime/site/export/ncbi_xml.py -> build/lib/nmdc_runtime/site/export 2025-08-30T23:29:30,600 copying nmdc_runtime/site/export/study_metadata.py -> build/lib/nmdc_runtime/site/export 2025-08-30T23:29:30,603 creating build/lib/nmdc_runtime/site/backup 2025-08-30T23:29:30,604 copying nmdc_runtime/site/backup/__init__.py -> build/lib/nmdc_runtime/site/backup 2025-08-30T23:29:30,606 copying nmdc_runtime/site/backup/nmdcdb_mongodump.py -> build/lib/nmdc_runtime/site/backup 2025-08-30T23:29:30,608 copying nmdc_runtime/site/backup/nmdcdb_mongoexport.py -> build/lib/nmdc_runtime/site/backup 2025-08-30T23:29:30,610 copying nmdc_runtime/site/backup/nmdcdb_mongoimport.py -> build/lib/nmdc_runtime/site/backup 2025-08-30T23:29:30,613 creating build/lib/nmdc_runtime/site/drsobjects 2025-08-30T23:29:30,614 copying nmdc_runtime/site/drsobjects/__init__.py -> build/lib/nmdc_runtime/site/drsobjects 2025-08-30T23:29:30,616 copying nmdc_runtime/site/drsobjects/ingest.py -> build/lib/nmdc_runtime/site/drsobjects 2025-08-30T23:29:30,618 copying nmdc_runtime/site/drsobjects/registration.py -> build/lib/nmdc_runtime/site/drsobjects 2025-08-30T23:29:30,620 creating build/lib/nmdc_runtime/site/repair 2025-08-30T23:29:30,622 copying nmdc_runtime/site/repair/__init__.py -> build/lib/nmdc_runtime/site/repair 2025-08-30T23:29:30,623 copying nmdc_runtime/site/repair/database_updater.py -> build/lib/nmdc_runtime/site/repair 2025-08-30T23:29:30,627 creating build/lib/nmdc_runtime/site/normalization 2025-08-30T23:29:30,628 copying nmdc_runtime/site/normalization/__init__.py -> build/lib/nmdc_runtime/site/normalization 2025-08-30T23:29:30,630 copying nmdc_runtime/site/normalization/gold.py -> build/lib/nmdc_runtime/site/normalization 2025-08-30T23:29:30,633 creating build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,634 copying nmdc_runtime/site/translation/emsl.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,636 copying nmdc_runtime/site/translation/__init__.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,638 copying nmdc_runtime/site/translation/submission_portal_translator.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,641 copying nmdc_runtime/site/translation/jgi.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,643 copying nmdc_runtime/site/translation/gold.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,645 copying nmdc_runtime/site/translation/neon_soil_translator.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,648 copying nmdc_runtime/site/translation/neon_surface_water_translator.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,651 copying nmdc_runtime/site/translation/neon_utils.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,653 copying nmdc_runtime/site/translation/translator.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,655 copying nmdc_runtime/site/translation/gold_translator.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,658 copying nmdc_runtime/site/translation/neon_benthic_translator.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,660 copying nmdc_runtime/site/translation/util.py -> build/lib/nmdc_runtime/site/translation 2025-08-30T23:29:30,718 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-08-30T23:29:30,719 !! 2025-08-30T23:29:30,720 ******************************************************************************** 2025-08-30T23:29:30,721 Please avoid running ``setup.py`` directly. 2025-08-30T23:29:30,721 Instead, use pypa/build, pypa/installer or other 2025-08-30T23:29:30,722 standards-based tools. 2025-08-30T23:29:30,723 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-08-30T23:29:30,723 or your builds will no longer be supported. 2025-08-30T23:29:30,724 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-08-30T23:29:30,725 ******************************************************************************** 2025-08-30T23:29:30,726 !! 2025-08-30T23:29:30,727 self.initialize_options() 2025-08-30T23:29:30,749 installing to build/bdist.linux-armv7l/wheel 2025-08-30T23:29:30,750 running install 2025-08-30T23:29:30,775 running install_lib 2025-08-30T23:29:30,804 creating build/bdist.linux-armv7l/wheel 2025-08-30T23:29:30,806 creating build/bdist.linux-armv7l/wheel/nmdc_runtime 2025-08-30T23:29:30,808 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/domain 2025-08-30T23:29:30,810 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/domain/users 2025-08-30T23:29:30,811 copying build/lib/nmdc_runtime/domain/users/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-08-30T23:29:30,813 copying build/lib/nmdc_runtime/domain/users/queriesInterface.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-08-30T23:29:30,814 copying build/lib/nmdc_runtime/domain/users/userService.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-08-30T23:29:30,816 copying build/lib/nmdc_runtime/domain/users/userSchema.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-08-30T23:29:30,818 copying build/lib/nmdc_runtime/domain/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain 2025-08-30T23:29:30,820 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/lib 2025-08-30T23:29:30,821 copying build/lib/nmdc_runtime/lib/extract_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-08-30T23:29:30,823 copying build/lib/nmdc_runtime/lib/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-08-30T23:29:30,825 copying build/lib/nmdc_runtime/lib/nmdc_dataframes.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-08-30T23:29:30,828 copying build/lib/nmdc_runtime/lib/load_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-08-30T23:29:30,830 copying build/lib/nmdc_runtime/lib/transform_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-08-30T23:29:30,832 copying build/lib/nmdc_runtime/lib/nmdc_etl_class.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-08-30T23:29:30,835 copying build/lib/nmdc_runtime/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-08-30T23:29:30,836 copying build/lib/nmdc_runtime/mongo_util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-08-30T23:29:30,839 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure 2025-08-30T23:29:30,840 copying build/lib/nmdc_runtime/infrastructure/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure 2025-08-30T23:29:30,842 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure/database 2025-08-30T23:29:30,843 copying build/lib/nmdc_runtime/infrastructure/database/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database 2025-08-30T23:29:30,846 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure/database/models 2025-08-30T23:29:30,847 copying build/lib/nmdc_runtime/infrastructure/database/models/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database/models 2025-08-30T23:29:30,849 copying build/lib/nmdc_runtime/infrastructure/database/models/user.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database/models 2025-08-30T23:29:30,851 copying build/lib/nmdc_runtime/infrastructure/database/db.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database 2025-08-30T23:29:30,853 copying build/lib/nmdc_runtime/containers.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-08-30T23:29:30,855 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core 2025-08-30T23:29:30,857 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core/exceptions 2025-08-30T23:29:30,858 copying build/lib/nmdc_runtime/core/exceptions/token.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-08-30T23:29:30,860 copying build/lib/nmdc_runtime/core/exceptions/base.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-08-30T23:29:30,862 copying build/lib/nmdc_runtime/core/exceptions/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-08-30T23:29:30,864 copying build/lib/nmdc_runtime/core/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core 2025-08-30T23:29:30,866 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core/db 2025-08-30T23:29:30,867 copying build/lib/nmdc_runtime/core/db/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/db 2025-08-30T23:29:30,869 copying build/lib/nmdc_runtime/core/db/Database.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/db 2025-08-30T23:29:30,872 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/client 2025-08-30T23:29:30,873 copying build/lib/nmdc_runtime/client/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/client 2025-08-30T23:29:30,875 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter 2025-08-30T23:29:30,877 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/domain 2025-08-30T23:29:30,878 copying build/lib/nmdc_runtime/minter/domain/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/domain 2025-08-30T23:29:30,880 copying build/lib/nmdc_runtime/minter/domain/model.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/domain 2025-08-30T23:29:30,882 copying build/lib/nmdc_runtime/minter/bootstrap.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-08-30T23:29:30,884 copying build/lib/nmdc_runtime/minter/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-08-30T23:29:30,887 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/adapters 2025-08-30T23:29:30,888 copying build/lib/nmdc_runtime/minter/adapters/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/adapters 2025-08-30T23:29:30,890 copying build/lib/nmdc_runtime/minter/adapters/repository.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/adapters 2025-08-30T23:29:30,893 copying build/lib/nmdc_runtime/minter/config.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-08-30T23:29:30,895 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/entrypoints 2025-08-30T23:29:30,896 copying build/lib/nmdc_runtime/minter/entrypoints/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/entrypoints 2025-08-30T23:29:30,898 copying build/lib/nmdc_runtime/minter/entrypoints/fastapi_app.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/entrypoints 2025-08-30T23:29:30,900 copying build/lib/nmdc_runtime/config.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-08-30T23:29:30,903 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site 2025-08-30T23:29:30,904 copying build/lib/nmdc_runtime/site/resources.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-08-30T23:29:30,907 copying build/lib/nmdc_runtime/site/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-08-30T23:29:30,909 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/changesheets 2025-08-30T23:29:30,910 copying build/lib/nmdc_runtime/site/changesheets/base.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/changesheets 2025-08-30T23:29:30,913 copying build/lib/nmdc_runtime/site/changesheets/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/changesheets 2025-08-30T23:29:30,915 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/validation 2025-08-30T23:29:30,916 copying build/lib/nmdc_runtime/site/validation/emsl.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-08-30T23:29:30,918 copying build/lib/nmdc_runtime/site/validation/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-08-30T23:29:30,920 copying build/lib/nmdc_runtime/site/validation/jgi.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-08-30T23:29:30,922 copying build/lib/nmdc_runtime/site/validation/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-08-30T23:29:30,924 copying build/lib/nmdc_runtime/site/validation/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-08-30T23:29:30,926 copying build/lib/nmdc_runtime/site/ops.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-08-30T23:29:30,930 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/export 2025-08-30T23:29:30,932 copying build/lib/nmdc_runtime/site/export/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-08-30T23:29:30,933 copying build/lib/nmdc_runtime/site/export/ncbi_xml_utils.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-08-30T23:29:30,936 copying build/lib/nmdc_runtime/site/export/ncbi_xml.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-08-30T23:29:30,940 copying build/lib/nmdc_runtime/site/export/study_metadata.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-08-30T23:29:30,943 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/backup 2025-08-30T23:29:30,944 copying build/lib/nmdc_runtime/site/backup/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-08-30T23:29:30,946 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongodump.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-08-30T23:29:30,948 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongoexport.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-08-30T23:29:30,951 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongoimport.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-08-30T23:29:30,953 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/drsobjects 2025-08-30T23:29:30,955 copying build/lib/nmdc_runtime/site/drsobjects/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-08-30T23:29:30,956 copying build/lib/nmdc_runtime/site/drsobjects/ingest.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-08-30T23:29:30,958 copying build/lib/nmdc_runtime/site/drsobjects/registration.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-08-30T23:29:30,961 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/repair 2025-08-30T23:29:30,962 copying build/lib/nmdc_runtime/site/repair/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/repair 2025-08-30T23:29:30,964 copying build/lib/nmdc_runtime/site/repair/database_updater.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/repair 2025-08-30T23:29:30,966 copying build/lib/nmdc_runtime/site/repository.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-08-30T23:29:30,970 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/normalization 2025-08-30T23:29:30,972 copying build/lib/nmdc_runtime/site/normalization/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/normalization 2025-08-30T23:29:30,974 copying build/lib/nmdc_runtime/site/normalization/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/normalization 2025-08-30T23:29:30,976 copying build/lib/nmdc_runtime/site/graphs.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-08-30T23:29:30,980 copying build/lib/nmdc_runtime/site/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-08-30T23:29:30,983 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/translation 2025-08-30T23:29:30,985 copying build/lib/nmdc_runtime/site/translation/emsl.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:30,987 copying build/lib/nmdc_runtime/site/translation/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:30,990 copying build/lib/nmdc_runtime/site/translation/submission_portal_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:30,993 copying build/lib/nmdc_runtime/site/translation/jgi.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:30,996 copying build/lib/nmdc_runtime/site/translation/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:30,999 copying build/lib/nmdc_runtime/site/translation/neon_soil_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:31,003 copying build/lib/nmdc_runtime/site/translation/neon_surface_water_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:31,007 copying build/lib/nmdc_runtime/site/translation/neon_utils.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:31,009 copying build/lib/nmdc_runtime/site/translation/translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:31,011 copying build/lib/nmdc_runtime/site/translation/gold_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:31,015 copying build/lib/nmdc_runtime/site/translation/neon_benthic_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:31,018 copying build/lib/nmdc_runtime/site/translation/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-08-30T23:29:31,021 copying build/lib/nmdc_runtime/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-08-30T23:29:31,025 copying build/lib/nmdc_runtime/main.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-08-30T23:29:31,027 running install_egg_info 2025-08-30T23:29:31,066 running egg_info 2025-08-30T23:29:31,097 writing nmdc_runtime.egg-info/PKG-INFO 2025-08-30T23:29:31,101 writing dependency_links to nmdc_runtime.egg-info/dependency_links.txt 2025-08-30T23:29:31,102 writing entry points to nmdc_runtime.egg-info/entry_points.txt 2025-08-30T23:29:31,104 writing top-level names to nmdc_runtime.egg-info/top_level.txt 2025-08-30T23:29:31,225 listing git files failed - pretending there aren't any 2025-08-30T23:29:31,230 reading manifest file 'nmdc_runtime.egg-info/SOURCES.txt' 2025-08-30T23:29:31,528 adding license file 'LICENSE' 2025-08-30T23:29:31,552 writing manifest file 'nmdc_runtime.egg-info/SOURCES.txt' 2025-08-30T23:29:31,555 Copying nmdc_runtime.egg-info to build/bdist.linux-armv7l/wheel/./nmdc_runtime-2.9.0-py3.11.egg-info 2025-08-30T23:29:31,566 running install_scripts 2025-08-30T23:29:31,580 creating build/bdist.linux-armv7l/wheel/nmdc_runtime-2.9.0.dist-info/WHEEL 2025-08-30T23:29:31,583 creating '/tmp/pip-wheel-9jnxyg07/nmdc_runtime-2.9.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-08-30T23:29:31,586 adding 'nmdc_runtime/__init__.py' 2025-08-30T23:29:31,588 adding 'nmdc_runtime/config.py' 2025-08-30T23:29:31,590 adding 'nmdc_runtime/containers.py' 2025-08-30T23:29:31,592 adding 'nmdc_runtime/main.py' 2025-08-30T23:29:31,594 adding 'nmdc_runtime/mongo_util.py' 2025-08-30T23:29:31,598 adding 'nmdc_runtime/util.py' 2025-08-30T23:29:31,601 adding 'nmdc_runtime/client/__init__.py' 2025-08-30T23:29:31,603 adding 'nmdc_runtime/core/__init__.py' 2025-08-30T23:29:31,605 adding 'nmdc_runtime/core/db/Database.py' 2025-08-30T23:29:31,607 adding 'nmdc_runtime/core/db/__init__.py' 2025-08-30T23:29:31,609 adding 'nmdc_runtime/core/exceptions/__init__.py' 2025-08-30T23:29:31,610 adding 'nmdc_runtime/core/exceptions/base.py' 2025-08-30T23:29:31,612 adding 'nmdc_runtime/core/exceptions/token.py' 2025-08-30T23:29:31,614 adding 'nmdc_runtime/domain/__init__.py' 2025-08-30T23:29:31,616 adding 'nmdc_runtime/domain/users/__init__.py' 2025-08-30T23:29:31,617 adding 'nmdc_runtime/domain/users/queriesInterface.py' 2025-08-30T23:29:31,619 adding 'nmdc_runtime/domain/users/userSchema.py' 2025-08-30T23:29:31,621 adding 'nmdc_runtime/domain/users/userService.py' 2025-08-30T23:29:31,623 adding 'nmdc_runtime/infrastructure/__init__.py' 2025-08-30T23:29:31,625 adding 'nmdc_runtime/infrastructure/database/__init__.py' 2025-08-30T23:29:31,626 adding 'nmdc_runtime/infrastructure/database/db.py' 2025-08-30T23:29:31,628 adding 'nmdc_runtime/infrastructure/database/models/__init__.py' 2025-08-30T23:29:31,630 adding 'nmdc_runtime/infrastructure/database/models/user.py' 2025-08-30T23:29:31,632 adding 'nmdc_runtime/lib/__init__.py' 2025-08-30T23:29:31,634 adding 'nmdc_runtime/lib/extract_nmdc_data.py' 2025-08-30T23:29:31,635 adding 'nmdc_runtime/lib/load_nmdc_data.py' 2025-08-30T23:29:31,639 adding 'nmdc_runtime/lib/nmdc_dataframes.py' 2025-08-30T23:29:31,642 adding 'nmdc_runtime/lib/nmdc_etl_class.py' 2025-08-30T23:29:31,648 adding 'nmdc_runtime/lib/transform_nmdc_data.py' 2025-08-30T23:29:31,651 adding 'nmdc_runtime/minter/__init__.py' 2025-08-30T23:29:31,652 adding 'nmdc_runtime/minter/bootstrap.py' 2025-08-30T23:29:31,654 adding 'nmdc_runtime/minter/config.py' 2025-08-30T23:29:31,655 adding 'nmdc_runtime/minter/adapters/__init__.py' 2025-08-30T23:29:31,657 adding 'nmdc_runtime/minter/adapters/repository.py' 2025-08-30T23:29:31,660 adding 'nmdc_runtime/minter/domain/__init__.py' 2025-08-30T23:29:31,661 adding 'nmdc_runtime/minter/domain/model.py' 2025-08-30T23:29:31,663 adding 'nmdc_runtime/minter/entrypoints/__init__.py' 2025-08-30T23:29:31,665 adding 'nmdc_runtime/minter/entrypoints/fastapi_app.py' 2025-08-30T23:29:31,667 adding 'nmdc_runtime/site/__init__.py' 2025-08-30T23:29:31,669 adding 'nmdc_runtime/site/graphs.py' 2025-08-30T23:29:31,678 adding 'nmdc_runtime/site/ops.py' 2025-08-30T23:29:31,682 adding 'nmdc_runtime/site/repository.py' 2025-08-30T23:29:31,685 adding 'nmdc_runtime/site/resources.py' 2025-08-30T23:29:31,687 adding 'nmdc_runtime/site/util.py' 2025-08-30T23:29:31,690 adding 'nmdc_runtime/site/backup/__init__.py' 2025-08-30T23:29:31,691 adding 'nmdc_runtime/site/backup/nmdcdb_mongodump.py' 2025-08-30T23:29:31,693 adding 'nmdc_runtime/site/backup/nmdcdb_mongoexport.py' 2025-08-30T23:29:31,695 adding 'nmdc_runtime/site/backup/nmdcdb_mongoimport.py' 2025-08-30T23:29:31,697 adding 'nmdc_runtime/site/changesheets/__init__.py' 2025-08-30T23:29:31,699 adding 'nmdc_runtime/site/changesheets/base.py' 2025-08-30T23:29:31,701 adding 'nmdc_runtime/site/drsobjects/__init__.py' 2025-08-30T23:29:31,703 adding 'nmdc_runtime/site/drsobjects/ingest.py' 2025-08-30T23:29:31,704 adding 'nmdc_runtime/site/drsobjects/registration.py' 2025-08-30T23:29:31,706 adding 'nmdc_runtime/site/export/__init__.py' 2025-08-30T23:29:31,710 adding 'nmdc_runtime/site/export/ncbi_xml.py' 2025-08-30T23:29:31,712 adding 'nmdc_runtime/site/export/ncbi_xml_utils.py' 2025-08-30T23:29:31,714 adding 'nmdc_runtime/site/export/study_metadata.py' 2025-08-30T23:29:31,716 adding 'nmdc_runtime/site/normalization/__init__.py' 2025-08-30T23:29:31,718 adding 'nmdc_runtime/site/normalization/gold.py' 2025-08-30T23:29:31,720 adding 'nmdc_runtime/site/repair/__init__.py' 2025-08-30T23:29:31,723 adding 'nmdc_runtime/site/repair/database_updater.py' 2025-08-30T23:29:31,725 adding 'nmdc_runtime/site/translation/__init__.py' 2025-08-30T23:29:31,727 adding 'nmdc_runtime/site/translation/emsl.py' 2025-08-30T23:29:31,729 adding 'nmdc_runtime/site/translation/gold.py' 2025-08-30T23:29:31,733 adding 'nmdc_runtime/site/translation/gold_translator.py' 2025-08-30T23:29:31,735 adding 'nmdc_runtime/site/translation/jgi.py' 2025-08-30T23:29:31,738 adding 'nmdc_runtime/site/translation/neon_benthic_translator.py' 2025-08-30T23:29:31,742 adding 'nmdc_runtime/site/translation/neon_soil_translator.py' 2025-08-30T23:29:31,746 adding 'nmdc_runtime/site/translation/neon_surface_water_translator.py' 2025-08-30T23:29:31,748 adding 'nmdc_runtime/site/translation/neon_utils.py' 2025-08-30T23:29:31,754 adding 'nmdc_runtime/site/translation/submission_portal_translator.py' 2025-08-30T23:29:31,756 adding 'nmdc_runtime/site/translation/translator.py' 2025-08-30T23:29:31,758 adding 'nmdc_runtime/site/translation/util.py' 2025-08-30T23:29:31,760 adding 'nmdc_runtime/site/validation/__init__.py' 2025-08-30T23:29:31,762 adding 'nmdc_runtime/site/validation/emsl.py' 2025-08-30T23:29:31,763 adding 'nmdc_runtime/site/validation/gold.py' 2025-08-30T23:29:31,765 adding 'nmdc_runtime/site/validation/jgi.py' 2025-08-30T23:29:31,767 adding 'nmdc_runtime/site/validation/util.py' 2025-08-30T23:29:31,770 adding 'nmdc_runtime-2.9.0.dist-info/licenses/LICENSE' 2025-08-30T23:29:31,772 adding 'nmdc_runtime-2.9.0.dist-info/METADATA' 2025-08-30T23:29:31,774 adding 'nmdc_runtime-2.9.0.dist-info/WHEEL' 2025-08-30T23:29:31,775 adding 'nmdc_runtime-2.9.0.dist-info/entry_points.txt' 2025-08-30T23:29:31,777 adding 'nmdc_runtime-2.9.0.dist-info/top_level.txt' 2025-08-30T23:29:31,779 adding 'nmdc_runtime-2.9.0.dist-info/RECORD' 2025-08-30T23:29:31,783 removing build/bdist.linux-armv7l/wheel 2025-08-30T23:29:31,927 Building wheel for nmdc-runtime (setup.py): finished with status 'done' 2025-08-30T23:29:31,931 Created wheel for nmdc-runtime: filename=nmdc_runtime-2.9.0-py3-none-any.whl size=146320 sha256=7f78e9b11db8724dc418c807ba632688ea1506ed6eb391757fb02a6df66265c1 2025-08-30T23:29:31,932 Stored in directory: /tmp/pip-ephem-wheel-cache-jm6e9qsn/wheels/21/aa/fd/b65081e4ef9dcf9b17e0ce6e5c8fa80102b82a0f44bd1f714d 2025-08-30T23:29:31,946 Successfully built nmdc-runtime 2025-08-30T23:29:31,953 Removed build tracker: '/tmp/pip-build-tracker-b3ethesf'