From ee4317eb63a66321d97153ad0e17b6651a6697ad Mon Sep 17 00:00:00 2001 From: Matvey Loshakov Date: Wed, 9 Oct 2024 14:46:48 +0200 Subject: [PATCH 1/2] Pilot HDC 1.2 --- .editorconfig | 18 + .env.schema | 27 + .gitignore | 12 + .pre-commit-config.yaml | 88 + CONTRIBUTING.md | 24 + COPYRIGHT | 5 + LICENSE | 661 ++++++ README.md | 19 +- bids-validator/.dockerignore | 16 + bids-validator/.env.schema | 15 + bids-validator/Dockerfile | 35 + bids-validator/README.md | 64 + bids-validator/poetry.lock | 1777 +++++++++++++++++ bids-validator/pyproject.toml | 29 + bids-validator/scripts/__init__.py | 5 + bids-validator/scripts/config.py | 86 + bids-validator/scripts/locks.py | 102 + bids-validator/scripts/logger.py | 16 + bids-validator/scripts/models.py | 29 + bids-validator/scripts/validate_dataset.py | 213 ++ bids-validator/tests/__init__.py | 5 + bids-validator/tests/conftest.py | 97 + bids-validator/tests/test_validate_dataset.py | 37 + filecopy/.dockerignore | 16 + filecopy/Dockerfile | 24 + filecopy/README.md | 65 + filecopy/operations/__init__.py | 5 + filecopy/operations/__main__.py | 18 + filecopy/operations/app.py | 12 + filecopy/operations/commands/__init__.py | 5 + filecopy/operations/commands/copy.py | 191 ++ filecopy/operations/commands/delete.py | 166 ++ filecopy/operations/config.py | 95 + filecopy/operations/duplicated_file_names.py | 49 + filecopy/operations/item_activity_schema.avsc | 56 + filecopy/operations/kafka_producer.py | 89 + filecopy/operations/logger.py | 16 + filecopy/operations/managers.py | 373 ++++ filecopy/operations/minio_boto3_client.py | 76 + filecopy/operations/models.py | 181 ++ filecopy/operations/services/__init__.py | 5 + .../operations/services/approval/__init__.py | 5 + .../operations/services/approval/client.py | 30 + .../operations/services/dataops/__init__.py | 5 + .../operations/services/dataops/client.py | 153 ++ .../operations/services/metadata/__init__.py | 5 + .../operations/services/metadata/client.py | 308 +++ .../services/notification/__init__.py | 5 + .../services/notification/client.py | 95 + .../services/notification/models.py | 67 + .../operations/services/redis/__init__.py | 5 + filecopy/operations/services/redis/client.py | 46 + filecopy/operations/traverser.py | 42 + filecopy/poetry.lock | 1748 ++++++++++++++++ filecopy/pyproject.toml | 31 + filecopy/tests/__init__.py | 5 + filecopy/tests/conftest.py | 11 + filecopy/tests/fixtures/__init__.py | 5 + filecopy/tests/fixtures/commands.py | 13 + filecopy/tests/fixtures/fake.py | 24 + filecopy/tests/fixtures/node.py | 87 + filecopy/tests/fixtures/services.py | 28 + filecopy/tests/services/__init__.py | 5 + filecopy/tests/services/approval/__init__.py | 5 + .../tests/services/approval/test_client.py | 15 + filecopy/tests/services/dataops/__init__.py | 5 + .../tests/services/dataops/test_client.py | 67 + filecopy/tests/services/metadata/__init__.py | 5 + .../tests/services/metadata/test_client.py | 132 ++ .../tests/services/notification/__init__.py | 5 + .../services/notification/test_client.py | 38 + filecopy/tests/test_duplicated_file_names.py | 42 + filecopy/tests/test_managers.py | 36 + filecopy/tests/test_models.py | 114 ++ filecopy/tests/test_traverser.py | 33 + freesurfer/.dockerignore | 11 + freesurfer/Dockerfile | 2 + freesurfer/build.sh | 1 + freesurfer/license.txt | 3 + 79 files changed, 8058 insertions(+), 1 deletion(-) create mode 100644 .editorconfig create mode 100644 .env.schema create mode 100644 .gitignore create mode 100644 .pre-commit-config.yaml create mode 100644 CONTRIBUTING.md create mode 100644 COPYRIGHT create mode 100644 LICENSE create mode 100644 bids-validator/.dockerignore create mode 100644 bids-validator/.env.schema create mode 100644 bids-validator/Dockerfile create mode 100644 bids-validator/README.md create mode 100644 bids-validator/poetry.lock create mode 100644 bids-validator/pyproject.toml create mode 100644 bids-validator/scripts/__init__.py create mode 100644 bids-validator/scripts/config.py create mode 100644 bids-validator/scripts/locks.py create mode 100644 bids-validator/scripts/logger.py create mode 100644 bids-validator/scripts/models.py create mode 100644 bids-validator/scripts/validate_dataset.py create mode 100644 bids-validator/tests/__init__.py create mode 100644 bids-validator/tests/conftest.py create mode 100644 bids-validator/tests/test_validate_dataset.py create mode 100644 filecopy/.dockerignore create mode 100644 filecopy/Dockerfile create mode 100644 filecopy/README.md create mode 100644 filecopy/operations/__init__.py create mode 100644 filecopy/operations/__main__.py create mode 100644 filecopy/operations/app.py create mode 100644 filecopy/operations/commands/__init__.py create mode 100644 filecopy/operations/commands/copy.py create mode 100644 filecopy/operations/commands/delete.py create mode 100644 filecopy/operations/config.py create mode 100644 filecopy/operations/duplicated_file_names.py create mode 100644 filecopy/operations/item_activity_schema.avsc create mode 100644 filecopy/operations/kafka_producer.py create mode 100644 filecopy/operations/logger.py create mode 100644 filecopy/operations/managers.py create mode 100644 filecopy/operations/minio_boto3_client.py create mode 100644 filecopy/operations/models.py create mode 100644 filecopy/operations/services/__init__.py create mode 100644 filecopy/operations/services/approval/__init__.py create mode 100644 filecopy/operations/services/approval/client.py create mode 100644 filecopy/operations/services/dataops/__init__.py create mode 100644 filecopy/operations/services/dataops/client.py create mode 100644 filecopy/operations/services/metadata/__init__.py create mode 100644 filecopy/operations/services/metadata/client.py create mode 100644 filecopy/operations/services/notification/__init__.py create mode 100644 filecopy/operations/services/notification/client.py create mode 100644 filecopy/operations/services/notification/models.py create mode 100644 filecopy/operations/services/redis/__init__.py create mode 100644 filecopy/operations/services/redis/client.py create mode 100644 filecopy/operations/traverser.py create mode 100644 filecopy/poetry.lock create mode 100644 filecopy/pyproject.toml create mode 100644 filecopy/tests/__init__.py create mode 100644 filecopy/tests/conftest.py create mode 100644 filecopy/tests/fixtures/__init__.py create mode 100644 filecopy/tests/fixtures/commands.py create mode 100755 filecopy/tests/fixtures/fake.py create mode 100644 filecopy/tests/fixtures/node.py create mode 100644 filecopy/tests/fixtures/services.py create mode 100644 filecopy/tests/services/__init__.py create mode 100644 filecopy/tests/services/approval/__init__.py create mode 100644 filecopy/tests/services/approval/test_client.py create mode 100644 filecopy/tests/services/dataops/__init__.py create mode 100644 filecopy/tests/services/dataops/test_client.py create mode 100644 filecopy/tests/services/metadata/__init__.py create mode 100644 filecopy/tests/services/metadata/test_client.py create mode 100644 filecopy/tests/services/notification/__init__.py create mode 100644 filecopy/tests/services/notification/test_client.py create mode 100644 filecopy/tests/test_duplicated_file_names.py create mode 100644 filecopy/tests/test_managers.py create mode 100644 filecopy/tests/test_models.py create mode 100644 filecopy/tests/test_traverser.py create mode 100644 freesurfer/.dockerignore create mode 100644 freesurfer/Dockerfile create mode 100644 freesurfer/build.sh create mode 100644 freesurfer/license.txt diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..f3515fd --- /dev/null +++ b/.editorconfig @@ -0,0 +1,18 @@ +root = true + +[*] +charset = utf-8 +tab_width = 4 +indent_style = space + +[*.py] +end_of_line = lf +indent_size = 4 +trim_trailing_whitespace = true +insert_final_newline = true + +[*.{yml,yaml}] +end_of_line = lf +indent_size = 2 +trim_trailing_whitespace = true +insert_final_newline = true diff --git a/.env.schema b/.env.schema new file mode 100644 index 0000000..a07a535 --- /dev/null +++ b/.env.schema @@ -0,0 +1,27 @@ +CONFIG_CENTER_ENABLED=false + +# If config center has been enabled +VAULT_URL= +VAULT_CRT= +VAULT_TOKEN= +S3_INTERNAL_HTTPS= +S3_PORT= +S3_HOST= +RDS_DBNAME= +RDS_HOST= +RDS_PORT= +AUDIT_TRAIL_SERVICE= +DATAOPS_SERVICE= +LINEAGE_SERVICE= +GREEN_ZONE_LABEL= +CORE_ZONE_LABEL= +METADATA_SERVICE= +PROJECT_SERVICE= +REDIS_HOST= +REDIS_PORT= +REDIS_PASSWORD= +KAFKA_URL= +S3_ACCESS_KEY= +S3_SECRET_KEY= +APPROVAL_SERVICE= +NOTIFICATION_SERVICE= diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..46dd3e2 --- /dev/null +++ b/.gitignore @@ -0,0 +1,12 @@ +*.pyc +*~ +*.swp +*.log +*.log.* +.braincodePassFile +test.sh +.DS_Store +# pycharm +.idea +.env +venv diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..9ffd5fa --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,88 @@ +default_language_version: + python: python3.10 + +repos: + + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: check-added-large-files + - id: check-docstring-first + - id: check-merge-conflict + - id: check-toml + - id: check-yaml + - id: double-quote-string-fixer + - id: end-of-file-fixer + - id: trailing-whitespace + + - repo: https://github.com/asottile/pyupgrade + rev: v3.17.0 + hooks: + - id: pyupgrade + args: [ + '--py310-plus', + ] + + - repo: https://github.com/psf/black + rev: 24.8.0 + hooks: + - id: black + args: [ + '--line-length=120', + '--skip-string-normalization', + ] + + - repo: https://github.com/PyCQA/isort + rev: 5.13.2 + hooks: + - id: isort + args: [ + '--line-length=120', + '--profile=black', + '--filter-files', + '--force-single-line-imports', + '--reverse-relative', + ] + + - repo: https://github.com/PyCQA/flake8 + rev: 5.0.4 + hooks: + - id: flake8 + additional_dependencies: [ + 'pycodestyle==2.9.1', # E,W + 'pyflakes==2.5.0', # F + 'mccabe==0.7.0', # C + 'flake8-bugbear==22.9.11', # B + 'flake8-builtins==1.5.3', # A + 'flake8-comprehensions==3.10.0', # C4 + 'flake8-debugger==4.1.2', # T1 + 'flake8-logging-format==0.7.5', # G + 'flake8-use-fstring==1.4.0', # FS + 'flake8-print==5.0.0', # T2 + ] + args: [ + '--select=E,W,F,C,B,A,C4,T1,G,FS,T2', + '--ignore=E203,W503,B008,B305,A003,G004', + '--max-complexity=10', + '--max-line-length=120', + ] + +# - repo: https://github.com/PyCQA/docformatter +# rev: v1.7.5 +# hooks: +# - id: docformatter +# args: [ +# '--wrap-summaries=120', +# '--wrap-descriptions=120', +# '--in-place', +# ] + + - repo: https://github.com/Lucas-C/pre-commit-hooks + rev: v1.5.5 + hooks: + - id: insert-license + files: \.py$ + args: [ + '--license-filepath=COPYRIGHT', + '--comment-style=#', + ] diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..3afd980 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,24 @@ +# Contribution Guide + +## Bug Reports + +For bug reports, [submit an issue](https://github.com/PilotDataPlatform/pipelines/issues). + +## Pull Requests + +1. Fork the [main repository](https://github.com/PilotDataPlatform/pipelines.git). +2. Create a feature branch to hold your changes. +3. Work on the changes in your feature branch. +4. Add [Unit Tests](#unit-tests). +5. Follow the Getting Started instruction to set up the service. +6. Create the Alembic [migration](#migrations) environment only when it's needed. +7. Test the code and create a pull request. + +### Unit Tests + +When adding a new feature or fixing a bug, unit tests are necessary to write. Currently we use Pytest as our testing framework and all test cases are written under the `tests` directory. + +Run test cases with Poetry and Pytest: +``` +poetry run pytest +``` diff --git a/COPYRIGHT b/COPYRIGHT new file mode 100644 index 0000000..d16efec --- /dev/null +++ b/COPYRIGHT @@ -0,0 +1,5 @@ +Copyright (C) 2022-Present Indoc Systems + +Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +You may not use this file except in compliance with the License. diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..0ad25db --- /dev/null +++ b/LICENSE @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/README.md b/README.md index 0f1b3fa..b9579f3 100644 --- a/README.md +++ b/README.md @@ -1 +1,18 @@ -# pilot-hdc-pipelines \ No newline at end of file +# pipelines + +Pipeline Services consists of different components to run and monitor pipeline, such as file pseudonymization pipeline. It contains different pipeline scripts, such as file/folder copy, delete pipeline script, and bids validator + +## Resources + +* [Pilot Platform API Documentation](https://pilotdataplatform.github.io/api-docs/) +* [Pilot Platform Helm Charts](https://github.com/PilotDataPlatform/helm-charts/) + +## Contribution + +You can contribute the project in following ways: + +* Report a bug. +* Suggest a feature. +* Open a pull request for fixing issues or adding functionality. Please consider + using [pre-commit](https://pre-commit.com) in this case. +* For general guidelines on how to contribute to the project, please take a look at the [contribution guides](CONTRIBUTING.md). diff --git a/bids-validator/.dockerignore b/bids-validator/.dockerignore new file mode 100644 index 0000000..4ebe4d4 --- /dev/null +++ b/bids-validator/.dockerignore @@ -0,0 +1,16 @@ +.git +.gitignore +.gitlab-ci* +gitlab-ci* +Dockerfile* +kubernetes +Jenkinsfile + +# Misc +.DS_Store +.env.local + +venv +env + +__pycache__ diff --git a/bids-validator/.env.schema b/bids-validator/.env.schema new file mode 100644 index 0000000..194c9ff --- /dev/null +++ b/bids-validator/.env.schema @@ -0,0 +1,15 @@ +CONFIG_CENTER_ENABLED=false + +# If config center has been enabled +VAULT_URL= +VAULT_CRT= +VAULT_TOKEN= + +S3_HOST= +S3_PORT= +S3_INTERNAL_HTTPS= +DATAOPS_SERVICE= +QUEUE_SERVICE= +METADATA_SERVICE= +RDS_HOST= +RDS_PORT= diff --git a/bids-validator/Dockerfile b/bids-validator/Dockerfile new file mode 100644 index 0000000..e0e3bf6 --- /dev/null +++ b/bids-validator/Dockerfile @@ -0,0 +1,35 @@ +FROM python:3.9-buster +USER root + +ENV PYTHONDONTWRITEBYTECODE=true \ + PYTHONIOENCODING=UTF-8 \ + POETRY_VERSION=1.3.2 \ + POETRY_HOME="/opt/poetry" \ + POETRY_VIRTUALENVS_CREATE=false + +ENV PATH="${POETRY_HOME}/bin:${PATH}" + +# RUN apt-get update -y && apt-get install -y rsync python3-pip python3-dev build-essential \ +# default-jre-headless locales nodejs npm && rm -rf /var/lib/apt/lists/* +RUN apt-get update -y +SHELL ["/bin/bash", "--login", "-c"] + +RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.35.3/install.sh | bash +RUN nvm install v18.12.1 +RUN npm install -g npm@9.2.0 +RUN npm install -g bids-validator@1.9.9 +RUN curl -sSL https://install.python-poetry.org | python3 - + +SHELL ["/bin/sh", "-c"] +RUN apt-get clean && apt-get update && apt-get install -y locales +COPY ./ /dataset-validate +WORKDIR /dataset-validate +RUN chmod 555 -R /dataset-validate +COPY poetry.lock pyproject.toml ./ +RUN poetry install --no-root --no-interaction +RUN locale-gen en_US.UTF-8 +ENV LANG en_US.UTF-8 +ENV LANGUAGE en_US:en +ENV LC_ALL en_US.UTF-8 +ENV PATH=/root/.nvm/versions/node/v18.12.1/bin:$PATH +RUN ls diff --git a/bids-validator/README.md b/bids-validator/README.md new file mode 100644 index 0000000..d47f643 --- /dev/null +++ b/bids-validator/README.md @@ -0,0 +1,64 @@ +# BIDS Validator + +[![Run Tests](https://github.com/PilotDataPlatform/pipelines/actions/workflows/run-tests-bids-validator.yml/badge.svg?branch=develop)](https://github.com/PilotDataPlatform/pipelines/actions/workflows/run-tests-bids-validator.yml) +[![Python](https://img.shields.io/badge/python-3.9-brightgreen.svg)](https://www.python.org/) +[![License](https://img.shields.io/badge/license-AGPL_v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0) + +This pipeline scripts provide functionality to validate dataset files against Brain Imaging Data Structure + +## Getting Started + +This is an example of how you may setting up your service locally. To get a local copy up and running follow these simple example steps. + +### Prerequisites + +This project is using [Poetry](https://python-poetry.org/docs/#installation) to handle the dependencies. + + curl -sSL https://install.python-poetry.org | python3 - + +### Installation & Quick Start + +1. Clone the project. + + https://github.com/PilotDataPlatform/pipelines.git + +2. Install dependencies. + + poetry install + +3. Add environment variables into `.env` in case it's needed. Use `.env.schema` as a reference. + +4. install bids-validator Command line version + ``` + npm install -g bids-validator + ``` + +5. run it locally: + ``` + python validate_dataset.py -d {dataset-id} -env dev --access-token 'access-token' + ``` + + + +### Startup using Docker + +This project can also be started using [Docker](https://www.docker.com/get-started/). + +1. To build and start the service within the Docker container, run: + + docker compose up + +## Resources + +* [Pilot Platform API Documentation](https://pilotdataplatform.github.io/api-docs/) +* [Pilot Platform Helm Charts](https://github.com/PilotDataPlatform/helm-charts/) + +## Contribution + +You can contribute the project in following ways: + +* Report a bug. +* Suggest a feature. +* Open a pull request for fixing issues or adding functionality. Please consider + using [pre-commit](https://pre-commit.com) in this case. +* For general guidelines on how to contribute to the project, please take a look at the [contribution guides](CONTRIBUTING.md). diff --git a/bids-validator/poetry.lock b/bids-validator/poetry.lock new file mode 100644 index 0000000..e8f6a17 --- /dev/null +++ b/bids-validator/poetry.lock @@ -0,0 +1,1777 @@ +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. + +[[package]] +name = "aioboto3" +version = "9.6.0" +description = "Async boto3 wrapper" +optional = false +python-versions = ">=3.7,<4.0" +files = [ + {file = "aioboto3-9.6.0-py3-none-any.whl", hash = "sha256:a62de3203c7372b5f1247057b9705eeb26c45ee65b5d1fab91767e4f31fd7b47"}, + {file = "aioboto3-9.6.0.tar.gz", hash = "sha256:abac5dcfa871627b7040e6586a69e3359e2dfc4e15dc66135969f2d26fbdcb3b"}, +] + +[package.dependencies] +aiobotocore = {version = "2.3.0", extras = ["boto3"]} + +[package.extras] +chalice = ["chalice 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b/bids-validator/pyproject.toml new file mode 100644 index 0000000..ede3d0f --- /dev/null +++ b/bids-validator/pyproject.toml @@ -0,0 +1,29 @@ +[tool.poetry] +name = "bids-validator" +version = "2.2.4" +description = "" +authors = ["Indoc Research"] + +[tool.poetry.dependencies] +python = "^3.9" +minio = "^7.1.7" +pydantic = "^1.9.0" +python-dotenv = "0.19.1" +python-json-logger = "^2.0.2" +psycopg2-binary = "2.9.3" +click = "8.1.2" +SQLAlchemy = "^1.4.36" +requests = "2.24.0" +asyncio = "^3.4.3" +pilot-platform-common = "0.3.0" + +[tool.poetry.dev-dependencies] +pytest = "7.1.2" +pytest-cov = "3.0.0" +pytest-httpserver = "1.0.2" +pytest-mock = "3.6.1" +Faker = "17.3.0" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/bids-validator/scripts/__init__.py b/bids-validator/scripts/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/bids-validator/scripts/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/bids-validator/scripts/config.py b/bids-validator/scripts/config.py new file mode 100644 index 0000000..dc09082 --- /dev/null +++ b/bids-validator/scripts/config.py @@ -0,0 +1,86 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import logging +from functools import lru_cache +from typing import Any +from typing import Dict +from typing import Optional + +from common import VaultClient +from pydantic import BaseSettings +from pydantic import Extra + + +class VaultConfig(BaseSettings): + """Store vault related configuration.""" + + APP_NAME: str = 'bids_validator' + CONFIG_CENTER_ENABLED: bool = False + + VAULT_URL: Optional[str] + VAULT_CRT: Optional[str] + VAULT_TOKEN: Optional[str] + + class Config: + env_file = '.env' + env_file_encoding = 'utf-8' + + +def load_vault_settings(settings: BaseSettings) -> Dict[str, Any]: + config = VaultConfig() + + if not config.CONFIG_CENTER_ENABLED: + return {} + + client = VaultClient(config.VAULT_URL, config.VAULT_CRT, config.VAULT_TOKEN) + return client.get_from_vault(config.APP_NAME) + + +class Settings(BaseSettings): + """Store service configuration settings.""" + + APP_NAME: str = 'bids_validator' + + LOGGING_LEVEL: int = logging.INFO + LOGGING_FORMAT: str = 'json' + + S3_HOST: str = '' + S3_PORT: int = 9000 + S3_INTERNAL_HTTPS: bool = False + S3_ACCESS_KEY: str = 'ACCESSKEY/CENLISDWYLOSADDFGMWZ' + S3_SECRET_KEY: str = 'SECRETKEY/DTRBFII/NJXVSJPLZMGPPVLELR' + + DATAOPS_SERVICE: str = 'http://127.0.0.1:5063' + QUEUE_SERVICE: str = 'http://127.0.0.1:6060' + METADATA_SERVICE: str = 'http://127.0.0.1:5066' + DATASET_SERVICE: str = 'http://127.0.0.1:5081' + + def __init__(self, *args: Any, **kwds: Any) -> None: + super().__init__(*args, **kwds) + + self.DATAOPS_SERVICE += '/v2/' + self.QUEUE_SERVICE += '/v1/' + self.METADATA_SERVICE = self.METADATA_SERVICE + '/v1/' + self.S3_URL = f'{self.S3_HOST}:{self.S3_PORT}' + + class Config: + env_file = '.env' + env_file_encoding = 'utf-8' + extra = Extra.allow + + @classmethod + def customise_sources(cls, init_settings, env_settings, file_secret_settings): + return init_settings, env_settings, load_vault_settings, file_secret_settings + + +@lru_cache() +def get_settings(): + settings = Settings() + return settings + + +ConfigClass = Settings() diff --git a/bids-validator/scripts/locks.py b/bids-validator/scripts/locks.py new file mode 100644 index 0000000..08f4201 --- /dev/null +++ b/bids-validator/scripts/locks.py @@ -0,0 +1,102 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from typing import Any +from typing import Dict +from typing import List + +import requests +from config import ConfigClass +from models import ItemStatus +from models import ResourceType + + +def get_all_children_nodes(parent_path: str, zone: str, container_code: str, access_token: str) -> List[Dict[str, Any]]: + item_zone = {'greenroom': 0, 'core': 1}.get(zone) + parameters = { + 'status': ItemStatus.ACTIVE, + 'zone': item_zone, + 'container_code': container_code, + 'container_type': 'dataset', + 'recursive': True, + } + if parent_path: + parameters['parent_path'] = parent_path + + header = {'Authorization': access_token} + + node_query_url = ConfigClass.METADATA_SERVICE + 'items/search/' + response = requests.get(node_query_url, params=parameters, headers=header) + ffs = response.json()['result'] + + return ffs + + +def lock_resource(resource_key: str, operation: str) -> dict: + # operation can be either read or write + url = ConfigClass.DATAOPS_SERVICE + 'resource/lock' + post_json = {'resource_key': resource_key, 'operation': operation} + + response = requests.post(url, json=post_json) + if response.status_code != 200: + raise Exception(f'resource {resource_key} already in used') + + return response.json() + + +def unlock_resource(resource_key: str, operation: str) -> dict: + # operation can be either read or write + url = ConfigClass.DATAOPS_SERVICE + 'resource/lock' + post_json = {'resource_key': resource_key, 'operation': operation} + + response = requests.delete(url, json=post_json) + if response.status_code != 200: + raise Exception(f'Error when unlock resource {resource_key}') + + return response.json() + + +def format_folder_path(node): + parent_path = node.get('parent_path', None) + if parent_path: + return f'{parent_path}/{node.get("name")}' + return node.get('name') + + +def lock_nodes(dataset_code: str, access_token: str): + """The function will recursively lock the node tree.""" + + # this is for crash recovery, if something trigger the exception + # we will unlock the locked node only. NOT the whole tree. The example + # case will be copy the same node, if we unlock the whole tree in exception + # then it will affect the processing one. + locked_node, err = [], None + + try: + nodes = get_all_children_nodes(None, 'core', dataset_code, access_token) + for ff_object in nodes: + # we will skip the deleted nodes + if ff_object.get('archived', False): + continue + + # conner case here, we DONT lock the name folder + # for the copy we will lock the both source and target + if ff_object.get('type') == ResourceType.FILE: + location = ff_object.get('storage')['location_uri'] + minio_path = location.split('//')[-1] + _, bucket, minio_obj_path = tuple(minio_path.split('/', 2)) + else: + bucket = ff_object.get('container') + minio_obj_path = format_folder_path(ff_object) + + source_key = f'{bucket}/{minio_obj_path}' + lock_resource(source_key, 'read') + locked_node.append((source_key, 'read')) + + except Exception as e: + err = e + + return locked_node, err diff --git a/bids-validator/scripts/logger.py b/bids-validator/scripts/logger.py new file mode 100644 index 0000000..3759de1 --- /dev/null +++ b/bids-validator/scripts/logger.py @@ -0,0 +1,16 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import logging + +from common import configure_logging +from scripts.config import get_settings + +settings = get_settings() + +logger = logging.getLogger('pilot.bids-validator') + +configure_logging(settings.LOGGING_LEVEL, settings.LOGGING_FORMAT) diff --git a/bids-validator/scripts/models.py b/bids-validator/scripts/models.py new file mode 100644 index 0000000..5b3a959 --- /dev/null +++ b/bids-validator/scripts/models.py @@ -0,0 +1,29 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from enum import Enum +from enum import unique + + +@unique +class ItemStatus(str, Enum): + # the new enum type for file status + # - REGISTERED means file is created by upload service + # but not complete yet. either in progress or fail. + # - ACTIVE means file uploading is complete. + # - ARCHIVED means the file has been deleted + + REGISTERED = 'REGISTERED' + ACTIVE = 'ACTIVE' + ARCHIVED = 'ARCHIVED' + + +@unique +class ResourceType(str, Enum): + """Store all possible types of resources.""" + + FOLDER = 'folder' + FILE = 'file' diff --git a/bids-validator/scripts/validate_dataset.py b/bids-validator/scripts/validate_dataset.py new file mode 100644 index 0000000..175b707 --- /dev/null +++ b/bids-validator/scripts/validate_dataset.py @@ -0,0 +1,213 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import argparse +import asyncio +import json +import os +import shutil +import subprocess +import time +import traceback +from datetime import datetime +from typing import Any +from typing import Dict +from typing import List + +import requests +from common.object_storage_adaptor.boto3_client import get_boto3_client +from config import ConfigClass +from locks import lock_nodes +from locks import unlock_resource +from models import ItemStatus +from models import ResourceType +from scripts.logger import logger + +TEMP_FOLDER = './dataset/' + + +def parse_inputs() -> dict: + parser = argparse.ArgumentParser( + description=__doc__, + formatter_class=argparse.RawDescriptionHelpFormatter, + ) + + parser.add_argument('-d', '--dataset-code', help='Dataset code', required=True) + parser.add_argument('-env', '--environment', help='Environment', required=True) + parser.add_argument('--access-token', '--access-token', help='Access Token', required=True) + + arguments = vars(parser.parse_args()) + return arguments + + +def send_message(dataset_code: str, status: str, bids_output: Dict[str, Any]) -> None: + queue_url = ConfigClass.QUEUE_SERVICE + 'broker/pub' + post_json = { + 'event_type': 'BIDS_VALIDATE_NOTIFICATION', + 'payload': { + 'status': status, # INIT/RUNNING/FINISH/ERROR + 'dataset': dataset_code, + 'payload': bids_output, + 'update_timestamp': datetime.utcfromtimestamp(time.time()).strftime('%Y-%m-%dT%H:%M:%S'), + }, + 'binary': True, + 'queue': 'socketio', + 'routing_key': 'socketio', + 'exchange': {'name': 'socketio', 'type': 'fanout'}, + } + + if status == 'failed': + post_json['payload']['payload'] = None + post_json['payload']['error_msg'] = bids_output + + try: + queue_res = requests.post(queue_url, json=post_json) + if queue_res.status_code != 200: + logger.info(f'code: {queue_res.status_code}: {queue_res.text}') + queue_res.raise_for_status() + logger.info('sent message to queue') + return + except Exception as e: + logger.error(f'Failed to send message to queue: {str(e)}') + raise + + +def get_files(dataset_code: str, access_token: str) -> List[str]: + all_files = [] + + query = { + 'status': ItemStatus.ACTIVE, + 'zone': 1, + 'container_code': dataset_code, + 'container_type': 'dataset', + 'recursive': True, + } + + header = {'Authorization': access_token} + + try: + resp = requests.get(ConfigClass.METADATA_SERVICE + 'items/search/', params=query, headers=header) + for node in resp.json()['result']: + if node['type'] == ResourceType.FILE: + all_files.append(node['storage']['location_uri']) + return all_files + except Exception as e: + logger.error(f'Error when get files: {str(e)}') + raise + + +async def download_from_minio(files_locations: List[str]) -> None: + boto3_client = await get_boto3_client( + ConfigClass.S3_URL, + access_key=ConfigClass.S3_ACCESS_KEY, + secret_key=ConfigClass.S3_SECRET_KEY, + https=ConfigClass.S3_INTERNAL_HTTPS, + ) + try: + for file_location in files_locations: + minio_path = file_location.split('//')[-1] + _, bucket, obj_path = tuple(minio_path.split('/', 2)) + await boto3_client.download_object(bucket, obj_path, TEMP_FOLDER + obj_path) + + logger.info('========Minio_Client download finished========') + + except Exception as e: + logger.error(f'Error when download data from minio: {str(e)}') + raise + + +def getProcessOutput() -> None: + f = open('result.txt', 'w') + try: + subprocess.run(['bids-validator', TEMP_FOLDER + 'data', '--json'], universal_newlines=True, stdout=f) + except Exception as e: + logger.error(f'BIDS validate fail: {str(e)}') + raise + + +def read_result_file() -> str: + f = open('result.txt', 'r') + output = f.read() + return output + + +def send_result_to_dataset(dataset_code: str, result: Dict[str, Any]) -> str: + query = {'validate_output': result} + try: + response = requests.put(ConfigClass.DATASET_SERVICE + f'/v1/dataset/bids-result/{dataset_code}', json=query) + logger.info('Submit the result to dataset service') + if response.status_code != 200: + logger.error(f'Failed to send result to dataset service {response.text}') + return + except Exception as e: + logger.error(f'Error when submit the result to dataset service: {str(e)}') + raise + + +def main(): + logger.info(f'Vault url: {os.getenv("VAULT_URL")}') + environment = args.get('environment', 'test') + logger.info(f'environment: {args.get("environment")}') + logger.info(f'config set: {environment}') + try: + # get arguments + dataset_code = args['dataset_code'] + access_token = args['access_token'] + + logger.info(f'dataset_code: {dataset_code}') + logger.info(f'access_token: {access_token}') + + locked_node = [] + files_locations = get_files(dataset_code, access_token) + # here add recursive read lock on the dataset + locked_node, err = lock_nodes(dataset_code, access_token) + if err: + raise err + + if len(files_locations) == 0: + send_message(dataset_code, 'failed', 'no files in dataset') + return + + # Download files folders from minio + loop = asyncio.get_event_loop() + loop.run_until_complete(download_from_minio(files_locations)) + logger.info('files are downloaded from minio') + + # Get bids validate result + getProcessOutput() + result = read_result_file() + + logger.info(f'BIDS validation result: {result}') + + bids_output = json.loads(result) + + # remove bids folder after validate + shutil.rmtree(TEMP_FOLDER) + + # Send the bids validation result to dataset service + send_result_to_dataset(dataset_code, bids_output) + + send_message(dataset_code, 'success', bids_output) + + except Exception as e: + logger.error(f'BIDs validator failed due to: {str(e)}') + send_message(dataset_code, 'failed', str(e)) + raise + + finally: + for resource_key, operation in locked_node: + unlock_resource(resource_key, operation) + + +if __name__ == '__main__': + try: + args = parse_inputs() + main() + except Exception as e: + logger.error(f'[Validate Failed] {str(e)}') + for info in traceback.format_stack(): + logger.error(info) + raise diff --git a/bids-validator/tests/__init__.py b/bids-validator/tests/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/bids-validator/tests/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/bids-validator/tests/conftest.py b/bids-validator/tests/conftest.py new file mode 100644 index 0000000..f6402de --- /dev/null +++ b/bids-validator/tests/conftest.py @@ -0,0 +1,97 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import random +import uuid +from typing import Any +from typing import Callable +from typing import Dict + +import faker +import pytest +from scripts.models import ItemStatus +from scripts.models import ResourceType + + +class Faker(faker.Faker): + def name(self) -> str: + return self.pystr(max_chars=10) + + +@pytest.fixture +def fake() -> Faker: + yield Faker() + + +@pytest.fixture +def create_node(fake) -> Callable[..., Dict[str, Any]]: + def _create_node( + id_=None, + parent=None, + parent_path=None, + name=None, + type_=None, + zone=0, + size=0, + owner='testuser', + container_code='testproject', + container_type='project', + created_time='2021-05-17 17:19:51.806591', + last_updated_time='2021-05-17 17:19:51.806591', + status=ItemStatus.ACTIVE, + tags=None, + attributes=None, + location_uri='minio_path', + version='fake_version', + ) -> Dict[str, Any]: + if id_ is None: + id_ = fake.pyint() + + if parent is None: + parent = f'{uuid.uuid4()}' + + if parent_path is None: + parent_path = 'fake' + + if name is None: + name = fake.word() + + if type_ is None: + type_ = random.choice(list(ResourceType)) + + if tags is None: + tags = fake.words() + + if attributes is None: + attributes = {} + + return { + 'id': id_, + 'parent': parent, + 'parent_path': parent_path, + 'restore_path': 'None', + 'status': status, + 'type': type_, + 'zone': zone, + 'name': name, + 'size': size, + 'owner': owner, + 'container_code': container_code, + 'container_type': container_type, + 'created_time': created_time, + 'last_updated_time': last_updated_time, + 'storage': {'id': 'fake_id', 'location_uri': location_uri, 'version': version}, + 'extended': { + 'id': 'fake_id', + 'extra': { + 'tags': tags, + 'system_tags': ['copied-to-core'], + 'attributes': attributes, + }, + }, + } + + return _create_node diff --git a/bids-validator/tests/test_validate_dataset.py b/bids-validator/tests/test_validate_dataset.py new file mode 100644 index 0000000..2a2967b --- /dev/null +++ b/bids-validator/tests/test_validate_dataset.py @@ -0,0 +1,37 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import os +import sys + +# TODO: Fix imports as a part of https://indocconsortium.atlassian.net/browse/PILOT-703 +sys.path.insert(0, f'{os.getcwd()}/scripts') + + +def test_send_message_makes_request_to_the_queue_service(mocker, httpserver): + from config import ConfigClass + from validate_dataset import send_message + + mocker.patch.object(ConfigClass, 'QUEUE_SERVICE', httpserver.url_for('/')) + httpserver.expect_oneshot_request('/broker/pub', method='POST').respond_with_json({}) + + send_message('dataset-code', 'init', {}) + + httpserver.check() + + +def test_get_files_get_correct_result(mocker, httpserver, create_node): + from config import ConfigClass + from models import ResourceType + from validate_dataset import get_files + + expected_body = {'result': [create_node(type_=ResourceType.FILE, location_uri='minio_path')]} + + mocker.patch.object(ConfigClass, 'METADATA_SERVICE', httpserver.url_for('/')) + httpserver.expect_oneshot_request('/items/search/', method='GET').respond_with_json(expected_body) + + received_response = get_files('dataset-code', 'access_token') + assert received_response == ['minio_path'] diff --git a/filecopy/.dockerignore b/filecopy/.dockerignore new file mode 100644 index 0000000..1789725 --- /dev/null +++ b/filecopy/.dockerignore @@ -0,0 +1,16 @@ +# Folders +.git +.venv +__pycache__ +venv +env +kubernetes + +# Files +.DS_Store +.env.local +.gitignore +.gitlab-ci* +gitlab-ci* +Dockerfile* +Jenkinsfile diff --git a/filecopy/Dockerfile b/filecopy/Dockerfile new file mode 100644 index 0000000..424b18a --- /dev/null +++ b/filecopy/Dockerfile @@ -0,0 +1,24 @@ +FROM docker-registry.ebrains.eu/hdc-services-image/base-image:python-3.10.14-v1 AS filecopy-image + +ENV PYTHONUNBUFFERED=true \ + PYTHONDONTWRITEBYTECODE=true \ + PYTHONIOENCODING=UTF-8 \ + POETRY_VERSION=1.3.2 \ + POETRY_HOME="/opt/poetry" \ + POETRY_VIRTUALENVS_CREATE=false + + +ENV PATH="${POETRY_HOME}/bin:${PATH}" + +RUN curl -sSL https://install.python-poetry.org | python3 - + +COPY poetry.lock pyproject.toml ./ + +RUN poetry install --no-root --no-interaction + +COPY operations ./operations + +RUN chown -R app:app /app +USER app + +ENTRYPOINT ["python3", "-m", "operations"] diff --git a/filecopy/README.md b/filecopy/README.md new file mode 100644 index 0000000..7c68e72 --- /dev/null +++ b/filecopy/README.md @@ -0,0 +1,65 @@ +# File copy and delete + +[![Run Tests](https://github.com/PilotDataPlatform/pipelines/actions/workflows/run-tests-filecopy.yml/badge.svg?branch=develop)](https://github.com/PilotDataPlatform/pipelines/actions/workflows/run-tests-filecopy.yml) +[![Python](https://img.shields.io/badge/python-3.9-brightgreen.svg)](https://www.python.org/) +[![License](https://img.shields.io/badge/license-AGPL_v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0) + +This pipeline scripts provide functionality for files and folders copy and delete in greenroom and core zone + +## Getting Started + +This is an example of how you may setting up your service locally. To get a local copy up and running follow these simple example steps. + +### Prerequisites + +This project is using [Poetry](https://python-poetry.org/docs/#installation) to handle the dependencies. + + curl -sSL https://install.python-poetry.org | python3 - + +### Installation & Quick Start + +1. Clone the project. + + https://github.com/PilotDataPlatform/pipelines.git + +2. Install dependencies. + + poetry install + +3. Add environment variables into `.env` in case it's needed. Use `.env.schema` as a reference. + +4. run it locally: + +File folder copy + ``` + python3 -m operations copy --source-id 'source folder id where the file copy from' --destination-id 'destination folder id where the file copy to' --project-code 'project_code' --operator 'operator' --job-id 'job id' --session-id 'session id' --include-ids 'Id of the copied file and folder' + --access-token 'access-token' + + ``` +File folder delete + ``` + python3 -m operations delete --source-id 'source folder id where the file delete from' --include-ids 'Id of the deleted file and folder' --project-code 'project_code' --operator 'operator' --job-id 'job id' --session-id 'session id' --access-token 'access-token' + ``` + +### Startup using Docker + +This project can also be started using [Docker](https://www.docker.com/get-started/). + +1. To build and start the service within the Docker container, run: + + docker compose up + +## Resources + +* [Pilot Platform API Documentation](https://pilotdataplatform.github.io/api-docs/) +* [Pilot Platform Helm Charts](https://github.com/PilotDataPlatform/helm-charts/) + +## Contribution + +You can contribute the project in following ways: + +* Report a bug. +* Suggest a feature. +* Open a pull request for fixing issues or adding functionality. Please consider + using [pre-commit](https://pre-commit.com) in this case. +* For general guidelines on how to contribute to the project, please take a look at the [contribution guides](CONTRIBUTING.md). diff --git a/filecopy/operations/__init__.py b/filecopy/operations/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/operations/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/operations/__main__.py b/filecopy/operations/__main__.py new file mode 100644 index 0000000..ff904f8 --- /dev/null +++ b/filecopy/operations/__main__.py @@ -0,0 +1,18 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import logging + +from operations.app import app +from operations.commands.copy import copy +from operations.commands.delete import delete + +if __name__ == '__main__': + logging.basicConfig(level=logging.DEBUG, format='%(asctime)s\t%(levelname)s\t[%(name)s]\t%(message)s') + + app.add_command(copy) + app.add_command(delete) + app() diff --git a/filecopy/operations/app.py b/filecopy/operations/app.py new file mode 100644 index 0000000..dc65b31 --- /dev/null +++ b/filecopy/operations/app.py @@ -0,0 +1,12 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import click + + +@click.group() +def app(): + """Main entry point.""" diff --git a/filecopy/operations/commands/__init__.py b/filecopy/operations/commands/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/operations/commands/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/operations/commands/copy.py b/filecopy/operations/commands/copy.py new file mode 100644 index 0000000..dbc1fc3 --- /dev/null +++ b/filecopy/operations/commands/copy.py @@ -0,0 +1,191 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import asyncio +import atexit +import json +from pathlib import Path +from typing import Optional + +import click +from common import ProjectClient +from operations.config import get_settings +from operations.kafka_producer import KafkaProducer +from operations.managers import CopyManager +from operations.managers import CopyPreparationManager +from operations.minio_boto3_client import MinioBoto3Client +from operations.models import get_timestamp +from operations.services.approval.client import ApprovalServiceClient +from operations.services.dataops.client import DataopsServiceClient +from operations.services.dataops.client import JobStatus +from operations.services.dataops.client import ResourceLockOperation +from operations.services.metadata.client import MetadataServiceClient +from operations.services.notification.client import NotificationServiceClient +from operations.services.notification.models import NotificationType +from operations.services.notification.models import PipelineAction +from operations.services.notification.models import PipelineStatus +from operations.traverser import Traverser + +atexit.register(KafkaProducer.close_connection) + + +@click.command() +@click.option('--source-id', type=str, required=True) +@click.option('--destination-id', type=str, required=True) +@click.option('--include-ids', type=str, multiple=True) +@click.option('--job-id', type=str, required=True) +@click.option('--session-id', type=str, required=True) +@click.option('--project-code', type=str, required=True) +@click.option('--operator', type=str, required=True) +@click.option('--request-info', type=str) +@click.option('--access-token', type=str, required=True) +def copy( + source_id: str, + destination_id: str, + include_ids: tuple[str], + job_id: str, + session_id: str, + project_code: str, + operator: str, + request_info: Optional[str], + access_token: str, +): + """Copy files from source geid into destination geid.""" + + click.echo(f'Starting copy process from "{source_id}" into "{destination_id}" including only "{set(include_ids)}".') + + settings = get_settings() + + project_client = ProjectClient(settings.PROJECT_SERVICE, settings.REDIS_URL) + + metadata_service_client = MetadataServiceClient( + settings.METADATA_SERVICE, + settings.S3_URL, + settings.CORE_ZONE_LABEL, + settings.TEMP_DIR, + project_client, + access_token, + ) + dataops_client = DataopsServiceClient(settings.DATAOPS_SERVICE) + + minio_client = MinioBoto3Client( + settings.S3_ACCESS_KEY, settings.S3_SECRET_KEY, settings.S3_URL, settings.S3_INTERNAL_HTTPS + ) + + loop = asyncio.get_event_loop() + loop.run_until_complete(KafkaProducer.init_connection()) + + approval_service_client = None + approved_entities = None + + # TODO: This sprint assume metadata service can always get info, + # Next sprint edit notification service client - https://indocconsortium.atlassian.net/browse/PILOT-1830 + nodes = metadata_service_client.get_items_by_ids([source_id, destination_id]) + include_nodes = metadata_service_client.get_items_by_ids(include_ids[0].split(',')) + source_folder = nodes[source_id] + destination_folder = nodes[destination_id] + target_names = [f'{item["parent_path"]}/{item["name"]}' for item in include_nodes.values()] + target_type = 'batch' if len(target_names) > 1 else next(iter(include_nodes.values()))['type'] + notification_client = NotificationServiceClient( + settings.NOTIFICATION_SERVICE, + include_nodes, + source_folder, + destination_folder, + project_code, + PipelineAction.COPY, + PipelineStatus.SUCCESS, + operator, + NotificationType.PIPELINE, + ) + + try: + if request_info: + request_dict = json.loads(request_info) + request_id = list(request_dict.keys())[0] + approved_entities = request_dict[request_id] + approval_service_client = ApprovalServiceClient(settings.APPROVAL_SERVICE, request_id) + + if destination_folder.is_archived: + raise ValueError('Destination is already in trash bin') + + source_bucket = Path(f'gr-{project_code}') + destination_bucket = Path(f'core-{project_code}') + timestamp = get_timestamp() + + copy_preparation_manager = CopyPreparationManager( + metadata_service_client, + approval_service_client, + approved_entities, + project_code, + settings.GREEN_ZONE_LABEL, + settings.CORE_ZONE_LABEL, + source_bucket, + destination_bucket, + set(include_ids[0].split(',')), + ) + + traverser = Traverser(copy_preparation_manager) + traverser.traverse_tree(source_folder, destination_folder) + registered_file_nodes = {} + + loop = asyncio.get_event_loop() + project = loop.run_until_complete(metadata_service_client.get_project_by_code(project_code)) + + try: + dataops_client.lock_resources(copy_preparation_manager.read_lock_paths, ResourceLockOperation.READ) + register_file_nodes = copy_preparation_manager.register_file_nodes + registered_file_nodes = metadata_service_client.register_nodes(register_file_nodes, project_code, timestamp) + source_file_node = copy_preparation_manager.source_file_node + source_folder_nodes = copy_preparation_manager.source_folder_nodes + + operation_type = 'copy' + + system_tags = [settings.COPIED_WITH_APPROVAL_TAG] + copy_manager = CopyManager( + metadata_service_client, + dataops_client, + approval_service_client, + approved_entities, + system_tags, + project, + operator, + minio_client, + operation_type, + ) + copy_manager.process_files(registered_file_nodes, source_file_node) + copy_manager.process_folders(source_folder_nodes) + finally: + dataops_client.unlock_resources(copy_preparation_manager.read_lock_paths, ResourceLockOperation.READ) + metadata_service_client.remove_registrated_nodes(registered_file_nodes) + + dataops_client.update_job( + session_id=session_id, + job_id=job_id, + target_names=target_names, + target_type=target_type, + container_code=project_code, + action_type='data_transfer', + status=JobStatus.SUCCEED, + ) + notification_client.send_notifications() + click.echo('Copy operation has been finished successfully.') + except Exception as e: + click.echo(f'Exception occurred while performing copy operation:{e}') + try: + notification_client.set_status(PipelineStatus.FAILURE) + notification_client.send_notifications() + dataops_client.update_job( + session_id=session_id, + job_id=job_id, + target_names=target_names, + target_type=target_type, + container_code=project_code, + action_type='data_transfer', + status=JobStatus.FAILED, + ) + except Exception as e: + click.echo(f'Update job error: {e}') + exit(1) diff --git a/filecopy/operations/commands/delete.py b/filecopy/operations/commands/delete.py new file mode 100644 index 0000000..45f4448 --- /dev/null +++ b/filecopy/operations/commands/delete.py @@ -0,0 +1,166 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import asyncio +import atexit +from pathlib import Path + +import click +from common import ProjectClient +from operations.config import get_settings +from operations.kafka_producer import KafkaProducer +from operations.managers import DeleteManager +from operations.managers import DeletePreparationManager +from operations.minio_boto3_client import MinioBoto3Client +from operations.models import ZoneType +from operations.services.dataops.client import DataopsServiceClient +from operations.services.dataops.client import JobStatus +from operations.services.dataops.client import ResourceLockOperation +from operations.services.metadata.client import MetadataServiceClient +from operations.services.notification.client import NotificationServiceClient +from operations.services.notification.models import NotificationType +from operations.services.notification.models import PipelineAction +from operations.services.notification.models import PipelineStatus +from operations.traverser import Traverser + +atexit.register(KafkaProducer.close_connection) + + +@click.command() +@click.option('--source-id', type=str, required=True) +@click.option('--include-ids', type=str, multiple=True) +@click.option('--job-id', type=str, required=True) +@click.option('--session-id', type=str, required=True) +@click.option('--project-code', type=str, required=True) +@click.option('--operator', type=str, required=True) +@click.option('--access-token', type=str, required=True) +def delete( + source_id: str, + include_ids: tuple[str], + job_id: str, + session_id: str, + project_code: str, + operator: str, + access_token: str, +): + """Move files from source geid into trash bin.""" + + click.echo(f'Starting delete process from "{source_id} including only "{set(include_ids)}".') + + settings = get_settings() + + project_client = ProjectClient(settings.PROJECT_SERVICE, settings.REDIS_URL) + + metadata_service_client = MetadataServiceClient( + settings.METADATA_SERVICE, + settings.S3_URL, + settings.CORE_ZONE_LABEL, + settings.TEMP_DIR, + project_client, + access_token, + ) + dataops_client = DataopsServiceClient(settings.DATAOPS_SERVICE) + + minio_client = MinioBoto3Client( + settings.S3_ACCESS_KEY, settings.S3_SECRET_KEY, settings.S3_URL, settings.S3_INTERNAL_HTTPS + ) + + loop = asyncio.get_event_loop() + loop.run_until_complete(KafkaProducer.init_connection()) + + # TODO: This sprint assume metadata service can always get info, + # Next sprint edit notification service client - https://indocconsortium.atlassian.net/browse/PILOT-1830 + source_folder = metadata_service_client.get_item_by_id(source_id) + destination_folder = Path() + include_nodes = metadata_service_client.get_items_by_ids(include_ids[0].split(',')) + target_names = [f'{item["parent_path"]}/{item["name"]}' for item in include_nodes.values()] + target_type = 'batch' if len(target_names) > 1 else next(iter(include_nodes.values()))['type'] + notification_client = NotificationServiceClient( + settings.NOTIFICATION_SERVICE, + include_nodes, + source_folder, + None, + project_code, + PipelineAction.DELETE, + PipelineStatus.SUCCESS, + operator, + NotificationType.PIPELINE, + ) + + try: + source_zone = settings.GREEN_ZONE_LABEL + source_bucket = Path(f'gr-{project_code}') + if source_folder['zone'] == ZoneType.CORE: + source_zone = settings.CORE_ZONE_LABEL + source_bucket = Path(f'core-{project_code}') + + delete_preparation_manager = DeletePreparationManager( + metadata_service_client, + project_code, + source_zone, + source_bucket, + set(include_ids[0].split(',')), + ) + traverser = Traverser(delete_preparation_manager) + traverser.traverse_tree(source_folder, destination_folder) + + loop = asyncio.get_event_loop() + project = loop.run_until_complete(metadata_service_client.get_project_by_code(project_code)) + + try: + dataops_client.lock_resources(delete_preparation_manager.write_lock_paths, ResourceLockOperation.WRITE) + + pipeline_name = 'data_delete_folder' + pipeline_desc = 'the script will delete the folder in greenroom/core recursively' + operation_type = 'delete' + + delete_manager = DeleteManager( + metadata_service_client, + dataops_client, + project, + operator, + minio_client, + settings.CORE_ZONE_LABEL, + settings.GREEN_ZONE_LABEL, + pipeline_name, + pipeline_desc, + operation_type, + set(include_ids[0].split(',')), + ) + + delete_manager.archive_nodes() + + finally: + dataops_client.unlock_resources(delete_preparation_manager.write_lock_paths, ResourceLockOperation.WRITE) + + dataops_client.update_job( + session_id=session_id, + job_id=job_id, + target_names=target_names, + target_type=target_type, + container_code=project_code, + action_type='data_delete', + status=JobStatus.SUCCEED, + ) + notification_client.send_notifications() + click.echo('Delete operation has been finished successfully.') + except Exception as e: + click.echo(f'An exception occurred while performing delete operation: {e}') + try: + notification_client.set_status(PipelineStatus.FAILURE) + notification_client.send_notifications() + dataops_client.update_job( + session_id=session_id, + job_id=job_id, + target_names=target_names, + target_type=target_type, + container_code=project_code, + action_type='data_delete', + status=JobStatus.FAILED, + ) + except Exception as e: + click.echo(f'Update job error: {e}') + exit(1) diff --git a/filecopy/operations/config.py b/filecopy/operations/config.py new file mode 100644 index 0000000..a5c9c85 --- /dev/null +++ b/filecopy/operations/config.py @@ -0,0 +1,95 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import logging +from functools import lru_cache +from typing import Any +from typing import Dict +from typing import Optional + +from common import VaultClient +from pydantic import BaseSettings +from pydantic import Extra + + +class VaultConfig(BaseSettings): + """Store vault related configuration.""" + + APP_NAME: str = 'pipelines' + CONFIG_CENTER_ENABLED: bool = False + + VAULT_URL: Optional[str] + VAULT_CRT: Optional[str] + VAULT_TOKEN: Optional[str] + + class Config: + env_file = '.env' + env_file_encoding = 'utf-8' + + +def load_vault_settings(settings: BaseSettings) -> Dict[str, Any]: + config = VaultConfig() + + if not config.CONFIG_CENTER_ENABLED: + return {} + + client = VaultClient(config.VAULT_URL, config.VAULT_CRT, config.VAULT_TOKEN) + return client.get_from_vault(config.APP_NAME) + + +class Settings(BaseSettings): + """Store service configuration settings.""" + + APP_NAME: str = 'pipelines' + + LOGGING_LEVEL: int = logging.INFO + LOGGING_FORMAT: str = 'json' + + S3_HOST: str = '' + S3_PORT: int = 9000 + S3_INTERNAL_HTTPS: bool = False + S3_ACCESS_KEY: str = 'ACCESSKEY/CENLISDWYLOSADDFGMWZ' + S3_SECRET_KEY: str = 'SECRETKEY/DTRBFII/NJXVSJPLZMGPPVLELR' + S3_URL: str = '' + + DATAOPS_SERVICE: str = 'http://127.0.0.1:5063' + METADATA_SERVICE: str = 'http://127.0.0.1:5066' + PROJECT_SERVICE: str = 'http://127.0.0.1:5064' + APPROVAL_SERVICE: str = 'http://127.0.0.1:8000' + NOTIFICATION_SERVICE: str = 'http://127.0.0.1:5065' + + GREEN_ZONE_LABEL: str = 'Greenroom' + CORE_ZONE_LABEL: str = 'Core' + + TEMP_DIR: str = './filecopy' + COPIED_WITH_APPROVAL_TAG: str = 'copied-to-core' + REDIS_USER: str = 'default' + REDIS_PASSWORD: str = '' + REDIS_HOST: str = '127.0.0.1' + REDIS_PORT: int = 6379 + REDIS_URL: str = '' + KAFKA_URL: str = '' + + def __init__(self, *args: Any, **kwds: Any) -> None: + super().__init__(*args, **kwds) + + self.REDIS_URL = f'redis://{self.REDIS_USER}:{self.REDIS_PASSWORD}@{self.REDIS_HOST}:{self.REDIS_PORT}' + self.S3_URL = f'{self.S3_HOST}:{self.S3_PORT}' + + class Config: + env_file = '.env' + env_file_encoding = 'utf-8' + extra = Extra.ignore + + @classmethod + def customise_sources(cls, init_settings, env_settings, file_secret_settings): + return init_settings, env_settings, load_vault_settings, file_secret_settings + + +@lru_cache(1) +def get_settings() -> Settings: + settings = Settings() + return settings diff --git a/filecopy/operations/duplicated_file_names.py b/filecopy/operations/duplicated_file_names.py new file mode 100644 index 0000000..12fd1fd --- /dev/null +++ b/filecopy/operations/duplicated_file_names.py @@ -0,0 +1,49 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from pathlib import Path +from typing import Optional +from typing import Union + +from operations.models import append_suffix_to_filepath +from operations.models import get_timestamp + + +class DuplicatedFileNames: + """Store information about source files that already exist at destination. + + File path should be used without the bucket name. + Use: 'admin/folder/file.txt' + Do not use: 'gr-project-code/admin/folder/file.txt' + """ + + def __init__(self) -> None: + self.filename_timestamp = get_timestamp() + self.files = {} + + def __str__(self) -> str: + return f'Count: {len(self.files)}' + + def add(self, filepath: Union[Path, str]) -> str: + """Store information about duplicated file and return new filename that should be used.""" + + path = Path(filepath) + + self.files[path] = append_suffix_to_filepath(path.name, self.filename_timestamp) + + return self.files[path] + + def get(self, filepath: Union[Path, str], default: Optional[str] = '') -> str: + """Return filename by filepath if it exists or return default value.""" + + path = Path(filepath) + + try: + return self.files[path] + except KeyError: + pass + + return default diff --git a/filecopy/operations/item_activity_schema.avsc b/filecopy/operations/item_activity_schema.avsc new file mode 100644 index 0000000..ef4b803 --- /dev/null +++ b/filecopy/operations/item_activity_schema.avsc @@ -0,0 +1,56 @@ +{ + "type": "record", + "name": "Activity", + "namespace": "metadata.items", + "fields": [ + { + "name": "item_id", + "type": ["null", { + "type": "string", + "logicalType": "uuid" + }] + }, { + "name": "item_name", + "type": "string" + }, { + "name": "item_type", + "type": "string" + }, { + "name": "item_parent_path", + "type": "string" + }, { + "name": "container_code", + "type": "string" + }, { + "name": "container_type", + "type": "string" + }, { + "name": "zone", + "type": "int" + }, { + "name": "user", + "type": "string" + }, { + "name": "imported_from", + "type": ["string", "null"] + }, { + "name": "activity_type", + "type": "string" + }, { + "name": "activity_time", + "type": { + "type": "long", + "logicalType": "timestamp-millis" + } + }, { + "name": "changes", + "type": { + "type": "array", + "items": { + "type": "map", + "values": "string" + } + } + } + ] +} diff --git a/filecopy/operations/kafka_producer.py b/filecopy/operations/kafka_producer.py new file mode 100644 index 0000000..ae23e2e --- /dev/null +++ b/filecopy/operations/kafka_producer.py @@ -0,0 +1,89 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import asyncio +import io +from datetime import datetime +from typing import Optional + +from aiokafka import AIOKafkaProducer +from fastavro import schema +from fastavro import schemaless_writer +from operations.config import get_settings +from operations.logger import logger +from operations.models import Node + +ConfigClass = get_settings() + + +class KafkaProducer: + endpoint = ConfigClass.KAFKA_URL + topic = 'metadata.items.activity' + schema = 'operations/item_activity_schema.avsc' + producer = None + + @classmethod + async def init_connection(self): + if self.producer is None: + logger.info('Initializing the kafka producer') + self.producer = AIOKafkaProducer(bootstrap_servers=self.endpoint, enable_idempotence=True) + try: + # Get cluster layout and initial topic/partition leadership information + await self.producer.start() + except Exception as e: + logger.error(f'Fail to start kafka producer:{str(e)}') + raise e + + @classmethod + def close_connection(self) -> None: + if self.producer is not None: + logger.info('Closing the kafka producer') + loop = asyncio.get_event_loop() + loop.run_until_complete(self.producer.stop()) + + @classmethod + async def create_file_operation_logs( + self, input_file: Node, operation_type: str, operator: str, output_file: Optional[Node] + ): + message = { + 'activity_type': operation_type, + 'activity_time': datetime.utcnow(), + 'item_id': input_file.id, + 'item_type': input_file.get('type'), + 'item_name': input_file.name, + 'item_parent_path': ('' if input_file.parent_path is None else input_file.parent_path), + 'container_code': input_file.get('container_code'), + 'container_type': input_file.get('container_type'), + 'zone': input_file.get('zone'), + 'user': operator, + 'imported_from': '', + 'changes': [], + } + if operation_type == 'delete': + message['item_parent_path'] = input_file.restore_path + + if operation_type == 'copy': + message['changes'] = [ + { + 'item_property': 'path', + 'old_value': str(input_file.display_path), + 'new_value': str(output_file.display_path), + }, + {'item_property': 'id', 'old_value': input_file.id, 'new_value': output_file.id}, + ] + try: + # Validate message + bio = io.BytesIO() + SCHEMA = schema.load_schema(self.schema) + schemaless_writer(bio, SCHEMA, message) + + validated_message = bio.getvalue() + + # Send message to kafka + await self.producer.send_and_wait(self.topic, validated_message) + except Exception as e: + logger.error(f'Fail to send message:{str(e)}') + raise Exception(f'Error when validate and send message to kafka producer: {e}') diff --git a/filecopy/operations/logger.py b/filecopy/operations/logger.py new file mode 100644 index 0000000..02c722b --- /dev/null +++ b/filecopy/operations/logger.py @@ -0,0 +1,16 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import logging + +from common import configure_logging +from operations.config import get_settings + +settings = get_settings() + +logger = logging.getLogger('pilot.pipelines') + +configure_logging(settings.LOGGING_LEVEL, settings.LOGGING_FORMAT) diff --git a/filecopy/operations/managers.py b/filecopy/operations/managers.py new file mode 100644 index 0000000..4dc440e --- /dev/null +++ b/filecopy/operations/managers.py @@ -0,0 +1,373 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import asyncio +import os +from pathlib import Path +from typing import Dict +from typing import List +from typing import Optional +from typing import Set +from typing import Union + +from operations.duplicated_file_names import DuplicatedFileNames +from operations.kafka_producer import KafkaProducer +from operations.logger import logger +from operations.minio_boto3_client import MinioBoto3Client +from operations.models import ItemStatus +from operations.models import Node +from operations.models import NodeList +from operations.models import NodeToRegister +from operations.models import ResourceType +from operations.models import get_timestamp +from operations.services.approval.client import ApprovalServiceClient +from operations.services.dataops.client import DataopsServiceClient +from operations.services.metadata.client import MetadataServiceClient +from operations.services.redis.client import RedisClient + + +class NodeManager: + """Base class for node manipulations that is used in the Traverser.""" + + def __init__(self, metadata_service_client: MetadataServiceClient) -> None: + self.metadata_service_client = metadata_service_client + + def get_tree(self, source_folder: Node) -> NodeList: + """Return child nodes from current source folder.""" + nodes = self.metadata_service_client.get_nodes_tree(source_folder.id, False) + return nodes + + def exclude_nodes(self, nodes: NodeList) -> Set[str]: + """Return set of ids that should be excluded when copying from this source folder.""" + + return set() + + def process_file(self, source_file: Node, destination_folder: Union[Path, Node]) -> None: + """Process one file.""" + + raise NotImplementedError + + def process_folder(self, source_folder: Node, destination_parent_folder: Union[Path, Node]) -> Union[Path, Node]: + """Process one folder.""" + + raise NotImplementedError + + +class BaseCopyManager(NodeManager): + """Base manager for copying process with approved entities.""" + + def __init__( + self, + metadata_service_client: MetadataServiceClient, + approval_service_client: Optional[ApprovalServiceClient], + approved_entities: Optional[List[str]], + include_ids: Optional[Set[str]], + ) -> None: + super().__init__(metadata_service_client) + + self.approval_service_client = approval_service_client + self.approved_entities = approved_entities + self.include_ids = include_ids + + def _is_node_approved(self, node: Node) -> bool: + """Check if node geid is in a list of approved entities. + + If approved entities are not set then node is considered approved. + """ + + if self.approved_entities is None: + return True + + return node.id in self.approved_entities + + def exclude_nodes(self, nodes: NodeList) -> Set[str]: + """Return set of geids that should be excluded when copying from this source folder.""" + if self.approved_entities is not None: + excluded_geids = nodes.ids.difference(self.approved_entities) + return excluded_geids + + if self.include_ids is None: + return set() + + if not self.include_ids.issubset(nodes.ids): + return set() + excluded_geids = nodes.ids.difference(self.include_ids) + + return excluded_geids + + def process_file(self, source_file: Node, destination_folder: Union[Path, Node]) -> None: + """Process one file.""" + + raise NotImplementedError + + def process_folder(self, source_folder: Node, destination_parent_folder: Union[Path, Node]) -> Union[Path, Node]: + """Process one folder.""" + + raise NotImplementedError + + +class CopyManager: + """Manager to copying files.""" + + def __init__( + self, + metadata_service_client: MetadataServiceClient, + dataops_client: DataopsServiceClient, + approval_service_client: Optional[ApprovalServiceClient], + approved_entities: List[str], + system_tags: List[str], + project: Node, + operator: str, + minio_client: MinioBoto3Client, + operation_type: str, + ) -> None: + + self.metadata_service_client = metadata_service_client + self.approval_service_client = approval_service_client + self.approved_entities = approved_entities + + self.dataops_client = dataops_client + self.system_tags = system_tags + self.project_code = project['code'] + self.operator = operator + self.minio_client = minio_client + self.operation_type = operation_type + + def _create_file_metadata(self, source_node: Node, target_node: Node, new_node_version_id: str) -> None: + self._copy_zip_preview_info(source_node.id, target_node.id) + + update_json = { + 'system_tags': self.system_tags, + 'version': new_node_version_id, + } + self.metadata_service_client.update_node(source_node, update_json) + + loop = asyncio.get_event_loop() + loop.run_until_complete( + KafkaProducer.create_file_operation_logs(source_node, self.operation_type, self.operator, target_node) + ) + + def _copy_zip_preview_info(self, old_geid, new_geid) -> None: + """Transfer the saved preview info to copied one.""" + + response = self.dataops_client.get_zip_preview(old_geid) + if response is None: + return + + self.dataops_client.create_zip_preview(new_geid, response['archive_preview']) + + def _update_approval_entity_copy_status_for_node(self, node: Node) -> None: + """Update copy status field for approval entity related to node.""" + if not self.approval_service_client: + return + + if not self.approved_entities: + return + + self.approval_service_client.update_copy_status(node.id) + + def _process_file(self, source_file: Node, destination_file: Node) -> Node: + + logger.info(f'Processing source file "{source_file}" against destination file "{destination_file}".') + + # TODO: Need to refactory the minio copy here: + # https://indocconsortium.atlassian.net/browse/PILOT-2501 + node, version_id = self.metadata_service_client.update_copied_file_node( + self.project_code, + destination_file, + self.system_tags, + source_file, + self.minio_client, + ) + + self._create_file_metadata(source_file, node, version_id) + + self._update_approval_entity_copy_status_for_node(source_file) + return node + + def process_files(self, registered_file_nodes: Dict[str, Node], source_file_node: Dict[str, Node]) -> None: + for item in registered_file_nodes: + updated_node = self._process_file(source_file_node[item], registered_file_nodes[item]) + registered_file_nodes[item] = updated_node + + def process_folders(self, source_folders: Dict[str, Node]) -> None: + update_json = {'system_tags': self.system_tags} + for _, item in source_folders.items(): + self.metadata_service_client.update_node(item, update_json) + + +class CopyPreparationManager(BaseCopyManager): + """Manager to prepare data before start of copying process.""" + + def __init__( + self, + metadata_service_client: MetadataServiceClient, + approval_service_client: Optional[ApprovalServiceClient], + approved_entities: List[str], + project_code: str, + source_zone: str, + destination_zone: str, + source_bucket: Path, + destination_bucket: Path, + include_geids: Optional[Set[str]], + ) -> None: + super().__init__(metadata_service_client, approval_service_client, approved_entities, include_geids) + + self.project_code = project_code + self.source_zone = source_zone + self.destination_zone = destination_zone + self.source_bucket = source_bucket + self.destination_bucket = destination_bucket + self.register_file_nodes = [] + self.source_file_node = {} + self.source_folder_nodes = {} + self.read_lock_paths = [] + + def process_file(self, source_file: Node, destination_folder: Node) -> None: + if not self._is_node_approved(source_file): + return + + logger.info(f'Processing source file "{source_file}" against destination path "{destination_folder}".') + source_filepath = self.source_bucket / source_file.display_path + + self.read_lock_paths.append(source_filepath) + + self.register_file_nodes.append(NodeToRegister(source_file, destination_folder)) + self.source_file_node[source_file.id] = source_file + + def process_folder(self, source_folder: Node, destination_parent: Node) -> Node: + logger.info( + f'Processing source folder "{source_folder}" ' f'against destination parent path "{destination_parent}".' + ) + source_path = self.source_bucket / source_folder.display_path + node = self.metadata_service_client.register_node( + self.project_code, source_folder, destination_parent, ResourceType.FOLDER, ItemStatus.ACTIVE, None + ) + self.source_folder_nodes[source_folder.id] = source_folder + self.read_lock_paths.append(source_path) + return node + + +class DeleteManager(NodeManager): + """Manager to deleting files.""" + + def __init__( + self, + metadata_service_client: MetadataServiceClient, + dataops_client: DataopsServiceClient, + project: Node, + operator: str, + minio_client: MinioBoto3Client, + core_zone_label: str, + green_zone_label: str, + pipeline_name: str, + pipeline_desc: str, + operation_type: str, + include_geids: Optional[Set[str]], + ) -> None: + super().__init__(metadata_service_client) + + self.dataops_client = dataops_client + + self.removal_timestamp = get_timestamp() + self.project_code = project['code'] + self.operator = operator + self.minio_client = minio_client + self.core_zone_label = core_zone_label + self.green_zone_label = green_zone_label + self.pipeline_name = pipeline_name + self.pipeline_desc = pipeline_desc + self.operation_type = operation_type + self.include_geids = include_geids + + self.redis_client = RedisClient() + + def exclude_nodes(self, nodes: NodeList) -> Set[str]: + if self.include_geids is None: + return set() + + if not self.include_geids.issubset(nodes.ids): + return set() + + excluded_geids = nodes.ids.difference(self.include_geids) + + return excluded_geids + + def process_file(self, source_file: Node, destination_folder: Node) -> None: + logger.info(f'Processing source file "{source_file}" against destination folder "{destination_folder}".') + + def process_folder(self, source_folder: Node, destination_parent_folder: Node) -> Node: + logger.info( + f'Processing source folder "{source_folder}" ' + f'against destination parent folder "{destination_parent_folder}".' + ) + + def archive_nodes(self) -> None: + for node_id in self.include_geids: + logger.info(f'Move the node "{node_id}" into trashbin recursively') + node = self.metadata_service_client.get_item_by_id(node_id) + self.metadata_service_client.archived_node(node, self.minio_client, self.operation_type, self.operator) + + # also remove the it from upload cache if it exists + # so the key will be // + # please make sure it is same in upload service + bucket_prefix = {1: 'core'}.get(node.zone, 'greenroom') + obj_path = os.path.join(bucket_prefix, node.container_code, node.parent_path, node.name) + + if self.redis_client.check_by_key(obj_path): + self.redis_client.delete_by_key(obj_path) + + +class DeletePreparationManager(NodeManager): + """Manager to prepare data before start of deleting process.""" + + def __init__( + self, + metadata_service_client: MetadataServiceClient, + project_code: str, + source_zone: str, + source_bucket: Path, + include_geids: Optional[Set[str]], + ) -> None: + super().__init__(metadata_service_client) + + self.project_code = project_code + self.source_zone = source_zone + self.source_bucket = source_bucket + self.include_geids = include_geids + + self.duplicated_files = DuplicatedFileNames() + self.write_lock_paths = [] + + def exclude_nodes(self, nodes: NodeList) -> Set[str]: + if self.include_geids is None: + return set() + + if not self.include_geids.issubset(nodes.ids): + return set() + + excluded_geids = nodes.ids.difference(self.include_geids) + + return excluded_geids + + def process_file(self, source_file: Node, destination_path: Path) -> None: + logger.info(f'Processing source file "{source_file}" against destination path "{destination_path}".') + + source_filepath = self.source_bucket / source_file.display_path + + self.write_lock_paths.append(source_filepath) + + def process_folder(self, source_folder: Node, destination_parent_path: Path) -> Path: + logger.info( + f'Processing source folder "{source_folder}" ' + f'against destination parent path "{destination_parent_path}".' + ) + + source_path = self.source_bucket / source_folder.display_path + + self.write_lock_paths.append(source_path) + + return destination_parent_path diff --git a/filecopy/operations/minio_boto3_client.py b/filecopy/operations/minio_boto3_client.py new file mode 100644 index 0000000..dabe7e8 --- /dev/null +++ b/filecopy/operations/minio_boto3_client.py @@ -0,0 +1,76 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import asyncio +import math +import os +import shutil + +from common.object_storage_adaptor.boto3_client import Boto3Client +from common.object_storage_adaptor.boto3_client import get_boto3_client +from operations.logger import logger + + +class MinioBoto3Client: + def __init__(self, access_key: str, secret_key: str, minio_endpoint: str, minio_https: bool) -> None: + self.minio_access_key = access_key + self.minio_secret_key = secret_key + self.minio_endpoint = minio_endpoint + self.minio_https = minio_https + self.client = self.connect_to_minio() + + def connect_to_minio(self) -> Boto3Client: + loop = asyncio.get_event_loop() + boto3_client = loop.run_until_complete( + get_boto3_client( + self.minio_endpoint, + access_key=self.minio_access_key, + secret_key=self.minio_secret_key, + https=self.minio_https, + ) + ) + return boto3_client + + async def download_object(self, src_bucket, src_path, temp_file_path): + await self.client.download_object(src_bucket, src_path, temp_file_path) + + async def copy_object(self, dest_bucket, dest_path, source_bucket, source_path): + result = await self.client.copy_object(source_bucket, source_path, dest_bucket, dest_path) + return result + + async def upload_object(self, bucket, object_name, file_path, temp_path): + # Here get the total size of the size and set up the max size of each chunk + try: + max_size = 5 * 1024 * 1024 + size = os.path.getsize(file_path) + logger.info(f'File total size is {size}') + total_parts = math.ceil(size / max_size) + + # Get upload id from upload pre + upload_id_list = await self.client.prepare_multipart_upload(bucket, [object_name]) + upload_id = upload_id_list[0] + logger.info(f'The upload id is {upload_id}') + parts = [] + with open(file_path, 'rb') as f: + for part_number in range(total_parts): + # Cut file into chunks and upload the chunk + file_data = f.read(max_size) + chunk_result = await self.client.part_upload( + bucket, object_name, upload_id, part_number + 1, file_data + ) + parts.append(chunk_result) + logger.info(f'Chunk upload result {chunk_result}') + res = await self.client.combine_chunks(bucket, object_name, upload_id, parts) + logger.info(f'Finalize the large file upload with version is {res}') + except Exception: + raise Exception('File upload failed') + finally: + shutil.rmtree(temp_path) + return res + + async def remove_object(self, src_bucket, src_obj_path): + result = await self.client.delete_object(src_bucket, src_obj_path) + return result diff --git a/filecopy/operations/models.py b/filecopy/operations/models.py new file mode 100644 index 0000000..eee2d5a --- /dev/null +++ b/filecopy/operations/models.py @@ -0,0 +1,181 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import time +from enum import Enum +from enum import unique +from pathlib import Path +from typing import Any +from typing import Dict +from typing import List +from typing import Set +from typing import Union + + +def get_timestamp() -> int: + """Return current timestamp.""" + + return round(time.time()) + + +def append_suffix_to_filepath(filename: str, suffix: Union[str, int], separator: str = '_') -> str: + """Append suffix to filepath before extension.""" + + path = Path(filename) + + current_extension = ''.join(path.suffixes) + new_extension = f'{separator}{suffix}{current_extension}' + + filename_parts = [path.name, ''] + if current_extension: + filename_parts = path.name.rsplit(current_extension, 1) + + filename = new_extension.join(filename_parts) + + filepath = str(path.parent / filename) + + return filepath + + +@unique +class ResourceType(str, Enum): + """Store all possible types of resources.""" + + FOLDER = 'folder' + FILE = 'file' + CONTAINER = 'Container' + + +@unique +class ZoneType(str, Enum): + GREENROOM = 0 + CORE = 1 + + +@unique +class ItemStatus(str, Enum): + # the new enum type for file status + # - REGISTERED means file is created by upload service + # but not complete yet. either in progress or fail. + # - ACTIVE means file uploading is complete. + # - ARCHIVED means the file has been deleted + + REGISTERED = 'REGISTERED' + ACTIVE = 'ACTIVE' + ARCHIVED = 'ARCHIVED' + + +class Node(dict): + """Store information about one node.""" + + def __str__(self) -> str: + return f'{self.id} | {self.name}' + + def __dict__(self) -> Dict[str, Any]: + return self + + @property + def parent(self) -> str: + return self['parent'] + + @property + def parent_path(self) -> str: + return self['parent_path'] + + @property + def id(self) -> str: + return self['id'] + + @property + def is_folder(self) -> bool: + return ResourceType.FOLDER == self['type'] + + @property + def is_file(self) -> bool: + return ResourceType.FILE == self['type'] + + @property + def is_archived(self) -> bool: + return ItemStatus.ARCHIVED == self['status'] + + @property + def status(self) -> ItemStatus: + return ItemStatus(self['status']) + + @property + def name(self) -> str: + return self['name'] + + @property + def tags(self) -> List[str]: + return self['extended']['extra']['tags'] + + @property + def size(self) -> int: + return self.get('size', 0) + + @property + def container_code(self) -> str: + return self.get('container_code') + + @property + def owner(self) -> str: + return self.get('owner') + + @property + def namespace(self) -> str: + result = {1: 'Core'}.get(self.get('zone'), 'Greenroom') + return result + + @property + def zone(self) -> int: + return self.get('zone') + + @property + def entity_type(self) -> str: + return self.get('type') + + @property + def restore_path(self) -> str: + return self.get('restore_path', '') + + @property + def display_path(self) -> Path: + if self['parent_path']: + full_path = f'{self["parent_path"]}/{self["name"]}' + else: + full_path = self['name'] + display_path = Path(full_path) + + if display_path.is_absolute(): + display_path = display_path.relative_to('/') + + return display_path + + def get_attributes(self) -> Dict[str, Any]: + return self['extended']['extra'].get('attributes', {}) + + +class NodeList(list): + """Store list of Nodes.""" + + def __init__(self, nodes: List[Dict[str, Any]]) -> None: + super().__init__([Node(node) for node in nodes]) + + @property + def ids(self) -> Set[str]: + return {node.id for node in self} + + def filter_files(self) -> 'NodeList': + return NodeList([node for node in self if node.is_file]) + + +class NodeToRegister: + """Object to store the registered nodes info.""" + + def __init__(self, source_node: Node, destination_node: Node) -> None: + self.source_node = source_node + self.destination_node = destination_node diff --git a/filecopy/operations/services/__init__.py b/filecopy/operations/services/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/operations/services/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/operations/services/approval/__init__.py b/filecopy/operations/services/approval/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/operations/services/approval/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/operations/services/approval/client.py b/filecopy/operations/services/approval/client.py new file mode 100644 index 0000000..0551e59 --- /dev/null +++ b/filecopy/operations/services/approval/client.py @@ -0,0 +1,30 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from typing import Any +from typing import Dict +from typing import List + +from requests import Session + + +class ApprovalServiceClient: + """Get information about approval request or entities for copy request.""" + + def __init__(self, endpoint: str, request_id: str) -> None: + self.endpoint = f'{endpoint}/v1' + self.request_id = request_id + self.client = Session() + + def update_copy_status(self, entity_id: str) -> List[Dict[str, Any]]: + """Update copy status field for approval entity.""" + payload = {'entities': [entity_id], 'copy_status': 'copied'} + response = self.client.put(f'{self.endpoint}/request/{self.request_id}/copy-status', json=payload) + if response.status_code == 200 and len(response.json()['result']) == 0: + raise Exception(f'Unable to update copy status for {entity_id}, entity is not found.') + if response.status_code != 200: + raise Exception(f'Unable to update copy status for {entity_id}') + return response.json()['result'] diff --git a/filecopy/operations/services/dataops/__init__.py b/filecopy/operations/services/dataops/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/operations/services/dataops/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/operations/services/dataops/client.py b/filecopy/operations/services/dataops/client.py new file mode 100644 index 0000000..a26a635 --- /dev/null +++ b/filecopy/operations/services/dataops/client.py @@ -0,0 +1,153 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from enum import Enum +from enum import unique +from pathlib import Path +from typing import Any +from typing import Dict +from typing import List +from typing import Optional + +from operations.logger import logger +from requests import Session + + +@unique +class ResourceLockOperation(str, Enum): + READ = 'read' + WRITE = 'write' + + class Config: + use_enum_values = True + + +@unique +class JobStatus(str, Enum): + SUCCEED = 'SUCCEED' + FAILED = 'FAILED' + + class Config: + use_enum_values = True + + +class DataopsServiceClient: + def __init__(self, endpoint: str) -> None: + self.endpoint_v1 = f'{endpoint}/v1' + self.endpoint_v2 = f'{endpoint}/v2' + self.client = Session() + + def lock_resources(self, resource_keys: List[Path], operation: ResourceLockOperation) -> Dict[str, Any]: + resource_keys = list(map(str, resource_keys)) + + logger.info(f'Performing "{operation}" lock for resource keys: {resource_keys}.') + response = self.client.post( + f'{self.endpoint_v2}/resource/lock/bulk', + json={ + 'resource_keys': resource_keys, + 'operation': operation, + }, + ) + + if response.status_code != 200: + message = f'Unable to lock resource keys: {resource_keys}.' + logger.info(message) + raise Exception(message) + + logger.info(f'Successfully "{operation}" locked resource keys: {resource_keys}.') + return response.json() + + def unlock_resources(self, resource_keys: List[Path], operation: ResourceLockOperation) -> Dict[str, Any]: + resource_keys = list(map(str, resource_keys)) + + logger.info(f'Performing "{operation}" unlock for resource keys: {resource_keys}.') + response = self.client.delete( + f'{self.endpoint_v2}/resource/lock/bulk', + json={ + 'resource_keys': resource_keys, + 'operation': operation, + }, + ) + + if response.status_code not in (200, 400): + message = f'Unable to unlock resource keys: {resource_keys}.' + logger.info(message) + raise Exception(message) + + logger.info(f'Successfully "{operation}" unlocked resource keys: {resource_keys}.') + return response.json() + + def update_job( + self, + session_id: str, + job_id: str, + target_names: list, + target_type: list, + container_code: str, + action_type: str, + status: JobStatus, + ) -> Dict[str, Any]: + """Create task-stream record for updated job status.""" + response = self.client.post( + f'{self.endpoint_v1}/task-stream/', + json={ + 'session_id': session_id, + 'target_names': target_names, + 'target_type': target_type, + 'container_code': container_code, + 'container_type': 'project', + 'action_type': action_type, + 'job_id': job_id, + 'status': status.name, + }, + ) + + if response.status_code != 200: + logger.error( + f'Unexpected status code received while updating job"{job_id}" Received response: "{response.text}".' + ) + raise Exception(f'Unable to update job "{job_id}".') + + return response.json() + + def get_zip_preview(self, file_geid: str) -> Optional[Dict[str, Any]]: + response = self.client.get( + f'{self.endpoint_v1}/archive', + params={ + 'file_id': file_geid, + }, + ) + if response.status_code == 404: + return None + + if response.status_code != 200: + logger.error( + 'Unexpected status code received while getting zip preview ' + f'for geid "{file_geid}". ' + f'Received response: "{response.text}".' + ) + raise Exception(f'Unable to get zip preview for id "{file_geid}".') + + return response.json() + + def create_zip_preview(self, file_id: str, archive_preview: Dict[str, Any]) -> Dict[str, Any]: + response = self.client.post( + f'{self.endpoint_v1}/archive', + json={ + 'file_id': file_id, + 'archive_preview': archive_preview, + }, + ) + + if response.status_code != 200: + logger.error( + 'Unexpected status code received while creating zip ' + f'preview for geid "{file_id}". ' + f'Received response: "{response.text}".' + ) + raise Exception(f'Unable to create zip preview for id "{file_id}".') + + return response.json() diff --git a/filecopy/operations/services/metadata/__init__.py b/filecopy/operations/services/metadata/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/operations/services/metadata/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/operations/services/metadata/client.py b/filecopy/operations/services/metadata/client.py new file mode 100644 index 0000000..14877fc --- /dev/null +++ b/filecopy/operations/services/metadata/client.py @@ -0,0 +1,308 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import asyncio +import time +from typing import Any +from typing import Dict +from typing import List +from typing import Optional +from typing import Tuple + +from common import ProjectClient +from common import ProjectException +from operations.kafka_producer import KafkaProducer +from operations.logger import logger +from operations.minio_boto3_client import MinioBoto3Client +from operations.models import ItemStatus +from operations.models import Node +from operations.models import NodeList +from operations.models import NodeToRegister +from operations.models import ResourceType +from operations.models import ZoneType +from operations.models import append_suffix_to_filepath +from requests import Session + + +class MetadataServiceClient: + def __init__( + self, + endpoint: str, + minio_endpoint: str, + core_zone_label: str, + temp_dir: str, + project_client: ProjectClient, + access_token: str, + ) -> None: + self.endpoint_v1 = f'{endpoint}/v1/' + self.client = Session() + + self.minio_endpoint = minio_endpoint + self.core_zone_label = core_zone_label + self.temp_dir = temp_dir + self.project_client = project_client + self.access_token = access_token + + def get_item_by_id(self, node_id: str) -> Node: + nodes = self.get_items_by_ids([node_id]) + return nodes[node_id] + + def get_items_by_ids(self, ids: list) -> Dict[str, Node]: + parameter = {'ids': ids} + response = self.client.get(f'{self.endpoint_v1}items/batch/', params=parameter) + if response.status_code != 200: + raise Exception(f'Unable to get nodes by ids "{ids}".') + + results = response.json()['result'] + + if len(results) != len(ids): + raise Exception(f'Number of returned nodes does not match number of requested ids "{ids}".') + + nodes = {node.id: node for node in NodeList(results)} + + return nodes + + async def get_project_by_code(self, project_code: str) -> Node: + try: + project = await self.project_client.get(code=project_code) + result = await project.json() + except ProjectException: + raise ProjectException(f'Unable to get project by code "{project_code}".') + + return Node(result) + + def get_nodes_tree(self, start_folder_id: str, traverse_subtrees: bool = False) -> NodeList: + parent_folder_response = self.client.get(f'{self.endpoint_v1}item/{start_folder_id}/') + if parent_folder_response.status_code != 200: + raise Exception( + f'Unable to get parent folder starting from "{start_folder_id}", "{parent_folder_response.url}".' + ) + parent_folder = parent_folder_response.json()['result'] + + header = {'Authorization': f'Bearer {self.access_token}'} + + parameters = { + 'status': ItemStatus.ACTIVE, + 'zone': parent_folder['zone'], + 'container_code': parent_folder['container_code'], + 'parent_path': self.format_folder_path(parent_folder, '/'), + 'recursive': traverse_subtrees, + 'page_size': 1000, + } + node_query_url = self.endpoint_v1 + 'items/search/' + response = self.client.get(node_query_url, params=parameters, headers=header) + + if response.status_code != 200: + raise Exception(f'Unable to get nodes tree starting from "{start_folder_id}".') + + nodes = NodeList(response.json()['result']) + return nodes + + def update_node(self, node: Node, update_json: Dict[str, Any]) -> Dict[str, Any]: + response = self.client.put(url=f'{self.endpoint_v1}item/', params={'id': node.get('id')}, json=update_json) + + if response.status_code != 200: + raise Exception(f'Unable to update node with node id "{node["id"]}".') + + return response.json() + + def update_copied_file_node( + self, project: str, node: Node, system_tags: List[str], source_file: Node, minio_client: MinioBoto3Client + ) -> Tuple[Dict[str, Any], str]: + try: + file_display_path = self.format_folder_path(node, '/') + location = f'minio://{self.minio_endpoint}/core-{project}/{file_display_path}' + payload = { + 'status': ItemStatus.ACTIVE, + 'location_uri': location, + 'system_tags': system_tags, + } + # minio location is + # minio://http:///bucket/user/object_path + src_minio_path = source_file['storage'].get('location_uri').split('//')[-1] + _, src_bucket, src_obj_path = tuple(src_minio_path.split('/', 2)) + target_minio_path = location.split('//')[-1] + _, target_bucket, target_obj_path = tuple(target_minio_path.split('/', 2)) + + version_id = self._copy_file_node( + node, src_bucket, src_obj_path, target_bucket, target_obj_path, minio_client + ) + payload['version'] = version_id + + response = self.client.put(url=f'{self.endpoint_v1}item/', params={'id': node.get('id')}, json=payload) + + if response.status_code != 200: + raise Exception(f'Unable to update node with node id "{node["id"]}".') + except Exception: + logger.exception('Error when copying.') + raise + return Node(response.json()['result']), version_id + + def _copy_file_node( + self, + node: Node, + src_bucket: str, + src_obj_path: str, + target_bucket: str, + target_obj_path: str, + minio_client: MinioBoto3Client, + ) -> str: + """The minio api only accept the 5GB in copy. + + if >5GB we need to download to local then reupload to target + """ + file_size_gb = node.size + loop = asyncio.get_event_loop() + if file_size_gb < 5e9: + logger.info('File size less than 5GiB') + logger.info(f'Copying object from "{src_bucket}/{src_obj_path}" to "{target_bucket}/{target_obj_path}".') + result = loop.run_until_complete( + minio_client.copy_object(target_bucket, target_obj_path, src_bucket, src_obj_path) + ) + version_id = result.get('VersionId', '') # empty in case versioning is unsupported + else: + logger.info('File size greater than 5GiB') + temp_path = self.temp_dir + str(time.time())[0:10] + temp_file_path = f'{temp_path}/{node.name}' + loop.run_until_complete(minio_client.download_object(src_bucket, src_obj_path, temp_file_path)) + logger.info(f'File fetched to local disk: {temp_path}') + result = loop.run_until_complete( + minio_client.upload_object(target_bucket, target_obj_path, temp_file_path, temp_path) + ) + version_id = result.get('VersionId', '') # empty in case versioning is unsupported + + logger.info(f'Minio Copy {src_bucket}/{src_obj_path} Success') + return version_id + + def register_node( + self, + project: str, + source_node: Node, + parent_node: Node, + item_type: ResourceType, + status: ItemStatus, + timestamp: Optional[int], + ) -> Node: + + payload = { + 'parent': parent_node.id, + 'parent_path': self.format_folder_path(parent_node, '/'), + 'type': item_type, + 'zone': ZoneType.CORE, + 'name': source_node.name, + 'size': source_node.size, + 'owner': source_node.owner, + 'container_code': project, + 'container_type': 'project', + 'tags': source_node.tags, + 'status': status, + } + # adding the attribute set if exist + manifest = source_node.get_attributes() + if manifest: + payload['attribute_template_id'] = list(manifest.keys())[0] + payload['attributes'] = manifest[list(manifest.keys())[0]] + + create_node_url = self.endpoint_v1 + 'item/' + response = self.client.post(create_node_url, json=payload) + if response.status_code == 409 and item_type == ResourceType.FILE: + payload['name'] = append_suffix_to_filepath(source_node.name, timestamp) + response = self.client.post(create_node_url, json=payload) + elif response.status_code == 409 and item_type == ResourceType.FOLDER: + folder_node = self.get_node_by_full_path( + source_node.name, self.format_folder_path(parent_node, '/'), project + ) + return Node(folder_node) + response.raise_for_status() + new_node = response.json()['result'] + return Node(new_node) + + def get_node_by_full_path(self, name: str, parent_path: str, container_code: str) -> Dict[str, Any]: + param = { + 'name': name, + 'parent_path': parent_path, + 'container_code': container_code, + 'container_type': 'project', + 'zone': ZoneType.CORE, + 'status': ItemStatus.ACTIVE, + } + get_node_url = self.endpoint_v1 + 'item/' + response = self.client.get(get_node_url, params=param) + if response.status_code != 200: + raise Exception(f'Item {parent_path}/{name} does not exist') + return response.json()['result'] + + def format_folder_path(self, node: Node, divider: str) -> str: + parent_path = node.get('parent_path', None) + if parent_path: + return f'{parent_path}{divider}{node.get("name")}' + return node.get('name') + + def move_node_to_trash(self, node_id: str) -> List: + patch_node_url = self.endpoint_v1 + 'item/' + parameter = {'id': node_id, 'status': ItemStatus.ARCHIVED} + response = self.client.patch(patch_node_url, params=parameter) + if response.status_code != 200: + raise Exception(f'Unable to patch node with node id "{node_id}".') + trash_node = response.json()['result'] + return trash_node + + def archived_node(self, source_file: Node, minio_client: MinioBoto3Client, operation_type, operator) -> Node: + trash_node = self.move_node_to_trash(source_file.id) + try: + # minio location is + # minio://http:///bucket/user/object_path + for item in trash_node: + if item['type'] == ResourceType.FILE: + # Remove from minio + src_minio_path = item['storage'].get('location_uri').split('//')[-1] + _, src_bucket, src_obj_path = tuple(src_minio_path.split('/', 2)) + + loop = asyncio.get_event_loop() + loop.run_until_complete(minio_client.remove_object(src_bucket, src_obj_path)) + logger.info(f'Minio Delete {src_bucket}/{src_obj_path} Success') + + # Add activity log + loop.run_until_complete( + KafkaProducer.create_file_operation_logs(Node(item), operation_type, operator, None) + ) + + except Exception as e: + logger.exception(f'Error when removing file: {e}') + raise + + return trash_node + + def remove_registrated_nodes(self, registered_file_nodes: Dict[str, Node]) -> None: + """Remove the registrated file nodes when copy failed for tear down.""" + delete_node_url = self.endpoint_v1 + 'item/' + for item in registered_file_nodes: + node = registered_file_nodes[item] + if node.status == ItemStatus.REGISTERED: + param = {'id': node.id} + response = self.client.delete(delete_node_url, params=param) + if response.status_code != 200: + raise Exception(f'Unable to patch node with node id "{node.id}".') + + def register_nodes( + self, register_file_nodes: List[NodeToRegister], project_code: str, timestamp: int + ) -> Dict[str, Node]: + """Registered the file nodes.""" + try: + registered_file_nodes = {} + for item in register_file_nodes: + node = self.register_node( + project_code, + item.source_node, + item.destination_node, + ResourceType.FILE, + ItemStatus.REGISTERED, + timestamp, + ) + registered_file_nodes[item.source_node.id] = node + except Exception as e: + raise Exception(f'Unable to registered nodes: {e}') + return registered_file_nodes diff --git a/filecopy/operations/services/notification/__init__.py b/filecopy/operations/services/notification/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/operations/services/notification/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/operations/services/notification/client.py b/filecopy/operations/services/notification/client.py new file mode 100644 index 0000000..32a9db9 --- /dev/null +++ b/filecopy/operations/services/notification/client.py @@ -0,0 +1,95 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from typing import List +from typing import Optional + +from operations.logger import logger +from operations.models import Node +from operations.services.notification.models import InvolvementType +from operations.services.notification.models import Location +from operations.services.notification.models import NotificationType +from operations.services.notification.models import PipelineAction +from operations.services.notification.models import PipelineNotification +from operations.services.notification.models import PipelineStatus +from operations.services.notification.models import Target +from operations.services.notification.models import TargetType +from requests import Session + + +class NotificationServiceClient: + """Client for sending notifications into Notification Service.""" + + def __init__( + self, + endpoint: str, + include_nodes: dict[str, Node], + source_folder: Node, + destination_folder: Optional[Node], + project_code: str, + pipeline_action: PipelineAction, + pipeline_status: PipelineStatus, + operator: str, + notification_type: NotificationType, + ) -> None: + self.endpoint = f'{endpoint}/v1/all/notifications/' + self.include_nodes = include_nodes + self.source_folder = source_folder + self.destination_folder = destination_folder + self.project_code = project_code + self.pipeline_action = pipeline_action + self.pipeline_status = pipeline_status + self.operator = operator + self.notification_type = notification_type + self.client = Session() + + def set_status(self, status: str) -> None: + self.pipeline_status = status + + def set_location(self, entity: Node) -> Location: + return Location(id=entity.id, path=str(entity.display_path), zone=entity.zone) + + def set_targets(self) -> List[Target]: + targets = [] + for _node, file_node in self.include_nodes.items(): + targets.append(Target(id=file_node.id, name=file_node.name, type=TargetType(file_node.entity_type))) + return targets + + def get_priority(self) -> dict[InvolvementType, str]: + involvers = {InvolvementType.INITIATOR: self.operator} + owner = self.source_folder.display_path.parts[0] + receiver = self.destination_folder.display_path.parts[0] if self.destination_folder else None + if owner != self.operator: + involvers[InvolvementType.OWNER] = owner + if receiver not in [owner, self.operator, None]: + involvers[InvolvementType.RECEIVER] = receiver + return involvers + + def send_notifications(self) -> None: + """Calling notification service API to create notifications.""" + source_folder = self.set_location(self.source_folder) + targets_entity = self.set_targets() + involvers = self.get_priority() + payload = [] + destination_folder = self.set_location(self.destination_folder) if self.destination_folder else None + for involvement, username in involvers.items(): + notification = PipelineNotification( + type=NotificationType.PIPELINE, + recipient_username=username, + involved_as=involvement, + action=self.pipeline_action, + status=self.pipeline_status, + initiator_username=self.operator, + project_code=self.project_code, + source=source_folder, + destination=destination_folder, + targets=targets_entity, + ).to_json() + payload.append(notification) + response = self.client.post(self.endpoint, json=payload) + if response.status_code != 204: + logger.error(f'Failed to create notification for file {self.pipeline_action}') + raise Exception(f'Unable to create notifications for file {self.pipeline_action}') diff --git a/filecopy/operations/services/notification/models.py b/filecopy/operations/services/notification/models.py new file mode 100644 index 0000000..e9bceea --- /dev/null +++ b/filecopy/operations/services/notification/models.py @@ -0,0 +1,67 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import json +from enum import Enum +from typing import Optional +from uuid import UUID + +from pydantic import BaseModel +from pydantic import conlist + + +class InvolvementType(str, Enum): + INITIATOR = 'initiator' + OWNER = 'owner' + RECEIVER = 'receiver' + + +class PipelineAction(str, Enum): + DELETE = 'delete' + COPY = 'copy' + + +class PipelineStatus(str, Enum): + SUCCESS = 'success' + FAILURE = 'failure' + + +class NotificationType(str, Enum): + PIPELINE = 'pipeline' + COPY_REQUEST = 'copy-request' + + +class TargetType(str, Enum): + FILE = 'file' + FOLDER = 'folder' + + +class Location(BaseModel): + id: UUID + path: str + zone: int + + +class Target(BaseModel): + id: UUID + name: str + type: TargetType + + +class PipelineNotification(BaseModel): + type: NotificationType + recipient_username: str + involved_as: InvolvementType + action: PipelineAction + status: PipelineStatus + initiator_username: str + project_code: str + source: Location + destination: Optional[Location] + targets: conlist(Target, min_items=1) + + def to_json(self): + return json.loads(self.json()) diff --git a/filecopy/operations/services/redis/__init__.py b/filecopy/operations/services/redis/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/operations/services/redis/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/operations/services/redis/client.py b/filecopy/operations/services/redis/client.py new file mode 100644 index 0000000..0a0f67f --- /dev/null +++ b/filecopy/operations/services/redis/client.py @@ -0,0 +1,46 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import asyncio + +from aioredis import StrictRedis +from operations.config import get_settings + +REDIS_INSTANCE = {} + + +class RedisClient: + """we should replace StrictRedis with aioredis https://aioredis.readthedocs.io/en/latest/getting-started/""" + + def __init__(self): + settings = get_settings() + self.loop = asyncio.new_event_loop() + + self.host = settings.REDIS_HOST + self.port = settings.REDIS_PORT + self.pwd = settings.REDIS_PASSWORD + self.connect() + + def __del__(self): + self.loop.close() + + def connect(self): + global REDIS_INSTANCE + if REDIS_INSTANCE: + self.__instance = REDIS_INSTANCE + pass + else: + REDIS_INSTANCE = StrictRedis(host=self.host, port=self.port, password=self.pwd) + self.__instance = REDIS_INSTANCE + + def set_by_key(self, key: str, content: str, expire_time: int = 86400): + return self.loop.run_until_complete(self.__instance.set(key, content, ex=expire_time)) + + def check_by_key(self, key: str): + return self.loop.run_until_complete(self.__instance.exists(key)) + + def delete_by_key(self, key: str): + return self.loop.run_until_complete(self.__instance.delete(key)) diff --git a/filecopy/operations/traverser.py b/filecopy/operations/traverser.py new file mode 100644 index 0000000..4e544e6 --- /dev/null +++ b/filecopy/operations/traverser.py @@ -0,0 +1,42 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from pathlib import Path +from typing import Union + +from operations.managers import NodeManager +from operations.models import Node +from operations.models import NodeList + + +class Traverser: + """Traverse the trees using node manipulations from node manager.""" + + def __init__(self, node_manager: NodeManager) -> None: + self.node_manager = node_manager + + def _traverse_tree(self, nodes: NodeList, source_folder: Node, destination_folder: Union[Path, Node]) -> None: + excluded_geids = self.node_manager.exclude_nodes(nodes) + errors = [] + + for source_entry in nodes: + if source_entry.id in excluded_geids: + continue + try: + if source_entry.is_folder: + existing_destination_folder = self.node_manager.process_folder(source_entry, destination_folder) + self.traverse_tree(source_entry, existing_destination_folder) + else: + self.node_manager.process_file(source_entry, destination_folder) + except Exception as e: + errors.append(e) + if errors: + raise Exception(errors) + + def traverse_tree(self, source_folder: Node, destination_folder: Union[Path, Node]) -> None: + """Start tree traversing.""" + nodes = self.node_manager.get_tree(source_folder) + self._traverse_tree(nodes, source_folder, destination_folder) diff --git a/filecopy/poetry.lock b/filecopy/poetry.lock new file mode 100644 index 0000000..807dbe8 --- /dev/null +++ b/filecopy/poetry.lock @@ -0,0 +1,1748 @@ +# This file is automatically @generated by Poetry 1.8.2 and should not be 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+requests = "2.24.0" +python-dotenv = "0.19.1" +SQLAlchemy = "1.4.27" +aioredis = "2.0.1" +fastavro = "^1.5.2" +aiokafka = "^0.7.2" +pilot-platform-common = "0.3.0" + +[tool.poetry.dev-dependencies] +pytest = "7.1.2" +pytest-cov = "^3.0.0" +pytest-httpserver = "1.0.2" +pytest-mock = "3.6.1" +Faker = "9.8.2" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/filecopy/tests/__init__.py b/filecopy/tests/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/tests/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/tests/conftest.py b/filecopy/tests/conftest.py new file mode 100644 index 0000000..e93646f --- /dev/null +++ b/filecopy/tests/conftest.py @@ -0,0 +1,11 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +pytest_plugins = [ + 'tests.fixtures.fake', + 'tests.fixtures.node', + 'tests.fixtures.services', +] diff --git a/filecopy/tests/fixtures/__init__.py b/filecopy/tests/fixtures/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/tests/fixtures/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/tests/fixtures/commands.py b/filecopy/tests/fixtures/commands.py new file mode 100644 index 0000000..71f3beb --- /dev/null +++ b/filecopy/tests/fixtures/commands.py @@ -0,0 +1,13 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import pytest +from click.testing import CliRunner + + +@pytest.fixture +def cli(): + yield CliRunner() diff --git a/filecopy/tests/fixtures/fake.py b/filecopy/tests/fixtures/fake.py new file mode 100755 index 0000000..8f8dbcf --- /dev/null +++ b/filecopy/tests/fixtures/fake.py @@ -0,0 +1,24 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import faker +import pytest +from common import GEIDClient + + +class Faker(faker.Faker): + def geid(self) -> str: + """Generate global entity id.""" + + return GEIDClient().get_GEID() + + def name(self) -> str: + return Faker().pystr(max_chars=10) + + +@pytest.fixture +def fake() -> Faker: + yield Faker() diff --git a/filecopy/tests/fixtures/node.py b/filecopy/tests/fixtures/node.py new file mode 100644 index 0000000..5a3ba94 --- /dev/null +++ b/filecopy/tests/fixtures/node.py @@ -0,0 +1,87 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import random +import uuid +from typing import Callable + +import pytest +from operations.models import ItemStatus +from operations.models import Node +from operations.models import ResourceType + + +@pytest.fixture +def create_node(fake) -> Callable[..., Node]: + def _create_node( + id_=None, + parent=None, + parent_path=None, + name=None, + type_=None, + zone=0, + size=0, + owner='testuser', + container_code='testproject', + container_type='project', + created_time='2021-05-17 17:19:51.806591', + last_updated_time='2021-05-17 17:19:51.806591', + status=ItemStatus.ACTIVE, + tags=None, + attributes=None, + location_uri='minio_path', + version='fake_version', + ) -> Node: + if id_ is None: + id_ = fake.pyint() + + if parent is None: + parent = f'{uuid.uuid4()}' + + if parent_path is None: + parent_path = 'fake' + + if name is None: + name = fake.word() + + if type_ is None: + type_ = random.choice(list(ResourceType)) + + if tags is None: + tags = fake.words() + + if attributes is None: + attributes = {} + + return Node( + { + 'id': id_, + 'parent': parent, + 'parent_path': parent_path, + 'restore_path': 'None', + 'status': status, + 'type': type_, + 'zone': zone, + 'name': name, + 'size': size, + 'owner': owner, + 'container_code': container_code, + 'container_type': container_type, + 'created_time': created_time, + 'last_updated_time': last_updated_time, + 'storage': {'id': 'fake_id', 'location_uri': location_uri, 'version': version}, + 'extended': { + 'id': 'fake_id', + 'extra': { + 'tags': tags, + 'system_tags': ['copied-to-core'], + 'attributes': attributes, + }, + }, + } + ) + + return _create_node diff --git a/filecopy/tests/fixtures/services.py b/filecopy/tests/fixtures/services.py new file mode 100644 index 0000000..02039a6 --- /dev/null +++ b/filecopy/tests/fixtures/services.py @@ -0,0 +1,28 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import pytest +from operations.services.approval.client import ApprovalServiceClient +from operations.services.dataops.client import DataopsServiceClient +from operations.services.metadata.client import MetadataServiceClient + + +@pytest.fixture +def dataops_client(httpserver) -> DataopsServiceClient: + yield DataopsServiceClient(httpserver.url_for('/')) + + +@pytest.fixture +def metadata_service_client(httpserver) -> MetadataServiceClient: + yield MetadataServiceClient( + httpserver.url_for('/'), 'minio-endpoint', 'core-zone', 'temp-dir', httpserver.url_for('/'), 'fake_token' + ) + + +@pytest.fixture +def approval_service_client(httpserver, fake) -> ApprovalServiceClient: + request_id = 'request_id' + yield ApprovalServiceClient(httpserver.url_for('/'), request_id) diff --git a/filecopy/tests/services/__init__.py b/filecopy/tests/services/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/tests/services/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/tests/services/approval/__init__.py b/filecopy/tests/services/approval/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/tests/services/approval/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/tests/services/approval/test_client.py b/filecopy/tests/services/approval/test_client.py new file mode 100644 index 0000000..65b5d63 --- /dev/null +++ b/filecopy/tests/services/approval/test_client.py @@ -0,0 +1,15 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + + +class TestApprovalServiceClient: + def test_update_copy_status_with_no_error_raised(self, approval_service_client, fake, httpserver): + entity_id = fake.uuid4() + expected_body = {'result': [{'entity_id': entity_id}]} + httpserver.expect_request('/v1/request/request_id/copy-status').respond_with_json(expected_body, status=200) + result = approval_service_client.update_copy_status(entity_id) + + assert len(result) == 1 diff --git a/filecopy/tests/services/dataops/__init__.py b/filecopy/tests/services/dataops/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/tests/services/dataops/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/tests/services/dataops/test_client.py b/filecopy/tests/services/dataops/test_client.py new file mode 100644 index 0000000..8719b78 --- /dev/null +++ b/filecopy/tests/services/dataops/test_client.py @@ -0,0 +1,67 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from pathlib import Path + +from operations.services.dataops.client import JobStatus +from operations.services.dataops.client import ResourceLockOperation + + +class TestDataopsServiceClient: + def test_lock_resources_returns_response_body(self, dataops_client, httpserver, fake): + expected_body = fake.pydict(value_types=['str', 'int']) + httpserver.expect_request('/v2/resource/lock/bulk').respond_with_json(expected_body) + + received_body = dataops_client.lock_resources([Path('key')], ResourceLockOperation.READ) + + assert received_body == expected_body + + def test_unlock_resources_returns_response_body(self, dataops_client, httpserver, fake): + expected_body = fake.pydict(value_types=['str', 'int']) + httpserver.expect_request('/v2/resource/lock/bulk').respond_with_json(expected_body, status=400) + + received_body = dataops_client.unlock_resources([Path('key')], ResourceLockOperation.READ) + + assert received_body == expected_body + + def test_update_job_returns_response_body(self, dataops_client, httpserver, fake): + expected_body = fake.pydict(value_types=['str', 'int']) + httpserver.expect_request('/v1/task-stream/').respond_with_json(expected_body) + + received_body = dataops_client.update_job( + session_id=fake.geid(), + job_id=fake.geid(), + target_names=[fake.file_path(depth=3)], + target_type='file', + container_code=fake.name(), + action_type='data_transfer', + status=JobStatus.SUCCEED, + ) + + assert received_body == expected_body + + def test_get_zip_preview_returns_response_body(self, dataops_client, httpserver, fake): + expected_body = fake.pydict(value_types=['str', 'int']) + httpserver.expect_request('/v1/archive').respond_with_json(expected_body) + + received_body = dataops_client.get_zip_preview(fake.geid()) + + assert received_body == expected_body + + def test_get_zip_preview_returns_none_when_archive_does_not_exist(self, dataops_client, httpserver, fake): + httpserver.expect_request('/v1/archive').respond_with_json({}, status=404) + + received_body = dataops_client.get_zip_preview(fake.geid()) + + assert received_body is None + + def test_create_zip_preview_returns_response_body(self, dataops_client, httpserver, fake): + expected_body = fake.pydict(value_types=['str', 'int']) + httpserver.expect_request('/v1/archive').respond_with_json(expected_body) + + received_body = dataops_client.create_zip_preview(fake.geid(), fake.pydict(value_types=['str'])) + + assert received_body == expected_body diff --git a/filecopy/tests/services/metadata/__init__.py b/filecopy/tests/services/metadata/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/tests/services/metadata/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/tests/services/metadata/test_client.py b/filecopy/tests/services/metadata/test_client.py new file mode 100644 index 0000000..4ada4a4 --- /dev/null +++ b/filecopy/tests/services/metadata/test_client.py @@ -0,0 +1,132 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from operations.minio_boto3_client import MinioBoto3Client +from operations.models import ItemStatus +from operations.models import NodeToRegister +from operations.models import ResourceType +from operations.models import get_timestamp + + +class TestMetadataServiceClient: + def test_get_items_by_ids_returns_correct_nodes(self, metadata_service_client, httpserver, create_node, fake): + _id = fake.pyint() + node = create_node(id_=_id) + expected_body = {'result': [node]} + httpserver.expect_request('/v1/items/batch/').respond_with_json(expected_body) + received_response = metadata_service_client.get_items_by_ids([_id]) + assert received_response[_id] == node + + def test_get_item_by_id_returns_correct_nodes(self, metadata_service_client, httpserver, create_node, fake): + _id = fake.pyint() + node = create_node(id_=_id) + expected_body = {'result': [node]} + httpserver.expect_request('/v1/items/batch/').respond_with_json(expected_body) + received_response = metadata_service_client.get_item_by_id(_id) + assert received_response == node + + def test_get_nodes_tree_returns_correct_nodes(self, metadata_service_client, httpserver, create_node, fake): + _id = fake.pyint() + start_node = create_node(id_=_id, name='test') + node = create_node(parent_path='test') + expected_query_body = {'result': start_node} + expected_body = {'result': [node]} + httpserver.expect_request(f'/v1/item/{_id}/').respond_with_json(expected_query_body) + httpserver.expect_request('/v1/items/search/').respond_with_json(expected_body) + received_response = metadata_service_client.get_nodes_tree(start_node.id) + assert received_response[0] == node + + def test_update_node_returns_correct_nodes(self, metadata_service_client, httpserver, create_node, fake): + _id = fake.pyint() + node = create_node(id_=_id) + updated_node = create_node(id_=_id, size=15) + expected_body = {'result': updated_node} + httpserver.expect_request('/v1/item/').respond_with_json(expected_body) + update_json = {'size': 15} + received_response = metadata_service_client.update_node(node, update_json) + assert received_response['result'] == updated_node + + def test_update_copied_file_node_successed(self, metadata_service_client, httpserver, create_node, mocker): + node = create_node(parent='admin', name='test', type_=ResourceType.FILE) + source_file = create_node( + location_uri='http://minio_path/core-testproject/admin/test', size=5, type_=ResourceType.FILE + ) + new_node = create_node(parent='admin', name='test', version='test_versionId') + expected_body = {'result': new_node} + + minio_client = MinioBoto3Client + + async def mock_copy_object(arg1, arg2, arg3, arg4): + return {'VersionId': 'test_versionId'} + + mocker.patch('operations.services.metadata.client.MinioBoto3Client.copy_object', mock_copy_object) + httpserver.expect_request('/v1/item/').respond_with_json(expected_body) + received_response, versionId = metadata_service_client.update_copied_file_node( + 'testproject', node, ['system_tag'], source_file, minio_client + ) + assert received_response == new_node + assert versionId == 'test_versionId' + + def test_register_node_get_correct_nodes(self, metadata_service_client, httpserver, create_node): + source_node = create_node(parent='admin', name='test') + parent_node = create_node(name='test') + node = create_node(container_code='testproject') + expected_body = {'result': node} + httpserver.expect_request('/v1/item/').respond_with_json(expected_body) + timestamp = get_timestamp() + received_response = metadata_service_client.register_node( + 'testproject', source_node, parent_node, 'file', ItemStatus.REGISTERED, timestamp + ) + assert received_response == node + + def test_archived_node_correctly(self, metadata_service_client, httpserver, create_node, mocker): + source_node = create_node(parent='admin', name='test') + trash_node = create_node( + parent='admin', + name='test', + type_=ResourceType.FILE, + status=ItemStatus.ARCHIVED, + location_uri='http://minio_path/core-testproject/admin/test', + ) + expected_body = {'result': [trash_node]} + httpserver.expect_request('/v1/item/').respond_with_json(expected_body) + + minio_client = MinioBoto3Client + + async def mock_remove_object(arg1, arg2): + return None + + mocker.patch('operations.services.metadata.client.MinioBoto3Client.remove_object', mock_remove_object) + + async def mock_create_file_operation_logs(arg1, arg2, arg3, arg4): + return None + + mocker.patch( + 'operations.services.metadata.client.KafkaProducer.create_file_operation_logs', + mock_create_file_operation_logs, + ) + received_response = metadata_service_client.archived_node(source_node, minio_client, 'delete', 'test') + assert received_response == [trash_node] + + def test_remove_registrated_nodes_not_raise_error(self, metadata_service_client, httpserver, create_node): + node = create_node(parent='admin', name='test', status=ItemStatus.REGISTERED) + registered_file_nodes = {node.id: node} + expected_body = {'result': [node]} + httpserver.expect_request('/v1/item/').respond_with_json(expected_body) + + received_response = metadata_service_client.remove_registrated_nodes(registered_file_nodes) + assert received_response is None + + def test_register_nodes_succeed(self, metadata_service_client, httpserver, create_node, mocker): + node = create_node(container_code='testproject', type_=ResourceType.FILE) + source_node = create_node(parent='admin', name='test') + parent_node = create_node(name='test') + register_file_nodes = [NodeToRegister(source_node, parent_node)] + expected_body = {'result': node} + httpserver.expect_request('/v1/item/').respond_with_json(expected_body) + timestamp = get_timestamp() + received_response = metadata_service_client.register_nodes(register_file_nodes, 'testproject', timestamp) + assert received_response == {source_node.id: node} diff --git a/filecopy/tests/services/notification/__init__.py b/filecopy/tests/services/notification/__init__.py new file mode 100644 index 0000000..105ee19 --- /dev/null +++ b/filecopy/tests/services/notification/__init__.py @@ -0,0 +1,5 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. diff --git a/filecopy/tests/services/notification/test_client.py b/filecopy/tests/services/notification/test_client.py new file mode 100644 index 0000000..4afd436 --- /dev/null +++ b/filecopy/tests/services/notification/test_client.py @@ -0,0 +1,38 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from operations.services.notification.client import NotificationServiceClient +from operations.services.notification.models import InvolvementType +from operations.services.notification.models import NotificationType +from operations.services.notification.models import PipelineAction +from operations.services.notification.models import PipelineStatus + + +class TestNotificationServiceClient: + def test_get_priority_returns_involvement_dictionary_for_all_participants(self, create_node): + source_folder = create_node(parent_path='user1') + destination_folder = create_node(parent_path='user2') + client = NotificationServiceClient( + '', + {}, + source_folder, + destination_folder, + '', + PipelineAction.COPY, + PipelineStatus.SUCCESS, + 'admin', + NotificationType.PIPELINE, + ) + + expected_priority = { + InvolvementType.INITIATOR: 'admin', + InvolvementType.OWNER: 'user1', + InvolvementType.RECEIVER: 'user2', + } + + received_priority = client.get_priority() + + assert received_priority == expected_priority diff --git a/filecopy/tests/test_duplicated_file_names.py b/filecopy/tests/test_duplicated_file_names.py new file mode 100644 index 0000000..88bfb52 --- /dev/null +++ b/filecopy/tests/test_duplicated_file_names.py @@ -0,0 +1,42 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from pathlib import Path + +import pytest +from operations.duplicated_file_names import DuplicatedFileNames + + +@pytest.fixture +def duplicated_files() -> DuplicatedFileNames: + yield DuplicatedFileNames() + + +class TestDuplicatedFileNames: + def test_add_stores_filename_with_timestamp_for_given_filepath(self, duplicated_files, fake): + filepath = fake.file_path(depth=3) + + expected_filename = f'{Path(filepath).stem}_{duplicated_files.filename_timestamp}{Path(filepath).suffix}' + + received_filename = duplicated_files.add(filepath) + + assert received_filename == expected_filename + + def test_get_returns_existing_filename_by_filepath(self, duplicated_files, fake): + filepath = fake.file_path(depth=3) + expected_filename = duplicated_files.add(filepath) + + received_filename = duplicated_files.get(filepath) + + assert received_filename == expected_filename + + def test_get_returns_default_value_if_filename_does_not_exist(self, duplicated_files, fake): + filepath = fake.file_path(depth=3) + expected_filename = fake.pystr() + + received_filename = duplicated_files.get(filepath, expected_filename) + + assert received_filename == expected_filename diff --git a/filecopy/tests/test_managers.py b/filecopy/tests/test_managers.py new file mode 100644 index 0000000..c75535a --- /dev/null +++ b/filecopy/tests/test_managers.py @@ -0,0 +1,36 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +import pytest +from operations.managers import NodeManager +from operations.models import Node +from operations.models import NodeList +from operations.models import ResourceType + + +@pytest.fixture +def node_manager(metadata_service_client) -> NodeManager: + yield NodeManager(metadata_service_client) + + +class TestNodeManager: + def test_get_tree_returns_node_list_with_parent_folder_geid(self, node_manager, httpserver, create_node, fake): + parent_node = create_node(type_=ResourceType.FOLDER, name='folder1', id_='parent_id') + parent_id = parent_node['id'] + httpserver.expect_request(f'/v1/item/{parent_id}/').respond_with_json({'result': parent_node}) + + expected_node = create_node(type_=ResourceType.FOLDER, parent=parent_node['id']) + body = {'result': [expected_node]} + httpserver.expect_request('/v1/items/search/').respond_with_json(body) + received_nodes = node_manager.get_tree(Node(parent_node)) + + assert received_nodes == [expected_node] + + def test_exclude_nodes_returns_empty_set(self, node_manager, create_node): + expected_set = set() + received_set = node_manager.exclude_nodes(NodeList([])) + + assert received_set == expected_set diff --git a/filecopy/tests/test_models.py b/filecopy/tests/test_models.py new file mode 100644 index 0000000..30f1a5b --- /dev/null +++ b/filecopy/tests/test_models.py @@ -0,0 +1,114 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from pathlib import Path + +import pytest +from operations.models import ItemStatus +from operations.models import Node +from operations.models import NodeList +from operations.models import ResourceType +from operations.models import append_suffix_to_filepath + + +@pytest.mark.parametrize( + 'filepath,suffix,expected', + [ + ('file.tar.gz', 'suffix', 'file_suffix.tar.gz'), + ('/path/to/file.tar.gz', 'outdated', '/path/to/file_outdated.tar.gz'), + ('folder.tar.gz/file.tar.gz', 'tar', 'folder.tar.gz/file_tar.tar.gz'), + ('image.jpg', 1638552343, 'image_1638552343.jpg'), + ('file', 'suffix', 'file_suffix'), + (Path('path/to/file'), 'suffix', 'path/to/file_suffix'), + ], +) +def test_append_suffix_to_filename_appends_suffix_as_expected(filepath, suffix, expected) -> None: + assert append_suffix_to_filepath(filepath, suffix) == expected + + +class TestNode: + def test_id_returns_node_id(self, create_node): + node = create_node() + expected_id = node['id'] + + assert node.id == expected_id + + def test_is_folder_returns_true_if_labels_contain_folder_type(self, create_node): + node = create_node(type_=ResourceType.FOLDER) + + assert node.is_folder is True + + def test_is_folder_returns_false_if_labels_does_not_contain_folder_type(self, create_node): + node = create_node(type_=ResourceType.FILE) + + assert node.is_folder is False + + def test_is_file_returns_true_if_labels_contain_file_type(self, create_node): + node = create_node(type_=ResourceType.FILE) + + assert node.is_file is True + + def test_is_file_returns_false_if_labels_does_not_contain_file_type(self, create_node): + node = create_node(type_=ResourceType.FOLDER) + + assert node.is_file is False + + def test_is_archived_returns_true_if_status_property_is_archived(self, create_node): + node = create_node(status=ItemStatus.ARCHIVED) + + assert node.is_archived is True + + def test_is_archived_returns_false_if_status_property_is_not_archived(self, create_node): + node = create_node(status=ItemStatus.ACTIVE) + + assert node.is_archived is False + + def test_id_returns_node_global_entity_id(self, create_node): + node = create_node() + expected_id = node['id'] + + assert node.id == expected_id + + def test_name_returns_node_name(self, create_node): + node = create_node() + expected_name = node['name'] + + assert node.name == expected_name + + def test_tags_returns_node_tags(self, create_node): + node = create_node() + expected_tags = node['extended']['extra']['tags'] + + assert node.tags == expected_tags + + def test_get_attributes_returns_attributes_which_starts_with_attr(self, create_node): + node = create_node(attributes={'attr_one': 1}) + expected_attributes = {'attr_one': 1} + + assert expected_attributes == node.get_attributes() + + +class TestNodeList: + def test_new_instance_converts_list_values_into_node_instances(self): + nodes = NodeList([{'key': 'value'}]) + + assert isinstance(nodes[0], Node) + + def test_ids_returns_set_with_all_node_ids(self, create_node): + node_1 = create_node() + node_2 = create_node() + nodes = NodeList([node_1, node_2]) + expected_ids = {node_1.id, node_2.id} + + assert expected_ids == nodes.ids + + def test_filter_files_returns_node_list_with_file_nodes_only(self, create_node): + node_1 = create_node(type_=ResourceType.FILE) + node_2 = create_node(type_=ResourceType.FOLDER) + nodes = NodeList([node_1, node_2]) + expected_nodes = NodeList([node_1]) + + assert expected_nodes == nodes.filter_files() diff --git a/filecopy/tests/test_traverser.py b/filecopy/tests/test_traverser.py new file mode 100644 index 0000000..421d4b0 --- /dev/null +++ b/filecopy/tests/test_traverser.py @@ -0,0 +1,33 @@ +# Copyright (C) 2022-Present Indoc Systems +# +# Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, +# Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html. +# You may not use this file except in compliance with the License. + +from operations.managers import NodeManager +from operations.models import Node +from operations.models import NodeList +from operations.models import ResourceType +from operations.traverser import Traverser + + +class TestTraverser: + def test_traverse_tree_works_with_one_level_of_nesting(self, metadata_service_client, create_node): + tree_nodes = NodeList([create_node(type_=ResourceType.FILE), create_node(type_=ResourceType.FILE)]) + + class Manager(NodeManager): + def get_tree(self, source_folder: Node): + return tree_nodes.copy() + + def process_file(self, source_file: Node, destination_folder: Node): + expected_node = tree_nodes.pop(0) + assert expected_node == source_file + + def process_folder(self, source_folder: Node, destination_parent_folder: Node): + pass + + traverser = Traverser(Manager(metadata_service_client)) + + traverser.traverse_tree(create_node(), create_node()) + + assert len(tree_nodes) == 0 diff --git a/freesurfer/.dockerignore b/freesurfer/.dockerignore new file mode 100644 index 0000000..c734437 --- /dev/null +++ b/freesurfer/.dockerignore @@ -0,0 +1,11 @@ +.git +.gitignore +.gitlab-ci* +gitlab-ci* +Dockerfile* +kubernetes +Jenkinsfile + +# Misc +.DS_Store +.env.local diff --git a/freesurfer/Dockerfile b/freesurfer/Dockerfile new file mode 100644 index 0000000..668d79c --- /dev/null +++ b/freesurfer/Dockerfile @@ -0,0 +1,2 @@ +FROM freesurfer/freesurfer:7.1.1 +COPY license.txt /usr/local/freesurfer/.license diff --git a/freesurfer/build.sh b/freesurfer/build.sh new file mode 100644 index 0000000..8e08edf --- /dev/null +++ b/freesurfer/build.sh @@ -0,0 +1 @@ +docker build -t freesurfer/freesurfer:7.1.1.0 . diff --git a/freesurfer/license.txt b/freesurfer/license.txt new file mode 100644 index 0000000..3878a83 --- /dev/null +++ b/freesurfer/license.txt @@ -0,0 +1,3 @@ +50177 + *CFMktIopx6LQ + FSHCDTQk2tit2 From e856969f9c58b4bfdf1020a60506b24956ca41fe Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 9 Oct 2024 12:48:39 +0000 Subject: [PATCH 2/2] Bump certifi from 2022.9.24 to 2024.7.4 in /filecopy Bumps [certifi](https://github.com/certifi/python-certifi) from 2022.9.24 to 2024.7.4. - [Commits](https://github.com/certifi/python-certifi/compare/2022.09.24...2024.07.04) --- updated-dependencies: - dependency-name: certifi dependency-type: indirect ... Signed-off-by: dependabot[bot] --- filecopy/poetry.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/filecopy/poetry.lock b/filecopy/poetry.lock index 807dbe8..f8b4710 100644 --- a/filecopy/poetry.lock +++ b/filecopy/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "aioboto3" @@ -327,13 +327,13 @@ crt = ["awscrt (==0.13.5)"] [[package]] name = "certifi" -version = "2022.9.24" +version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2022.9.24-py3-none-any.whl", hash = "sha256:90c1a32f1d68f940488354e36370f6cca89f0f106db09518524c88d6ed83f382"}, - {file = "certifi-2022.9.24.tar.gz", hash = "sha256:0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14"}, + {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, + {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, ] [[package]]