From 4e87f7a90644e3ff3b6ae4e0cc717606e4ddcc13 Mon Sep 17 00:00:00 2001 From: Matvey Loshakov Date: Wed, 9 Oct 2024 14:46:48 +0200 Subject: [PATCH] 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 | 22 +- 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, 8061 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..18672cf 100644 --- a/README.md +++ b/README.md @@ -1 +1,21 @@ -# 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). + +## Acknowledgements +The development of the HealthDataCloud open source software was supported by the EBRAINS research infrastructure, funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3) and H2020 Research and Innovation Action Grant Interactive Computing E-Infrastructure for the Human Brain Project ICEI 800858. 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