From 4b643de9833a95b0ffa6126a6ae1f2d838a08c40 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 6 Feb 2024 12:37:35 -0600 Subject: [PATCH 1/9] Local file to S3 upload. --- example/download.yaml | 18 + kghub_downloader/download_utils.py | 19 +- poetry.lock | 932 ++++++++++++++++++----------- pyproject.toml | 5 +- 4 files changed, 608 insertions(+), 366 deletions(-) diff --git a/example/download.yaml b/example/download.yaml index a3e5ff4..e5cad80 100644 --- a/example/download.yaml +++ b/example/download.yaml @@ -12,6 +12,24 @@ - url: https://drive.google.com/uc?id=10ojJffrPSl12OMcu4gyx0fak2CNu6qOs local_name: gdrive_test_2.txt +- base_url: https://rest.uniprot.org/uniprotkb/ + api: uniprot + url: 'gdrive:1Ai52w4fu4XPu5w4wdE8y3rymEgN0BDqe' + local_name: 'uniprot_genome_features' + fields: [ + "organism_id", + "id", + "accession", + "protein_name", + "ec", + "ft_binding" + ] + keywords: [ + "Reference+proteome" + ] + size: 500 + batch_size: 1 + test: True # - url: https://www.ebi.ac.uk/chembl/elk/es/ # api: elasticsearch # query_file: example/query.json diff --git a/kghub_downloader/download_utils.py b/kghub_downloader/download_utils.py index 8d426ee..435ec63 100644 --- a/kghub_downloader/download_utils.py +++ b/kghub_downloader/download_utils.py @@ -20,6 +20,8 @@ from google.cloud.storage.blob import Blob from typing import List, Optional import gdown +import boto3 +from botocore.exceptions import NoCredentialsError GDOWN_MAP = {"gdrive": "https://drive.google.com/uc?id="} @@ -188,9 +190,20 @@ def mirror_to_bucket(local_file, bucket_url, remote_file) -> None: blob.upload_from_filename(local_file) elif bucket_url.startswith("s3://"): - raise ValueError("Currently, only Google Cloud storage is supported.") - # bashCommand = f"aws s3 cp {outfile} {mirror}" - # subprocess.run(bashCommand.split()) + # Create an S3 client + s3 = boto3.client('s3') + + try: + # Upload the file + s3.upload_file(local_file, bucket_name, remote_file) + print(f"File {local_file} uploaded to {bucket_name}/{remote_file}") + return True + except FileNotFoundError: + print(f"The file {local_file} was not found") + return False + except NoCredentialsError: + print("Credentials not available") + return False else: raise ValueError("Currently, only Google Cloud storage is supported.") diff --git a/poetry.lock b/poetry.lock index 44b447b..6d21e09 100644 --- a/poetry.lock +++ b/poetry.lock @@ -12,84 +12,215 @@ files = [ [[package]] name = "attrs" -version = "22.1.0" +version = "23.2.0" description = "Classes Without Boilerplate" optional = false -python-versions = ">=3.5" +python-versions = ">=3.7" files = [ - {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"}, - 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url: https://drive.google.com/uc?id=10ojJffrPSl12OMcu4gyx0fak2CNu6qOs local_name: gdrive_test_2.txt -- base_url: https://rest.uniprot.org/uniprotkb/ - api: uniprot - url: 'gdrive:1Ai52w4fu4XPu5w4wdE8y3rymEgN0BDqe' - local_name: 'uniprot_genome_features' - fields: [ - "organism_id", - "id", - "accession", - "protein_name", - "ec", - "ft_binding" - ] - keywords: [ - "Reference+proteome" - ] - size: 500 - batch_size: 1 - test: True # - url: https://www.ebi.ac.uk/chembl/elk/es/ # api: elasticsearch # query_file: example/query.json From ddf7960d66a3f87930fa0206ead17a35f766fc98 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 6 Feb 2024 12:45:02 -0600 Subject: [PATCH 3/9] formatted --- kghub_downloader/download_utils.py | 2 +- test/integration/test_download.py | 5 +---- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/kghub_downloader/download_utils.py b/kghub_downloader/download_utils.py index 435ec63..970536d 100644 --- a/kghub_downloader/download_utils.py +++ b/kghub_downloader/download_utils.py @@ -191,7 +191,7 @@ def mirror_to_bucket(local_file, bucket_url, remote_file) -> None: elif bucket_url.startswith("s3://"): # Create an S3 client - s3 = boto3.client('s3') + s3 = boto3.client("s3") try: # Upload the file diff --git a/test/integration/test_download.py b/test/integration/test_download.py index 554bfce..3732f26 100644 --- a/test/integration/test_download.py +++ b/test/integration/test_download.py @@ -24,10 +24,7 @@ def test_download(): def test_tag(): - files = [ - "test/output/zfin/fish_phenotype.txt", - "test/output/test_file.yaml" - ] + files = ["test/output/zfin/fish_phenotype.txt", "test/output/test_file.yaml"] tagged_files = ["test/output/gdrive_test_1.txt"] for file in files: From 2728e2d0b488041f9fc7faf9f961d8934ec839c3 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 6 Feb 2024 13:06:08 -0600 Subject: [PATCH 4/9] typo --- kghub_downloader/download_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kghub_downloader/download_utils.py b/kghub_downloader/download_utils.py index 970536d..0a0e275 100644 --- a/kghub_downloader/download_utils.py +++ b/kghub_downloader/download_utils.py @@ -206,7 +206,7 @@ def mirror_to_bucket(local_file, bucket_url, remote_file) -> None: return False else: - raise ValueError("Currently, only Google Cloud storage is supported.") + raise ValueError("Currently, only Google Cloud and S3 storage is supported.") return None From 6f40d18696554a976866d15c7ae7671fd93bb0c3 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 8 Feb 2024 15:39:04 -0600 Subject: [PATCH 5/9] Added comment --- kghub_downloader/download_utils.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/kghub_downloader/download_utils.py b/kghub_downloader/download_utils.py index 0a0e275..08c8263 100644 --- a/kghub_downloader/download_utils.py +++ b/kghub_downloader/download_utils.py @@ -195,6 +195,8 @@ def mirror_to_bucket(local_file, bucket_url, remote_file) -> None: try: # Upload the file + # ! This will only work if the user has the AWS IAM user + # ! access keys set up as environment variables. s3.upload_file(local_file, bucket_name, remote_file) print(f"File {local_file} uploaded to {bucket_name}/{remote_file}") return True From 973f7fd1b0fd854db9785912d02b4a718b4c9daf Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 8 Feb 2024 16:16:34 -0600 Subject: [PATCH 6/9] Added mock test for s3 and formatted code --- kghub_downloader/download_utils.py | 39 ++--- kghub_downloader/main.py | 3 +- poetry.lock | 222 ++++++++++++++++++++++++++++- pyproject.toml | 3 + test/integration/test_download.py | 5 +- test/unit/test_mirror.py | 48 ++++++- test/unit/test_parse_url.py | 6 +- 7 files changed, 301 insertions(+), 25 deletions(-) diff --git a/kghub_downloader/download_utils.py b/kghub_downloader/download_utils.py index 08c8263..7b0bff7 100644 --- a/kghub_downloader/download_utils.py +++ b/kghub_downloader/download_utils.py @@ -1,27 +1,30 @@ -import os, pathlib, re +import json import logging +import os +import pathlib +import re +from multiprocessing.sharedctypes import Value +from typing import List, Optional +from urllib.error import URLError +from urllib.request import Request, urlopen -import json, yaml +import boto3 import compress_json # type: ignore +import elasticsearch +import elasticsearch.helpers +import gdown +import yaml +from botocore.exceptions import NoCredentialsError +from google.cloud import storage +from google.cloud.storage.blob import Blob +from tqdm.auto import tqdm # type: ignore # from compress_json import compress_json -from multiprocessing.sharedctypes import Value -from urllib.error import URLError -from urllib.request import Request, urlopen -import elasticsearch -import elasticsearch.helpers -from tqdm.auto import tqdm # type: ignore -from google.cloud import storage -from google.cloud.storage.blob import Blob -from typing import List, Optional -import gdown -import boto3 -from botocore.exceptions import NoCredentialsError GDOWN_MAP = {"gdrive": "https://drive.google.com/uc?id="} @@ -159,6 +162,8 @@ def download_from_yaml( def mirror_to_bucket(local_file, bucket_url, remote_file) -> None: + bucket_split = bucket_url.split("/") + bucket_name = bucket_split[2] with open(local_file, "rb"): if bucket_url.startswith("gs://"): @@ -167,8 +172,6 @@ def mirror_to_bucket(local_file, bucket_url, remote_file) -> None: # Connect to GCS Bucket storage_client = storage.Client() - bucket_split = bucket_url.split("/") - bucket_name = bucket_split[2] bucket = storage_client.bucket(bucket_name) # Upload blob from local file @@ -208,7 +211,9 @@ def mirror_to_bucket(local_file, bucket_url, remote_file) -> None: return False else: - raise ValueError("Currently, only Google Cloud and S3 storage is supported.") + raise ValueError( + "Currently, only Google Cloud and S3 storage is supported." + ) return None diff --git a/kghub_downloader/main.py b/kghub_downloader/main.py index e1283e4..c107bc6 100644 --- 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testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "617f9988bfa7d6337fb01a73f90db9c2b30b8db61e369042b802183042b3428a" +content-hash = "947cc7d417271825a033f0a51f789f916b5461d5e9ff09bda3eb872da009983a" diff --git a/pyproject.toml b/pyproject.toml index cebc2d6..e504606 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,6 +24,9 @@ boto3 = ">=1.34.35" [tool.poetry.dev-dependencies] pytest = "^6.2.5" +[tool.poetry.group.dev.dependencies] +moto = "^5.0.1" + [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" diff --git a/test/integration/test_download.py b/test/integration/test_download.py index 3732f26..6f2fa78 100644 --- a/test/integration/test_download.py +++ b/test/integration/test_download.py @@ -1,6 +1,7 @@ -from kghub_downloader.download_utils import download_from_yaml -from os.path import exists import os +from os.path import exists + +from kghub_downloader.download_utils import download_from_yaml # Integration test using example configuration diff --git a/test/unit/test_mirror.py b/test/unit/test_mirror.py index 17f8042..9442de4 100644 --- a/test/unit/test_mirror.py +++ b/test/unit/test_mirror.py @@ -1,7 +1,13 @@ -from kghub_downloader.download_utils import * - +import os from unittest import mock +import boto3 +import moto +import pytest + +from kghub_downloader.download_utils import mirror_to_bucket + + # proper test @mock.patch("google.cloud.storage.Client") def test_mirror(client): @@ -16,3 +22,41 @@ def test_mirror(client): blob = bucket().blob blob.assert_called_with("kghub_test_upload.txt") + + +@pytest.fixture(scope="session") +def aws_credentials(): + """Mocked AWS Credentials for moto.""" + os.environ["AWS_ACCESS_KEY_ID"] = "testing" + os.environ["AWS_SECRET_ACCESS_KEY"] = "testing" + os.environ["AWS_SECURITY_TOKEN"] = "testing" + os.environ["AWS_SESSION_TOKEN"] = "testing" + os.environ["AWS_DEFAULT_REGION"] = "us-east-1" + + +@pytest.fixture(scope="function") +def empty_bucket(aws_credentials): + moto_fake = moto.mock_aws() + try: + moto_fake.start() + conn = boto3.resource("s3") + conn.create_bucket(Bucket="monarch-test") # or the name of the bucket you use + yield conn + finally: + moto_fake.stop() + + +def test_mirror_to_bucket_s3(empty_bucket): + # Call the function under test + result = mirror_to_bucket( + local_file="test/resources/testfile.txt", + bucket_url="s3://monarch-test/", + remote_file="kghub_test_upload.txt", + ) + + # Check if the file was created in the bucket + bucket = empty_bucket.Bucket("monarch-test") + files_in_bucket = list(bucket.objects.all()) + assert len(files_in_bucket) == 1 + assert files_in_bucket[0].key == "kghub_test_upload.txt" + assert result is True diff --git a/test/unit/test_parse_url.py b/test/unit/test_parse_url.py index af66870..b470807 100644 --- a/test/unit/test_parse_url.py +++ b/test/unit/test_parse_url.py @@ -1,6 +1,8 @@ -from kghub_downloader.download_utils import * +import os + +import pytest -import os, pytest +from kghub_downloader.download_utils import * os.environ["TEST_URL"] = "https://testurl.com/fake/download/rootpath" os.environ["TEST_KEY"] = "123456789987654321" From d4d319fab3c06fb7d1a47318701cb135ea0d8c48 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 8 Feb 2024 18:28:41 -0600 Subject: [PATCH 7/9] Added documentation --- docs/index.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/index.md b/docs/index.md index 4ff5d30..2d02134 100644 --- a/docs/index.md +++ b/docs/index.md @@ -23,6 +23,7 @@ Available options are: - `http(s)` - Google Cloud Storage (`gs://`) - Google Drive (`gdrive://` or https://drive.google.com/...). The file must be publicly accessible. + - Amazon AWS S3 bucket (`s3://`) - **local_name**: The name to save the file as locally - **tag**: A tag to use to filter downloads - **api**: The API to use to download the file. Currently supported: `elasticsearch` @@ -36,6 +37,11 @@ Available options are: > - [add the service account to the relevant bucket](https://cloud.google.com/storage/docs/access-control/using-iam-permissions#bucket-iam) and > - [download a JSON key](https://cloud.google.com/iam/docs/keys-create-delete) for that service account. > Then, set the `GOOGLE_APPLICATION_CREDENTIALS` environment variable to point to that file. +> +> Mirorring local files to Amazon AWS S3 bucket requires the following: +> - [Create an AWS account](https://portal.aws.amazon.com/) +> - [Create an IAM user in AWS](https://docs.aws.amazon.com/IAM/latest/UserGuide/getting-started.html): This enables getting the `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` needed for authentication. These two shoul dbe stored as environment variables in the user's system. +> - [Create an S3 bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/creating-bucket.html): This will be the destination for pushing local files. You can also include any secrets like API keys you have set as environment variables using `{VARIABLE_NAME}`, for example: ```yaml From 5b976cd1444868e796f44c03d4ed599397d3e038 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 8 Feb 2024 18:59:41 -0600 Subject: [PATCH 8/9] Added code for download from s3 --- example/download.yaml | 3 +++ kghub_downloader/download_utils.py | 5 +++++ 2 files changed, 8 insertions(+) diff --git a/example/download.yaml b/example/download.yaml index a3e5ff4..9a4f7e3 100644 --- a/example/download.yaml +++ b/example/download.yaml @@ -12,6 +12,9 @@ - url: https://drive.google.com/uc?id=10ojJffrPSl12OMcu4gyx0fak2CNu6qOs local_name: gdrive_test_2.txt +- url: s3://monarch-kg-test/kghub_downloader_test_file.yaml + local_name: test_file.yaml + # - url: https://www.ebi.ac.uk/chembl/elk/es/ # api: elasticsearch # query_file: example/query.json diff --git a/kghub_downloader/download_utils.py b/kghub_downloader/download_utils.py index 7b0bff7..c0e2b96 100644 --- a/kghub_downloader/download_utils.py +++ b/kghub_downloader/download_utils.py @@ -109,6 +109,11 @@ def download_from_yaml( Blob.from_string(url, client=storage.Client()).download_to_filename( outfile ) + elif url.startswith("s3://"): + s3 = boto3.client("s3") + bucket_name = url.split("/")[2] + remote_file = "/".join(url.split("/")[3:]) + s3.download_file(bucket_name, remote_file, outfile) elif any( url.startswith(str(i)) for i in list(GDOWN_MAP.keys()) + list(GDOWN_MAP.values()) From fb474f928077e24e968efa6ea092570939f8b0fa Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 8 Feb 2024 19:00:26 -0600 Subject: [PATCH 9/9] formatted --- kghub_downloader/download_utils.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/kghub_downloader/download_utils.py b/kghub_downloader/download_utils.py index c0e2b96..77ed9f6 100644 --- a/kghub_downloader/download_utils.py +++ b/kghub_downloader/download_utils.py @@ -22,10 +22,6 @@ # from compress_json import compress_json - - - - GDOWN_MAP = {"gdrive": "https://drive.google.com/uc?id="}