From 712e360d4892218e447b58aa17a6cbcf64f641e0 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 24 Apr 2024 15:32:00 -0600 Subject: [PATCH] update deps and readme --- docs/index.md | 61 +++-- poetry.lock | 722 ++++++++++++++++++++++++++++++++++--------------- pyproject.toml | 8 +- 3 files changed, 536 insertions(+), 255 deletions(-) diff --git a/docs/index.md b/docs/index.md index b3b73fd..dfbea0e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,6 @@ # KG-Hub Downloader -| [Documentation](https://monarch-initiative.github.io/kghub-downloader) | +| [Documentation](https://monarch-initiative.github.io/kghub-downloader) | [Repository](https://github.com/monarch-initiative/kghub-downloader) | [PyPI](https://pypi.org/project/kghub-downloader) | ### Overview @@ -9,17 +9,19 @@ This is a configuration based file caching downloader with initial support for h ### Installation KGHub Downloader is available to install via pip: + ``` pip install kghub-downloader ``` -### Configure +### Configure The downloader requires a YAML file which contains a list of target URLs to download, and local names to save those downloads. For an example, see [example/download.yaml](example/download.yaml) Available options are: -- \***url**: The URL to download from. Currently supported: + +- \***url**: The URL to download from. Currently supported: - `http(s)` - `ftp` - with `glob:` option to download files with specific extensions (only with ftp as of now and looks recursively). @@ -29,29 +31,33 @@ Available options are: - **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` -- elastic search options +- elastic search options - **query_file**: The file containing the query to run against the index - **index**: The elastic search index for query > \* Note: -> Google Cloud Storage URLs require that you have set up your credentials as described [here](https://cloud.google.com/artifact-registry/docs/python/authentication#keyring-user). You must: -> - [create a service account](https://cloud.google.com/iam/docs/service-accounts-create) -> - [add the service account to the relevant bucket](https://cloud.google.com/storage/docs/access-control/using-iam-permissions#bucket-iam) and +> Google Cloud Storage URLs require that you have set up your credentials as described [here](https://cloud.google.com/artifact-registry/docs/python/authentication#keyring-user). You must: +> +> - [create a service account](https://cloud.google.com/iam/docs/service-accounts-create) +> - [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. +> 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 should be 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. +> +> - [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 should be 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: -You can also include any secrets like API keys you have set as environment variables using `{VARIABLE_NAME}`, for example: ```yaml --- - url: "https://example.com/myfancyfile.json?key={YOUR_SECRET}" localname: myfancyfile.json ``` -Note: `YOUR_SECRET` *MUST* as an environment variable, and be sure to include the {curly braces} in the url string. + +Note: `YOUR_SECRET` _MUST_ as an environment variable, and be sure to include the {curly braces} in the url string. ### Usage @@ -67,30 +73,31 @@ download_from_yaml(yaml_file="download.yaml", output_dir="data") #### Command Line +To download files listed in a download.yaml file: + ```bash $ downloader [OPTIONS] ARGS ``` -╰ Download files listed in a download.yaml file -| OPTIONS | | -| --- | --- | -| yaml_file | A string pointing to the download.yaml file, to be parsed for things to download.
Defaults to `./download.yaml` | -| ignore_cache | Ignore cache and download files even if they exist [false] | -| snippet_only | Downloads only the first 5 kB of each uncompressed source, for testing and file checks | -| tags | Limit to only downloads with this tag | -| mirror | Remote storage URL to mirror download to. Supported buckets: Google Cloud Storage | +| OPTIONS | | +| ------------ | ----------------------------------------------------------------------------------------------------- | +| yaml_file | Path to the download.yaml file, to be parsed for things to download.
Defaults to `./download.yaml` | +| ignore_cache | Ignore cache and download files even if they exist (Default `False`) | +| snippet_only | Downloads only the first 5 kB of each uncompressed source, for testing and file checks | +| tags | Limit to only downloads with this tag | +| mirror | Remote storage URL to upload downloaded files to.
Supported buckets: Google Cloud Storage | - -| ARGUMENTS | | -| --- | --- | -| output_dir | A string pointing to where to write out downloaded files. | +| ARGUMENTS | | +| ---------- | ------------------------------- | +| output_dir | Where to save downloaded files. | Examples: + ```bash $ downloader --output_dir example_output --tags zfin_gene_to_phenotype example.yaml $ downloader --output_dir example_output --mirror gs://your-bucket/desired/directory -# Note that if your YAML file is named `download.yaml`, +# Note that if your YAML file is named `download.yaml`, # the argument can be omitted from the CLI call. $ downloader --output_dir example_output ``` @@ -111,4 +118,4 @@ poetry install poetry run pytest ``` -NOTE: The tests require gcloud credentials to be set up as described above, using the monarch github actions service account. \ No newline at end of file +NOTE: The tests require gcloud credentials to be set up as described above, using the Monarch github actions service account. diff --git a/poetry.lock b/poetry.lock index 7a75043..3bd2fff 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,19 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. + +[[package]] +name = "astunparse" +version = "1.6.3" +description = "An AST unparser for Python" +optional = false +python-versions = "*" +files = [ + {file = "astunparse-1.6.3-py2.py3-none-any.whl", hash = "sha256:c2652417f2c8b5bb325c885ae329bdf3f86424075c4fd1a128674bc6fba4b8e8"}, + {file = "astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872"}, +] + +[package.dependencies] +six = ">=1.6.1,<2.0" +wheel = ">=0.23.0,<1.0" [[package]] name = "atomicwrites" @@ -29,6 +44,23 @@ tests = ["attrs[tests-no-zope]", "zope-interface"] tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] +[[package]] +name = "babel" +version = "2.14.0" +description = "Internationalization utilities" +optional = false +python-versions = ">=3.7" +files = [ + {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"}, + {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"}, +] + +[package.dependencies] +pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} + +[package.extras] +dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] + [[package]] name = "beautifulsoup4" version = "4.12.3" @@ -52,17 +84,17 @@ lxml = ["lxml"] [[package]] name = "boto3" -version = "1.34.38" +version = "1.34.91" description = "The AWS SDK for Python" optional = false -python-versions = ">= 3.8" +python-versions = ">=3.8" files = [ - {file = "boto3-1.34.38-py3-none-any.whl", hash = "sha256:7c70c6ceb2706c7fad6466a5de174fe6d0d6f5f8f1e052bfaad9cbe4e53b64cd"}, - {file = "boto3-1.34.38.tar.gz", hash = "sha256:e74fbad79bc921a74a9a276ef9f38e1e31153f76690fe9bc5ec790007de36572"}, + {file = "boto3-1.34.91-py3-none-any.whl", hash = "sha256:97fac686c47647db4b44e4789317e4aeecd38511d71e84f8d20abe33eb630ff1"}, + {file = "boto3-1.34.91.tar.gz", hash = "sha256:5077917041adaaae15eeca340289547ef905ca7e11516e9bd22d394fb5057d2a"}, ] [package.dependencies] -botocore = ">=1.34.38,<1.35.0" +botocore = ">=1.34.91,<1.35.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -71,13 +103,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.34.38" +version = "1.34.91" description = "Low-level, data-driven core of boto 3." optional = false -python-versions = ">= 3.8" +python-versions = ">=3.8" files = [ - {file = "botocore-1.34.38-py3-none-any.whl", hash = "sha256:773e49f5bf596191e796b2a15096ff381e61778cbe7c982b381bb9f6bfe5fef3"}, - {file = "botocore-1.34.38.tar.gz", hash = "sha256:da9754a8e1798706427ede9c9c0a55263bd8e57f217c021807b2946eb4a0c2d8"}, + {file = "botocore-1.34.91-py3-none-any.whl", hash = "sha256:4d1b13f2b1c28ce1743b1e5895ae62bb7e67f892b51882164ea19c27a130852b"}, + {file = "botocore-1.34.91.tar.gz", hash = "sha256:93ef7071292a1b2b9fc26537f8ae3a8227da1177969241939ea3fbdb1a1a1d0c"}, ] [package.dependencies] @@ -85,21 +117,21 @@ jmespath = ">=0.7.1,<2.0.0" python-dateutil = ">=2.1,<3.0.0" urllib3 = [ {version = ">=1.25.4,<1.27", markers = "python_version < \"3.10\""}, - {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""}, + {version = ">=1.25.4,<2.2.0 || >2.2.0,<3", markers = "python_version >= \"3.10\""}, ] [package.extras] -crt = ["awscrt (==0.19.19)"] +crt = ["awscrt (==0.20.9)"] [[package]] name = "cachetools" -version = "5.3.2" +version = "5.3.3" description = "Extensible memoizing collections and decorators" optional = false python-versions = ">=3.7" files = [ - {file = 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google-cloud-storage = "^2.1.0" -typer = "^0.7.0" -mkdocs = "^1.4.0" -mkdocs-material = "^8.5.6" +typer ="^0.12.3" +mkdocs = ">=1.4" +mkdocs-material = ">=9.5" mkdocstrings = {extras = ["python"], version = "^0.20.0"} gdown = ">=4.7.1" boto3 = ">=1.34.35"