gentroutils 0.1.5__py3-none-any.whl

gentroutils/__init__.py

@@ -0,0 +1,44 @@
+"""Cli for gentroutils."""
+
+from __future__ import annotations
+
+import logging
+import time
+
+import click
+import pyfiglet
+
+from gentroutils.commands.update_gwas_curation_metadata import (
+    update_gwas_curation_metadata_command,
+)
+from gentroutils.commands.utils import set_log_file, set_log_lvl, teardown_cli
+
+logger = logging.getLogger("gentroutils")
+logger.setLevel(logging.DEBUG)
+
+
+@click.group()
+@click.option("-d", "--dry-run", is_flag=True, default=False)
+@click.option(
+    "-v",
+    count=True,
+    default=0,
+    callback=set_log_lvl,
+    help="Increase verbosity of the logging. Can be used multiple times. The default log level is ERROR, -v is INFO, -vv is DEBUG",
+)
+@click.option("-q", "--log-file", callback=set_log_file, required=False)
+@click.pass_context
+def cli(ctx: click.Context, **kwargs: dict[str, str]) -> None:
+    r"""Gentroutils Command Line Interface."""
+    ascii_art = pyfiglet.Figlet(font="serifcap").renderText("Gentroutils")
+    click.echo(click.style(ascii_art, fg="blue"))
+    ctx.max_content_width = 200
+    ctx.ensure_object(dict)
+    ctx.obj["dry_run"] = kwargs["dry_run"]
+    ctx.obj["execution_start"] = time.time()
+    ctx.call_on_close(lambda: teardown_cli(ctx))
+
+
+cli.add_command(update_gwas_curation_metadata_command)
+
+__all__ = ["cli"]

gentroutils/commands/__init__.py

@@ -0,0 +1,7 @@
+"""CLI submodules for gentroutils package."""
+
+from gentroutils.commands.update_gwas_curation_metadata import (
+    update_gwas_curation_metadata_command,
+)
+
+__all__ = ["update_gwas_curation_metadata_command"]

gentroutils/commands/update_gwas_curation_metadata.py

@@ -0,0 +1,313 @@
+"""Update gwas catalog metadata."""
+
+from __future__ import annotations
+
+import asyncio
+import io
+import logging
+import re
+import sys
+from ftplib import FTP
+from urllib.parse import ParseResult, urlparse
+
+import click
+import requests
+from google.cloud import storage
+
+from gentroutils.commands.utils import coro
+
+logger = logging.getLogger("gentroutils")
+MAX_CONCURRENT_CONNECTIONS = 10
+CURATED_INPUTS = (
+    (
+        "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-associations_ontology-annotated.tsv",
+        "gs://gwas_catalog_data/curated_inputs/gwas_catalog_associations_ontology_annotated.tsv",
+    ),
+    (
+        "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-download-studies-v1.0.3.1.txt",
+        "gs://gwas_catalog_data/curated_inputs/gwas_catalog_download_studies.tsv",
+    ),
+    (
+        "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-unpublished-studies-v1.0.3.1.tsv",
+        "gs://gwas_catalog_data/curated_inputs/gwas_catalog_unpublished_studies.tsv",
+    ),
+    (
+        "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-download-ancestries-v1.0.3.1.txt",
+        "gs://gwas_catalog_data/curated_inputs/gwas_catalog_download_ancestries.tsv",
+    ),
+    (
+        "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-unpublished-ancestries-v1.0.3.1.tsv",
+        "gs://gwas_catalog_data/curated_inputs/gwas_catalog_unpublished_ancestries.tsv",
+    ),
+    (
+        "ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/harmonised_list.txt",
+        "gs://gwas_catalog_data/curated_inputs/harmonised_list.txt",
+    ),
+)
+
+
+@click.command(name="update-gwas-curation-metadata")
+@click.option(
+    "--file-to-transfer",
+    "-f",
+    metavar="<ftp_file|http(s) file> <gcp_file>",
+    type=(str, str),
+    multiple=True,
+    default=CURATED_INPUTS,
+)
+@click.option(
+    "--gwas-catalog-release-info-url",
+    "-g",
+    metavar="<url>",
+    default="https://www.ebi.ac.uk/gwas/api/search/stats",
+    type=click.STRING,
+)
+@click.pass_context
+@coro
+async def update_gwas_curation_metadata_command(
+    ctx: click.Context,
+    file_to_transfer: list[tuple[str, str]],
+    gwas_catalog_release_info_url: str,
+) -> None:
+    """Update GWAS Catalog metadata directly to cloud bucket.
+
+    \b
+    This is the script to fetch the latest GWAS Catalog data files that include:
+    - [x] gwas-catalog-associations_ontology-annotated.tsv - list of associations with ontology annotations by GWAS Catalog
+    - [x] gwas-catalog-download-studies-v1.0.3.1.txt - list of published studies by GWAS Catalog
+    - [x] gwas-catalog-unpublished-studies-v1.0.3.1.tsv - list of unpublished studies by GWAS Catalog
+    - [x] gwas-catalog-download-ancestries-v1.0.3.1.txt - list of published studies by GWAS Catalog
+    - [x] gwas-catalog-unpublished-ancestries-v1.0.3.1.tsv - list of unpublished studies by GWAS Catalog
+
+    \b
+    By default all GWAS Catalog data files are uploaded from GWAS Catalog FTP server to Open Targets GCP bucket.
+    The script also captures the latest release metadata from GWAS Catalog release info url.
+    One can overwrite this script to sync data files from FTP or HTTP(s) to GCP bucket. The example usage is as follows:
+
+    \b
+    gentroutils --log-file gs://gwas_catalog_data/curated_inputs/log.txt update-gwas-curation-metadata \\
+    -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-associations_ontology-annotated.tsv gs://gwas_catalog_data/curated_inputs/gwas_catalog_associations_ontology_annotated.tsv \\
+    -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-download-studies-v1.0.3.1.txt gs://gwas_catalog_data/curated_inputs/gwas_catalog_download_studies.tsv \\
+    -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-unpublished-studies-v1.0.3.1.tsv gs://gwas_catalog_data/curated_inputs/gwas_catalog_unpublished_studies.tsv \\
+    -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-download-ancestries-v1.0.3.1.txt gs://gwas_catalog_data/curated_inputs/gwas_catalog_download_ancestries.tsv \\
+    -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-unpublished-ancestries-v1.0.3.1.tsv gs://gwas_catalog_data/curated_inputs/gwas_catalog_unpublished_ancestries.tsv \\
+    -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/harmonised_list.txt gs://gwas_catalog_data/curated_inputs/harmonised_list.txt \\
+    -f https://raw.githubusercontent.com/opentargets/curation/master/genetics/GWAS_Catalog_study_curation.tsv gs://gwas_catalog_data/manifests/gwas_catalog_study_curation.tsv \\
+    -g https://www.ebi.ac.uk/gwas/api/search/stats
+
+
+    To preserve the logs from this command, you can specify the log file path using `--log-file` option. The log file can point to local or GCP path.
+    Currently only FTP and HTTP(s) protocols are supported for input and GCP protocol is supported for output.
+    """
+    # we always want to have the logs from this command uploaded to the target bucket
+    logger.debug("Running gwas_curation_update step.")
+    dry_run = ctx.obj["dry_run"]
+    if len(file_to_transfer) > MAX_CONCURRENT_CONNECTIONS:
+        logger.error(
+            "File transfer limit exceeded! Max %s connections allowed.",
+            MAX_CONCURRENT_CONNECTIONS,
+        )
+        sys.exit(1)
+    uri_map = [
+        {"input": urlparse(ftp_file), "output": urlparse(gcp_file)}
+        for ftp_file, gcp_file in file_to_transfer
+    ]
+    transfer_tasks = generate_transfer_tasks(uri_map, dry_run)
+
+    # capture latest release metadata
+    with requests.get(gwas_catalog_release_info_url) as response:
+        if not response.ok:
+            logger.error("Failed to fetch release info.")
+            sys.exit(1)
+        release_info = response.json()
+        for key, value in release_info.items():
+            logger.debug("%s: %s", key, value)
+
+        efo_version = release_info.get("efoversion")
+        logger.info("Diseases were mapped to %s EFO release.", efo_version)
+        logger.info("EFO version: %s", efo_version)
+        ensembl_build = release_info.get("ensemblbuild")
+        logger.info("Genes were mapped to v%s Ensembl release.", ensembl_build)
+
+    results = await asyncio.gather(*transfer_tasks)
+    if not dry_run:
+        logger.info("Transferred %s files.", len(results))
+    logger.info("gwas_curation_update step completed.")
+
+
+def generate_transfer_tasks(
+    uri_map: list[dict[str, ParseResult]], dry_run: bool
+) -> list[asyncio.Task[None]]:
+    """Generate transfer tasks.
+
+    Args:
+        uri_map (list[dict[str, ParseResult]]): list of transferable tasks, each should have `input` and `output` keys.
+        dry_run (bool): dry run flag.
+
+    Returns:
+        list[asyncio.Task[None]]: list of asyncio tasks.
+    """
+    ftp_transfer_list = []
+    http_transfer_list = []
+    for uri in uri_map:
+        if uri["input"].scheme != "ftp" and not uri["input"].scheme.startswith("http"):
+            logger.error("Only FTP and HTTP(s) protocols is supported at input.")
+            sys.exit(1)
+        if uri["output"].scheme != "gs":
+            logger.error("Only GCP protocol is supported at output.")
+            sys.exit(1)
+        in_server = uri["input"].netloc
+        out_server = uri["output"].netloc
+        in_prefix = "/".join(uri["input"].path.strip("/").split("/")[:-1])
+        in_file = uri["input"].path.strip("/").split("/")[-1]
+        out_prefix = "/".join(uri["output"].path[1:-1].split("/")[:-1])
+        out_bucket = uri["output"].path.split("/")[-1]
+        if uri["input"].scheme == "ftp":
+            ftp_transfer_list.append(
+                {
+                    "ftp_server": in_server,
+                    "ftp_prefix": in_prefix,
+                    "ftp_filename": in_file,
+                    "gcp_bucket": out_server,
+                    "gcp_prefix": out_prefix,
+                    "gcp_filename": out_bucket,
+                }
+            )
+        if uri["input"].scheme.startswith("http"):
+            http_transfer_list.append(
+                {
+                    "http_url": uri["input"].geturl(),
+                    "gcp_bucket": out_server,
+                    "gcp_prefix": out_prefix,
+                    "gcp_filename": out_bucket,
+                }
+            )
+    transfer_tasks = []
+    for transfer_obj in ftp_transfer_list:
+        transfer_tasks.append(
+            asyncio.create_task(
+                sync_from_ftp_to_gcp(
+                    transfer_obj["ftp_server"],
+                    transfer_obj["ftp_prefix"],
+                    transfer_obj["ftp_filename"],
+                    transfer_obj["gcp_bucket"],
+                    transfer_obj["gcp_prefix"],
+                    transfer_obj["gcp_filename"],
+                    dry_run=dry_run,
+                )
+            )
+        )
+
+    for transfer_obj in http_transfer_list:
+        transfer_tasks.append(
+            asyncio.create_task(
+                sync_from_http_to_gcp(
+                    transfer_obj["http_url"],
+                    transfer_obj["gcp_bucket"],
+                    transfer_obj["gcp_prefix"],
+                    transfer_obj["gcp_filename"],
+                    dry_run=dry_run,
+                )
+            )
+        )
+
+    return transfer_tasks
+
+
+async def sync_from_http_to_gcp(
+    url: str, gcp_bucket: str, gcp_prefix: str, gcp_file: str, *, dry_run: bool = True
+) -> None:
+    """Sync file from HTTP and upload to GCP.
+
+    This function fetches the data from the provided HTTP URL and uploads the content
+    directly to provided GCP bucket blob.
+
+    Args:
+        url (str): HTTP URL to fetch the data.
+        gcp_bucket (str): GCP bucket name.
+        gcp_prefix (str): GCP prefix.
+        gcp_file (str): GCP file name.
+        dry_run (bool, optional): Dry run flag. Defaults to True.
+    """
+    if dry_run:
+        logger.info(
+            "Attempting to transfer data from %s to gs://%s/%s/%s.",
+            url,
+            gcp_bucket,
+            gcp_prefix,
+            gcp_file,
+        )
+        return
+    logger.info("Retriving data from: %s.", url)
+    response = requests.get(url)
+    if not response.ok:
+        logger.error("Failed to fetch data from %s.", url)
+        return
+
+    content = response.content
+    bucket = storage.Client().bucket(gcp_bucket)
+    gcp_path = f"{gcp_prefix}/{gcp_file}" if gcp_prefix else gcp_file
+
+    blob = bucket.blob(gcp_path)
+    logger.info("Uploading the data to: gs://%s/%s.", gcp_bucket, gcp_path)
+    blob.upload_from_string(content.decode("utf-8"))
+
+
+async def sync_from_ftp_to_gcp(
+    ftp_server: str,
+    ftp_prefix: str,
+    ftp_file: str,
+    gcp_bucket: str,
+    gcp_prefix: str,
+    gcp_file: str,
+    *,
+    dry_run: bool = True,
+) -> None:
+    """Fetch files from FTP and upload to GCP.
+
+    This function fetches the data from the provided FTP server and uploads the content directly
+    to the provided GCP bucket blob.
+
+    Args:
+        ftp_server (str): FTP server.
+        ftp_prefix (str): FTP prefix.
+        ftp_file (str): FTP file name.
+        gcp_bucket (str): GCP bucket name.
+        gcp_prefix (str): GCP prefix.
+        gcp_file (str): GCP file name.
+        dry_run (bool, optional): Dry run flag. Defaults to True.
+
+    """
+    if dry_run:
+        logger.info(
+            "Attempting to transfer data from ftp://%s/%s/%s to gs://%s/%s/%s.",
+            ftp_server,
+            ftp_prefix,
+            ftp_file,
+            gcp_bucket,
+            gcp_prefix,
+            gcp_file,
+        )
+        return
+    with FTP(ftp_server) as ftp:
+        ftp.login()
+        bucket = storage.Client().bucket(gcp_bucket)
+        gcp_path = f"{gcp_prefix}/{gcp_file}" if gcp_prefix else gcp_file
+        blob = bucket.blob(gcp_path)
+        logger.info("Changing directory to %s.", ftp_prefix)
+        ftp.cwd(ftp_prefix)
+        dir_match = re.match(r"^.*(?P<release_date>\d{4}\/\d{2}\/\d{2}){1}$", ftp.pwd())
+        if dir_match:
+            logger.info("Found release date!: %s", dir_match.group("release_date"))
+        buffer = io.BytesIO()
+        logger.info(
+            "Retrieving data from: ftp://%s/%s/%s.", ftp_server, ftp_prefix, ftp_file
+        )
+        ftp.retrbinary(f"RETR {ftp_file}", lambda x: buffer.write(x))
+        content = buffer.getvalue().decode("utf-8")
+        buffer.close()
+        logger.info("Uploading data to: gs://%s/%s.", gcp_bucket, gcp_path)
+        blob.upload_from_string("".join(content))
+
+
+__all__ = ["update_gwas_curation_metadata_command"]

gentroutils/commands/utils.py

@@ -0,0 +1,135 @@
+"""Ütility functions for the CLI."""
+
+import asyncio
+import logging
+import sys
+import time
+from functools import wraps
+from pathlib import Path
+from urllib.parse import urlparse
+
+import click
+from google.cloud import storage
+
+logger = logging.getLogger("gentroutils")
+
+
+def set_log_file(ctx: click.Context, param: click.Option, log_file: str) -> str:
+    """Set logging file based on provided `log-file` flag.
+
+    This is a callback function called by the click.Option [--log-file] flag.
+    In case of the `log_file` being path to the GCP bucket the returned value
+    will be the local temporary file path. both log file paths (remote and local)
+    will be stored in the click context object for further reference at the end of the CLI run.
+
+
+    Args:
+        ctx (click.Context): click context
+        param (click.Option): click option
+        log_file (str): log file path
+
+    Raises:
+        click.BadParameter: If the log file is a directory or the URI scheme is not GCS.
+
+    Returns:
+        str: log file path
+    """
+    ctx.ensure_object(dict)
+    if not log_file:
+        return ""
+    logger.info("Extracting log file from the %s", param)
+    upload_to_gcp = False
+    if "://" in log_file:
+        upload_to_gcp = True
+    if upload_to_gcp:
+        parsed_uri = urlparse(log_file)
+        ctx.obj["gcp_log_file"] = log_file
+        if parsed_uri.scheme != "gs":
+            raise click.BadParameter("Only GCS is supported for logging upload")
+        log_file = parsed_uri.path.strip("/")
+        ctx.obj["local_log_file"] = log_file
+    ctx.obj["upload_to_gcp"] = upload_to_gcp
+
+    local_file = Path(log_file)
+    if local_file.exists() and local_file.is_dir():
+        raise click.BadParameter("Log file is a directory")
+    if local_file.exists() and local_file.is_file():
+        local_file.unlink()
+    if not local_file.exists():
+        local_file.touch()
+    logger.info("Logging to %s", local_file)
+    handler = logging.FileHandler(local_file)
+    formatter = logging.Formatter(
+        "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+    )
+    handler.setFormatter(formatter)
+    handler.setLevel(logging.DEBUG)
+    logger.addHandler(handler)
+    return str(local_file)
+
+
+def teardown_cli(ctx: click.Context) -> None:
+    """Teardown the gentroutils cli.
+
+    This function is used to as a teardown function for the CLI.
+    This will upload the log file to the GCP bucket if the `upload_to_gcp` flag is set in the context object.
+
+    Args:
+        ctx (click.Context): click context
+    """
+    if "upload_to_gcp" in ctx.obj and ctx.obj["upload_to_gcp"]:
+        gcp_file = ctx.obj["gcp_log_file"]
+        local_file = ctx.obj["local_log_file"]
+        client = storage.Client()
+        bucket_name = urlparse(gcp_file).netloc
+        bucket = client.bucket(bucket_name=bucket_name)
+        blob = bucket.blob(Path(local_file).name)
+        logger.info("Uploading %s to %s", local_file, gcp_file)
+        blob.upload_from_filename(local_file)
+        Path(local_file).unlink()
+    logger.info(
+        "Finished, elapsed time %s seconds", time.time() - ctx.obj["execution_start"]
+    )
+
+
+def set_log_lvl(_: click.Context, param: click.Option, value: int) -> int:
+    """Set logging level based on the number of provided `v` flags.
+
+    This is a callback function called by the click.Option [-v] flag.
+    For example
+    `-vv` - DEBUG
+    `-v`  - INFO
+    `no flag - ERROR
+
+    Args:
+        param (click.Option): click option
+        value (int): logging level
+
+    Returns:
+        int: logging level
+    """
+    logger.info("Extracting log level from the %s", param)
+    log_lvls = {0: logging.ERROR, 1: logging.INFO, 2: logging.DEBUG}
+    log_lvl = log_lvls.get(value, logging.DEBUG)
+    handler = logging.StreamHandler(sys.stdout)
+    formatter = logging.Formatter(
+        "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+    )
+    handler.setFormatter(formatter)
+    handler.setLevel(log_lvl)
+    logger.addHandler(handler)
+    return log_lvl
+
+
+def coro(f):
+    """Corutine wrapper for synchronous functions."""
+
+    @wraps(f)
+    def wrapper(*args, **kwargs):
+        """Wrapper around the synchronous function."""
+        return asyncio.run(f(*args, **kwargs))
+
+    return wrapper
+
+
+__all__ = ["set_log_file", "set_log_lvl", "coro", "logger", "teardown_cli"]

gentroutils-0.1.5.dist-info/METADATA

@@ -0,0 +1,71 @@
+Metadata-Version: 2.3
+Name: gentroutils
+Version: 0.1.5
+Summary: Add your description here
+Author-email: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: click>=8.1.7
+Requires-Dist: google-cloud-storage>=2.18.1
+Requires-Dist: pyfiglet>=1.0.2
+Requires-Dist: requests>=2.32.3
+Description-Content-Type: text/markdown
+
+# gentroutils
+
+[![Tests](https://github.com/opentargets/gentroutils/actions/workflows/test.yaml/badge.svg?event=push)](https://github.com/opentargets/gentroutils/actions/workflows/test.yaml)
+![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)
+
+Set of Command Line Interface tools to process Open Targets Genetics GWAS data.
+
+## Installation
+
+```
+pip install gentroutils
+```
+
+## Available commands
+
+To see all available commands after installation run
+
+```{bash}
+gentroutils --help
+```
+
+## Contribute
+
+To be able to contribute to the project you need to set it up. This project
+runs on:
+
+- [x] python 3.10.8
+- [x] rye (package manager)
+- [x] uv (dependency manager)
+
+To set up the project run
+
+```{bash}
+make dev
+```
+
+The command will install above dependencies (initial requirements are curl and bash) if not present and
+install all python dependencies listed in `pyproject.toml`. Finally the command will install `pre-commit` hooks
+requred to be run before the commit is created.
+
+The project has additional `dev` dependencies that include the list of packages used for testing purposes.
+All of the `dev` depnendencies are automatically installed by `rye`.
+
+To see all available dev commands
+
+Run following command to see all available dev commands
+
+```{bash}
+make help
+```
+
+### Manual testing of CLI module
+
+To check CLI execution manually you need to run
+
+```{bash}
+rye run gentroutils
+```

gentroutils-0.1.5.dist-info/RECORD

@@ -0,0 +1,9 @@
+gentroutils/__init__.py,sha256=aHDzbBMrnsgdcO_FfsYCbbPXProynwB7_2nfyc4UGp8,1281
+gentroutils/commands/__init__.py,sha256=avkqzwa1ck__rLVN0Wqfpr3eHtKS6TvyPeeaHcguJuw,210
+gentroutils/commands/update_gwas_curation_metadata.py,sha256=7pBBkB6JF3VfT12xiP78MT_pmn0Wv4CF7Tm5TPgBXf8,12525
+gentroutils/commands/utils.py,sha256=9Wyptjww9hiAufCFILdnjdDOE6X6TdtyTWJOTkoIRqg,4316
+gentroutils-0.1.5.dist-info/METADATA,sha256=9PFlHuJakF2bnJfF9d6kPepH0jdRJM3g70GevV5Q7fM,1795
+gentroutils-0.1.5.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+gentroutils-0.1.5.dist-info/entry_points.txt,sha256=IvxZyBBD71Ota0aPMtVaJzI9OSX5_f-iH4ZJx6sY53w,48
+gentroutils-0.1.5.dist-info/licenses/LICENSE,sha256=RFhQPdSOiMTguUX7JSoIuTxA7HVzCbj_p8WU36HjUQQ,10947
+gentroutils-0.1.5.dist-info/RECORD,,

gentroutils-0.1.5.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.25.0
+Root-Is-Purelib: true
+Tag: py3-none-any

gentroutils-0.1.5.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+gentroutils = gentroutils:cli

gentroutils-0.1.5.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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