gentroutils 0.2.0__py3-none-any.whl → 1.6.0.dev1__py3-none-any.whl

gentroutils/commands/utils.py

@@ -1,160 +0,0 @@
-"""Ütility functions for the CLI."""
-
-import asyncio
-import logging
-import sys
-import time
-from functools import wraps
-from pathlib import Path
-from tempfile import NamedTemporaryFile
-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
-    ctx.obj["upload_to_gcp"] = upload_to_gcp
-
-    if upload_to_gcp:
-        parsed_uri = urlparse(log_file)
-        if parsed_uri.scheme != "gs":
-            raise click.BadParameter("Only GCS is supported for logging upload")
-        tmp_file = NamedTemporaryFile(delete=False)
-        logger.info("Logging to temporary file %s", tmp_file.name)
-        handler = logging.FileHandler(tmp_file.name)
-        formatter = logging.Formatter(
-            "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-        )
-        handler.setFormatter(formatter)
-        handler.setLevel(logging.DEBUG)
-        logger.addHandler(handler)
-        ctx.obj["local_log_file"] = tmp_file.name
-        ctx.obj["local_log_file_obj"] = tmp_file
-        ctx.obj["gcp_log_file"] = log_file
-        return tmp_file.name
-
-    else:
-        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.parent.mkdir(parents=True, exist_ok=True)
-            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"]
-        with open(local_file, "r") as f:
-            content = f.read()
-        try:
-            client = storage.Client()
-            bucket_name = urlparse(gcp_file).netloc
-            bucket = client.bucket(bucket_name=bucket_name)
-            file_name = urlparse(gcp_file).path.lstrip("/")
-            blob = bucket.blob(file_name)
-            logger.info("Uploading %s to %s", local_file, gcp_file)
-            if ctx.obj["dry_run"]:
-                logger.info("Dry run, skipping the upload of the log file")
-            else:
-                blob.upload_from_string(content)
-                ctx.obj["local_log_file_obj"].close()
-        except Exception as e:
-            msg = f"Failed to upload log file to GCP {e}"
-            logger.error(click.style(msg, fg="red"))
-    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-0.2.0.dist-info/METADATA

@@ -1,107 +0,0 @@
-Metadata-Version: 2.3
-Name: gentroutils
-Version: 0.2.0
-Summary: Open Targets python genetics utility CLI tools
-Author-email: Szymon Szyszkowski <ss60@sanger.ac.uk>
-License: Apache-2.0
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Healthcare Industry
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Operating System :: Unix
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-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
-```
-
-### Updating gwas catalog metadata
-
-To update gwas catalog metadata run folliwing command
-
-```bash
-gentroutils  -vvv -q gs://ot_orchestration/tests/gentroutils/log.txt  update-gwas-curation-metadata \
--f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-associations_ontology-annotated.tsv gs://ot_orchestration/tests/gentroutils/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://ot_orchestration/tests/gentroutils/gwas-catalog-download-studies-v1.0.3.1.txt \
--f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-download-ancestries-v1.0.3.1.txt gs://ot_orchestration/tests/gentroutils/gwas-catalog-download-ancestries-v1.0.3.1.txt \
--g https://www.ebi.ac.uk/gwas/api/search/stats
-```
-
-The command `update-gwas-curation-metadata` fetches the data from the ftp server and transfers them to the gcp without intermediate temporary files. The download(s) and upload(s) are made asyncronously.
-
-The logs from the command are saved under the `-q` log file, if specified `gcp` log file, then the file will be uploaded after the command has run.
-
-To test the command run it with `-d` == `--dry-run`, this will just mark the input and output destinations.
-To allow for full logs to be transmitted to the log file, use `-vvv` to increase the verbosity of the logs
-
-> [!NOTE]
-> Change the path to the output `gcp` files to make sure they are saved under requested path
-
-> [!WARNING]
-> Please read before running the command!:
->
-> * The above command has some default values set for the input and output files, make sure you test them in `--dry-run` so the existing files will not get overwritten!
-> * Make sure to run `gcloud auth application-default login` to allow to use Google Cloud Python SDK before running the command
-
-## 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-0.2.0.dist-info/RECORD

@@ -1,9 +0,0 @@
-gentroutils/__init__.py,sha256=aHDzbBMrnsgdcO_FfsYCbbPXProynwB7_2nfyc4UGp8,1281
-gentroutils/commands/__init__.py,sha256=avkqzwa1ck__rLVN0Wqfpr3eHtKS6TvyPeeaHcguJuw,210
-gentroutils/commands/update_gwas_curation_metadata.py,sha256=4Pb2YdEnfulQklFh0KBvAOBnylCsDIAye7Keq2dC0mY,10937
-gentroutils/commands/utils.py,sha256=zYIzu47f-_a3nBeVXRR5xg5QiklrwES8uYNNhjed7gA,5384
-gentroutils-0.2.0.dist-info/METADATA,sha256=lMJ2JdqokHojQaY-hWhs9IvCJ4ei4vBpOfsOAfgBw4E,4061
-gentroutils-0.2.0.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-gentroutils-0.2.0.dist-info/entry_points.txt,sha256=IvxZyBBD71Ota0aPMtVaJzI9OSX5_f-iH4ZJx6sY53w,48
-gentroutils-0.2.0.dist-info/licenses/LICENSE,sha256=RFhQPdSOiMTguUX7JSoIuTxA7HVzCbj_p8WU36HjUQQ,10947
-gentroutils-0.2.0.dist-info/RECORD,,

gentroutils-0.2.0.dist-info/entry_points.txt

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