metahq-cli 0.1.1__tar.gz → 1.0.0rc1__tar.gz

metahq_cli-1.0.0rc1/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Krishnan Lab
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

{metahq_cli-0.1.1 → metahq_cli-1.0.0rc1}/PKG-INFO

@@ -1,8 +1,9 @@
 Metadata-Version: 2.4
 Name: metahq-cli
-Version: 0.1.1
+Version: 1.0.0rc1
 Summary: The meta-hq CLI.
 Author-email: Parker Hicks <parker.hicks@cuanschutz.edu>, Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
+License-File: LICENSE
 Keywords: CLI,Data Curation,Database,Public Biomedical Data
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
@@ -20,23 +21,32 @@ Provides-Extra: dev
 Requires-Dist: black; extra == 'dev'
 Requires-Dist: flake8; extra == 'dev'
 Requires-Dist: isort; extra == 'dev'
+Requires-Dist: mkdocs-click; extra == 'dev'
+Requires-Dist: mkdocs-material; extra == 'dev'
+Requires-Dist: mkdocs>=1.6.1; extra == 'dev'
+Requires-Dist: mkdocstrings[python]; extra == 'dev'
 Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: pymdown-extensions; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
 Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: vulture; extra == 'dev'
 Provides-Extra: test
 Requires-Dist: pytest-benchmark; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
 Requires-Dist: pytest>=8.0; extra == 'test'
 Description-Content-Type: text/markdown
 
-<img src="media/metahq_logo.png" alt="Logo" width="400" height="200"/>
+<div align="left">
+    <img src="https://raw.githubusercontent.com/krishnanlab/meta-hq/main/media/metahq_cli_logo.png" alt="CLI Logo" width="400" height="200" />
+</div>
 
 ![CLI Tests](https://github.com/krishnanlab/meta-hq/workflows/CLI%20Tests/badge.svg)
-![Python](https://img.shields.io/badge/python-3.11+-blue.svg)
+![Python](https://img.shields.io/badge/python-3.12+-blue.svg)
 ![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)
 ![pypi](https://img.shields.io/pypi/v/metahq-cli.svg)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
-A package to query the MetaHQ database.
+A command line interface to query the MetaHQ database.
 
 ## Key features
 

{metahq_cli-0.1.1 → metahq_cli-1.0.0rc1}/README.md

@@ -1,11 +1,14 @@
-<img src="media/metahq_logo.png" alt="Logo" width="400" height="200"/>
+<div align="left">
+    <img src="https://raw.githubusercontent.com/krishnanlab/meta-hq/main/media/metahq_cli_logo.png" alt="CLI Logo" width="400" height="200" />
+</div>
 
 ![CLI Tests](https://github.com/krishnanlab/meta-hq/workflows/CLI%20Tests/badge.svg)
-![Python](https://img.shields.io/badge/python-3.11+-blue.svg)
+![Python](https://img.shields.io/badge/python-3.12+-blue.svg)
 ![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)
 ![pypi](https://img.shields.io/pypi/v/metahq-cli.svg)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
-A package to query the MetaHQ database.
+A command line interface to query the MetaHQ database.
 
 ## Key features
 

{metahq_cli-0.1.1 → metahq_cli-1.0.0rc1}/pyproject.toml

@@ -34,6 +34,12 @@ dev = [
     "isort",
     "flake8",
     "mypy",
+    "mkdocs>=1.6.1",
+    "mkdocstrings[python]",
+    "mkdocs-material",
+    "mkdocs-click",
+    "pymdown-extensions",
+    "vulture",
 ]
 
 test = [

metahq_cli-1.0.0rc1/src/metahq_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.0.0-rc.1"

{metahq_cli-0.1.1 → metahq_cli-1.0.0rc1}/src/metahq_cli/commands/__init__.py

@@ -1,6 +1,8 @@
+from metahq_cli.commands.delete import delete
 from metahq_cli.commands.retrieve import retrieve_commands
 from metahq_cli.commands.search import search
 from metahq_cli.commands.setup import setup
 from metahq_cli.commands.supported import supported
+from metahq_cli.commands.validate import validate
 
-__all__ = ["retrieve_commands", "setup", "search", "supported"]
+__all__ = ["retrieve_commands", "setup", "search", "supported", "validate", "delete"]

metahq_cli-1.0.0rc1/src/metahq_cli/commands/delete.py

@@ -0,0 +1,63 @@
+"""
+CLI command to delete old version of MetaHQ
+"""
+
+import click
+import os
+import shutil
+import sys
+from metahq_core.util.progress import console
+from pathlib import Path
+
+from metahq_cli.logger import setup_logger
+from metahq_cli.util.common_args import logging_args
+from metahq_core.util.supported import get_default_log_dir
+from metahq_cli.util.helpers import set_verbosity
+
+from metahq_core.util.supported import get_config, get_config_file
+
+@click.command(name="delete", context_settings={"help_option_names": ["-h", "--help"]})
+@click.option(
+    "-l",
+    "--log-dir",
+    type=click.Path(),
+    default="default",
+    help="Path to directory storing logs. Default is `/home/path/MetaHQ`.",
+)
+@click.option(
+    "--all",
+    "-a",
+    is_flag=True,
+    default=False,
+    help="Will delete everything in MetaHQ directory",
+)
+@logging_args
+def delete(log_level: str, log_dir: str, quiet: bool, all: bool):
+    """Delete old version of MetaHQ"""
+    if log_dir == "default":
+        log_dir = str(get_default_log_dir())
+
+    logger = setup_logger(__name__, level=log_level, log_dir=log_dir, console=console)
+    verbose = set_verbosity(quiet)
+    
+    # read in config
+    config = get_config()
+    config_path = get_config_file()
+    logger.info(f"The path to config file is found at: {config_path}")
+    logger.info(f"Information in the config file is: {config}")
+         
+    if click.confirm(
+        f"Delete MetaHQ database and config file or config directory?",
+        default=False,
+    ):
+        logger.info("Deleting existing data directory...")
+        shutil.rmtree(config["data_dir"])
+        if all:
+            logger.info("Deleting existing config directory...")
+            shutil.rmtree(config_path.parent)
+        else:
+            logger.info("Deleting existing config file...")
+            os.remove(config_path)
+    else:
+        logger.info("Keeping existing data directory and config file.")
+        sys.exit("Terminating...")

{metahq_cli-0.1.1 → metahq_cli-1.0.0rc1}/src/metahq_cli/commands/retrieve.py

@@ -4,7 +4,7 @@ CLI command to retrieve annotations and labels from meta-hq.
 Author: Parker Hicks
 Date: 2025-09-05
 
-Last updated: 2025-11-24 by Parker Hicks
+Last updated: 2025-12-01 by Parker Hicks
 """
 
 import click
@@ -61,15 +61,17 @@ def retrieve_commands():
     """Retrieval commands for tissue, disease, sex, and age annotations."""
 
 
-@retrieve_commands.command("tissues")
-@logging_args
+@retrieve_commands.command("age")
+@click.option(
+    "--terms",
+    type=AGE_GROUP_OPT,
+    default="all",
+    help="Age groups to choose. Can combine like 'fetus,adult'.",
+)
 @retrieval_args
-@ontology_retrieval_args
-@click.option("--terms", type=str, default="UBERON:0000948,UBERON:0000955")
-def retrieve_tissues(
-    terms, level, mode, fmt, metadata, filters, output, log_level, quiet, direct
-):
-    """Retrieval command for tissue ontology terms."""
+@logging_args
+def retrieve_age(terms, level, fmt, metadata, filters, output, log_level, quiet):
+    """Retrieval command for age group annotations."""
     if metadata == "default":
         metadata = level
 
@@ -78,17 +80,17 @@ def retrieve_tissues(
         __name__, console=get_console(), level=log_level, log_dir=get_log_dir()
     )
 
-    # hidden from user. Used to test annotation quality.
-    mode = check_direct(mode, direct, verbose, log)
     builder = Builder(logger=log, verbose=verbose)
 
     # parse and check filters
     filters = builder.get_filters(filters)
 
     # make configs
-    query_config = builder.query_config("geo", "tissue", level, filters)
-    curation_config = builder.curation_config(terms, mode, "uberon")
-    output_config = builder.output_config(output, fmt, metadata, level=level)
+    query_config = builder.query_config("geo", "age", level, filters)
+    curation_config = builder.curation_config(terms, "direct", "age")
+    output_config = builder.output_config(
+        output, fmt, metadata, level=level, attribute="age"
+    )
 
     # retrieve
     retriever = Retriever(
@@ -98,10 +100,10 @@ def retrieve_tissues(
 
 
 @retrieve_commands.command("diseases")
-@logging_args
+@click.option("--terms", type=str, default="MONDO:0004994,MONDO:0018177")
 @retrieval_args
 @ontology_retrieval_args
-@click.option("--terms", type=str, default="MONDO:0004994,MONDO:0018177")
+@logging_args
 def retrieve_diseases(
     terms, level, mode, fmt, metadata, filters, output, log_level, quiet, direct
 ):
@@ -124,7 +126,9 @@ def retrieve_diseases(
     # make configs
     query_config = builder.query_config("geo", "disease", level, filters)
     curation_config = builder.curation_config(terms, mode, "mondo")
-    output_config = builder.output_config(output, fmt, metadata, level=level)
+    output_config = builder.output_config(
+        output, fmt, metadata, level=level, attribute="disease"
+    )
 
     # retrieve
     retriever = Retriever(
@@ -134,9 +138,9 @@ def retrieve_diseases(
 
 
 @retrieve_commands.command("sex")
-@logging_args
-@retrieval_args
 @click.option("--terms", type=str, default="male,female")
+@retrieval_args
+@logging_args
 def retrieve_sex(terms, level, fmt, metadata, filters, output, log_level, quiet):
     """Retrieval command for sex annotations."""
     if metadata == "default":
@@ -155,7 +159,9 @@ def retrieve_sex(terms, level, fmt, metadata, filters, output, log_level, quiet)
     # make configs
     query_config = builder.query_config("geo", "sex", level, filters)
     curation_config = builder.curation_config(terms, "direct", "sex")
-    output_config = builder.output_config(output, fmt, metadata, level=level)
+    output_config = builder.output_config(
+        output, fmt, metadata, level=level, attribute="sex"
+    )
 
     # retrieve
     retriever = Retriever(
@@ -164,17 +170,15 @@ def retrieve_sex(terms, level, fmt, metadata, filters, output, log_level, quiet)
     retriever.retrieve()
 
 
-@retrieve_commands.command("age")
-@logging_args
+@retrieve_commands.command("tissues")
+@click.option("--terms", type=str, default="UBERON:0000948,UBERON:0000955")
 @retrieval_args
-@click.option(
-    "--terms",
-    type=AGE_GROUP_OPT,
-    default="all",
-    help="Age groups to choose. Can combine like 'fetus,adult'.",
-)
-def retrieve_age(terms, level, fmt, metadata, filters, output, log_level, quiet):
-    """Retrieval command for age group annotations."""
+@ontology_retrieval_args
+@logging_args
+def retrieve_tissues(
+    terms, level, mode, fmt, metadata, filters, output, log_level, quiet, direct
+):
+    """Retrieval command for tissue ontology terms."""
     if metadata == "default":
         metadata = level
 
@@ -183,15 +187,19 @@ def retrieve_age(terms, level, fmt, metadata, filters, output, log_level, quiet)
         __name__, console=get_console(), level=log_level, log_dir=get_log_dir()
     )
 
+    # hidden from user. Used to test annotation quality.
+    mode = check_direct(mode, direct, verbose, log)
     builder = Builder(logger=log, verbose=verbose)
 
     # parse and check filters
     filters = builder.get_filters(filters)
 
     # make configs
-    query_config = builder.query_config("geo", "age", level, filters)
-    curation_config = builder.curation_config(terms, "direct", "age")
-    output_config = builder.output_config(output, fmt, metadata, level=level)
+    query_config = builder.query_config("geo", "tissue", level, filters)
+    curation_config = builder.curation_config(terms, mode, "uberon")
+    output_config = builder.output_config(
+        output, fmt, metadata, level=level, attribute="tissue"
+    )
 
     # retrieve
     retriever = Retriever(

{metahq_cli-0.1.1 → metahq_cli-1.0.0rc1}/src/metahq_cli/commands/search.py

@@ -22,7 +22,6 @@ DEFAULT_TOP_HITS = 3
 
 
 @click.command(name="search", context_settings={"help_option_names": ["-h", "--help"]})
-@logging_args
 @click.option("--query", type=str, required=True, help="Search query")
 @click.option(
     "--db",
@@ -30,6 +29,7 @@ DEFAULT_TOP_HITS = 3
     type=str,
     default="default",
     help="DuckDB file",
+    hidden=True,
 )
 @click.option(
     "--type",
@@ -65,6 +65,7 @@ DEFAULT_TOP_HITS = 3
 @click.option(
     "--scopes", "-x", is_flag=True, default=False, help="Include scopes in synonym list"
 )
+@logging_args
 def search(
     query,
     db,

{metahq_cli-0.1.1 → metahq_cli-1.0.0rc1}/src/metahq_cli/commands/setup.py

@@ -4,15 +4,14 @@ Command to set up the meta-hq CLI.
 Author: Parker Hicks
 Date: 2025-09-05
 
-Last updated: 2025-11-24 by Parker Hicks
+Last updated: 2025-11-26 by Parker Hicks
 """
 
+from pathlib import Path
+
 import click
 from metahq_core.util.progress import console
-from metahq_core.util.supported import (
-    get_default_data_dir,
-    get_default_log_dir,
-)
+from metahq_core.util.supported import get_default_data_dir, get_default_log_dir
 
 from metahq_cli.logger import setup_logger
 from metahq_cli.setup.config import Config
@@ -22,18 +21,31 @@ from metahq_cli.util.helpers import set_verbosity
 from metahq_cli.util.supported import LATEST_DATABASE
 
 
-@click.command
-@logging_args
-@click.option("--doi", type=str, default="latest")
-@click.option("--data-dir", type=click.Path(), default="default")
+@click.command(name="setup", context_settings={"help_option_names": ["-h", "--help"]})
 @click.option(
-    "--log-dir",
+    "-d",
+    "--doi",
     type=str,
+    default="latest",
+    help="Zenodo DOI of the MetaHQ database. Default is `latest`.",
+)
+@click.option(
+    "-o",
+    "--data-dir",
+    type=click.Path(),
     default="default",
-    help="Path to directory storing logs.",
+    help="Path to directory to store the database. Default is `/home/path/.metahq_data`.",
 )
+@click.option(
+    "-l",
+    "--log-dir",
+    type=click.Path(),
+    default="default",
+    help="Path to directory storing logs. Default is `/home/path/MetaHQ`.",
+)
+@logging_args
 def setup(doi: str, data_dir: str, log_level: str, log_dir: str, quiet: bool):
-    """Creates the meta-hq package configuration file."""
+    """Download the MetaHQ database and configure the CLI."""
     if log_dir == "default":
         log_dir = str(get_default_log_dir())
 
@@ -48,7 +60,7 @@ def setup(doi: str, data_dir: str, log_level: str, log_dir: str, quiet: bool):
 
     logger.info("Downloading MetaHQ database...")
     downloader = Downloader(
-        doi, data_dir, logger=logger, logdir=log_dir, verbose=verbose
+        doi, data_dir, logger=logger, logdir=str(log_dir), verbose=verbose
     )
     downloader.get()
     downloader.extract()

metahq_cli-1.0.0rc1/src/metahq_cli/commands/validate.py

@@ -0,0 +1,51 @@
+"""
+CLI command to validate data hasen't changed.
+"""
+
+import click
+from metahq_core.util.progress import console
+from pathlib import Path
+import hashlib
+
+from metahq_cli.logger import setup_logger
+from metahq_cli.util.common_args import logging_args
+from metahq_core.util.supported import get_default_log_dir
+from metahq_cli.util.helpers import set_verbosity
+
+from metahq_core.util.supported import get_config, get_config_file
+from metahq_cli.util._validate import check_md5_match
+
+@click.command(name="validate", context_settings={"help_option_names": ["-h", "--help"]})
+@click.option(
+    "-l",
+    "--log-dir",
+    type=click.Path(),
+    default="default",
+    help="Path to directory storing logs. Default is `/home/path/MetaHQ`.",
+)
+@logging_args
+def validate(log_level: str, log_dir: str, quiet: bool):
+    """Validate files are unchanged"""
+    if log_dir == "default":
+        log_dir = str(get_default_log_dir())
+
+    logger = setup_logger(__name__, level=log_level, log_dir=log_dir, console=console)
+    verbose = set_verbosity(quiet)
+    
+    # read in config
+    config = get_config()
+    config_path = get_config_file()
+    logger.info(f"The path to config file is found at: {config_path}")
+    logger.info(f"Validating the files for the config options: {config}")
+    
+    changed_files = check_md5_match(config["zenodo_doi"], config["data_dir"])
+    
+    if len(changed_files) == 0:
+        logger.info("Validation Passed: All files validated to be correct")
+    elif len(changed_files) > 0:
+        logger.warning(
+            f"Validation Failed: The following files are not the same as when downloaded. "
+            "Run `metahq setup` again."
+        )
+        for afile in changed_files:
+            logger.warning(afile)

{metahq_cli-0.1.1 → metahq_cli-1.0.0rc1}/src/metahq_cli/logger.py

@@ -4,13 +4,12 @@ Logger setup.
 Author: Parker Hicks
 Date: 2025-10-16
 
-Last updated: 2025-11-21 by Parker Hicks
+Last updated: 2026-02-04 by Parker Hicks
 """
 
 from __future__ import annotations
 
 import logging
-from logging.handlers import TimedRotatingFileHandler
 from pathlib import Path
 from typing import TYPE_CHECKING
 
@@ -46,22 +45,22 @@ def setup_logger(
     log_dir: str | Path,
     level: int | str = logging.INFO,
 ) -> logging.Logger:
-    """
-    Sets up a logger.
+    """Sets up a logger.
+
+    Arguments:
+        name (str):
+            Logger name.
 
-    Parameters
-    ----------
-    name: str
-        Logger name.
+        console (rich.Console):
+            Console object to send logging information to.
 
-    log_dir: str | Path
-        Path to logging directory. Default is ~/metahq/logs
+        log_dir (str | Path):
+            Path to logging directory.
 
-    level: int
-        Logging level.
+        level (int):
+            Logging level.
 
-    Returns
-    -------
+    Returns:
         Configured logger.
 
     """
@@ -94,11 +93,8 @@ def setup_logger(
     logger.addHandler(console_handler)
 
     # file handler
-    file_handler = TimedRotatingFileHandler(
+    file_handler = logging.FileHandler(
         Path(log_dir) / "log.log",
-        when="midnight",
-        interval=1,
-        backupCount=30,
         encoding="utf-8",
     )
     # file formatter

{metahq_cli-0.1.1 → metahq_cli-1.0.0rc1}/src/metahq_cli/main.py

@@ -9,7 +9,7 @@ Last updated: 2025-09-05
 
 import click
 
-from metahq_cli.commands import retrieve_commands, search, setup, supported
+from metahq_cli.commands import retrieve_commands, search, setup, supported, validate, delete
 
 
 @click.group()
@@ -21,6 +21,8 @@ main.add_command(setup)
 main.add_command(search)
 main.add_command(supported)
 main.add_command(retrieve_commands, name="retrieve")
+main.add_command(validate)
+main.add_command(delete)
 
 if __name__ == "__main__":
     main()