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maxibormaxibor
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remove amdirt capitalization
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‎.github/workflows/ci_test.yml‎

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name: AMDirT-CI
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name: amdirt-CI
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on: [push, pull_request]
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‎.github/workflows/publish_pypi.yml‎

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- name: Setup Python
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uses: actions/setup-python@v3
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with:
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python-version: "3.9"
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- name: Build AMDirT
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python-version: "3.12"
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- name: Build amdirt
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run: |
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pip install wheel
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python setup.py sdist bdist_wheel

‎AMDirT/__init__.py‎

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__version__ = "1.6.3"
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__version__ = "1.6.4"

‎AMDirT/assets/tables.json‎

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"ancientmetagenome-environmental": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv",
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"ancientmetagenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv",
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"ancientsinglegenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv",
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"test": "https://raw.githubusercontent.com/SPAAM-community/AMDirT/dev/tests/data/valid.tsv"
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"test": "https://raw.githubusercontent.com/SPAAM-community/amdirt/dev/tests/data/valid.tsv"
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},
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"samples_schema": {
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"ancientmetagenome-environmental": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples_schema.json",
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"ancientmetagenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples_schema.json",
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"ancientsinglegenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples_schema.json",
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"test": "https://raw.githubusercontent.com/SPAAM-community/AMDirT/dev/tests/data/schema.json"
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"test": "https://raw.githubusercontent.com/SPAAM-community/amdirt/dev/tests/data/schema.json"
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},
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"libraries": {
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"ancientmetagenome-environmental": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv",
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"ancientmetagenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv",
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"ancientsinglegenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv",
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"test": "https://raw.githubusercontent.com/SPAAM-community/AMDirT/dev/tests/data/valid_libaries.tsv"
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"test": "https://raw.githubusercontent.com/SPAAM-community/amdirt/dev/tests/data/valid_libaries.tsv"
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},
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"libraries_schema": {
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"ancientmetagenome-environmental": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries_schema.json",
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"ancientmetagenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries_schema.json",
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"ancientsinglegenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries_schema.json",
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"test": "https://raw.githubusercontent.com/SPAAM-community/AMDirT/dev/tests/data/libraries_schema.json"
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"test": "https://raw.githubusercontent.com/SPAAM-community/amdirt/dev/tests/data/libraries_schema.json"
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}
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}

‎AMDirT/autofill/__init__.py‎

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@@ -1,7 +1,7 @@
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from AMDirT.validate.domain import DatasetValidator
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from AMDirT.core import get_json_path, logger
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from AMDirT.core.ena import ENAPortalAPI
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from AMDirT.validate.exceptions import NetworkError
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from amdirt.validate.domain import DatasetValidator
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from amdirt.core import get_json_path, logger
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from amdirt.core.ena import ENAPortalAPI
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from amdirt.validate.exceptions import NetworkError
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import json
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import sys

‎AMDirT/cli.py‎

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import click
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from AMDirT import __version__
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from AMDirT.validate import run_validation
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from AMDirT.viewer import run_app
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from AMDirT.convert import run_convert
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from AMDirT.core import get_json_path, get_amdir_tags, get_latest_tag
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from AMDirT.autofill import run_autofill
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from AMDirT.merge import merge_new_df
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from AMDirT.download import download as download_amdir
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from amdirt import __version__
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from amdirt.validate import run_validation
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from amdirt.viewer import run_app
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from amdirt.convert import run_convert
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from amdirt.core import get_json_path, get_amdir_tags, get_latest_tag
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from amdirt.autofill import run_autofill
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from amdirt.merge import merge_new_df
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from amdirt.download import download as download_amdir
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from json import load
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@click.option("--verbose", is_flag=True, help="Verbose mode")
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def cli(ctx, verbose, no_args_is_help=True, **kwargs):
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"""\b
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AMDirT: Performs validity check of AncientMetagenomeDir datasets
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Authors: AMDirT development team and the SPAAM community
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Homepage & Documentation: https://github.com/SPAAM-community/AMDirT
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amdirt: Performs validity check of AncientMetagenomeDir datasets
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Authors: amdirt development team and the SPAAM community
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Homepage & Documentation: https://github.com/SPAAM-community/amdirt
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\b
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"""
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ctx.ensure_object(dict)
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)
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def download(no_args_is_help=True, **kwargs):
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"""\b
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Download a table from the AMDirT repository
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Download a table from the amdirt repository
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"""
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download_amdir(**kwargs)
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‎AMDirT/convert/__init__.py‎

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from sys import path
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import os
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from AMDirT.core import (
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from amdirt.core import (
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prepare_accession_table,
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prepare_bibtex_file,
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prepare_eager_table,
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get_remote_resources,
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get_json_path,
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)
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from AMDirT.validate import AMDirValidator
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from AMDirT.validate.exceptions import DatasetValidationError
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from amdirt.validate import AMDirValidator
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from amdirt.validate.exceptions import DatasetValidationError
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from json import load
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from AMDirT.core import logger
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from amdirt.core import logger
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import pandas as pd
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import warnings
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mag=False,
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verbose=False,
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):
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"""Run the AMDirT conversion application to input samplesheet tables for different pipelines
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"""Run the amdirt conversion application to input samplesheet tables for different pipelines
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Args:
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samples (str): Path to AncientMetagenomeDir filtered samples tsv file

‎AMDirT/core/__init__.py‎

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colorlog.ColoredFormatter("%(log_color)s%(name)s [%(levelname)s]: %(message)s")
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)
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logger = colorlog.getLogger("AMDirT")
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logger = colorlog.getLogger("amdirt")
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logger.addHandler(handler)
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logger.propagate = False
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def get_json_path():
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path = get_module_dir("AMDirT.assets").joinpath("tables.json")
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path = get_module_dir("amdirt.assets").joinpath("tables.json")
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return path
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‎AMDirT/core/ena.py‎

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import requests
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from AMDirT.core import logger
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from amdirt.core import logger
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import os
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from typing import List, Dict
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‎AMDirT/download/__init__.py‎

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from AMDirT.core import (
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from amdirt.core import (
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logger,
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get_amdir_tags,
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get_remote_resources,
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def download(table: str, table_type: str, release: str, output: str = ".") -> str:
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"""
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Download a table from the AMDirT repository.
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Download a table from the amdirt repository.
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Parameters
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----------

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