text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
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# Copyright©2021, Regents of the University of California
# http://creativecommons.org/licenses/BSD
"""List existing shoulders
"""
import argparse
import logging
import django.core.management
import impl.nog_sql.shoulder
import impl.nog_sql.util
log = logging.getLogger(__name__)
class Command(django.core.manag... | CDLUC3/ezid | ezidapp/management/commands/shoulder-list.py | .py | 15afef2926b6a555 | 7.56 | 12 |
# Copyright©2021, Regents of the University of California
# http://creativecommons.org/licenses/BSD
"""Mint one or more new identifiers on an existing shoulder
"""
import argparse
import logging
import django.core.management
import ezidapp.models.shoulder
import impl.nog_sql.ezid_minter
import impl.nog_sql.util
... | CDLUC3/ezid | ezidapp/management/commands/shoulder-mint.py | .py | 1475e7af8116672f | 7.56 | 12 |
# Copyright©2021, Regents of the University of California
# http://creativecommons.org/licenses/BSD
"""Update the Datacenter for an existing DOI shoulder
"""
import argparse
import logging
import django.core.management
import ezidapp.models.datacenter
import ezidapp.models.shoulder
import impl.nog_sql.shoulder
im... | CDLUC3/ezid | ezidapp/management/commands/shoulder-update-datacenter.py | .py | 2af2286a4c5bec09 | 7.56 | 12 |
#!/usr/bin/env -S uv run --script
# /// script
# requires-python = ">=3.11"
# dependencies = ["youtube-transcript-api==1.2.4"]
# ///
"""
Extract transcript from a YouTube video.
Usage:
get-transcript.py <video_id_or_url> [--timestamps] [--language LANGUAGE]
"""
import argparse
import re
import sys
from youtube_t... | ipruning/dotfiles | modules/bin/get-transcript.py | .py | 94c6fb5c09fba818 | 7.57 | 13 |
#!/usr/bin/env -S uv run --script
# /// script
# requires-python = ">=3.11"
# dependencies = [
# "loguru==0.7.3",
# "rich==15.0.0",
# ]
# ///
import os
import re
import subprocess
import sys
from loguru import logger
from rich.console import Console
from rich.text import Text
logger.remove()
logger.add(
... | ipruning/dotfiles | modules/bin/link.py | .py | b903ae043c12a94c | 7.57 | 13 |
#!/usr/bin/env -S uv run --script
# /// script
# requires-python = ">=3.11"
# ///
import logging
import os
import sys
def _setup_logger():
logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s")
return logging.getLogger(__name__)
def _read_text_file(path: str) -> str:
expanded = os... | ipruning/dotfiles | modules/bin/pmt.py | .py | fa98a135f3bfcbbe | 7.57 | 13 |
"""Host-owned policy that can make this repository audit-only."""
from __future__ import annotations
import tomllib
from dataclasses import dataclass
from pathlib import Path
POLICY_RELATIVE_PATH = Path(".config/dotfiles/policy.toml")
MANAGED_MODE = "managed"
AUDIT_ONLY_MODE = "audit-only"
class HostPolicyError(Ru... | ipruning/dotfiles | scripts/host_policy.py | .py | 87833a2c4fb189cb | 7.57 | 13 |
"""Shared ownership policy for the mise executable."""
from __future__ import annotations
import os
from pathlib import Path
from .host_policy import configured_mise_path
MISE_RELATIVE_PATH = Path(".local/bin/mise")
def canonical_mise_path(home: Path) -> Path:
return configured_mise_path(home) or home / MISE_... | ipruning/dotfiles | scripts/mise.py | .py | f34ed0e94e124138 | 7.57 | 13 |
"""Host profiles shared by inspection and explicit setup commands."""
from __future__ import annotations
import platform
from enum import StrEnum
class HostProfile(StrEnum):
AUTO = "auto"
LINUX_LITE = "linux-lite"
MACOS = "macos"
FULL = "full"
LINUX_LITE_APPLICATIONS = frozenset(
{"atuin", "bt... | ipruning/dotfiles | scripts/profiles.py | .py | 7acec3c92d6380ad | 7.57 | 13 |
"""Shared fixtures for repository behavior tests."""
from __future__ import annotations
import os
import subprocess
import sys
from functools import cache
from pathlib import Path
REPO_ROOT = Path(__file__).resolve().parents[1]
def mackup_cfg(applications: str = "") -> str:
"""Return a minimal Mackup storage c... | ipruning/dotfiles | tests/conftest.py | .py | b02fae44ea522bed | 8.07 | 13 |
import os
from itertools import cycle
from runez.system import flattened
class AsciiAnimation:
"""Progress spinner animations"""
env_var = "SPINNER" # Env var overriding which predefined spinner to use
default = "dots" # Default spinner to use
@classmethod
def available_names(cls, include_vir... | codrsquad/runez | src/runez/ascii.py | .py | 1657e5be4c991213 | 7.5 | 9 |
"""
Convenience commonly used click options:
@runez.click.version()
@runez.click.debug()
@runez.click.dryrun("-n") # If you wanted an extra `-n` flag to mean `--dryrun` as well
@runez.click.log()
def main(debug, dryrun, log, ...):
...
"""
import argparse
import errno
import logging
import... | codrsquad/runez | src/runez/click.py | .py | a72395493b760d94 | 7.5 | 9 |
import os
from runez.colors import NamedColors, NamedStyles, PlainBackend, Renderable
from runez.convert import to_int
VALID_FLAVORS = {"dark", "light", "neutral"}
class AnsiCode:
"""Compute ANSI escape codes to use for a given RGB color"""
bg_offset = 40
fg_offset = 30
@classmethod
def enhanc... | codrsquad/runez | src/runez/colors/terminal.py | .py | 2625bc566484d300 | 7.5 | 9 |
"""
Import this only from your test cases
Example:
from runez.conftest import cli, temp_folder
"""
from __future__ import annotations
import logging
import os
import re
import sys
import traceback
from pathlib import Path
from typing import TYPE_CHECKING
import _pytest.logging
import pytest
if TYPE_CHECKING:
... | codrsquad/runez | src/runez/conftest.py | .py | 659f118c4c1d4be9 | 8 | 9 |
"""
Daemon thread that can be used to run periodical background tasks.
Assumptions:
- Tasks should be reasonably short running (do not use this for long operations)
- Execution frequency should be >= 1 second (this is not designed for very quick frequency)
- Frequency does not dynamically change (stated once at task c... | codrsquad/runez | src/runez/heartbeat.py | .py | 696c5397c1d82e88 | 7.5 | 9 |
"""
This module holds less often used conveniences, it is not available via `import runez`
Functions from this module must be explicitly imported, for example:
>>> from runez.inspector import auto_import_siblings
"""
import importlib
from runez.system import find_caller
def auto_import_siblings(skip=None, caller=... | codrsquad/runez | src/runez/inspector.py | .py | 62356516536835d7 | 8 | 9 |
from __future__ import annotations
import inspect
import os
from runez.colors import ColorManager
from runez.convert import to_int
from runez.system import _R, flattened, joined, OptionalColor, short, Slotted, stringified, SYS_INFO, UNSET, wcswidth
NAMED_BORDERS = {
"ascii": "rstgrid,t:+++=,m:+++-",
"compact... | codrsquad/runez | src/runez/render.py | .py | 72b8483b4e6a40a3 | 7.5 | 9 |
import threading
THREAD_LOCAL = threading.local()
class thread_local_property:
"""
A property that is computed once per thread
Use this in rare cases where you need just a property (or 2) to be thread local in a given object
If you need an entire object to be thread-local, then use class `ThreadLoca... | codrsquad/runez | src/runez/thread.py | .py | 9e32785fa17f79ad | 7.5 | 9 |
import os
import pytest
import runez
from runez.__main__ import main
from runez.conftest import cli, ClickRunner, IsolatedLogSetup, logged, temp_folder
from runez.http import GlobalHttpCalls
from runez.logsetup import LogManager
from runez.system import CaptureOutput, short
# Re-export fixtures so pytest discovers t... | codrsquad/runez | tests/conftest.py | .py | 14f93fc5bf6a141e | 8 | 9 |
"""
Test click related methods
"""
import errno
import logging
import os
import sys
import click
import pytest
import runez
import runez.config
from .conftest import exception_raiser
def my_formatter(text):
return text.format(placeholder="epilog")
@runez.click.group()
@runez.click.version(message="%(prog)s,... | codrsquad/runez | tests/test_click.py | .py | fa58608d760bed9d | 8 | 9 |
import os
import sys
import pytest
import runez
from runez.inspector import auto_import_siblings
def importable_test_py_files(folder):
"""Finds all .py files in tests/ folder, used for auto-import validation"""
for fname in os.listdir(folder):
fpath = os.path.join(folder, fname)
if os.path.i... | codrsquad/runez | tests/test_inspector.py | .py | 667479ab1b85a416 | 8 | 9 |
import os
from unittest.mock import patch
import pytest
import runez
from runez.prompt import ask_once
def custom_serializer(value):
if value == "invalid":
return None
return {"value": value}
def mocked_input(x):
return x
def test_no_tty(logged):
assert ask_once("test", "Please enter va... | codrsquad/runez | tests/test_prompt.py | .py | c165aa17fd4b06b8 | 7 | 9 |
import logging
import os
import re
import sys
import pytest
import runez
import runez.conftest
def sample_main():
args = sys.argv[1:]
runez.log.trace("Running main() with: %s" % args)
if args:
args = runez.flattened(args, shellify=True)
if args[0] == "TypeError":
# Raise a Ty... | codrsquad/runez | tests/test_testing.py | .py | 3abc9d74e11ece3d | 7 | 9 |
"""Interface for ``python -m scanspec``."""
import logging
import string
import click
# Need this so we can eval() below
from .specs import * # noqa
@click.group(invoke_without_command=True)
@click.option(
"--log-level",
default="INFO",
type=click.Choice(
["CRITICAL", "ERROR", "WARNING", "INFO... | bluesky/scanspec | src/scanspec/cli.py | .py | 315cbbf46ae7fcb1 | 8.04 | 11 |
"""Core classes like `Dimension` and `Path`."""
from __future__ import annotations
import itertools
import sys
import warnings
from collections.abc import Callable, Iterable, Iterator, Sequence
from dataclasses import dataclass
from functools import lru_cache
from inspect import isclass
from typing import (
Any,
... | bluesky/scanspec | src/scanspec/core.py | .py | 8f791ed99184702a | 7.04 | 11 |
"""`plot_spec` to visualize a scan."""
from collections.abc import Generator, Iterable
from itertools import cycle
from typing import Any
import numpy as np
import numpy.typing as npt
from matplotlib import colors, patches
from matplotlib import pyplot as plt
from matplotlib.axes import Axes
from mpl_toolkits.mplot3d... | bluesky/scanspec | src/scanspec/plot.py | .py | 63610b0abf182812 | 8.04 | 11 |
"""FastAPI service to query information about Specs."""
import base64
import json
from collections.abc import Mapping
from enum import StrEnum
from typing import Any
import numpy as np
import numpy.typing as npt
from fastapi import Body, FastAPI
from fastapi.middleware.cors import CORSMiddleware
from fastapi.openapi.... | bluesky/scanspec | src/scanspec/service.py | .py | c9ab38759eab0568 | 7.04 | 11 |
"""An example_spec directive."""
from contextlib import contextmanager
from typing import Any, cast
from docutils.statemachine import StringList
from matplotlib.sphinxext import plot_directive
from sphinx.application import Sphinx
from . import __version__
@contextmanager
def always_create_figures():
"""Force ... | bluesky/scanspec | src/scanspec/sphinxext.py | .py | dcfc281321a3edc2 | 8.04 | 11 |
from typing import Any
import pytest
def approx(
expected: Any,
rel: float | None = None,
abs: float | None = None,
nan_ok: bool = False,
) -> Any:
"""
Temporary loosely typed wrapper around approx.
To be removed pending:
https://github.com/pytest-dev/pytest/issues/7469
Args:
... | bluesky/scanspec | tests/__init__.py | .py | 4460fe069307a2cf | 7.04 | 11 |
import json
import pathlib
import subprocess
import sys
from typing import cast
from unittest.mock import patch
import matplotlib.pyplot as plt
import numpy as np
import numpy.typing as npt
from click.testing import CliRunner
from matplotlib.lines import Line2D
from matplotlib.text import Annotation
from mpl_toolkits.... | bluesky/scanspec | tests/test_cli.py | .py | 25b99a61152f218b | 7.04 | 11 |
import json
import logging
import os
import sys
import uuid
from dataclasses import dataclass
from datetime import datetime, timedelta
from http.client import HTTPConnection, HTTPSConnection
from logging import LogRecord
from logging.handlers import QueueHandler, QueueListener
from queue import Queue
from typing import... | Jellyfish-AI/jf_agent | jf_agent/agent_logging.py | .py | ad773e1a3cb4a31f | 7.63 | 17 |
import logging
import string
import traceback
from typing import Optional
from jf_ingest import diagnostics, logging_helper
from jf_ingest.config import IngestionConfig
from jf_ingest.jf_jira import load_and_push_jira_to_s3
from jf_ingest.jf_jira.auth import get_jira_connection as get_jira_connection_from_jf_ingest
fr... | Jellyfish-AI/jf_agent | jf_agent/jf_jira/jira_download.py | .py | 7b5c80d6393a9953 | 7.63 | 17 |
import logging
import time
from typing import Any, Callable, Optional
from jf_ingest import logging_helper
logger = logging.getLogger(__name__)
def get_wait_time(e: Optional[Exception], retries: int) -> int:
"""
This function attempts to standardize determination of a wait time on a retryable failure.
I... | Jellyfish-AI/jf_agent | jf_agent/jf_jira/utils.py | .py | ca643a13e088d178 | 7.63 | 17 |
import bisect
import logging
import threading
import time
from collections import defaultdict, namedtuple
from contextlib import contextmanager
from datetime import datetime, timedelta
import requests
from jf_ingest import logging_helper
logger = logging.getLogger(__name__)
RateLimitRealmConfig = namedtuple('RateLim... | Jellyfish-AI/jf_agent | jf_agent/ratelimit.py | .py | 2e92dccbffb63f9d | 7.63 | 17 |
import requests
from requests.adapters import HTTPAdapter
from requests.packages.urllib3.util.retry import Retry
class ReauthSession(requests.Session):
def __init__(self, **kwargs):
super().__init__(**kwargs)
def request(self, method, url, **kwargs):
# If we get HTTP 401, re-authenticate and ... | Jellyfish-AI/jf_agent | jf_agent/session.py | .py | ab7dbc1a053e0aec | 7.63 | 17 |
import logging
from collections import namedtuple
from itertools import islice
from time import sleep
from typing import Any, List
import requests
from jf_ingest import logging_helper
from jf_agent.exception import BadConfigException
from jf_agent.session import retry_session
logger = logging.getLogger(__name__)
U... | Jellyfish-AI/jf_agent | jf_agent/util.py | .py | 3029a3f78309cc88 | 7.63 | 17 |
import logging
import os
import shutil
import traceback
from typing import Optional
import psutil
import requests
from jf_ingest.validation import (
GitConnectionHealthCheckResult,
IngestionHealthCheckResult,
IngestionType,
JiraConnectionHealthCheckResult,
validate_git,
validate_jira,
)
from j... | Jellyfish-AI/jf_agent | jf_agent/validation.py | .py | 98a9cecc844371fc | 7.63 | 17 |
"""
Audit how many cross-references make_chebi_relations() takes out of ChEBI's database_accession.tsv.
The file identifies each xref's database only by a numeric source_id, and a row's `type` decides
whether `accession_number` is that database's own identifier at all. Both columns therefore have to
be matched, and th... | NCATSTranslator/Babel | docs/sources/CHEBI/scripts/audit_database_accession.py | .py | ac1532a8977acc0a | 7.63 | 17 |
"""
Audit the ChEBI SDF's data-item tags against the keys make_chebi_relations() asks for.
ChEBI renames SDF tags between releases without notice. Because chebi_sdf_entry_to_dict()
matches tags by exact (normalized) string and simply omits anything it doesn't recognize, a
rename is silent: the ingest keeps running and... | NCATSTranslator/Babel | docs/sources/CHEBI/sdf_tags/audit_sdf_tags.py | .py | 71116e9bb5a4d7a4 | 7.63 | 17 |
"""Measure what DOID's ICD xrefs do to disease clique sizes.
Prints the four-scenario table quoted in ``docs/sources/DOID/mappings.md``:
* **ICD kept** -- every DOID ICD xref fed to glom(), the merge problem in the raw.
* **overuse-filtered** -- ``remove_overused_xrefs`` over the whole DOID concord, unscoped.
* **ICD... | NCATSTranslator/Babel | docs/sources/DOID/mappings/scripts/measure_icd_xrefs.py | .py | cdb19d7efb2ab87e | 7.63 | 17 |
#!/usr/bin/env python
"""Regenerate the two DrugBank food-and-extract audit CSVs in this directory (issue #828).
This is the committed generator for the sibling files:
- ``food-and-extracts.csv`` (File A) — every structureless DrugBank food/material this PR retypes,
with the type it ships now (``biolink:Food`` ... | NCATSTranslator/Babel | docs/sources/DRUGBANK/food-and-extracts/scripts/generate_csvs.py | .py | e3c0e73f57d22335 | 7.63 | 17 |
#!/usr/bin/env python
"""Replay create_typed_sets() over a completed build's Food.txt to check the #935 type vote.
Issue #918 typed a chemical clique as ``biolink:Food`` whenever *any* member carried DrugBank
food evidence, overriding the per-identifier type vote entirely. That was asserted to be safe
because "every c... | NCATSTranslator/Babel | docs/sources/DRUGBANK/food-and-extracts/scripts/replay_type_vote.py | .py | e4f4ce5876ac9a88 | 7.63 | 17 |
"""
List every UBERON term that cross-references more than one EMAPA term.
These are the cliques that decided whether `EMAPA` belongs in `anatomy_unique_prefixes`
(config.yaml). Restricting a prefix makes `glom()` refuse any merge whose union would hold two
identifiers sharing it, so each UBERON term below would have ... | NCATSTranslator/Babel | docs/sources/EMAPA/scripts/multi_emapa_uberon_xrefs.py | .py | ae4abf8adbb8ddb3 | 7.63 | 17 |
"""Characterize the quoting/punctuation used in the two NCBIGene free-text synonym columns.
NCBI's ``gene_info.gz`` packs multiple values into two pipe-delimited free-text columns:
- ``Synonyms`` (column index 4) -- the NCBI "otheraliases" field
- ``Other_designations`` (column index 13) -- the NCBI "other... | NCATSTranslator/Babel | docs/sources/NCBIGene/quoting/analyze_quoting.py | .py | a75d044ece56b803 | 7.63 | 17 |
"""Report on '' occurrences in NCBIGene gene_info.gz that could be *genuine* name components
(e.g. double-prime nomenclature) rather than issue-#744 pipe-split artifacts.
Classification of a '' occurrence:
- **open-marker artifact**: a pipe-fragment that STARTS with '' (e.g. ``''cytochrome P450``) --
the opening of... | NCATSTranslator/Babel | docs/sources/NCBIGene/quoting/double_prime_report.py | .py | 587adc3f92fbfbb4 | 7.63 | 17 |
"""Report every synonym that the issue-#932 fix removes from NCBIGene's shredded alias fields.
NCBI wraps a comma-containing alias in ''...'' and then turns that value's internal commas into
'|' -- the ``Synonyms`` column's own delimiter -- so the value arrives shredded into pipe-fragments.
The #744 fix drops the two ... | NCATSTranslator/Babel | docs/sources/NCBIGene/quoting/shredded_pieces_report.py | .py | 264bf8b9998d3f93 | 7.63 | 17 |
#!/usr/bin/env python3
"""Archive a build's summary reports into ``releases/<build>/``.
A finished build directory is hundreds of gigabytes and lives on a cluster that will eventually be
cleaned. A small part of it -- the summary tables, the per-compendium content reports, and the
provenance metadata -- is what people... | NCATSTranslator/Babel | releases/scripts/archive_build.py | .py | fafb60aaae70be55 | 7.63 | 17 |
# standard modules
from typing import NamedTuple
# logger = LoggingUtil.init_logging(__name__, logging.ERROR)
class LabeledID(NamedTuple):
"""
Labeled Thing Object
---
schema:
id: LabeledID
required:
- identifier
properties:
identifer:
t... | NCATSTranslator/Babel | src/LabeledID.py | .py | ac0d54dbfa641e8e | 7.63 | 17 |
import logging
from collections import defaultdict
import jsonlines
from src.babel_utils import glom
from src.categories import GENE
from src.metadata.provenance import write_concord_metadata
from src.prefixes import NCBIGENE, UNIPROTKB
from src.util import LoggingUtil
logger = LoggingUtil.init_logging(__name__, lev... | NCATSTranslator/Babel | src/createcompendia/geneprotein.py | .py | 5113e7d119e98081 | 7.63 | 17 |
from collections import defaultdict
import src.datahandlers.ec as ec
import src.datahandlers.obo as obo
import src.datahandlers.reactome as reactome
import src.datahandlers.rhea as rhea
import src.datahandlers.umls as umls
from src.babel_utils import get_prefixes, glom, read_identifier_file, remove_overused_xrefs, wri... | NCATSTranslator/Babel | src/createcompendia/processactivitypathway.py | .py | a9d5d9e9c7c6bb21 | 7.63 | 17 |
import logging
import src.datahandlers.mesh as mesh
import src.datahandlers.umls as umls
from src.babel_utils import glom, read_identifier_file, write_compendium
from src.categories import ORGANISM_TAXON
from src.metadata.provenance import write_concord_metadata
from src.prefixes import MESH, NCBITAXON, UMLS
from src.... | NCATSTranslator/Babel | src/createcompendia/taxon.py | .py | 0d3de85b3c0796a1 | 7.63 | 17 |
import ftplib
import pyoxigraph
from src.babel_utils import parse_rdf_literal, pull_via_ftp
from src.prefixes import CHEMBLCOMPOUND
def pull_chembl(moleculefilename):
fname = get_latest_chembl_name()
if fname is not None:
# fname should be like chembl_28.0_molecule.ttl.gz
# Pull via ftp is g... | NCATSTranslator/Babel | src/datahandlers/chembl.py | .py | b605b560031c6bd8 | 7.63 | 17 |
import logging
import pyoxigraph
from src.babel_utils import parse_rdf_literal, pull_via_urllib
from src.categories import CELL_LINE
from src.metadata.provenance import write_download_metadata
from src.prefixes import CLO, ORPHANET
from src.util import LoggingUtil, Text
logger = LoggingUtil.init_logging(__name__, le... | NCATSTranslator/Babel | src/datahandlers/clo.py | .py | 1190143a5113597d | 7.63 | 17 |
import json
from src.babel_utils import norm, pull_via_urllib
from src.prefixes import DOID, OIO
def pull_doid():
pull_via_urllib(
"https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/main/src/ontology/",
"doid.json",
subpath="DOID",
decompress=False,
)
de... | NCATSTranslator/Babel | src/datahandlers/doid.py | .py | 3b186f096721af29 | 7.63 | 17 |
# Download CC-0 licensed data from DrugBank (https://go.drugbank.com/releases/latest)
import csv
import os.path
import shutil
from zipfile import ZipFile
import requests
from src.categories import COMPLEX_MOLECULAR_MIXTURE, FOOD
from src.datahandlers.ncit import read_ncit_code_set
from src.datahandlers.unii import re... | NCATSTranslator/Babel | src/datahandlers/drugbank.py | .py | 485d2127a82e3dd0 | 7.63 | 17 |
import pyoxigraph
from src.babel_utils import parse_rdf_literal, pull_via_urllib
from src.categories import MOLECULAR_ACTIVITY
from src.prefixes import EC
def pull_ec():
pull_via_urllib("https://ftp.expasy.org/databases/enzyme/", "enzyme.rdf", subpath="EC", decompress=False)
class ECgraph:
"""Load the mesh... | NCATSTranslator/Babel | src/datahandlers/ec.py | .py | 3bfbffee384ebe42 | 7.63 | 17 |
import logging
import pyoxigraph
from src.babel_utils import parse_rdf_literal, pull_via_urllib
from src.metadata.provenance import write_concord_metadata
from src.prefixes import EFO, ORPHANET
from src.util import LoggingUtil, Text
logger = LoggingUtil.init_logging(__name__, level=logging.WARNING)
def pull_efo():... | NCATSTranslator/Babel | src/datahandlers/efo.py | .py | 3ddc5a48a574b29c | 7.63 | 17 |
from bs4 import BeautifulSoup
from src.babel_utils import pull_via_urllib
from src.prefixes import GTOPDB
def pull_gtopdb_ligands():
pull_via_urllib("https://www.guidetopharmacology.org/DATA/", "ligands.tsv", decompress=False, subpath="GTOPDB")
def strip_html_tags(name):
"""
GtoPDB contains HTML tags, ... | NCATSTranslator/Babel | src/datahandlers/gtopdb.py | .py | e53e1afb78c4820b | 7.63 | 17 |
import warnings
from collections import defaultdict
import pyoxigraph
from src.babel_utils import make_local_name, pull_via_ftp
from src.categories import ANATOMICAL_ENTITY, CELL, CELLULAR_COMPONENT
from src.prefixes import MESH
MESH_IRI_PREFIX = "http://id.nlm.nih.gov/mesh/"
def get_mesh_id_from_iri(iri) -> str:
... | NCATSTranslator/Babel | src/datahandlers/mesh.py | .py | 735274ec69f2ba05 | 7.63 | 17 |
from __future__ import with_statement
import os
from logging.config import fileConfig
from pathlib import Path # Python 3.6+ only
from alembic import context
from dotenv import load_dotenv
from sqlalchemy import create_engine
if not load_dotenv():
env_path = Path('.') / '..' / '..' / '.env'
load_dotenv(dote... | dbvis-ukon/coronavis | Backend/migrations/alembic/env.py | .py | a766c3db65950882 | 7.63 | 17 |
"""create germany materialized view
Revision ID: 00a7bf4dae6c
Revises: 8175af65a5b9
Create Date: 2020-11-26 14:37:50.902921
"""
from alembic import op
# revision identifiers, used by Alembic.
revision = '00a7bf4dae6c'
down_revision = '8175af65a5b9'
branch_labels = None
depends_on = None
def upgrade():
op.get_b... | dbvis-ukon/coronavis | Backend/migrations/alembic/versions/00a7bf4dae6c_create_germany_materialized_view.py | .py | cf38ffbbee80bf75 | 7.63 | 17 |
"""create cases_lk_risklayer table
Revision ID: 2ea7edb628ac
Revises: 3610493d8979
Create Date: 2020-11-25 20:43:50.998184
"""
from alembic import op
# revision identifiers, used by Alembic.
revision = '2ea7edb628ac'
down_revision = '3610493d8979'
branch_labels = None
depends_on = None
def upgrade():
op.get_bi... | dbvis-ukon/coronavis | Backend/migrations/alembic/versions/2ea7edb628ac_create_cases_lk_risklayer_table.py | .py | 6abdffe1eedd90f8 | 7.63 | 17 |
"""create cases table
Revision ID: 3610493d8979
Revises:
Create Date: 2020-11-25 20:42:26.698495
"""
from alembic import op
# revision identifiers, used by Alembic.
revision = '3610493d8979'
down_revision = None
branch_labels = None
depends_on = None
def upgrade():
op.get_bind().execute("""
create table c... | dbvis-ukon/coronavis | Backend/migrations/alembic/versions/3610493d8979_create_cases_table.py | .py | f333effb34085005 | 7.63 | 17 |
"""add columns to divi_meldungen
Revision ID: a3a5ae77b6b9
Revises: bbaf5488b4fe
Create Date: 2021-03-23 11:42:48.229731
"""
from alembic import op
# revision identifiers, used by Alembic.
revision = 'a3a5ae77b6b9'
down_revision = 'bbaf5488b4fe'
branch_labels = None
depends_on = None
def upgrade():
op.get_bind... | dbvis-ukon/coronavis | Backend/migrations/alembic/versions/a3a5ae77b6b9_add_columns_to_divi_meldungen.py | .py | a8e10683f8e91789 | 7.63 | 17 |
"""create cases_current view
Revision ID: b84312f6532e
Revises: 00a7bf4dae6c
Create Date: 2020-11-26 14:43:32.346113
"""
from alembic import op
# revision identifiers, used by Alembic.
revision = 'b84312f6532e'
down_revision = '00a7bf4dae6c'
branch_labels = None
depends_on = None
def upgrade():
op.get_bind().e... | dbvis-ukon/coronavis | Backend/migrations/alembic/versions/b84312f6532e_create_cases_current_view.py | .py | 06117aa51b71c766 | 7.63 | 17 |
"""create risklayer_prognosis table
Revision ID: c34d4cef2dad
Revises: 91aca0bccf3f
Create Date: 2020-11-25 21:28:24.950572
"""
from alembic import op
# revision identifiers, used by Alembic.
revision = 'c34d4cef2dad'
down_revision = '91aca0bccf3f'
branch_labels = None
depends_on = None
def upgrade():
op.get_b... | dbvis-ukon/coronavis | Backend/migrations/alembic/versions/c34d4cef2dad_create_risklayer_prognosis_table.py | .py | f98b6791c88f2b08 | 7.63 | 17 |
from sqlalchemy.dialects.postgresql import JSONB
from sqlalchemy.orm import deferred
from db import db
class Crawl(db.Model):
"""
Hospital data class
"""
__tablename__ = 'crawl'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
url = db.Column(db.String, nullable=False)
te... | dbvis-ukon/coronavis | Backend/models/crawl.py | .py | 813bc3ab5fa28255 | 7.63 | 17 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import json
import os
# noinspection PyUnresolvedReferences
from datetime import datetime
from flasgger import Swagger
from flask import Flask, jsonify, redirect
from flask_compress import Compress
from flask_cors import CORS, cross_origin
from flask_mail import Mail
from... | dbvis-ukon/coronavis | Backend/server.py | .py | a3423eb109eafe75 | 7.63 | 17 |
"""
Govspeak markdown rendering module.
Provides markdown rendering with GOV.UK-specific extensions including:
- Call-to-action blocks ($CTA...$CTA)
- Information callouts (^...^)
- Warning callouts (%...%)
- Numbered steps (s1., s2., etc.)
- Email address links (<email@example.com>)
"""
import re
import markdown
fro... | digital-land/specification | bin/govspeak.py | .py | bb792a858ca7094f | 7.45 | 7 |
#!/usr/bin/env python3
import sys
import csv
from pathlib import Path
import frontmatter
def output_to_file(file_path, output_string):
with open(file_path, "a") as file:
file.write(output_string)
def generate(specification_path, output_path=None):
svg_content = []
tables = {
"dataset":... | digital-land/specification | bin/specification-svg.py | .py | 70b7fa5282c921d5 | 7.95 | 7 |
"""Builds the memory-mapped domain index the workers read.
Runs in the librarian, after the lists have been downloaded and cleaned. Writes
beside the live path and renames, so a worker holding an mmap keeps reading a
consistent file until it chooses to reopen.
"""
import os
import struct
import time
from libtb.index... | MelonSmasher/TurkeyBite | src/libtb/index/builder.py | .py | 1e736341a55bf2ac | 7.5 | 9 |
"""Moves the domain index from the librarian to the workers.
Only one node runs the librarian, and ./vols/lists is a per-node bind mount, so
a worker on another host cannot see the file the librarian wrote. This module
ships it through Valkey, which both nodes already reach and authenticate to, so
distribution needs n... | MelonSmasher/TurkeyBite | src/libtb/index/transport.py | .py | 463dd6ca5673c482 | 7.5 | 9 |
import json
import sys
from rq import Queue
from redis import Redis
from libtb.util import dig
def describe(data, verdict):
"""Builds the log line for an observed packet.
Every field is read through dig() or checked for its type first. This code
used to reach straight into nested keys, and since the call... | MelonSmasher/TurkeyBite | src/libtb/inlet/__init__.py | .py | 436e66b707d5af46 | 7.5 | 9 |
"""Registrable domains, using the Public Suffix List.
The question is where the name somebody registered ends and the subdomains that
registrant controls begin. Taking the last two labels is the obvious answer and
it is wrong whenever the public part of the name is itself more than one label:
news.bbc.co.uk ... | MelonSmasher/TurkeyBite | src/libtb/psl/__init__.py | .py | c40daffcb064e40a | 7.5 | 9 |
import socket
class Facility:
"""Syslog facilities"""
KERN, USER, MAIL, DAEMON, AUTH, SYSLOG, \
LPR, NEWS, UUCP, CRON, AUTHPRIV, FTP = range(12)
LOCAL0, LOCAL1, LOCAL2, LOCAL3, \
LOCAL4, LOCAL5, LOCAL6, LOCAL7 = range(16, 24)
class Level:
"""Syslog levels"""
EMERG, ALERT, CRIT, ERR, \
... | MelonSmasher/TurkeyBite | src/libtb/tbsyslog/__init__.py | .py | 4efa7d69e2d447c0 | 7.5 | 9 |
"""Tests for retiring the Valkey host list keyspace.
Two things can go wrong here and both are quiet. Sweeping too widely takes the
domain index manifest and chunks with it, because they share the turkey-bite:
prefix. Gating too widely stops populating the keyspace that `compare` mode
reads as authoritative, which tur... | MelonSmasher/TurkeyBite | tests/test_host_list_keyspace.py | .py | 5a8da3dc070bc32e | 8 | 9 |
"""
Benchmark: get()'s simple-path fast path vs the walk() machinery (issue #58).
Simple paths (literal Key/Attr/Slot chains) resolve via engine.simple_get();
everything else goes through walk(). This times both on the same paths by
driving the walk machinery directly, so the comparison stays valid as long
as both cod... | freywaid/dotted | benchmarks/bench_simple_get.py | .py | ca193341ff84afaf | 7.57 | 13 |
"""
Root conftest. Adds the `--all` flag and the skip logic for integration
tests. Tests under `tests/integration/` auto-mark themselves via that
directory's conftest; by default they're skipped. They run when either
`--all` is passed or the caller explicitly targets the directory.
"""
import pytest
def pytest_addopt... | freywaid/dotted | conftest.py | .py | b40230478d0ed077 | 8.07 | 13 |
"""
Base classes, sentinels, and infrastructure for the dotted element system.
"""
import collections
import pyparsing as pp
from .utypes import marker, ANY, CUT_SENTINEL, BRANCH_CUT, BRANCH_SOFTCUT, resolve_types # noqa: F401
# Generator safety (data): keep lazy things lazy as long as possible. Avoid needlessly co... | freywaid/dotted | dotted/base.py | .py | dd5b4ad23855809c | 7.57 | 13 |
"""
CLI entry point for dq — dotted notation query tool.
"""
import json
import signal
import sys
import dotted
from dotted.api import ParseError
from .formats import READERS, WRITERS, validate_reader, validate_writer
OPERATIONS = {'get', 'update', 'remove'}
def parse_value(s):
"""
Parse a string as JSON,... | freywaid/dotted | dotted/cli/main.py | .py | 840f9aedf371874e | 7.57 | 13 |
"""
Traversal engine for dotted path operations.
Core traversal functions (walk, gets, updates, removes, expands).
"""
import copy
from . import base
from . import matchers
from . import wrappers
from .access import Attr, Slot
from .results import Dotted
def _needs_parents(ops):
"""
True if any op in the ch... | freywaid/dotted | dotted/engine.py | .py | 250c3400dcc645cf | 7.57 | 13 |
"""
Dotted result model and transform registry.
"""
import itertools
from . import predicates
from . import utils
from .access import Attr, Invert, Key, Slot
from .matchers import Const
from .utils import lazyprop
class rdoc(str):
def expandtabs(*args, **kwargs):
title = 'Supported transforms\n\n'
... | freywaid/dotted | dotted/results.py | .py | 2cc97ce44a8706bc | 7.57 | 13 |
"""
Shared type-checking helpers (duck-typing).
"""
class lazyprop:
"""
Non-data descriptor: compute once on first access, cache the result
in the instance __dict__ (which then shadows the descriptor). Like
functools.cached_property but lock-free and available on 3.6+.
"""
def __init__(self, fn... | freywaid/dotted | dotted/utils.py | .py | 81a35111c637ad49 | 7.57 | 13 |
"""
Type specification, sentinels, and registry for the dotted element system.
"""
# Sentinel used as a "missing" marker and as the ANY constant for remove.
marker = object()
class _ANYMeta(type):
"""Metaclass for ANY: isinstance(x, ANY) is always True."""
def __instancecheck__(cls, instance):
return... | freywaid/dotted | dotted/utypes.py | .py | 9fd3c56e906ccfb9 | 7.57 | 13 |
"""
Fixtures and collection rules for integration tests.
Every test collected under `tests/integration/` is auto-marked as
`integration`. Root `conftest.py` handles the default skip + `--all`
override.
A session-scoped fixture creates a dedicated `dotted_test` schema and
seeds a sample table; per-test transaction rol... | freywaid/dotted | tests/integration/conftest.py | .py | 705adc1b57c8bc3c | 8.07 | 13 |
"""
Smoke tests: minimum infrastructure check. Confirms the DSN is
reachable, the schema was created, and the seed data is present.
"""
def test_conn_reachable(query):
rows = query('SELECT 1 AS one')
assert rows == [{'one': 1}]
def test_seed_row_count(query):
rows = query('SELECT count(*) AS c FROM dott... | freywaid/dotted | tests/integration/test_smoke.py | .py | 1c13cffb6b555551 | 7.57 | 13 |
"""
End-to-end integration tests: run dotted.sql output against the
seeded Postgres schema and verify row-level semantics.
The seeded table `dotted_test.items` has columns:
id, status, age, deleted_at, data (JSONB)
Seed (from tests/integration/conftest.py):
id=1: status=active age=25 user.age=... | freywaid/dotted | tests/integration/test_sqlize_e2e.py | .py | 3e12a7e3dc8e1bf2 | 8.07 | 13 |
"""
Tests for API functions
"""
import pytest
import dotted
# quote
def test_quote_string():
assert dotted.quote('hello') == 'hello'
# spaces and reserved chars require quoting
assert dotted.quote('has space') == "'has space'"
assert dotted.quote('has.dot') == "'has.dot'"
assert dotted.quote('a[0... | freywaid/dotted | tests/test_api.py | .py | 2216338967aaeaef | 7.07 | 13 |
"""
Tests for template bindings and resolution in parse() and traversal APIs.
"""
import pytest
import dotted
def test_parse_template_partial_true_default():
"""
parse() with default partial=True allows templates through.
"""
ops = dotted.parse('a.$0.b')
assert dotted.is_template(ops)
def test_p... | freywaid/dotted | tests/test_bindings.py | .py | 8c3061bfb88d688d | 7.07 | 13 |
"""
Tests for the + concatenation operator in key construction.
"""
import pytest
import dotted
from dotted.api import parse, get, update, remove, replace, is_template
from dotted.matchers import Concat, ConcatPart, Word, Numeric, Subst, Reference
from dotted.results import assemble
# ---- parsing: key context ----
... | freywaid/dotted | tests/test_concat.py | .py | 328d5757c4d8178d | 7.07 | 13 |
"""
Tests for empty path operations (root access).
"""
import dotted
def test_get_empty_returns_root():
data = {'a': 1, 'b': 2}
assert dotted.get(data, '') == data
def test_get_empty_list():
data = [1, 2, 3]
assert dotted.get(data, '') == data
def test_get_empty_primitive():
assert dotted.get(... | freywaid/dotted | tests/test_empty.py | .py | ce64dcde6186d21e | 7.07 | 13 |
import pytest
import dotted
def test_parse_lookahead_keyvalue():
dotted.parse('hello&id=1')
dotted.parse('*&id=1')
dotted.parse('a[id=1]')
dotted.parse('a[*]')
dotted.parse('a[*&id=1]')
def test_parse_not_equal():
"""!= parses as its own filter (same semantics as !(key=val), repr stays id!=1... | freywaid/dotted | tests/test_filter_keyvalue.py | .py | 95bb31f22da9e7da | 7.07 | 13 |
import pytest
import dotted
def test_get_key():
d = {'hello': {'there': [1, '2', 3]}}
r = dotted.get(d, 'hello.there')
assert r == [1, '2', 3]
def test_get_dot_index():
"""Test dot notation for list index access (items.0 instead of items[0])"""
# Basic list index
data = {'items': [1, 2, 3]}... | freywaid/dotted | tests/test_get.py | .py | d60503dec13047dc | 8.07 | 13 |
"""
Tests for guard transforms: field|transform=value, [slot]|transform=value,
**|transform=value, filter transforms [*&field|transform=value], and
template-level guards.
Guard transforms are matching-only: yielded values are originals (untransformed).
"""
import dotted
# --- Parse / Assemble round-trips ---
def t... | freywaid/dotted | tests/test_guard_transforms.py | .py | ee26b4ba02a16c83 | 7.07 | 13 |
"""
"""
import dotted
def test_invert_get():
r = dotted.get({'hello': 'there'}, '-hello')
assert r == 'there'
r = dotted.get([], '-[0]')
assert r is None
def test_invert_remove_via_update():
r = dotted.update({'hello': {'there': 'me', 'not': 'this'}}, '-hello.there', dotted.ANY)
assert r ==... | freywaid/dotted | tests/test_invert.py | .py | 4ae4a0300984236f | 7.07 | 13 |
"""
Tests for dotted.keys, dotted.values, and dotted.items.
"""
import dotted
def test_keys_flat():
d = {'a': 1, 'b': 2}
assert list(dotted.keys(d)) == ['a', 'b']
def test_keys_nested():
d = {'a': {'b': 1}, 'x': 2}
assert list(dotted.keys(d)) == ['a.b', 'x']
def test_keys_deep():
d = {'a': {'b... | freywaid/dotted | tests/test_keys_values.py | .py | ac3748854913757f | 7.07 | 13 |
"""
Direct tests for _match_from declarations and the generic matchable method.
"""
from dotted.matchers import (
Const, Word, Numeric, String,
Wildcard, WildcardFirst, Regex, RegexFirst,
Special, Appender,
Subst, Reference, Concat, ConcatPart,
)
from dotted.utypes import ANY, resolve_types
# -- ANY t... | freywaid/dotted | tests/test_matchable.py | .py | 225427c359b9edb2 | 8.07 | 13 |
# SPDX-FileCopyrightText: 2026 Open Source Robotics Foundation, Inc.
# SPDX-License-Identifier: Apache-2.0
"""Build-time helpers for the JSON-domain schema reference rendered by schema.md."""
import re
from pathlib import Path
import yaml
_HERE = Path(__file__).parent
SCHEMA_SRC = _HERE / '..' / '..' / 'nodl_schema'... | ros-tooling/nodl | nodl/doc/schema_reference.py | .py | fb9e82bbcec4baf0 | 7.63 | 17 |
# SPDX-FileCopyrightText: 2026 Open Source Robotics Foundation, Inc.
# SPDX-License-Identifier: Apache-2.0
"""Static type checking with pyright."""
import subprocess
import sys
from pathlib import Path
# The importable package source lives one level up from this test directory.
_SOURCE_DIR = Path(__file__).resolve().... | ros-tooling/nodl | nodl_docgen/test/test_pyright.py | .py | 21c637d40fef251e | 7.13 | 17 |
# SPDX-FileCopyrightText: 2026 Open Source Robotics Foundation, Inc.
# SPDX-License-Identifier: Apache-2.0
import argparse
import sys
from pathlib import Path
from nodl_generator_cpp.generate import cmake_deps, generate_cpp
from nodl_generator_cpp.params import generate_parameter_header
def main(argv: list[str] | No... | ros-tooling/nodl | nodl_generator_cpp/nodl_generator_cpp/cli.py | .py | c22c5595e915c157 | 7.63 | 17 |
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