Merge pull request #18003 from mvdbeek/add_galaxy_to_user_agent

Add galaxy to user agent

cron/build_chrom_db.py

@@ -18,7 +18,8 @@
 from urllib.parse import urlencode
 
 import parse_builds  # noqa: I100,I202
-import requests
+
+from galaxy.util import requests
 
 
 def getchrominfo(url, db):

cron/parse_builds.py

@@ -8,7 +8,7 @@
 import sys
 import xml.etree.ElementTree as ElementTree
 
-import requests
+from galaxy.util import requests
 
 
 def getbuilds(url):

cron/parse_builds_3_sites.py

@@ -5,7 +5,7 @@
 
 import xml.etree.ElementTree as ElementTree
 
-import requests
+from galaxy.util import requests
 
 sites = [
     "http://genome.ucsc.edu/cgi-bin/",

lib/galaxy/app.py

@@ -133,6 +133,7 @@
     build_tours_registry,
     ToursRegistry,
 )
+from galaxy.util import user_agent  # noqa: F401
 from galaxy.util import (
     ExecutionTimer,
     heartbeat,

lib/galaxy/authnz/custos_authnz.py

@@ -16,7 +16,6 @@
 from urllib.parse import quote
 
 import jwt
-import requests
 from oauthlib.common import generate_nonce
 from requests_oauthlib import OAuth2Session
 
@@ -30,6 +29,7 @@
 )
 from galaxy.model.base import transaction
 from galaxy.model.orm.util import add_object_to_object_session
+from galaxy.util import requests
 from . import IdentityProvider
 
 try:

lib/galaxy/authnz/managers.py

@@ -6,7 +6,6 @@
 import random
 import string
 
-import requests
 from cloudauthz import CloudAuthz
 from cloudauthz.exceptions import CloudAuthzBaseException
 
@@ -19,6 +18,7 @@
     etree,
     listify,
     parse_xml,
+    requests,
     string_as_bool,
     unicodify,
 )

lib/galaxy/authnz/psa_authnz.py

@@ -3,7 +3,6 @@
 import time
 
 import jwt
-import requests
 from msal import ConfidentialClientApplication
 from social_core.actions import (
     do_auth,
@@ -27,7 +26,10 @@
     UserAuthnzToken,
 )
 from galaxy.model.base import transaction
-from galaxy.util import DEFAULT_SOCKET_TIMEOUT
+from galaxy.util import (
+    DEFAULT_SOCKET_TIMEOUT,
+    requests,
+)
 from . import IdentityProvider
 
 log = logging.getLogger(__name__)

lib/galaxy/files/sources/invenio.py

@@ -11,7 +11,6 @@
 )
 from urllib.parse import quote
 
-import requests
 from typing_extensions import (
     Literal,
     TypedDict,
@@ -37,6 +36,7 @@
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     get_charset_from_http_headers,
+    requests,
     stream_to_open_named_file,
 )
 

lib/galaxy/files/sources/util.py

@@ -7,8 +7,6 @@
     Union,
 )
 
-import requests
-
 from galaxy import exceptions
 from galaxy.files import (
     ConfiguredFileSources,
@@ -17,7 +15,10 @@
 from galaxy.files.sources import FilesSourceOptions
 from galaxy.files.sources.http import HTTPFilesSourceProperties
 from galaxy.files.uris import stream_url_to_file
-from galaxy.util import DEFAULT_SOCKET_TIMEOUT
+from galaxy.util import (
+    DEFAULT_SOCKET_TIMEOUT,
+    requests,
+)
 from galaxy.util.config_parsers import IpAllowedListEntryT
 
 TargetPathT = Union[str, PathLike]

lib/galaxy/job_execution/container_monitor.py

@@ -9,10 +9,11 @@
 from functools import partial
 from typing import Callable
 
-import requests
-
 from galaxy.tool_util.deps import docker_util
-from galaxy.util import DEFAULT_SOCKET_TIMEOUT
+from galaxy.util import (
+    DEFAULT_SOCKET_TIMEOUT,
+    requests,
+)
 from galaxy.util.sockets import get_ip
 
 GetIpCallable = Callable[[], str]

lib/galaxy/jobs/runners/godocker.py

@@ -3,15 +3,14 @@
 import time
 from datetime import datetime
 
-import requests
-
 from galaxy import model
 from galaxy.jobs.runners import (
     AsynchronousJobRunner,
     AsynchronousJobState,
 )
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
+    requests,
     unicodify,
 )
 

lib/galaxy/managers/citations.py

@@ -1,12 +1,14 @@
 import functools
 import logging
 
-import requests
 from beaker.cache import CacheManager
 from beaker.util import parse_cache_config_options
 
 from galaxy.structured_app import BasicSharedApp
-from galaxy.util import DEFAULT_SOCKET_TIMEOUT
+from galaxy.util import (
+    DEFAULT_SOCKET_TIMEOUT,
+    requests,
+)
 
 log = logging.getLogger(__name__)
 

lib/galaxy/model/store/load_objects.py

@@ -8,9 +8,10 @@
     Dict,
 )
 
-import requests
 import yaml
 
+from galaxy.util import requests
+
 DESCRIPTION = """Load a Galaxy model store into a running Galaxy instance.
 
 See the corresponding galaxy-build-objects script for one possible way to

lib/galaxy/selenium/has_driver.py

@@ -14,7 +14,6 @@
     Union,
 )
 
-import requests
 from axe_selenium_python import Axe
 from selenium.common.exceptions import (
     NoSuchElementException,
@@ -29,6 +28,7 @@
 from selenium.webdriver.support.wait import WebDriverWait
 
 from galaxy.navigation.components import Target
+from galaxy.util import requests
 from .axe_results import (
     AxeResults,
     NullAxeResults,

lib/galaxy/selenium/navigates_galaxy.py

@@ -24,7 +24,6 @@
     Union,
 )
 
-import requests
 import yaml
 from selenium.webdriver.common.by import By
 from selenium.webdriver.remote.webdriver import WebDriver
@@ -36,7 +35,10 @@
     HasText,
 )
 from galaxy.navigation.data import load_root_component
-from galaxy.util import DEFAULT_SOCKET_TIMEOUT
+from galaxy.util import (
+    DEFAULT_SOCKET_TIMEOUT,
+    requests,
+)
 from . import sizzle
 from .has_driver import (
     exception_indicates_click_intercepted,

lib/galaxy/tool_util/biotools/source.py

@@ -8,9 +8,10 @@
     Optional,
 )
 
-import requests
-
-from galaxy.util import DEFAULT_SOCKET_TIMEOUT
+from galaxy.util import (
+    DEFAULT_SOCKET_TIMEOUT,
+    requests,
+)
 from .interface import BiotoolsEntry
 
 

lib/galaxy/tool_util/cwl/cwltool_deps.py

@@ -10,7 +10,7 @@
 
 warnings.filterwarnings("ignore", message=r"[\n.]DEPRECATION: Python 2", module="cwltool")
 
-import requests
+from galaxy.util import requests
 
 try:
     from cwltool import (

lib/galaxy/tool_util/data/__init__.py

@@ -34,7 +34,6 @@
     Union,
 )
 
-import requests
 from typing_extensions import (
     Protocol,
     TypedDict,
@@ -44,6 +43,7 @@
 from galaxy.exceptions import MessageException
 from galaxy.util import (
     Element,
+    requests,
     RW_R__R__,
 )
 from galaxy.util.compression_utils import decompress_path_to_directory

lib/galaxy/tool_util/deps/mulled/get_tests.py

@@ -15,9 +15,10 @@
     Optional,
 )
 
-import requests
 import yaml
 
+from galaxy.util import requests
+
 try:
     from jinja2 import Template
     from jinja2.exceptions import UndefinedError
@@ -130,7 +131,10 @@ def find_anaconda_versions(name, anaconda_channel="bioconda"):
     """
     Find a list of available anaconda versions for a given container name
     """
-    r = requests.get(f"https://anaconda.org/{anaconda_channel}/{name}/files", timeout=MULLED_SOCKET_TIMEOUT)
+    r = requests.get(
+        f"https://anaconda.org/{anaconda_channel}/{name}/files",
+        timeout=MULLED_SOCKET_TIMEOUT,
+    )
     r.raise_for_status()
     urls = []
     for line in r.text.splitlines():
@@ -147,7 +151,8 @@ def open_recipe_file(file, recipes_path=None, github_repo="bioconda/bioconda-rec
         return open(f"{recipes_path}/{file}").read()
     else:  # if no clone of the repo is available locally, download from GitHub
         r = requests.get(
-            f"https://raw.githubusercontent.com/{github_repo}/master/{file}", timeout=MULLED_SOCKET_TIMEOUT
+            f"https://raw.githubusercontent.com/{github_repo}/master/{file}",
+            timeout=MULLED_SOCKET_TIMEOUT,
         )
         if r.status_code == 404:
             raise OSError
@@ -163,7 +168,10 @@ def get_alternative_versions(filepath, filename, recipes_path=None, github_repo=
         return [n.replace(f"{recipes_path}/", "") for n in glob(f"{recipes_path}/{filepath}/*/{filename}")]
     # else use the GitHub API:
     versions = []
-    r = requests.get(f"https://api.github.com/repos/{github_repo}/contents/{filepath}", timeout=MULLED_SOCKET_TIMEOUT)
+    r = requests.get(
+        f"https://api.github.com/repos/{github_repo}/contents/{filepath}",
+        timeout=MULLED_SOCKET_TIMEOUT,
+    )
     check_github_api_response_rate_limit(r)
     r.raise_for_status()
     for subfile in json.loads(r.text):

lib/galaxy/tool_util/deps/mulled/mulled_build_channel.py

@@ -22,8 +22,7 @@
 import sys
 import time
 
-import requests
-
+from galaxy.util import requests
 from ._cli import arg_parser
 from .mulled_build import (
     add_build_arguments,

lib/galaxy/tool_util/deps/mulled/mulled_list.py

@@ -5,8 +5,7 @@
 from glob import glob
 from html.parser import HTMLParser
 
-import requests
-
+from galaxy.util import requests
 from .util import MULLED_SOCKET_TIMEOUT
 
 QUAY_API_ENDPOINT = "https://quay.io/api/v1/repository"

lib/galaxy/tool_util/deps/mulled/mulled_search.py

@@ -6,11 +6,10 @@
 import sys
 import tempfile
 
-import requests
-
 from galaxy.tool_util.deps.conda_util import CondaContext
 from galaxy.util import (
     check_github_api_response_rate_limit,
+    requests,
     which,
 )
 from .mulled_list import get_singularity_containers

lib/galaxy/tool_util/deps/mulled/util.py

@@ -18,7 +18,6 @@
     Union,
 )
 
-import requests
 from conda_package_streaming.package_streaming import stream_conda_info
 from conda_package_streaming.url import stream_conda_info as stream_conda_info_from_url
 from packaging.version import Version
@@ -29,6 +28,7 @@
     LegacyVersion,
     parse_version,
 )
+from galaxy.util import requests
 
 if TYPE_CHECKING:
     from galaxy.tool_util.deps.container_resolvers import ResolutionCache

lib/galaxy/tool_util/locations/dockstore.py

@@ -1,9 +1,11 @@
 from urllib.parse import quote
 
-import requests
 import yaml
 
-from galaxy.util import DEFAULT_SOCKET_TIMEOUT
+from galaxy.util import (
+    DEFAULT_SOCKET_TIMEOUT,
+    requests,
+)
 from . import ToolLocationResolver
 
 

lib/galaxy/tool_util/verify/interactor.py

@@ -24,7 +24,6 @@
     Union,
 )
 
-import requests
 from packaging.version import Version
 from requests import Response
 from requests.cookies import RequestsCookieJar
@@ -41,6 +40,7 @@
     TestCollectionDef,
     TestCollectionOutputDef,
 )
+from galaxy.util import requests
 from galaxy.util.bunch import Bunch
 from galaxy.util.hash_util import (
     memory_bound_hexdigest,

lib/galaxy/tools/data_fetch.py

@@ -26,6 +26,7 @@
     stream_to_file,
     stream_url_to_file,
 )
+from galaxy.util import user_agent  # noqa: F401
 from galaxy.util import (
     in_directory,
     safe_makedirs,