Merge pull request #13664 from... (06d37d99) · Commits · NDIP / Galaxy

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

+33 −8

Original line number	Diff line number	Diff line
		@@ -5,6 +5,10 @@ import json
		import logging
		import sys
		import tempfile
		from datetime import (
		datetime,
		timezone,
		)

		import requests

		@@ -140,13 +144,31 @@ class GitHubSearch():
		Tool to search the GitHub bioconda-recipes repo
		"""

		@staticmethod
		def _check_response_rate_limit(response):
		if response.status_code == 403 and "API rate limit exceeded" in response.json()["message"]:
		# It can take tens of minutes before the rate limit window resets
		message = "GitHub API rate limit exceeded."
		rate_limit_reset_UTC_timestamp = response.headers.get("X-RateLimit-Reset")
		if rate_limit_reset_UTC_timestamp:
		rate_limit_reset_datetime = datetime.fromtimestamp(int(rate_limit_reset_UTC_timestamp), tz=timezone.utc)
		message += f" The rate limit window will reset at {rate_limit_reset_datetime.isoformat()}."
		raise Exception(message)

		def get_json(self, search_string):
		"""
		Takes search_string variable and return results from the bioconda-recipes github repository in JSON format

		DEPRECATED: this method is currently unreliable because the API query
		sometimes succeeds but returns no items.
		"""
		response = requests.get(
		"https://api.github.com/search/code?q=%s+in:path+repo:bioconda/bioconda-recipes+path:recipes" % search_string, timeout=MULLED_SOCKET_TIMEOUT).json()
		return response
		f"https://api.github.com/search/code?q={search_string}+in:path+repo:bioconda/bioconda-recipes+path:recipes",
		timeout=MULLED_SOCKET_TIMEOUT,
		)
		self._check_response_rate_limit(response)
		response.raise_for_status()
		return response.json()

		def process_json(self, json, search_string):
		"""
		@@ -164,10 +186,12 @@ class GitHubSearch():
		"""
		Check if a recipe exists in bioconda-recipes which matches search_string exactly
		"""
		if requests.get("https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/%s" % search_string, timeout=MULLED_SOCKET_TIMEOUT).status_code == 200:
		return True
		else:
		return False
		response = requests.get(
		f"https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/{search_string}",
		timeout=MULLED_SOCKET_TIMEOUT,
		)
		self._check_response_rate_limit(response)
		return response.status_code == 200


		def get_package_hash(packages, versions):
		@@ -338,10 +362,11 @@ def main(argv=None):
		github = GitHubSearch()

		for item in args.search:
		github_json = github.get_json(item)
		github_results[item] = github.process_json(github_json, item)
		if github.recipe_present(item):
		github_recipe_present.append(item)
		else:
		github_json = github.get_json(item)
		github_results[item] = github.process_json(github_json, item)

		json_results['github'] = github_results
		json_results['github_recipe_present'] = {

test/unit/tool_util/mulled/test_mulled_search.py

+14 −5

Original line number	Diff line number	Diff line
		@@ -27,12 +27,21 @@ def test_conda_search():


		@external_dependency_management
		def test_github_search():
		def test_github_recipe_present():
		t = GitHubSearch()
		search1 = t.process_json(t.get_json("adsfasdf"), "adsfasdf")
		search2 = t.process_json(t.get_json("bioconductor-gosemsim"), "bioconductor-gosemsim")
		assert search1 == []
		assert {'path': 'recipes/bioconductor-gosemsim/meta.yaml', 'name': 'meta.yaml'} in search2

		search_string2expected = {
		"adsfasdf": False,
		"bioconductor-gosemsim": True,
		}
		for search_string, expected in search_string2expected.items():
		try:
		is_recipe_present = t.recipe_present(search_string)
		except Exception as e:
		if "API rate limit" in str(e):
		pytest.skip("Hitting GitHub API rate limit")
		raise
		assert is_recipe_present is expected


		@external_dependency_management