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import os
import unittest
import bioblend
import bioblend.toolshed
from . import test_util
@test_util.skip_unless_toolshed()
class TestToolshed(unittest.TestCase):
def setUp(self):
toolshed_url = os.environ["BIOBLEND_TOOLSHED_URL"]
self.ts = bioblend.toolshed.ToolShedInstance(url=toolshed_url)
def test_categories_client(self):
# get_categories
categories = self.ts.categories.get_categories()
assert "Assembly" in [c["name"] for c in categories]
# we cannot test get_categories with deleted=True as it requires administrator status
# show_category
visualization_category_id = [c for c in categories if c["name"] == "Visualization"][0]["id"]
visualization_category = self.ts.categories.show_category(visualization_category_id)
assert visualization_category["description"] == "Tools for visualizing data"
# get_repositories
repositories = self.ts.categories.get_repositories(visualization_category_id)
repositories_reversed = self.ts.categories.get_repositories(visualization_category_id, sort_order="desc")
assert repositories["repositories"][0]["model_class"] == "Repository"
assert len(repositories["repositories"]) > 200
assert repositories["repositories"][0] == repositories_reversed["repositories"][-1]
def test_repositories_client(self):
# get_repositories
repositories = self.ts.repositories.get_repositories()
assert len(repositories) > 5000
assert repositories[0]["model_class"] == "Repository"
repositories = self.ts.repositories.get_repositories(name="bam_to_sam", owner="devteam")
assert len(repositories) == 1
bam_to_sam_repo = repositories[0]
assert bam_to_sam_repo["name"] == "bam_to_sam"
assert bam_to_sam_repo["owner"] == "devteam"
# search_repositories
samtools_search = self.ts.repositories.search_repositories("samtools", page_size=5)
assert int(samtools_search["total_results"]) > 20
assert len(samtools_search["hits"]) == 5
# show_repository
show_bam_to_sam_repo = self.ts.repositories.show_repository(bam_to_sam_repo["id"])
assert "SAM" in show_bam_to_sam_repo["long_description"]
# test_create_repository
# need to provide an API key to test this
# test_update_repository
# need to provide an API key to test this
def test_repositories_revisions(self):
# get_ordered_installable_revisions
bam_to_sam_revisions = self.ts.repositories.get_ordered_installable_revisions("bam_to_sam", "devteam")
assert len(bam_to_sam_revisions) >= 4
# get_repository_revision_install_info
bam_to_sam_revision_install_info = self.ts.repositories.get_repository_revision_install_info(
"bam_to_sam", "devteam", bam_to_sam_revisions[0]
)
assert len(bam_to_sam_revision_install_info) == 3
assert bam_to_sam_revision_install_info[0].get("model_class") == "Repository"
assert bam_to_sam_revision_install_info[1].get("model_class") == "RepositoryMetadata"
assert bam_to_sam_revision_install_info[2].get("model_class") is None
def test_tools_client(self):
# search_tools
samtools_search = self.ts.tools.search_tools("samtools", page_size=5)
assert int(samtools_search["total_results"]) > 2000
assert len(samtools_search["hits"]) == 5
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