def test_make_fileitem_from_path_GIVEN_annotation_file_THEN_name_lacks_csv(
self, ):
source = FileItemSource(tempfile.gettempdir(), "local")
item = source.make_fileitem_from_path("customanno.csv",
"someh5ad_annotations", True)
self.assertEqual(item.name, "customanno")
self.assertEqual(item.descriptor,
"someh5ad_annotations/customanno.csv")
def test_launch_GIVEN_no_stdout_THEN_throw_ProcessException(self, popen):
subprocess = MagicMock()
subprocess.stdout.readline().decode.return_value = ""
subprocess.stderr.read().decode.return_value = "An unexpected error"
popen.return_value = subprocess
key = CacheKey(
FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
FileItemSource("/tmp", "local"),
)
entry = CacheEntry.for_key(key, 8000)
from cellxgene_gateway.subprocess_backend import SubprocessBackend
backend = SubprocessBackend()
cellxgene_loc = "/some/cellxgene"
scripts = [
"http://example.com/script.js", "http://example.com/script2.js"
]
with self.assertRaises(ProcessException) as context:
backend.launch(cellxgene_loc, scripts, entry)
popen.assert_called_once_with(
[
"yes | /some/cellxgene launch /tmp/czi/pbmc3k.h5ad --port 8000 --host 127.0.0.1 --disable-annotations --scripts http://example.com/script.js --scripts http://example.com/script2.js"
],
shell=True,
stderr=-1,
stdout=-1,
)
self.assertEqual("An unexpected error", context.exception.stderr)
def main():
cellxgene_data = os.environ.get("CELLXGENE_DATA", None)
cellxgene_bucket = os.environ.get("CELLXGENE_BUCKET", None)
#global default_item_source
if cellxgene_bucket is not None:
from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
item_sources.append(S3ItemSource(cellxgene_bucket, name="s3"))
default_item_source = "s3"
if cellxgene_data is not None:
from cellxgene_gateway.items.file.fileitem_source import FileItemSource
item_sources.append(FileItemSource(cellxgene_data, name="local"))
default_item_source = "local"
if len(item_sources) == 0:
raise Exception("Please specify CELLXGENE_DATA or CELLXGENE_BUCKET")
flask_util.include_source_in_url = len(item_sources) > 1
launch()
def main():
logging.basicConfig(
level=logging.INFO,
format="%(asctime)s:%(name)s:%(levelname)s:%(message)s",
)
cellxgene_data = os.environ.get("CELLXGENE_DATA", None)
cellxgene_bucket = os.environ.get("CELLXGENE_BUCKET", None)
if cellxgene_bucket is not None:
from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
item_sources.append(S3ItemSource(cellxgene_bucket, name="s3"))
default_item_source = "s3"
if cellxgene_data is not None:
from cellxgene_gateway.items.file.fileitem_source import FileItemSource
item_sources.append(FileItemSource(cellxgene_data, name="local"))
default_item_source = "local"
if len(item_sources) == 0:
raise Exception("Please specify CELLXGENE_DATA or CELLXGENE_BUCKET")
flask_util.include_source_in_url = len(item_sources) > 1
launch()
import unittest
from unittest.mock import MagicMock, patch
from cellxgene_gateway.filecrawl import render_item
from cellxgene_gateway.items.file.fileitem import FileItem
from cellxgene_gateway.items.file.fileitem_source import FileItemSource
from cellxgene_gateway.items.item import ItemType
source = FileItemSource("/tmp")
class TestRenderEntry(unittest.TestCase):
def test_GIVEN_path_both_slash_THEN_view_has_single_slash(self):
entry = FileItem(subpath="/somepath/",
name="entry",
type=ItemType.h5ad)
rendered = render_item(entry, source)
self.assertIn("view/somepath/entry/'", rendered)
def test_GIVEN_path_starts_slash_THEN_view_has_single_slash(self):
entry = FileItem(subpath="/somepath", name="entry", type=ItemType.h5ad)
rendered = render_item(entry, source)
self.assertIn("view/somepath/entry/'", rendered)
def test_GIVEN_path_ends_slash_THEN_view_has_single_slash(self):
entry = FileItem(subpath="somepath/", name="entry", type=ItemType.h5ad)
rendered = render_item(entry, source)
self.assertIn("view/somepath/entry/'", rendered)
def test_GIVEN_path_no_slash_THEN_view_has_single_slash(self):
entry = FileItem(subpath="somepath", name="entry", type=ItemType.h5ad)
def test_make_fileitem_from_path_GIVEN_h5ad_file_THEN_returns_name(self):
source = FileItemSource(tempfile.gettempdir(), "local")
item = source.make_fileitem_from_path("someanalysis.h5ad", "studydir")
self.assertEqual(item.name, "someanalysis.h5ad")
self.assertEqual(item.descriptor, "studydir/someanalysis.h5ad")
import unittest
from flask import Flask
from cellxgene_gateway import flask_util
from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
from cellxgene_gateway.cache_key import CacheKey
from cellxgene_gateway.gateway import app
from cellxgene_gateway.items.file.fileitem import FileItem
from cellxgene_gateway.items.file.fileitem_source import FileItemSource
from cellxgene_gateway.items.item import ItemType
key = CacheKey(
FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
FileItemSource("/tmp", "local"),
)
class TestRenderEntry(unittest.TestCase):
def setUp(self):
self.app = app
self.app_context = self.app.test_request_context()
self.app_context.push()
self.client = self.app.test_client()
def test_GIVEN_key_and_port_THEN_returns_loading_CacheEntry(self):
entry = CacheEntry.for_key("some-key", 1)
self.assertEqual(entry.status, CacheEntryStatus.loading)
def test_GIVEN_absolute_static_url_THEN_include_path(self):
flask_util.include_source_in_url = False
def test_list_items_GIVEN_subpath_THEN_checks_subpath(self, listdir, path):
stub_join(path)
source = FileItemSource("/tmp/unittest", "local")
source.list_items("foo")
path.exists.assert_called_once_with("/tmp/unittest/foo")
