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 make_fileitem_from_path(
self, filename, subpath, is_annotation=False, is_shallow=False
) -> FileItem:
if is_annotation and filename.endswith(self.annotation_file_suffix):
name = filename[: -len(self.annotation_file_suffix)]
ext = self.annotation_file_suffix
else:
name = filename
ext = ""
item = FileItem(
subpath=subpath,
name=name,
ext=ext,
type=ItemType.annotation if is_annotation else ItemType.h5ad,
)
if not is_annotation and not is_shallow:
annotations = self.make_annotations_for_fileitem(item)
item.annotations = annotations
return item
def test_GIVEN_path_no_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 create_annotation(self, item: FileItem, name: str) -> FileItem:
annotation = self.make_fileitem_from_path(
name, self.get_annotations_subpath(item), is_annotation=True)
item.annotations = (item.annotations or []).append(annotation)
return annotation
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