def get_key(path):
if path == "/" or path == "":
raise CellxgeneException(
"No matching dataset found.", status.HTTP_404_NOT_FOUND
)
trimmed = path[:-1] if path[-1] == "/" else path
try:
# valid paths come in three forms:
if trimmed.endswith('.h5ad') and data_file_exists(trimmed):
# 1) somedir/dataset.h5ad: a dataset
return CacheKey(trimmed, trimmed, None)
elif trimmed.endswith('.csv'):
# 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotations file.
annotations_dir = os.path.split(trimmed)[0]
dataset = make_h5ad(annotations_dir)
if data_file_exists(dataset):
data_dir_ensure(annotations_dir)
return CacheKey(trimmed, dataset, trimmed)
elif trimmed.endswith('_annotations') and data_dir_exists(trimmed):
# 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
dataset = make_h5ad(trimmed)
if data_file_exists(dataset):
return CacheKey(trimmed, dataset, '')
except CellxgeneException:
pass
split = os.path.split(trimmed)
return get_key(split[0])
def do_view(path, source_name=None):
source = matching_source(source_name)
match = cache.check_path(source, path)
if match is None:
lookup = source.lookup(path)
if lookup is None:
raise CellxgeneException(
f"Could not find item for path {path} in source {source.name}",
404,
)
key = CacheKey.for_lookup(source, lookup)
print(
f"view path={path}, source_name={source_name}, dataset={key.file_path}, annotation_file= {key.annotation_file_path}, key={key.descriptor}, source={key.source_name}"
)
with entry_lock:
match = cache.check_entry(key)
if match is None:
uascripts = get_extra_scripts()
match = cache.create_entry(key, uascripts)
match.timestamp = current_time_stamp()
if (match.status == CacheEntryStatus.loaded
or match.status == CacheEntryStatus.loading):
return match.serve_content(path)
elif match.status == CacheEntryStatus.error:
raise ProcessException.from_cache_entry(match)
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 do_terminate(path):
source_name = request.args.get("source_name") or default_item_source.name
source = matching_source(source_name)
key = CacheKey.for_lookup(source, source.lookup(path))
match = cache.check_entry(key)
if not match is None:
match.terminate()
return redirect(url_for("do_GET_status"), code=302)
def do_relaunch(path):
source_name = request.args.get("source_name") or default_item_source.name
source = matching_source(source_name)
key = CacheKey.for_lookup(source, source.lookup(path))
match = cache.check_entry(key)
if not match is None:
match.terminate()
return redirect(
key.view_url,
code=302,
)
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
import unittest
from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
from cellxgene_gateway.cache_key import CacheKey
key = CacheKey("czi/pbmc3k.h5ad", "pbmc3k.h5ad", "tmp.csv")
class TestRenderEntry(unittest.TestCase):
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):
actual = CacheEntry.for_key(
key, 8000).rewrite_text_content("src:url(/static/assets/")
expected = (
"src:url(http://localhost:5005/view/czi/pbmc3k.h5ad/static/assets/"
)
self.assertEqual(actual, expected)
def test_GIVEN_absolute_src_THEN_include_path(self):
actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
'<link rel="shortcut icon" href="/static/assets/favicon.ico">')
expected = '<link rel="shortcut icon" href="http://localhost:5005/view/czi/pbmc3k.h5ad/static/assets/favicon.ico">'
self.assertEqual(actual, expected)
if __name__ == "__main__":
unittest.main()