def filecrawl(path=None):
source_name = request.args.get("source")
sources = (
filter(
lambda x: x.name == urllib.parse.unquote_plus(source_name),
item_sources,
)
if source_name
else item_sources
)
# loop all data sources --
rendered_sources = [
render_item_source(item_source, path) for item_source in sources
] # will we need to make this async in the page???
rendered_html = "\n".join(rendered_sources)
resp = make_response(
render_template(
"filecrawl.html",
extra_scripts=get_extra_scripts(),
rendered_html=rendered_html,
path=path,
)
)
set_no_cache(resp)
return resp
def test_GIVEN_bare_string_THEN_throws_Exception(self):
with self.assertRaises(Exception) as context:
self.assertEqual(get_extra_scripts(), [])
self.assertEqual(
'Error parsing GATEWAY_EXTRA_SCRIPTS, expected JSON array e.g. ["https://example.com/path/to/script.js"]',
str(context.exception),
)
def index():
return render_template(
"index.html",
ip=env.ip,
cellxgene_data=env.cellxgene_data,
extra_scripts=get_extra_scripts(),
)
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 filecrawl():
entries = recurse_dir(env.cellxgene_data)
rendered_html = render_entries(entries)
resp = make_response(
render_template(
"filecrawl.html",
extra_scripts=get_extra_scripts(),
rendered_html=rendered_html,
))
return set_no_cache(resp)
def handle_invalid_usage(error):
message = f"{error.http_status} Error : {error.message}"
return (
render_template(
"cellxgene_error.html",
extra_scripts=get_extra_scripts(),
message=message,
),
error.http_status,
)
def do_filecrawl(path):
filecrawl_path = os.path.join(env.cellxgene_data, path)
if not os.path.isdir(filecrawl_path):
raise CellxgeneException("Path is not directory: " + filecrawl_path,
status.HTTP_400_BAD_REQUEST)
entries = recurse_dir(filecrawl_path)
rendered_html = render_entries(entries)
return render_template(
"filecrawl.html",
extra_scripts=get_extra_scripts(),
rendered_html=rendered_html,
path=path,
)
def index():
users = [
name for name in os.listdir(env.cellxgene_data)
if os.path.isdir(os.path.join(env.cellxgene_data, name))
]
return render_template(
"index.html",
ip=env.ip,
cellxgene_data=env.cellxgene_data,
extra_scripts=get_extra_scripts(),
users=users,
enable_upload=env.enable_upload,
)
def filecrawl():
entries = recurse_dir(env.cellxgene_data)
rendered_html = render_entries(entries)
resp = make_response(
render_template(
"filecrawl.html",
extra_scripts=get_extra_scripts(),
rendered_html=rendered_html,
))
resp.headers["Cache-Control"] = "no-cache, no-store, must-revalidate"
resp.headers["Pragma"] = "no-cache"
resp.headers["Expires"] = "0"
resp.headers['Cache-Control'] = 'public, max-age=0'
return resp
def do_view(path):
key = get_key(path)
print(
f"view path={path}, dataset={key.dataset}, annotation_file= {key.annotation_file}, key={key.pathpart}"
)
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 == "loaded" or match.status == "loading":
return match.serve_content(path)
elif match.status == "error":
raise ProcessException.from_cache_entry(match)
def handle_invalid_process(error):
message = []
message.append(error.message)
message.append(f"{error.http_status} Error.")
message.append(f"Stdout: {error.stdout}")
message.append(f"Stderr: {error.stderr}")
return (
render_template(
"process_error.html",
extra_scripts=get_extra_scripts(),
message=error.message,
http_status=error.http_status,
stdout=error.stdout,
stderr=error.stderr,
relaunch_url=error.key.relaunch_url(),
annotation_file=error.key.annotation_descriptor,
),
error.http_status,
)
def filecrawl(path=None):
source_name = request.args.get("source")
sources = (filter(
lambda x: x.name == urllib.parse.unquote_plus(source_name),
item_sources,
) if source_name else item_sources)
# loop all data sources --
rendered_sources = [
render_item_source(item_source, path) for item_source in sources
] # will we need to make this async in the page???
rendered_html = "\n".join(rendered_sources)
resp = make_response(
render_template(
"filecrawl.html",
extra_scripts=get_extra_scripts(),
rendered_html=rendered_html,
path=path,
))
resp.headers["Cache-Control"] = "no-cache, no-store, must-revalidate"
resp.headers["Pragma"] = "no-cache"
resp.headers["Expires"] = "0"
resp.headers["Cache-Control"] = "public, max-age=0"
return resp
def do_GET_status():
return render_template(
"cache_status.html",
entry_list=cache.entry_list,
extra_scripts=get_extra_scripts(),
)
def test_GIVEN_two_scripts_THEN_returns_two_strings(self):
self.assertEqual(get_extra_scripts(), ["abc", "def"])
def test_GIVEN_empty_string_THEN_returns_empty_array(self):
self.assertEqual(get_extra_scripts(), [])
def test_GIVEN_two_scripts_THEN_returns_two_strings(self):
self.assertEqual(get_extra_scripts(), ['abc', 'def'])