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):
if source.is_authorized(match.key.descriptor):
return match.serve_content(path)
else:
raise CellxgeneException("User not authorized to access this data",
403)
elif match.status == CacheEntryStatus.error:
raise ProcessException.from_cache_entry(match)
def create_dir(parent_path, dir_name):
full_path = os.path.join(parent_path, dir_name)
if "/" in dir_name:
raise CellxgeneException(
"Please have no slashes in the intended directory.",
status.HTTP_400_BAD_REQUEST,
)
elif not os.path.exists(parent_path):
raise CellxgeneException(
"The selected User directory does not exist.",
status.HTTP_400_BAD_REQUEST,
)
elif os.path.exists(full_path):
raise CellxgeneException(
"The provided subdirectory already exists within Directory.",
status.HTTP_400_BAD_REQUEST,
)
elif not is_subdir(full_path, parent_path):
raise CellxgeneException(
"The directory must be a subdirectory of the parent path.",
status.HTTP_400_BAD_REQUEST,
)
elif not os.path.isdir(parent_path):
raise CellxgeneException(
"The parent is not a directory.", status.HTTP_400_BAD_REQUEST
)
else:
os.mkdir(full_path)
def upload_file():
upload_dir = request.form["path"]
full_upload_path = os.path.join(env.cellxgene_data, upload_dir)
if is_subdir(full_upload_path,
env.cellxgene_data) and os.path.isdir(full_upload_path):
if request.method == "POST":
if "file" in request.files:
f = request.files["file"]
if f and f.filename.endswith(".h5ad"):
f.save(
os.path.join(full_upload_path,
secure_filename(f.filename)))
return redirect("/filecrawl.html", code=302)
else:
raise CellxgeneException(
"Uploaded file must be in anndata (.h5ad) format.",
status.HTTP_400_BAD_REQUEST,
)
else:
raise CellxgeneException(
"A file must be chosen to upload.",
status.HTTP_400_BAD_REQUEST,
)
else:
raise CellxgeneException("Invalid directory.",
status.HTTP_400_BAD_REQUEST)
return redirect(location, code=302)
def validate_is_dir(file_path):
validate_exists(file_path)
if not os.path.isdir(file_path):
raise CellxgeneException(
"Path is not dir: " + file_path, status.HTTP_400_BAD_REQUEST
)
return
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_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 check_entry(self, key):
contents = self.entry_list
matches = [
c for c in contents
if c.key.equals(key) and c.status != CacheEntryStatus.terminated
]
if len(matches) == 0:
return None
elif len(matches) == 1:
return matches[0]
else:
raise CellxgeneException(
status.HTTP_500_INTERNAL_SERVER_ERROR,
"Found " + str(len(matches)) + " for " + key.dataset,
)
def check_path(self, source, path):
contents = self.entry_list
matches = [
c for c in contents
if c.key.source.name == source.name and path.startswith(
c.key.descriptor) and c.status != CacheEntryStatus.terminated
]
if len(matches) == 0:
return None
elif len(matches) == 1:
return matches[0]
else:
raise CellxgeneException(
status.HTTP_500_INTERNAL_SERVER_ERROR,
"Found " + str(len(matches)) + " for " + path,
)
def validate_exists(file_path):
if not os.path.exists(file_path):
raise CellxgeneException(
"File does not exist: " + file_path, status.HTTP_400_BAD_REQUEST
)
def serve_content(self, path):
gateway_basepath = self.key.gateway_basepath()
subpath = path[len(self.key.descriptor):] # noqa: E203
if len(subpath) == 0:
r = make_response(f"Redirect to {gateway_basepath}\n", 302)
r.headers["location"] = gateway_basepath + querystring()
return r
elif self.status == CacheEntryStatus.loading:
launch_time = datetime.datetime.fromtimestamp(self.launchtime)
return render_template(
"loading.html",
launchtime=launch_time,
all_output=self.all_output,
)
headers = {}
copy_headers = [
"accept",
"accept-encoding",
"accept-language",
"cache-control",
"connection",
"content-length",
"content-type",
"cookie",
"host",
"origin",
"pragma",
"referer",
"sec-fetch-mode",
"sec-fetch-site",
"user-agent",
]
for h in copy_headers:
if h in request.headers:
headers[h] = request.headers[h]
full_path = self.cellxgene_basepath() + subpath + querystring()
if request.method in ["GET", "HEAD", "OPTIONS"]:
cellxgene_response = get(full_path, headers=headers)
elif request.method == "PUT":
cellxgene_response = put(
full_path,
headers=headers,
data=request.data,
)
elif request.method == "POST":
cellxgene_response = post(
full_path,
headers=headers,
data=request.data,
)
else:
raise CellxgeneException(f"Unexpected method {request.method}",
400)
content_type = cellxgene_response.headers["content-type"]
if "text" in content_type:
gateway_content = self.rewrite_text_content(
cellxgene_response.content.decode())
else:
gateway_content = cellxgene_response.content
resp_headers = {}
for h in copy_headers:
if h in cellxgene_response.headers:
resp_headers[h] = cellxgene_response.headers[h]
gateway_response = make_response(
gateway_content,
cellxgene_response.status_code,
resp_headers,
)
return gateway_response
def serve_content(self, path):
gateway_basepath = (
f"{env.external_protocol}://{env.external_host}/view/{self.key.pathpart}/"
)
subpath = path[len(self.key.pathpart) :] # noqa: E203
if len(subpath) == 0:
r = make_response(f"Redirect to {gateway_basepath}\n", 301)
r.headers["location"] = gateway_basepath+querystring()
return r
elif self.status == "loading":
launch_time = datetime.datetime.fromtimestamp(self.launchtime)
return render_template(
"loading.html", launchtime=launch_time, all_output=self.all_output
)
port = self.port
cellxgene_basepath = f"http://127.0.0.1:{port}"
headers = {}
copy_headers = [
'accept',
'accept-encoding',
'accept-language',
'cache-control',
'connection',
'content-length',
'content-type',
'cookie',
'host',
'origin',
'pragma',
'referer',
'sec-fetch-mode',
'sec-fetch-site',
'user-agent'
]
for h in copy_headers:
if h in request.headers:
headers[h] = request.headers[h]
full_path = cellxgene_basepath + subpath + querystring()
if request.method in ["GET", "HEAD", "OPTIONS"]:
cellxgene_response = get(
full_path, headers=headers
)
elif request.method == "PUT":
cellxgene_response = put(
full_path,
headers=headers,
data=request.data,
)
elif request.method == "POST":
cellxgene_response = post(
full_path,
headers=headers,
data=request.data,
)
else:
raise CellxgeneException(
f"Unexpected method {request.method}", 400
)
content_type = cellxgene_response.headers["content-type"]
if "text" in content_type:
cellxgene_content = cellxgene_response.content.decode()
gateway_content = cellxgene_content.replace(
"http://fonts.gstatic.com", "https://fonts.gstatic.com"
).replace(cellxgene_basepath, gateway_basepath)
else:
gateway_content = cellxgene_response.content
resp_headers = {}
for h in copy_headers:
if h in cellxgene_response.headers:
resp_headers[h] = cellxgene_response.headers[h]
gateway_response = make_response(
gateway_content,
cellxgene_response.status_code,
resp_headers,
)
return gateway_response