def clear_harakiri(_):
if uwsgi:
try:
# Setting user harakiri to 0 means to clear pending timeout if any
uwsgi.set_user_harakiri(0)
except:
# teardown_request must not fail
app.logger.exception("Failed to clear user harakiri")
def apply_reverse_proxy_timeout():
timestamp = request.environ.get("GEN3_REQUEST_TIMESTAMP")
timeout = request.environ.get("GEN3_TIMEOUT_SECONDS")
if not timestamp or not timeout:
return None
timeout = float(timestamp) + float(timeout.rstrip("s")) - time.time()
if timeout < 1:
# We don't proceed if the time remaining is less than 1 second because the
# minimal harakiri time is 1 second. Therefore it is important to set
# GEN3_TIMEOUT_SECONDS larger than 1 second, not even close.
app.logger.info(
"Not enough time to handle the request; discarding now.")
abort(504)
if uwsgi:
# GOTCHA: the int here is intentional over round, because we need a smaller
# timeout than reverse proxy
timeout = int(timeout)
uwsgi.set_user_harakiri(timeout)
app.logger.debug("Set user harakiri in %d seconds.", timeout)
def real_call(self, *args, **kwargs):
uwsgi.set_user_harakiri(self.s)
r = self.f(*args, **kwargs)
uwsgi.set_user_harakiri(0)
return r
def export_entities(program, project):
"""
Return a file with the requested entities as an attachment.
Either ``ids`` or ``node_label`` must be provided in the parameters. When both are
provided, ``node_label`` is ignored and ``ids`` is used.
If ``ids`` is provided, all entities matching given ``ids`` will be exported. If
there is only one entity type in the output, it will return a ``{node_type}.tsv`` or
``{node_type}.json`` file, e.g.: ``aliquot.tsv``. If there are multiple entity
types, it returns ``gdc_export_{one_time_sha}.tar.gz`` for TSV format, or
``gdc_export_{one_time_sha}.json`` for JSON format. CSV is similar to TSV.
If ``node_label`` is provided, it will export all entities of type with name
``node_label`` to a TSV file or JSON file. CSV is not supported yet in this case.
Summary:
Export entities
Tags:
export
Args:
program (str): |program_id|
project (str): |project_id|
Query Args:
ids (str): one or a list of node IDs seperated by commas.
node_label (str): type of nodes to look up, for example ``'case'``
format (str): output format, ``json`` or ``tsv`` or ``csv``; default is ``tsv``
with_children (str): whether to recursively find children or not; default is False
category (str): category of node to filter on children. Example: ``clinical``
without_id (bool): whether to include the ids in the export file; default is False
Responses:
200: Success
400: Bad Request
404: No id is found
403: Unauthorized request.
"""
try:
import uwsgi
except ImportError:
# not in uWSGI, skip
pass
else:
if hasattr(uwsgi, "set_user_harakiri"):
# disable HARAKIRI because export is meant to take a long time
uwsgi.set_user_harakiri(0)
if flask.request.method == "GET":
# Unpack multidict, or values will unnecessarily be lists.
kwargs = {k: v for k, v in flask.request.args.items()}
else:
kwargs = utils.parse.parse_request_json()
# Convert `format` argument to `file_format`.
if "format" in kwargs:
kwargs["file_format"] = kwargs["format"]
del kwargs["format"]
without_id = kwargs.get("without_id", "false").lower() == "true"
node_label = kwargs.get("node_label")
project_id = "{}-{}".format(program, project)
file_format = kwargs.get("file_format") or "tsv"
mimetype = (
"application/json"
if file_format.lower() == "json"
else "application/octet-stream"
)
if not kwargs.get("ids"):
if not node_label:
raise UserError("expected either `ids` or `node_label` parameter")
filename = "{}.{}".format(node_label, file_format)
content_disp = "attachment; filename={}".format(filename)
headers = {"Content-Disposition": content_disp}
utils.transforms.graph_to_doc.validate_export_node(node_label)
return flask.Response(
flask.stream_with_context(
utils.transforms.graph_to_doc.export_all(
node_label,
project_id,
file_format,
flask.current_app.db,
without_id,
)
),
mimetype=mimetype,
headers=headers,
)
else:
output = utils.transforms.graph_to_doc.ExportFile(
program=program, project=project, **kwargs
)
content_disp = "attachment; filename={}".format(output.filename)
headers = {"Content-Disposition": content_disp}
return flask.Response(
flask.stream_with_context(output.get_response()),
mimetype=mimetype,
headers=headers,
)
"""
uwsgi.chunked_read_nb()
"""
def uwsgi_pypy_chunked_read_nb():
wsgi_req = uwsgi_pypy_current_wsgi_req();
rlen = ffi.new("size_t*")
chunk = lib.uwsgi_chunked_read(wsgi_req, rlen, 0, 1)
if chunk == ffi.NULL:
if lib.uwsgi_is_again() > 0:
return None
raise IOError("unable to receive chunked part")
return ffi.string(chunk, rlen[0])
uwsgi.chunked_read_nb = uwsgi_pypy_chunked_read_nb
"""
uwsgi.set_user_harakiri(sec)
"""
uwsgi.set_user_harakiri = lambda x: lib.set_user_harakiri(x)
print "Initialized PyPy with Python", sys.version
print "PyPy Home:", sys.prefix
"""
Continulets support
"""
# this is the dictionary of continulets (one per-core)
uwsgi_pypy_continulets = {}
"""
uwsgi.chunked_read_nb()
"""
def uwsgi_pypy_chunked_read_nb():
wsgi_req = uwsgi_pypy_current_wsgi_req();
rlen = ffi.new("size_t*")
chunk = lib.uwsgi_chunked_read(wsgi_req, rlen, 0, 1)
if chunk == ffi.NULL:
if lib.uwsgi_is_again() > 0:
return None
raise IOError("unable to receive chunked part")
return ffi.string(chunk, rlen[0])
uwsgi.chunked_read_nb = uwsgi_pypy_chunked_read_nb
"""
uwsgi.set_user_harakiri(sec)
"""
uwsgi.set_user_harakiri = lambda x: lib.set_user_harakiri(x)
print "Initialized PyPy with Python", sys.version
print "PyPy Home:", sys.prefix
"""
Continulets support
"""
# this is the dictionary of continulets (one per-core)
uwsgi_pypy_continulets = {}