app.router.add_get('/nodestate/{nodetype}/{nodenumber}', nodestate)
app.router.add_get('/nodeinfo', nodeinfo)
app.router.add_get('/nodeinfo/{statkey}', nodeinfo)
app.router.add_get('/info', info)
app.router.add_post('/register', register)
return app
#
# Main
#
if __name__ == '__main__':
loop = asyncio.get_event_loop()
app = loop.run_until_complete(init(loop))
# create a client Session here so that all client requests
# will share the same connection pool
max_tcp_connections = int(config.get("max_tcp_connections"))
app['client'] = ClientSession(loop=loop, connector=TCPConnector(limit=max_tcp_connections))
session = aiobotocore.get_session(loop=loop)
app["session"] = session
app["loop"] = loop
asyncio.ensure_future(healthCheck(app), loop=loop)
head_port = config.get("head_port")
log.info("Starting service on port: {}".format(head_port))
log.debug("debug test")
run_app(app, port=int(head_port))
async def GET_Link(request):
"""HTTP method to return JSON for a group link"""
log.request(request)
app = request.app
group_id = request.match_info.get('id')
if not group_id:
msg = "Missing group id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(group_id, obj_class="Group"):
msg = "Invalid group id: {}".format(group_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
link_title = request.match_info.get('title')
validateLinkName(link_title)
username, pswd = getUserPasswordFromRequest(request)
if username is None and app['allow_noauth']:
username = "******"
else:
await validateUserPassword(app, username, pswd)
domain = getDomainFromRequest(request)
if not isValidDomain(domain):
msg = "Invalid host value: {}".format(domain)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
await validateAction(app, domain, group_id, username, "read")
req = getDataNodeUrl(app, group_id)
req += "/groups/" + group_id + "/links/" + link_title
log.debug("get LINK: " + req)
link_json = await http_get(app, req)
log.debug("got link_json: " + str(link_json))
resp_link = {}
resp_link["title"] = link_title
resp_link["class"] = link_json["class"]
if link_json["class"] == "H5L_TYPE_HARD":
resp_link["id"] = link_json["id"]
resp_link["collection"] = getCollectionForId(link_json["id"])
elif link_json["class"] == "H5L_TYPE_SOFT":
resp_link["h5path"] = link_json["h5path"]
elif link_json["class"] == "H5L_TYPE_EXTERNAL":
resp_link["h5path"] = link_json["h5path"]
resp_link["h5domain"] = link_json["h5domain"]
else:
log.warn("Unexpected link class: {}".format(link_json["class"]))
resp_json = {}
resp_json["link"] = resp_link
resp_json["created"] = link_json["created"]
# links don't get modified, so use created timestamp as lastModified
resp_json["lastModified"] = link_json["created"]
hrefs = []
group_uri = '/groups/' + group_id
hrefs.append({
'rel': 'self',
'href': getHref(request, group_uri + '/links/' + link_title)
})
hrefs.append({'rel': 'home', 'href': getHref(request, '/')})
hrefs.append({'rel': 'owner', 'href': getHref(request, group_uri)})
if link_json["class"] == "H5L_TYPE_HARD":
target = '/' + resp_link["collection"] + '/' + resp_link["id"]
hrefs.append({'rel': 'target', 'href': getHref(request, target)})
resp_json["hrefs"] = hrefs
resp = await jsonResponse(request, resp_json)
log.response(request, resp=resp)
return resp
async def GET_Links(request):
"""HTTP method to return JSON for link collection"""
log.request(request)
app = request.app
params = request.rel_url.query
group_id = request.match_info.get('id')
if not group_id:
msg = "Missing group id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(group_id, obj_class="Group"):
msg = "Invalid group id: {}".format(group_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
limit = None
if "Limit" in params:
try:
limit = int(params["Limit"])
except ValueError:
msg = "Bad Request: Expected int type for limit"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
marker = None
if "Marker" in params:
marker = params["Marker"]
username, pswd = getUserPasswordFromRequest(request)
if username is None and app['allow_noauth']:
username = "******"
else:
await validateUserPassword(app, username, pswd)
domain = getDomainFromRequest(request)
if not isValidDomain(domain):
msg = "Invalid host value: {}".format(domain)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
await validateAction(app, domain, group_id, username, "read")
req = getDataNodeUrl(app, group_id)
req += "/groups/" + group_id + "/links"
query_sep = '?'
if limit is not None:
req += query_sep + "Limit=" + str(limit)
query_sep = '&'
if marker is not None:
req += query_sep + "Marker=" + marker
log.debug("get LINKS: " + req)
links_json = await http_get(app, req)
log.debug("got links json from dn for group_id: {}".format(group_id))
links = links_json["links"]
# mix in collection key, target and hrefs
for link in links:
if link["class"] == "H5L_TYPE_HARD":
collection_name = getCollectionForId(link["id"])
link["collection"] = collection_name
target_uri = '/' + collection_name + '/' + link["id"]
link["target"] = getHref(request, target_uri)
link_uri = '/groups/' + group_id + '/links/' + link['title']
link["href"] = getHref(request, link_uri)
resp_json = {}
resp_json["links"] = links
hrefs = []
group_uri = '/groups/' + group_id
hrefs.append({
'rel': 'self',
'href': getHref(request, group_uri + '/links')
})
hrefs.append({'rel': 'home', 'href': getHref(request, '/')})
hrefs.append({'rel': 'owner', 'href': getHref(request, group_uri)})
resp_json["hrefs"] = hrefs
resp = await jsonResponse(request, resp_json)
log.response(request, resp=resp)
return resp
async def PUT_Chunk(request):
log.request(request)
app = request.app
params = request.rel_url.query
chunk_id = request.match_info.get('id')
if not chunk_id:
msg = "Missing chunk id"
log.error(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(chunk_id, "Chunk"):
msg = "Invalid chunk id: {}".format(chunk_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not request.has_body:
msg = "PUT Value with no body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
content_type = "application/octet-stream"
if "Content-Type" in request.headers:
# client should use "application/octet-stream" for binary transfer
content_type = request.headers["Content-Type"]
if content_type != "application/octet-stream":
msg = "Unexpected content_type: {}".format(content_type)
log.error(msg)
raise HTTPBadRequest(reason=msg)
validateInPartition(app, chunk_id)
log.debug("request params: {}".format(list(params.keys())))
if "dset" not in params:
msg = "Missing dset in GET request"
log.error(msg)
raise HTTPBadRequest(reason=msg)
dset_json = json.loads(params["dset"])
log.debug("dset_json: {}".format(dset_json))
dims = getChunkLayout(dset_json)
if "root" not in dset_json:
msg = "expected root key in dset_json"
log.error(msg)
raise KeyError(msg)
rank = len(dims)
# get chunk selection from query params
selection = []
for i in range(rank):
dim_slice = getSliceQueryParam(request, i, dims[i])
selection.append(dim_slice)
selection = tuple(selection)
log.debug("got selection: {}".format(selection))
type_json = dset_json["type"]
itemsize = 'H5T_VARIABLE'
if "size" in type_json:
itemsize = type_json["size"]
dt = createDataType(type_json)
log.debug("dtype: {}".format(dt))
if rank == 0:
msg = "No dimension passed to PUT chunk request"
log.error(msg)
raise HTTPBadRequest(reason=msg)
if len(selection) != rank:
msg = "Selection rank does not match shape rank"
log.error(msg)
raise HTTPBadRequest(reason=msg)
for i in range(rank):
s = selection[i]
log.debug("selection[{}]: {}".format(i, s))
mshape = getSelectionShape(selection)
log.debug(f"mshape: {mshape}")
num_elements = 1
for extent in mshape:
num_elements *= extent
# check that the content_length is what we expect
if itemsize != 'H5T_VARIABLE':
log.debug("expect content_length: {}".format(num_elements*itemsize))
log.debug("actual content_length: {}".format(request.content_length))
if itemsize != 'H5T_VARIABLE' and (num_elements * itemsize) != request.content_length:
msg = "Expected content_length of: {}, but got: {}".format(num_elements*itemsize, request.content_length)
log.error(msg)
raise HTTPBadRequest(reason=msg)
# create a numpy array for incoming data
input_bytes = await request_read(request) # TBD - will it cause problems when failures are raised before reading data?
if len(input_bytes) != request.content_length:
msg = "Read {} bytes, expecting: {}".format(len(input_bytes), request.content_length)
log.error(msg)
raise HTTPInternalServerError()
input_arr = bytesToArray(input_bytes, dt, mshape)
chunk_arr = await getChunk(app, chunk_id, dset_json, chunk_init=True)
# update chunk array
chunk_arr[selection] = input_arr
chunk_cache = app["chunk_cache"]
chunk_cache.setDirty(chunk_id)
log.info(f"PUT_Chunk dirty cache count: {chunk_cache.dirtyCount}")
# async write to S3
dirty_ids = app["dirty_ids"]
now = int(time.time())
dirty_ids[chunk_id] = now
# chunk update successful
resp = json_response({}, status=201)
log.response(request, resp=resp)
return resp
async def POST_Chunk(request):
log.request(request)
app = request.app
params = request.rel_url.query
put_points = False
num_points = 0
if "count" in params:
num_points = int(params["count"])
if "action" in params and params["action"] == "put":
log.info("POST Chunk put points, num_points: {}".format(num_points))
put_points = True
else:
log.info("POST Chunk get points")
chunk_id = request.match_info.get('id')
if not chunk_id:
msg = "Missing chunk id"
log.error(msg)
raise HTTPBadRequest(reason=msg)
log.info("POST chunk_id: {}".format(chunk_id))
chunk_index = getChunkIndex(chunk_id)
log.debug("chunk_index: {}".format(chunk_index))
if not isValidUuid(chunk_id, "Chunk"):
msg = "Invalid chunk id: {}".format(chunk_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
validateInPartition(app, chunk_id)
log.debug("request params: {}".format(list(params.keys())))
if "dset" not in params:
msg = "Missing dset in GET request"
log.error(msg)
raise HTTPBadRequest(reason=msg)
dset_json = json.loads(params["dset"])
log.debug("dset_json: {}".format(dset_json))
chunk_layout = getChunkLayout(dset_json)
chunk_coord = getChunkCoordinate(chunk_id, chunk_layout)
log.debug("chunk_coord: {}".format(chunk_coord))
if not request.has_body:
msg = "POST Value with no body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
content_type = "application/octet-stream"
if "Content-Type" in request.headers:
# client should use "application/octet-stream" for binary transfer
content_type = request.headers["Content-Type"]
if content_type != "application/octet-stream":
msg = "Unexpected content_type: {}".format(content_type)
log.error(msg)
raise HTTPBadRequest(reason=msg)
type_json = dset_json["type"]
dset_dtype = createDataType(type_json)
log.debug("dtype: {}".format(dset_dtype))
dims = getChunkLayout(dset_json)
log.debug("got dims: {}".format(dims))
rank = len(dims)
if rank == 0:
msg = "POST chunk request with no dimensions"
log.error(msg)
raise HTTPBadRequest(reason=msg)
# create a numpy array for incoming points
input_bytes = await request_read(request)
if len(input_bytes) != request.content_length:
msg = "Read {} bytes, expecting: {}".format(len(input_bytes), request.content_length)
log.error(msg)
raise HTTPInternalServerError()
# get chunk from cache/s3. If not found init a new chunk if this is a write request
chunk_arr = await getChunk(app, chunk_id, dset_json, chunk_init=put_points)
if put_points:
# writing point data
# create a numpy array with the following type:
# (coord1, coord2, ...) | dset_dtype
if rank == 1:
coord_type_str = "uint64"
else:
coord_type_str = "({},)uint64".format(rank)
comp_dtype = np.dtype([("coord", np.dtype(coord_type_str)), ("value", dset_dtype)])
point_arr = np.fromstring(input_bytes, dtype=comp_dtype)
if len(point_arr) != num_points:
msg = "Unexpected size of point array, got: {} expected: {}".format(len(point_arr), num_points)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
for i in range(num_points):
elem = point_arr[i]
if rank == 1:
coord = int(elem[0])
else:
coord = tuple(elem[0]) # index to update
val = elem[1] # value
chunk_arr[coord] = val # update the point
chunk_cache = app["chunk_cache"]
chunk_cache.setDirty(chunk_id)
# async write to S3
dirty_ids = app["dirty_ids"]
now = int(time.time())
dirty_ids[chunk_id] = now
log.info("set {} to dirty".format(chunk_id))
else:
# reading point data
point_dt = np.dtype('uint64') # use unsigned long for point index
point_arr = np.fromstring(input_bytes, dtype=point_dt) # read points as unsigned longs
if len(point_arr) % rank != 0:
msg = "Unexpected size of point array"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
num_points = len(point_arr) // rank
log.debug("got {} points".format(num_points))
point_arr = point_arr.reshape((num_points, rank))
output_arr = np.zeros((num_points,), dtype=dset_dtype)
for i in range(num_points):
point = point_arr[i,:]
tr_point = getChunkRelativePoint(chunk_coord, point)
val = chunk_arr[tuple(tr_point)]
output_arr[i] = val
if put_points:
# write empty response
resp = json_response({})
else:
# get data
output_data = output_arr.tobytes()
# write response
try:
resp = StreamResponse()
resp.headers['Content-Type'] = "application/octet-stream"
resp.content_length = len(output_data)
await resp.prepare(request)
await resp.write(output_data)
except Exception as e:
log.error(f"Exception during binary data write: {e}")
raise HTTPInternalServerError()
finally:
await resp.write_eof()
return resp
async def k8s_register(app):
log.info("k8s_register")
# TBD - find more elegant way to avoid this warning
import urllib3
urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
k8s_config.load_incluster_config(
) #get the config from within the cluster and set it as the default config for all new clients
c = k8s_client.Configuration() #go and get a copy of the default config
c.verify_ssl = False #set verify_ssl to false in that config
k8s_client.Configuration.set_default(
c) #make that config the default for all new clients
v1 = k8s_client.CoreV1Api()
# TBD - use the async version
ret = v1.list_pod_for_all_namespaces(watch=False)
pod_ips = []
sn_urls = {}
dn_urls = {}
for i in ret.items:
pod_ip = i.status.pod_ip
if not pod_ip:
continue
labels = i.metadata.labels
if "app" in labels and labels["app"] == "hsds":
log.info(f"hsds pod - ip: {pod_ip}")
pod_ips.append(pod_ip)
if not pod_ips:
log.error("Expected to find at least one hsds pod")
return
pod_ips.sort() # for assigning node numbers
node_count = len(pod_ips)
ready_count = 0
this_node_id = app["id"]
sn_port = config.get("sn_port")
dn_port = config.get("dn_port")
for node_number in range(node_count):
for port in (sn_port, dn_port):
# send an info request to the node
pod_ip = pod_ips[node_number]
url = f"http://{pod_ip}:{port}"
if port == sn_port:
sn_urls[node_number] = url
else:
dn_urls[node_number] = url
info_rsp = await get_info(app, url)
if not info_rsp:
# timeout or other failure
continue
if "node" not in info_rsp:
log.error("expected to find node key in info resp")
continue
node_rsp = info_rsp["node"]
log.debug(f"got info resp: {node_rsp}")
for key in ("type", "id", "node_number", "node_count"):
if key not in node_rsp:
log.error(
f"unexpected node type in node state, expected to find key: {key}"
)
continue
if node_rsp["type"] not in ("sn", "dn"):
log.error(f"expected node_type to be sn or dn")
continue
node_id = node_rsp["id"]
if node_id == this_node_id:
# set node_number and node_count
log.debug("got info_rsp for this node")
if app["node_number"] != node_number:
old_number = app["node_number"]
log.info(
f"node_number has changed - old value was {old_number} new number is {node_number}"
)
if app["node_type"] == "dn":
meta_cache = app["meta_cache"]
chunk_cache = app["chunk_cache"]
if meta_cache.dirtyCount > 0 or chunk_cache.dirtyCount > 0:
# set the node state to waiting till the chunk cache have been flushed
if app["node_state"] == "READY":
log.info(
"setting node_state to waiting while cache is flushing"
)
app["node_state"] = "WAITING"
else:
meta_cache.clearCache()
chunk_cache.clearCache()
log.info(
f"node number was: {old_number} setting to: {node_number}"
)
app["node_number"] = node_number
app['register_time'] = time.time()
else:
# SN nodes can update node_number immediately
log.info(
f"node number was: {old_number} setting to: {node_number}"
)
app["node_number"] = node_number
app['register_time'] = time.time()
if app["node_count"] != node_count:
old_count = app["node_count"]
log.info(
f"node count was: {old_count} setting to: {node_count}"
)
app["node_count"] = node_count
if node_number == node_rsp[
"node_number"] and node_count == node_rsp["node_count"]:
ready_count += 1
log.debug(f"incremented ready_count to {ready_count}")
else:
log.info(f"differing node_number/node_count for url: {url}")
log.info(
f"expected node_number: {node_number} actual: {node_rsp['node_number']}"
)
log.info(
f"expected node_count: {node_count} actual: {node_rsp['node_count']}"
)
if ready_count == node_count * 2:
if app["node_state"] != "READY":
log.info("setting node state to READY")
app["node_state"] = "READY"
app["node_count"] = node_count
app["sn_urls"] = sn_urls
app["dn_urls"] = dn_urls
else:
log.info(
f"not all pods ready - ready_count: {ready_count}/{node_count*2}")
if app["node_state"] == "READY":
log.info("setting node state to SCALING")
app["node_state"] = "SCALING"
async def info(request):
"""HTTP Method to retun node state to caller"""
log.debug("info request")
app = request.app
answer = {}
# copy relevant entries from state dictionary to response
node = {}
node['id'] = request.app['id']
node['type'] = request.app['node_type']
node['start_time'] = app["start_time"] #unixTimeToUTC(app['start_time'])
node['state'] = app['node_state']
node['node_number'] = app['node_number']
node['node_count'] = app['node_count']
answer["node"] = node
# psutil info
# see: http://pythonhosted.org/psutil/ for description of different fields
cpu = {}
cpu["percent"] = psutil.cpu_percent()
cpu["cores"] = psutil.cpu_count()
answer["cpu"] = cpu
diskio = psutil.disk_io_counters()
disk_stats = {}
disk_stats["read_count"] = diskio.read_count
disk_stats["read_time"] = diskio.read_time
disk_stats["read_bytes"] = diskio.read_bytes
disk_stats["write_count"] = diskio.write_count
disk_stats["write_time"] = diskio.write_time
disk_stats["write_bytes"] = diskio.write_bytes
answer["diskio"] = disk_stats
netio = psutil.net_io_counters()
net_stats = {}
net_stats["bytes_sent"] = netio.bytes_sent
net_stats["bytes_sent"] = netio.bytes_recv
net_stats["packets_sent"] = netio.packets_sent
net_stats["packets_recv"] = netio.packets_recv
net_stats["errin"] = netio.errin
net_stats["errout"] = netio.errout
net_stats["dropin"] = netio.dropin
net_stats["dropout"] = netio.dropout
answer["netio"] = net_stats
mem_stats = {}
svmem = psutil.virtual_memory()
mem_stats["phys_total"] = svmem.total
mem_stats["phys_available"] = svmem.available
sswap = psutil.swap_memory()
mem_stats["swap_total"] = sswap.total
mem_stats["swap_used"] = sswap.used
mem_stats["swap_free"] = sswap.free
mem_stats["percent"] = sswap.percent
answer["memory"] = mem_stats
disk_stats = {}
sdiskusage = psutil.disk_usage('/')
disk_stats["total"] = sdiskusage.total
disk_stats["used"] = sdiskusage.used
disk_stats["free"] = sdiskusage.free
disk_stats["percent"] = sdiskusage.percent
answer["disk"] = disk_stats
answer["log_stats"] = app["log_count"]
answer["req_count"] = app["req_count"]
if "s3_stats" in app:
answer["s3_stats"] = app["s3_stats"]
mc_stats = {}
if "meta_cache" in app:
mc = app["meta_cache"] # only DN nodes have this
mc_stats["count"] = len(mc)
mc_stats["dirty_count"] = mc.dirtyCount
mc_stats["utililization_per"] = mc.cacheUtilizationPercent
mc_stats["mem_used"] = mc.memUsed
mc_stats["mem_target"] = mc.memTarget
answer["meta_cache_stats"] = mc_stats
cc_stats = {}
if "chunk_cache" in app:
cc = app["chunk_cache"] # only DN nodes have this
cc_stats["count"] = len(cc)
cc_stats["dirty_count"] = cc.dirtyCount
cc_stats["utililization_per"] = cc.cacheUtilizationPercent
cc_stats["mem_used"] = cc.memUsed
cc_stats["mem_target"] = cc.memTarget
answer["chunk_cache_stats"] = cc_stats
dc_stats = {}
if "domain_cache" in app:
dc = app["domain_cache"] # only DN nodes have this
dc_stats["count"] = len(dc)
dc_stats["dirty_count"] = dc.dirtyCount
dc_stats["utililization_per"] = dc.cacheUtilizationPercent
dc_stats["mem_used"] = dc.memUsed
dc_stats["mem_target"] = dc.memTarget
answer["domain_cache_stats"] = dc_stats
resp = await jsonResponse(request, answer)
log.response(request, resp=resp)
return resp
async def GET_Domain(request):
"""HTTP method to return JSON for given domain"""
log.request(request)
app = request.app
params = request.rel_url.query
(username, pswd) = getUserPasswordFromRequest(request)
if username is None and app['allow_noauth']:
username = "******"
else:
await validateUserPassword(app, username, pswd)
domain = None
try:
domain = getDomainFromRequest(request)
except ValueError:
log.warn("Invalid domain")
raise HTTPBadRequest(reason="Invalid domain name")
verbose = False
if "verbose" in params and params["verbose"]:
verbose = True
if not domain:
log.info("no domain passed in, returning all top-level domains")
# no domain passed in, return top-level domains for this request
domains = await get_domains(request)
rsp_json = {"domains": domains}
rsp_json["hrefs"] = []
resp = await jsonResponse(request, rsp_json)
log.response(request, resp=resp)
return resp
log.info("got domain: {}".format(domain))
domain_json = await getDomainJson(app, domain, reload=True)
if domain_json is None:
log.warn("domain: {} not found".format(domain))
raise HTTPNotFound()
if 'owner' not in domain_json:
log.error("No owner key found in domain")
raise HTTPInternalServerError()
if 'acls' not in domain_json:
log.error("No acls key found in domain")
raise HTTPInternalServerError()
log.debug("got domain_json: {}".format(domain_json))
# validate that the requesting user has permission to read this domain
aclCheck(domain_json, "read",
username) # throws exception if not authorized
if "h5path" in params:
# if h5path is passed in, return object info for that path
# (if exists)
h5path = params["h5path"]
root_id = domain_json["root"]
obj_id = await getObjectIdByPath(app, root_id,
h5path) # throws 404 if not found
log.info("get obj_id: {} from h5path: {}".format(obj_id, h5path))
# get authoritative state for object from DN (even if it's in the meta_cache).
obj_json = await getObjectJson(app, obj_id, refresh=True)
obj_json["domain"] = domain
# Not bothering with hrefs for h5path lookups...
resp = await jsonResponse(request, obj_json)
log.response(request, resp=resp)
return resp
# return just the keys as per the REST API
rsp_json = await get_domain_response(app, domain_json, verbose=verbose)
# include domain objects if requested
if "getobjs" in params and params["getobjs"] and "root" in domain_json:
root_id = domain_json["root"]
include_attrs = False
if "include_attrs" in params and params["include_attrs"]:
include_attrs = True
domain_objs = await getDomainObjects(app,
root_id,
include_attrs=include_attrs)
rsp_json["domain_objs"] = domain_objs
hrefs = []
hrefs.append({'rel': 'self', 'href': getHref(request, '/')})
if "root" in domain_json:
root_uuid = domain_json["root"]
hrefs.append({
'rel': 'database',
'href': getHref(request, '/datasets')
})
hrefs.append({'rel': 'groupbase', 'href': getHref(request, '/groups')})
hrefs.append({
'rel': 'typebase',
'href': getHref(request, '/datatypes')
})
hrefs.append({
'rel': 'root',
'href': getHref(request, '/groups/' + root_uuid)
})
hrefs.append({'rel': 'acls', 'href': getHref(request, '/acls')})
parent_domain = getParentDomain(domain)
log.debug("href parent domain: {}".format(parent_domain))
if parent_domain:
hrefs.append({
'rel': 'parent',
'href': getHref(request, '/', domain=parent_domain)
})
rsp_json["hrefs"] = hrefs
resp = await jsonResponse(request, rsp_json)
log.response(request, resp=resp)
return resp
async def PUT_Domain(request):
"""HTTP method to create a new domain"""
log.request(request)
app = request.app
params = request.rel_url.query
# verify username, password
username, pswd = getUserPasswordFromRequest(
request) # throws exception if user/password is not valid
await validateUserPassword(app, username, pswd)
# inital perms for owner and default
owner_perm = {
'create': True,
'read': True,
'update': True,
'delete': True,
'readACL': True,
'updateACL': True
}
default_perm = {
'create': False,
'read': True,
'update': False,
'delete': False,
'readACL': False,
'updateACL': False
}
try:
domain = getDomainFromRequest(request)
except ValueError:
msg = "Invalid domain"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
log.info("PUT domain: {}, username: {}".format(domain, username))
body = None
if request.has_body:
body = await request.json()
log.debug("PUT domain with body: {}".format(body))
if ("flush" in params and params["flush"]) or (body and "flush" in body
and body["flush"]):
# flush domain - update existing domain rather than create a new resource
domain_json = await getDomainJson(app, domain, reload=True)
log.debug("got domain_json: {}".format(domain_json))
if domain_json is None:
log.warn("domain: {} not found".format(domain))
raise HTTPNotFound()
if 'owner' not in domain_json:
log.error("No owner key found in domain")
raise HTTPInternalServerError()
if 'acls' not in domain_json:
log.error("No acls key found in domain")
raise HTTPInternalServerError()
aclCheck(domain_json, "update",
username) # throws exception if not allowed
if "root" in domain_json:
# nothing to do for folder objects
await doFlush(app, domain_json["root"])
# flush successful
resp = await jsonResponse(request, None, status=204)
log.response(request, resp=resp)
return resp
is_folder = False
owner = username
linked_domain = None
root_id = None
if body and "folder" in body:
if body["folder"]:
is_folder = True
if body and "owner" in body:
owner = body["owner"]
if body and "linked_domain" in body:
if is_folder:
msg = "Folder domains can not be used for links"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
linked_domain = body["linked_domain"]
log.info(f"linking to domain: {linked_domain}")
if owner != username and username != "admin":
log.warn("Only admin users are allowed to set owner for new domains")
raise HTTPForbidden()
parent_domain = getParentDomain(domain)
log.debug("Parent domain: [{}]".format(parent_domain))
if (not parent_domain or parent_domain == '/') and not is_folder:
msg = "Only folder domains can be created at the top-level"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if (not parent_domain or parent_domain == '/') and username != "admin":
msg = "creation of top-level domains is only supported by admin users"
log.warn(msg)
raise HTTPForbidden()
parent_json = None
if parent_domain and parent_domain != '/':
try:
parent_json = await getDomainJson(app, parent_domain, reload=True)
except ClientResponseError as ce:
if ce.code == 404:
msg = "Parent domain: {} not found".format(parent_domain)
log.warn(msg)
raise HTTPNotFound()
elif ce.code == 410:
msg = "Parent domain: {} removed".format(parent_domain)
log.warn(msg)
raise HTTPGone()
else:
log.error(f"Unexpected error: {ce.code}")
raise HTTPInternalServerError()
log.debug("parent_json {}: {}".format(parent_domain, parent_json))
if "root" in parent_json and parent_json["root"]:
msg = "Parent domain must be a folder"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if parent_json:
aclCheck(parent_json, "create",
username) # throws exception if not allowed
if linked_domain:
linked_json = await getDomainJson(app, linked_domain, reload=True)
log.debug(f"got linked json: {linked_json}")
if "root" not in linked_json:
msg = "Folder domains cannot ber used as link target"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
root_id = linked_json["root"]
aclCheck(linked_json, "read", username)
aclCheck(linked_json, "delete", username)
else:
linked_json = None
if not is_folder and not linked_json:
# create a root group for the new domain
root_id = createObjId("roots")
log.debug("new root group id: {}".format(root_id))
group_json = {"id": root_id, "root": root_id, "domain": domain}
log.debug("create group for domain, body: " + json.dumps(group_json))
# create root group
req = getDataNodeUrl(app, root_id) + "/groups"
try:
group_json = await http_post(app, req, data=group_json)
except ClientResponseError as ce:
msg = "Error creating root group for domain -- " + str(ce)
log.error(msg)
raise HTTPInternalServerError()
else:
log.debug("no root group, creating folder")
domain_json = {}
domain_acls = {}
# owner gets full control
domain_acls[owner] = owner_perm
if config.get("default_public") or is_folder:
# this will make the domain public readable
log.debug("adding default perm for domain: {}".format(domain))
domain_acls["default"] = default_perm
# construct dn request to create new domain
req = getDataNodeUrl(app, domain)
req += "/domains"
body = {"owner": owner, "domain": domain}
body["acls"] = domain_acls
if root_id:
body["root"] = root_id
log.debug("creating domain: {} with body: {}".format(domain, body))
try:
domain_json = await http_put(app, req, data=body)
except ClientResponseError as ce:
msg = "Error creating domain state -- " + str(ce)
log.error(msg)
raise HTTPInternalServerError()
# domain creation successful
# maxin limits
domain_json["limits"] = getLimits()
domain_json["version"] = getVersion()
resp = await jsonResponse(request, domain_json, status=201)
log.response(request, resp=resp)
return resp
async def GET_Datatypes(request):
"""HTTP method to return datatype collection for given domain"""
log.request(request)
app = request.app
params = request.rel_url.query
(username, pswd) = getUserPasswordFromRequest(request)
if username is None and app['allow_noauth']:
username = "******"
else:
await validateUserPassword(app, username, pswd)
try:
domain = getDomainFromRequest(request)
except ValueError:
msg = "Invalid domain"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
# use reload to get authoritative domain json
try:
domain_json = await getDomainJson(app, domain, reload=True)
except ClientResponseError as ce:
if ce.code in (404, 410):
msg = "domain not found"
log.warn(msg)
raise HTTPNotFound()
else:
log.error(f"Unexpected Error: {ce.code})")
raise HTTPInternalServerError()
if 'owner' not in domain_json:
log.error("No owner key found in domain")
raise HTTPInternalServerError()
if 'acls' not in domain_json:
log.error("No acls key found in domain")
raise HTTPInternalServerError()
log.debug("got domain_json: {}".format(domain_json))
# validate that the requesting user has permission to read this domain
aclCheck(domain_json, "read",
username) # throws exception if not authorized
limit = None
if "Limit" in params:
try:
limit = int(params["Limit"])
except ValueError:
msg = "Bad Request: Expected int type for limit"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
marker = None
if "Marker" in params:
marker = params["Marker"]
# get the datatype collection list
obj_ids = []
if "root" in domain_json or domain_json["root"]:
# get the groups collection list
collections = await get_collections(app, domain_json["root"])
objs = collections["datatypes"]
obj_ids = getIdList(objs, marker=marker, limit=limit)
# create hrefs
hrefs = []
hrefs.append({'rel': 'self', 'href': getHref(request, '/datatypes')})
if "root" in domain_json:
root_uuid = domain_json["root"]
hrefs.append({
'rel': 'root',
'href': getHref(request, '/groups/' + root_uuid)
})
hrefs.append({'rel': 'home', 'href': getHref(request, '/')})
# return obj ids and hrefs
rsp_json = {}
rsp_json["datatypes"] = obj_ids
rsp_json["hrefs"] = hrefs
resp = await jsonResponse(request, rsp_json)
log.response(request, resp=resp)
return resp
async def get_domains(request):
""" This method is called by GET_Domains and GET_Domain """
app = request.app
# if there is no domain passed in, get a list of top level domains
if "domain" not in request.rel_url.query:
prefix = '/'
else:
prefix = request.rel_url.query["domain"]
log.info(f"get_domains for: {prefix}")
if not prefix.startswith('/'):
msg = "Prefix must start with '/'"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
# always use "verbose" to pull extra info
if "verbose" in request.rel_url.query and request.rel_url.query["verbose"]:
verbose = True
else:
verbose = False
limit = None
if "Limit" in request.rel_url.query:
try:
limit = int(request.rel_url.query["Limit"])
log.debug(f"GET_Domains - using Limit: {limit}")
except ValueError:
msg = "Bad Request: Expected int type for limit"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
marker = None
if "Marker" in request.rel_url.query:
marker = request.rel_url.query["Marker"]
log.debug(f"got Marker request param: {marker}")
# list the S3 keys for this prefix
domainNames = []
if prefix == "/":
# search for domains from the top_level domains config
domainNames = config.get("top_level_domains")
else:
s3prefix = prefix[1:]
log.debug(f"listing S3 keys for {s3prefix}")
s3keys = await getS3Keys(app,
include_stats=False,
prefix=s3prefix,
deliminator='/')
log.debug(f"getS3Keys returned: {len(s3keys)} keys")
log.debug(f"s3keys {s3keys}")
for s3key in s3keys:
if s3key[-1] != '/':
log.debug(f"ignoring key: {s3key}")
continue
log.debug(f"got s3key: {s3key}")
domain = "/" + s3key[:-1]
if marker:
if marker == domain:
marker = None
continue
log.debug(f"adding domain: {domain} to domain list")
domainNames.append(domain)
if limit and len(domainNames) == limit:
# got to requested limit
break
# get domain info for each domain
domains = []
for domain in domainNames:
try:
# query DN's for domain json
# TBD - multicast to DN nodes
log.debug(f"getDomainJson for {domain}")
domain_json = await getDomainJson(app, domain, reload=True)
if domain_json:
domain_rsp = await get_domain_response(app,
domain_json,
verbose=verbose)
# mixin domain anme
domain_rsp["name"] = domain
domains.append(domain_rsp)
except HTTPNotFound:
# One of the dmains not found, but continue through the list
log.debug(f"not found error for: {domain}")
return domains
async def GET_Group(request):
"""HTTP method to return JSON for group"""
log.request(request)
app = request.app
params = request.rel_url.query
h5path = None
getAlias = False
include_links = False
include_attrs = False
group_id = request.match_info.get('id')
if not group_id and "h5path" not in params:
# no id, or path provided, so bad request
msg = "Missing group id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if group_id:
log.info(f"GET_Group, id: {group_id}")
# is the id a group id and not something else?
if not isValidUuid(group_id, "Group"):
msg = f"Invalid group id: {group_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "getalias" in params:
if params["getalias"]:
getAlias = True
if "h5path" in params:
h5path = params["h5path"]
if not group_id and h5path[0] != '/':
msg = "h5paths must be absolute if no parent id is provided"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
log.info(f"GET_Group, h5path: {h5path}")
if "include_links" in params and params["include_links"]:
include_links = True
if "include_attrs" in params and params["include_attrs"]:
include_attrs = True
username, pswd = getUserPasswordFromRequest(request)
if username is None and app['allow_noauth']:
username = "******"
else:
await validateUserPassword(app, username, pswd)
domain = getDomainFromRequest(request)
if not isValidDomain(domain):
msg = f"Invalid domain: {domain}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
bucket = getBucketForDomain(domain)
if h5path and h5path[0] == '/':
# ignore the request path id (if given) and start
# from root group for absolute paths
domain_json = await getDomainJson(app, domain)
if "root" not in domain_json:
msg = f"Expected root key for domain: {domain}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
group_id = domain_json["root"]
if h5path:
group_id = await getObjectIdByPath(app,
group_id,
h5path,
bucket=bucket
) # throws 404 if not found
if not isValidUuid(group_id, "Group"):
msg = f"No group exist with the path: {h5path}"
log.warn(msg)
raise HTTPNotFound()
log.info(f"get group_id: {group_id} from h5path: {h5path}")
# verify authorization to read the group
await validateAction(app, domain, group_id, username, "read")
# get authoritative state for group from DN (even if it's in the meta_cache).
group_json = await getObjectJson(app,
group_id,
refresh=True,
include_links=include_links,
include_attrs=include_attrs,
bucket=bucket)
log.debug(f"domain from request: {domain}")
group_json["domain"] = getPathForDomain(domain)
if bucket:
group_json["bucket"] = bucket
if getAlias:
root_id = group_json["root"]
alias = []
if group_id == root_id:
alias.append('/')
else:
idpath_map = {root_id: '/'}
h5path = await getPathForObjectId(app,
root_id,
idpath_map,
tgt_id=group_id,
bucket=bucket)
if h5path:
alias.append(h5path)
group_json["alias"] = alias
hrefs = []
group_uri = '/groups/' + group_id
hrefs.append({'rel': 'self', 'href': getHref(request, group_uri)})
hrefs.append({
'rel': 'links',
'href': getHref(request, group_uri + '/links')
})
root_uri = '/groups/' + group_json["root"]
hrefs.append({'rel': 'root', 'href': getHref(request, root_uri)})
hrefs.append({'rel': 'home', 'href': getHref(request, '/')})
hrefs.append({
'rel': 'attributes',
'href': getHref(request, group_uri + '/attributes')
})
group_json["hrefs"] = hrefs
resp = await jsonResponse(request, group_json)
log.response(request, resp=resp)
return resp
async def POST_Group(request):
"""HTTP method to create new Group object"""
log.request(request)
app = request.app
username, pswd = getUserPasswordFromRequest(request)
# write actions need auth
await validateUserPassword(app, username, pswd)
domain = getDomainFromRequest(request)
if not isValidDomain(domain):
msg = f"Invalid domain: {domain}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
bucket = getBucketForDomain(domain)
domain_json = await getDomainJson(app, domain, reload=True)
aclCheck(domain_json, "create",
username) # throws exception if not allowed
if "root" not in domain_json:
msg = f"Expected root key for domain: {domain}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
link_id = None
link_title = None
if request.has_body:
body = await request.json()
log.info(f"POST Group body: {body}")
if body:
if "link" in body:
link_body = body["link"]
log.debug(f"link_body: {link_body}")
if "id" in link_body:
link_id = link_body["id"]
if "name" in link_body:
link_title = link_body["name"]
if link_id and link_title:
log.debug(f"link id: {link_id}")
# verify that the referenced id exists and is in this domain
# and that the requestor has permissions to create a link
await validateAction(app, domain, link_id, username,
"create")
if not link_id or not link_title:
log.warn(f"POST Group body with no link: {body}")
domain_json = await getDomainJson(
app, domain) # get again in case cache was invalidated
root_id = domain_json["root"]
group_id = createObjId("groups", rootid=root_id)
log.info(f"new group id: {group_id}")
group_json = {"id": group_id, "root": root_id}
log.debug("create group, body: " + json.dumps(group_json))
req = getDataNodeUrl(app, group_id) + "/groups"
params = {}
if bucket:
params["bucket"] = bucket
group_json = await http_post(app, req, data=group_json, params=params)
# create link if requested
if link_id and link_title:
link_json = {}
link_json["id"] = group_id
link_json["class"] = "H5L_TYPE_HARD"
link_req = getDataNodeUrl(app, link_id)
link_req += "/groups/" + link_id + "/links/" + link_title
log.debug("PUT link - : " + link_req)
put_json_rsp = await http_put(app,
link_req,
data=link_json,
params=params)
log.debug(f"PUT Link resp: {put_json_rsp}")
log.debug("returning resp")
# group creation successful
resp = await jsonResponse(request, group_json, status=201)
log.response(request, resp=resp)
return resp
def scanRootCallback(app, s3keys):
log.debug(f"scanRootCallback, {len(s3keys)} items")
if isinstance(s3keys, list):
log.error("got list result for s3keys callback")
raise ValueError("unexpected callback format")
results = app["scanRoot_results"]
if results:
log.debug(f"previous scanRoot_results:".format(results))
for s3key in s3keys.keys():
if not isS3ObjKey(s3key):
log.info(f"not s3obj key, ignoring: {s3key}")
continue
objid = getObjId(s3key)
etag = None
obj_size = None
lastModified = None
item = s3keys[s3key]
if "ETag" in item:
etag = item["ETag"]
if "Size" in item:
obj_size = item["Size"]
if "LastModified" in item:
lastModified = item["LastModified"]
log.debug(f"{objid}: {etag} {obj_size} {lastModified}")
if lastModified > results["lastModified"]:
log.debug(f"changing lastModified from: {results['lastModified']} to {lastModified}")
results["lastModified"] = lastModified
is_chunk = False
if isValidChunkId(objid):
is_chunk = True
results["num_chunks"] += 1
results["allocated_bytes"] += obj_size
else:
results["metadata_bytes"] += obj_size
if is_chunk or getCollectionForId(objid) == "datasets":
if is_chunk:
dsetid = getDatasetId(objid)
else:
dsetid = objid
datasets = results["datasets"]
if dsetid not in datasets:
dataset_info = {}
dataset_info["lastModified"] = 0
dataset_info["num_chunks"] = 0
dataset_info["allocated_bytes"] = 0
datasets[dsetid] = dataset_info
dataset_info = datasets[dsetid]
if lastModified > dataset_info["lastModified"]:
dataset_info["lastModified"] = lastModified
if is_chunk:
dataset_info["num_chunks"] += 1
dataset_info["allocated_bytes"] += obj_size
elif getCollectionForId(objid) == "groups":
results["num_groups"] += 1
elif getCollectionForId(objid) == "datatypes":
results["num_datatypes"] += 1
else:
log.error(f"Unexpected collection type for id: {objid}")
async def put_object(self, key, data, bucket=None):
""" Write data to given key.
Returns client specific dict on success
"""
if not bucket:
log.error("put_object - bucket not set")
raise HTTPInternalServerError()
start_time = time.time()
log.debug(
f"azureBlobClient.put_object({bucket}/{key} start: {start_time}")
try:
async with self._client.get_blob_client(container=bucket,
blob=key) as blob_client:
blob_rsp = await blob_client.upload_blob(data,
blob_type='BlockBlob',
overwrite=True)
finish_time = time.time()
ETag = blob_rsp["etag"]
lastModified = int(blob_rsp["last_modified"].timestamp())
data_size = len(data)
rsp = {
"ETag": ETag,
"size": data_size,
"LastModified": lastModified
}
log.debug(f"put_object {key} returning: {rsp}")
log.info(
f"azureBlobClient.put_object({key} bucket={bucket}) start={start_time:.4f} finish={finish_time:.4f} elapsed={finish_time-start_time:.4f} bytes={len(data)}"
)
except CancelledError as cle:
self._azure_stats_increment("error_count")
msg = f"azureBlobClient.CancelledError for put_object {key}: {cle}"
log.error(msg)
raise HTTPInternalServerError()
except Exception as e:
if isinstance(e, AzureError):
if e.status_code == 404:
msg = f"azureBlobClient.key: {key} not found "
log.warn(msg)
raise HTTPNotFound()
elif e.status_code in (401, 403):
msg = f"azureBlobClient.access denied for get key: {key}"
log.info(msg)
raise HTTPForbidden()
else:
self._azure_stats_increment("error_count")
log.error(
f"azureBlobClient.got unexpected AzureError for get_object {key}: {e.message}"
)
raise HTTPInternalServerError()
else:
log.error(
f"azureBlobClient.Unexpected exception for put_object {key}: {e}"
)
raise HTTPInternalServerError()
if data and len(data) > 0:
self._azure_stats_increment("bytes_out", inc=len(data))
log.debug(f"azureBlobClient.put_object {key} complete, rsp: {rsp}")
return rsp
async def fetch(self, obj_id):
log.debug(f"DomainCrawler - fetch for obj_id: {obj_id}")
obj_json = await getObjectJson(self._app,
obj_id,
include_links=True,
include_attrs=self._include_attrs)
log.debug(f"DomainCrawler - for {obj_id} got json: {obj_json}")
# including links, so don't need link count
if "link_count" in obj_json:
del obj_json["link_count"]
self._obj_dict[obj_id] = obj_json
if self._include_attrs:
del obj_json["attributeCount"]
# if this is a group, iterate through all the hard links and
# add to the lookup ids set
if getCollectionForId(obj_id) == "groups":
links = obj_json["links"]
log.debug(f"DomainCrawler links: {links}")
for title in links:
log.debug(f"DomainCrawler - got link: {title}")
link_obj = links[title]
if link_obj["class"] != 'H5L_TYPE_HARD':
continue
link_id = link_obj["id"]
if link_id not in self._obj_dict:
# haven't seen this object yet, get obj json
log.debug(f"DomainCrawler - adding link_id: {link_id}")
self._obj_dict[link_id] = {} # placeholder for obj id
self._q.put_nowait(link_id)
log.debug(f"DomainCrawler - fetch conplete obj_id: {obj_id}")
async def oio_register(app):
""" register with oio conscience
"""
log.info("oio_register")
oio_proxy = app["oio_proxy"]
host_ip = app["host_ip"]
if not host_ip:
log.error("host ip not set")
return
node_type = app["node_type"]
if node_type not in ("sn", "dn"):
log.error("unexpected node type")
return
service_name = "hdf" + node_type
req = oio_proxy + "/v3.0/OPENIO/conscience/register"
body = {
"addr": host_ip + ":" + str(app["node_port"]),
"tags": {
"stat.cpu": 100,
"tag.up": True
},
"type": service_name
}
log.debug(f"conscience register: body: {body}")
try:
await http_post(app, req, data=body)
except ClientError as client_exception:
log.error(
f"got ClientError registering with oio_proxy: {client_exception}")
return
except CancelledError as cancelled_exception:
log.error(
f"got CanceeledError registering with oio_proxy: {cancelled_exception}"
)
return
log.info("oio registration successful")
# get list of DN containers
req = oio_proxy + "/v3.0/OPENIO/conscience/list?type=hdfdn"
try:
dn_node_list = await http_get(app, req)
except ClientError as client_exception:
log.error(
f"got ClientError listing dn nodes with oio_proxy: {client_exception}"
)
return
except CancelledError as cancelled_exception:
log.error(
f"got CanceeledError listing dn nodes with oio_proxy: {cancelled_exception}"
)
return
log.info(f"got {len(dn_node_list)} conscience list items")
# create map keyed by dn addr
dn_node_map = {}
for dn_node in dn_node_list:
log.debug(f"checking dn conscience list item: {dn_node}")
if "addr" not in dn_node:
log.warn(f"conscience list item with no addr: {dn_node}")
continue
addr = dn_node["addr"]
if "score" not in dn_node:
log.warn(f'conscience list item with no score key: {dn_node}')
continue
if dn_node["score"] <= 0:
log.debug(f"zero score - skipping conscience list addr: {addr}")
continue
if addr in dn_node_map:
# shouldn't ever get this?
log.warn(f"duplicate entry for node: {dn_node}")
continue
# send an info request to the node
info_rsp = await get_info(app, "http://" + addr)
if not info_rsp:
# timeout or other failure
continue
if "node" not in info_rsp:
log.error("expecteed to find node key in info resp")
continue
info_node = info_rsp["node"]
log.debug(f"got info resp: {info_node}")
for key in ("type", "id", "node_number", "node_count"):
if key not in info_node:
log.error(
f"unexpected node type in node state, expected to find key: {key}"
)
continue
if info_node["type"] != "dn":
log.error(f"expecteed node_type to be dn")
continue
# mix in node id, node number, node_count to the conscience info
dn_node["node_id"] = info_node["id"]
dn_node["node_number"] = info_node["node_number"]
dn_node["node_count"] = info_node["node_count"]
dn_node_map[addr] = dn_node
log.info(f"done with dn_node_list, got: {len(dn_node_map)} active nodes")
if len(dn_node_map) == 0:
if app["node_state"] != "INITIALIZING":
log.info(
"no active DN nodes, setting cluster state to INITIALIZING")
app["node_state"] = "INITIALIZING"
return
# sort map by address
addrs = list(dn_node_map.keys())
addrs.sort()
# check that node number is set and is the expected value for each node key
invalid_count = 0
node_index = 0
node_count = len(addrs)
dn_urls = {}
this_node_found = False
this_node_id = app["id"]
for addr in addrs:
dn_node = dn_node_map[addr]
log.debug(f"dn_node for index {node_index}: {dn_node}")
node_id = dn_node["node_id"]
if node_id == this_node_id:
this_node_found = True
node_number = dn_node["node_number"]
dn_urls[node_number] = "http://" + dn_node["addr"]
if node_index != node_number or dn_node["node_count"] != node_count:
if node_number == -1:
log.info(f"node {node_index} not yet initialized")
elif node_index != node_number:
log.warn(
f"node_id {node_id}, expected node_number of {node_index} but found {node_number}"
)
invalid_count += 1
if node_id == app["id"]:
# this is us, update our node_number, node_count
if app["node_number"] != node_index:
# TBD - clean cache items
log.info(
f"setting node_number for this node to: {node_index}")
app["node_number"] = node_index
if app["node_count"] != node_count:
# TBD - clean cache items
log.info(
f"setting node_count for this node to: {node_count}")
app["node_count"] = node_count
invalid_count += 1
else:
log.debug(f"node {node_id} node number is correct")
node_index += 1
if invalid_count == 0:
log.debug("no invalid nodes!")
if app["node_state"] != "READY":
if app["node_type"] == "dn" and not this_node_found:
# don't go to READY unless this node shows up
log.info(
f"node {this_node_id} not yet showing in proxy list, stay in INITIALIZING"
)
else:
log.info("setting node state to READY")
app["node_state"] = "READY"
if app["node_type"] == "sn" and app["node_number"] == -1:
# node number shouldn't matter for SN nodes, so set to 1
app["node_number"] = 1
if app["node_count"] != node_count:
log.info(f"setting node_count to: {node_count}")
app["node_count"] = node_count
app["dn_urls"] = dn_urls
else:
log.debug(f"number invalid nodes: {invalid_count}")
if app["node_state"] == "READY":
log.warn("invalid nodes found, setting node state to INITIALIZING")
app["node_state"] = "INITIALIZING"
log.info("oio_register done")
async def DELETE_Domain(request):
"""HTTP method to delete a domain resource"""
log.request(request)
app = request.app
params = request.rel_url.query
domain = None
meta_only = False # if True, just delete the meta cache value
keep_root = False
if request.has_body:
body = await request.json()
if "domain" in body:
domain = body["domain"]
else:
msg = "No domain in request body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "meta_only" in body:
meta_only = body["meta_only"]
if "keep_root" in body:
keep_root = body["keep_root"]
else:
# get domain from request uri
try:
domain = getDomainFromRequest(request)
except ValueError:
msg = "Invalid domain"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "keep_root" in params:
keep_root = params["keep_root"]
log.info("meta_only domain delete: {}".format(meta_only))
if meta_only:
# remove from domain cache if present
domain_cache = app["domain_cache"]
if domain in domain_cache:
log.info("deleting {} from domain_cache".format(domain))
del domain_cache[domain]
resp = await jsonResponse(request, {})
return resp
username, pswd = getUserPasswordFromRequest(request)
await validateUserPassword(app, username, pswd)
parent_domain = getParentDomain(domain)
if (not parent_domain or parent_domain == '/') and username != "admin":
msg = "Deletion of top-level domains is only supported by admin users"
log.warn(msg)
raise HTTPForbidden()
try:
domain_json = await getDomainJson(app, domain, reload=True)
except ClientResponseError as ce:
if ce.code == 404:
log.warn("domain not found")
raise HTTPNotFound()
elif ce.code == 410:
log.warn("domain has been removed")
raise HTTPGone()
else:
log.error(f"unexpected error: {ce.code}")
raise HTTPInternalServerError()
aclCheck(domain_json, "delete",
username) # throws exception if not allowed
# check for sub-objects if this is a folder
if "root" not in domain_json:
s3prefix = domain[1:] + '/'
log.info(f"checking kets with prefix: {s3prefix} ")
s3keys = await getS3Keys(app,
include_stats=False,
prefix=s3prefix,
deliminator='/')
for s3key in s3keys:
if s3key.endswith("/"):
log.warn(f"attempt to delete folder {domain} with sub-items")
log.debug(f"got prefix: {s3keys[0]}")
raise HTTPConflict(reason="folder has sub-items")
req = getDataNodeUrl(app, domain)
req += "/domains"
body = {"domain": domain}
rsp_json = await http_delete(app, req, data=body)
if "root" in domain_json and not keep_root:
# delete the root group
root_id = domain_json["root"]
req = getDataNodeUrl(app, root_id)
req += "/groups/" + root_id
await http_delete(app, req)
# remove from domain cache if present
domain_cache = app["domain_cache"]
if domain in domain_cache:
del domain_cache[domain]
# delete domain cache from other sn_urls
sn_urls = app["sn_urls"]
body["meta_only"] = True
for node_no in sn_urls:
if node_no == app["node_number"]:
continue # don't send to ourselves
sn_url = sn_urls[node_no]
req = sn_url + "/"
log.info("sending sn request: {}".format(req))
try:
sn_rsp = await http_delete(app, req, data=body)
log.info("{} response: {}".format(req, sn_rsp))
except ClientResponseError as ce:
log.warn("got error for sn_delete: {}".format(ce))
resp = await jsonResponse(request, rsp_json)
log.response(request, resp=resp)
return resp
async def healthCheck(app):
""" Periodic method that either registers with headnode (if state in INITIALIZING) or
calls headnode to verify vitals about this node (otherwise)"""
# let the server event loop startup before sarting the health check
await asyncio.sleep(1)
log.info("health check start")
sleep_secs = config.get("node_sleep_time")
while True:
print("node_state:", app["node_state"])
if "oio_proxy" in app:
# for OIO post registration request every time interval
await oio_register(app)
elif "is_k8s" in app:
await k8s_register(app)
elif app["node_state"] == "INITIALIZING" or (
app["node_state"] == "WAITING" and app["node_number"] < 0):
# startup docker registration
await register(app)
else:
# check in with the head node and make sure we are still active
head_url = getHeadUrl(app)
req_node = "{}/nodestate".format(head_url)
log.debug("health check req {}".format(req_node))
try:
rsp_json = await http_get(app, req_node)
if rsp_json is None or not isinstance(rsp_json, dict):
log.warn(
"invalid health check response: type: {} text: {}".
format(type(rsp_json), rsp_json))
else:
log.debug("cluster_state: {}".format(
rsp_json["cluster_state"]))
if rsp_json["cluster_state"] != "READY" and app[
"node_state"] == "READY":
log.info("changing node_state to WAITING")
app["node_state"] = "WAITING"
#print("rsp_json: ", rsp_json)
# save the url's to each of the active nodes'
sn_urls = {}
dn_urls = {}
# or rsp_json["host"] is None or rsp_json["id"] != app["id"]
this_node = None
for node in rsp_json["nodes"]:
if node["node_type"] == app["node_type"] and node[
"node_number"] == app["node_number"]:
# this should be this node
if node["id"] != app["id"]:
# flag - to re-register
log.warn(
"mis-match node ids, app: {} vs head: {} - re-initializing"
.format(node["id"], app["id"]))
app["node_state"] == "INITIALIZING"
app["node_number"] = -1
break
if not node["host"]:
# flag - to re-register
log.warn(
"host not set for this node - re-initializing"
.format(node["id"], app["id"]))
app["node_state"] == "INITIALIZING"
app["node_number"] = -1
break
if not node["host"]:
continue # not online
this_node = copy(node)
url = "http://" + node["host"] + ":" + str(
node["port"])
node_number = node["node_number"]
if node["node_type"] == "dn":
dn_urls[node_number] = url
elif node["node_type"] == "sn":
sn_urls[node_number] = url
else:
log.error(
"Unexpected node_type for node: {}".format(
node))
app["sn_urls"] = sn_urls
log.debug(f"sn_urls: {sn_urls}")
app["dn_urls"] = dn_urls
log.debug(f"dn_urls: {dn_urls}")
if this_node is None and rsp_json[
"cluster_state"] != "READY":
log.warn("this node not found, re-initialize")
app["node_state"] == "INITIALIZING"
app["node_number"] = -1
if app["node_state"] == "WAITING" and rsp_json[
"cluster_state"] == "READY" and app[
"node_number"] >= 0:
log.info(
"setting node_state to READY, node_number: {}".
format(app["node_number"]))
app["node_state"] = "READY"
log.info("health check ok")
except ClientError as ce:
log.warn(f"ClientError: {ce} for health check")
except HTTPInternalServerError as he:
log.warn(
f"HTTPInternalServiceError <{he.code}> for health check")
except HTTPNotFound as hnf:
log.warn(f"HTTPNotFound <{hnf.code}> for health check")
except HTTPGone as hg:
log.warn(f"HTTPGone <{hg.code}> for health heck")
svmem = psutil.virtual_memory()
num_tasks = len(asyncio.Task.all_tasks())
active_tasks = len(
[task for task in asyncio.Task.all_tasks() if not task.done()])
log.debug(
f"health check sleep: {sleep_secs}, vm: {svmem.percent} num tasks: {num_tasks} active tasks: {active_tasks}"
)
await asyncio.sleep(sleep_secs)
async def GET_ACL(request):
"""HTTP method to return JSON for given domain/ACL"""
log.request(request)
app = request.app
acl_username = request.match_info.get('username')
if not acl_username:
msg = "Missing username for ACL"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
(username, pswd) = getUserPasswordFromRequest(request)
if username is None and app['allow_noauth']:
username = "******"
else:
await validateUserPassword(app, username, pswd)
try:
domain = getDomainFromRequest(request)
except ValueError:
msg = "Invalid domain"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
# use reload to get authoritative domain json
try:
domain_json = await getDomainJson(app, domain, reload=True)
except ClientResponseError as ce:
if ce.code in (404, 410):
msg = "domain not found"
log.warn(msg)
raise HTTPNotFound()
else:
log.error(f"unexpected error: {ce.code}")
raise HTTPInternalServerError()
# validate that the requesting user has permission to read ACLs in this domain
if acl_username in (username, "default"):
# allow read access for a users on ACL, or default
aclCheck(domain_json, "read",
username) # throws exception if not authorized
else:
aclCheck(domain_json, "readACL",
username) # throws exception if not authorized
if 'owner' not in domain_json:
log.warn("No owner key found in domain")
raise HTTPInternalServerError()
if 'acls' not in domain_json:
log.warn("No acls key found in domain")
raise HTTPInternalServerError()
acls = domain_json["acls"]
log.debug("got domain_json: {}".format(domain_json))
if acl_username not in acls:
msg = "acl for username: [{}] not found".format(acl_username)
log.warn(msg)
raise HTTPNotFound()
acl = acls[acl_username]
acl_rsp = {}
for k in acl.keys():
acl_rsp[k] = acl[k]
acl_rsp["userName"] = acl_username
# return just the keys as per the REST API
rsp_json = {}
rsp_json["acl"] = acl_rsp
hrefs = []
hrefs.append({'rel': 'self', 'href': getHref(request, '/acls')})
if "root" in domain_json:
hrefs.append({
'rel': 'root',
'href': getHref(request, '/groups/' + domain_json["root"])
})
hrefs.append({'rel': 'home', 'href': getHref(request, '/')})
hrefs.append({'rel': 'owner', 'href': getHref(request, '/')})
rsp_json["hrefs"] = hrefs
resp = await jsonResponse(request, rsp_json)
log.response(request, resp=resp)
return resp
async def PUT_Group(request):
""" Handler for PUT /groups"""
""" Used to flush all objects under a root group to S3 """
FLUSH_TIME_OUT = 10.0 # TBD make config
FLUSH_SLEEP_INTERVAL = 0.1 # TBD make config
log.request(request)
app = request.app
root_id = request.match_info.get('id')
log.info("PUT group: {} (flush)".format(root_id))
if not isValidUuid(root_id, obj_class="group"):
log.error(f"Unexpected group_id: {root_id}")
raise HTTPInternalServerError()
schema2 = isSchema2Id(root_id)
if schema2 and not isRootObjId(root_id):
log.error(f"Expected root id for flush but got: {root_id}")
raise HTTPInternalServerError()
flush_start = time.time()
flush_set = set()
dirty_ids = app["dirty_ids"]
for obj_id in dirty_ids:
if schema2:
if isValidUuid(obj_id) and getRootObjId(obj_id) == root_id:
flush_set.add(obj_id)
else:
# for schema1 not easy to determine if a given id is in a domain,
# so just wait on all of them
flush_set.add(obj_id)
log.debug(f"flushop - waiting on {len(flush_set)} items")
while time.time() - flush_start < FLUSH_TIME_OUT:
# check to see if the items in our flush set are still there
remaining_set = set()
for obj_id in flush_set:
if not obj_id in dirty_ids:
log.debug(f"flush - {obj_id} has been written")
elif dirty_ids[obj_id] > flush_start:
log.debug(
f"flush - {obj_id} has been updated after flush start")
else:
log.debug(f"flush - {obj_id} still pending")
remaining_set.add(obj_id)
flush_set = remaining_set
if len(flush_set) == 0:
log.debug("flush op - all objects have been written")
break
log.debug(
f"flushop - {len(flush_set)} item remaining, sleeping for {FLUSH_SLEEP_INTERVAL}"
)
await asyncio.sleep(FLUSH_SLEEP_INTERVAL)
if len(flush_set) > 0:
log.warn(
f"flushop - {len(flush_set)} items not updated after {FLUSH_TIME_OUT}"
)
raise HTTPServiceUnavailable()
resp = json_response(None, status=204) # NO Content response
log.response(request, resp=resp)
return resp
async def GET_ACLs(request):
"""HTTP method to return JSON for domain/ACLs"""
log.request(request)
app = request.app
(username, pswd) = getUserPasswordFromRequest(request)
if username is None and app['allow_noauth']:
username = "******"
else:
await validateUserPassword(app, username, pswd)
try:
domain = getDomainFromRequest(request)
except ValueError:
msg = "Invalid domain"
log.warn(msg)
raise HTTPBadRequest(message=msg)
# use reload to get authoritative domain json
try:
domain_json = await getDomainJson(app, domain, reload=True)
except ClientResponseError:
log.warn("domain not found")
log.warn(msg)
raise HTTPNotFound()
if 'owner' not in domain_json:
log.error("No owner key found in domain")
raise HTTPInternalServerError()
if 'acls' not in domain_json:
log.error("No acls key found in domain")
raise HTTPInternalServerError()
acls = domain_json["acls"]
log.debug("got domain_json: {}".format(domain_json))
# validate that the requesting user has permission to read this domain
aclCheck(domain_json, "readACL",
username) # throws exception if not authorized
acl_list = []
acl_usernames = list(acls.keys())
acl_usernames.sort()
for acl_username in acl_usernames:
entry = {"userName": acl_username}
acl = acls[acl_username]
for k in acl.keys():
entry[k] = acl[k]
acl_list.append(entry)
# return just the keys as per the REST API
rsp_json = {}
rsp_json["acls"] = acl_list
hrefs = []
hrefs.append({'rel': 'self', 'href': getHref(request, '/acls')})
if "root" in domain_json:
hrefs.append({
'rel': 'root',
'href': getHref(request, '/groups/' + domain_json["root"])
})
hrefs.append({'rel': 'home', 'href': getHref(request, '/')})
hrefs.append({'rel': 'owner', 'href': getHref(request, '/')})
rsp_json["hrefs"] = hrefs
resp = await jsonResponse(request, rsp_json)
log.response(request, resp=resp)
return resp
async def GET_Chunk(request):
log.request(request)
app = request.app
params = request.rel_url.query
chunk_id = request.match_info.get('id')
if not chunk_id:
msg = "Missing chunk id"
log.error(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(chunk_id, "Chunk"):
msg = "Invalid chunk id: {}".format(chunk_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
validateInPartition(app, chunk_id)
log.debug("request params: {}".format(list(params.keys())))
if "dset" not in params:
msg = "Missing dset in GET request"
log.error(msg)
raise HTTPBadRequest(reason=msg)
dset_json = json.loads(params["dset"])
log.debug("dset_json: {}".format(dset_json))
type_json = dset_json["type"]
dims = getChunkLayout(dset_json)
log.debug("got dims: {}".format(dims))
rank = len(dims)
# get chunk selection from query params
if "select" in params:
log.debug("select: {}".format(params["select"]))
selection = []
for i in range(rank):
dim_slice = getSliceQueryParam(request, i, dims[i])
selection.append(dim_slice)
selection = tuple(selection)
log.debug("got selection: {}".format(selection))
dt = createDataType(type_json)
log.debug("dtype: {}".format(dt))
rank = len(dims)
if rank == 0:
msg = "No dimension passed to GET chunk request"
log.error(msg)
raise HTTPBadRequest(reason=msg)
if len(selection) != rank:
msg = "Selection rank does not match shape rank"
log.error(msg)
raise HTTPBadRequest(reason=msg)
for i in range(rank):
s = selection[i]
log.debug("selection[{}]: {}".format(i, s))
s3path = None
s3offset = 0
s3size = 0
if "s3path" in params:
s3path = params["s3path"]
log.debug(f"GET_Chunk - useing s3path: {s3path}")
if "s3offset" in params:
try:
s3offset = int(params["s3offset"])
except ValueError:
log.error(f"invalid s3offset params: {params['s3offset']}")
raise HTTPBadRequest()
if "s3size" in params:
try:
s3size = int(params["s3size"])
except ValueError:
log.error(f"invalid s3size params: {params['s3sieze']}")
raise HTTPBadRequest()
chunk_arr = await getChunk(app, chunk_id, dset_json, s3path=s3path, s3offset=s3offset, s3size=s3size)
if chunk_arr is None:
# return a 404
msg = "Chunk {} does not exist".format(chunk_id)
log.info(msg)
raise HTTPNotFound()
resp = None
if "query" in params:
# do query selection
query = params["query"]
log.info("query: {}".format(query))
if rank != 1:
msg = "Query selection only supported for one dimensional arrays"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
limit = 0
if "Limit" in params:
limit = int(params["Limit"])
values = []
indices = []
field_names = []
if dt.fields:
field_names = list(dt.fields.keys())
x = chunk_arr[selection]
log.debug("x: {}".format(x))
eval_str = getEvalStr(query, "x", field_names)
log.debug("eval_str: {}".format(eval_str))
where_result = np.where(eval(eval_str))
log.debug("where_result: {}".format(where_result))
where_result_index = where_result[0]
log.debug("whare_result index: {}".format(where_result_index))
log.debug("boolean selection: {}".format(x[where_result_index]))
s = selection[0]
count = 0
for index in where_result_index:
log.debug("index: {}".format(index))
value = x[index].tolist()
log.debug("value: {}".format(value))
json_val = bytesArrayToList(value)
log.debug("json_value: {}".format(json_val))
json_index = index.tolist() * s.step + s.start # adjust for selection
indices.append(json_index)
values.append(json_val)
count += 1
if limit > 0 and count >= limit:
log.info("got limit items")
break
query_result = {}
query_result["index"] = indices
query_result["value"] = values
log.info(f"query_result retiurning: {len(indices)} rows")
log.debug(f"query_result: {query_result}")
resp = json_response(query_result)
else:
# get requested data
output_arr = chunk_arr[selection]
output_data = arrayToBytes(output_arr)
# write response
try:
resp = StreamResponse()
resp.headers['Content-Type'] = "application/octet-stream"
resp.content_length = len(output_data)
await resp.prepare(request)
await resp.write(output_data)
except Exception as e:
log.error(f"Exception during binary data write: {e}")
raise HTTPInternalServerError()
finally:
await resp.write_eof()
return resp
async def PUT_DatasetShape(request):
"""HTTP method to update dataset's shape"""
log.request(request)
app = request.app
dset_id = request.match_info.get('id')
if not isValidUuid(dset_id, obj_class="dataset"):
log.error("Unexpected type_id: {}".format(dset_id))
raise HTTPInternalServerError()
body = await request.json()
log.info("PUT datasetshape: {}, body: {}".format(dset_id, body))
if "shape" not in body and "extend" not in body:
log.error("Expected shape or extend keys")
raise HTTPInternalServerError()
dset_json = await get_metadata_obj(app, dset_id)
shape_orig = dset_json["shape"]
log.debug("shape_orig: {}".format(shape_orig))
if "maxdims" not in shape_orig:
log.error("expected maxdims in dataset json")
raise HTTPInternalServerError()
dims = shape_orig["dims"]
maxdims = shape_orig["maxdims"]
resp_json = {}
if "extend" in body:
# extend the shape by the give value and return the
# newly extended area
extension = body["extend"]
extend_dim = 0
if "extend_dim" in body:
extend_dim = body["extend_dim"]
log.info(f"datashape extend: {extension} dim: {extend_dim}")
selection = "["
for i in range(len(dims)):
if i == extend_dim:
lb = dims[i]
ub = lb + extension
if maxdims[extend_dim] != 0 and ub > maxdims[extend_dim]:
msg = "maximum extent exceeded"
log.warn(msg)
raise HTTPConflict()
selection += f"{lb}:{ub}"
dims[i] = ub
else:
if dims[i] == 0:
dims[i] = 1 # each dimension must be non-zero
selection += ":"
if i < len(dims) - 1:
selection += ","
selection += "]"
resp_json["selection"] = selection
else:
# verify that the extend request is still valid
# e.g. another client has already extended the shape since the SN
# verified it
shape_update = body["shape"]
log.debug("shape_update: {}".format(shape_update))
for i in range(len(dims)):
if shape_update[i] < dims[i]:
msg = "Dataspace can not be made smaller"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
# Update the shape!
for i in range(len(dims)):
dims[i] = shape_update[i]
# write back to S3, save to metadata cache
log.info(f"Updated dimensions: {dims}")
await save_metadata_obj(app, dset_id, dset_json)
resp = json_response(resp_json, status=201)
log.response(request, resp=resp)
return resp
async def getChunk(app, chunk_id, dset_json, s3path=None, s3offset=0, s3size=0, chunk_init=False):
# if the chunk cache has too many dirty items, wait till items get flushed to S3
MAX_WAIT_TIME = 10.0 # TBD - make this a config
chunk_cache = app['chunk_cache']
if chunk_init and s3offset > 0:
log.error(f"unable to initiale chunk {chunk_id} for reference layouts ")
raise HTTPInternalServerError()
log.debug(f"getChunk cache utilization: {chunk_cache.cacheUtilizationPercent} per, dirty_count: {chunk_cache.dirtyCount}, mem_dirty: {chunk_cache.memDirty}")
chunk_arr = None
dset_id = getDatasetId(chunk_id)
dims = getChunkLayout(dset_json)
type_json = dset_json["type"]
dt = createDataType(type_json)
bucket = None
s3key = None
if s3path:
if not s3path.startswith("s3://"):
# TBD - verify these at dataset creation time?
log.error(f"unexpected s3path for getChunk: {s3path}")
raise HTTPInternalServerError()
path = s3path[5:]
index = path.find('/') # split bucket and key
if index < 1:
log.error(f"s3path is invalid: {s3path}")
raise HTTPInternalServerError()
bucket = path[:index]
log.debug(f"using bucket: {bucket}")
s3key = path[(index+1):]
log.debug(f"Using bucket: {bucket} and s3key: {s3key}")
else:
s3key = getS3Key(chunk_id)
log.debug("getChunk s3key: {}".format(s3key))
if chunk_id in chunk_cache:
chunk_arr = chunk_cache[chunk_id]
else:
if s3path and s3size == 0:
obj_exists = False
else:
obj_exists = await isS3Obj(app, s3key, bucket=bucket)
# TBD - potential race condition?
if obj_exists:
pending_s3_read = app["pending_s3_read"]
if chunk_id in pending_s3_read:
# already a read in progress, wait for it to complete
read_start_time = pending_s3_read[chunk_id]
log.info(f"s3 read request for {chunk_id} was requested at: {read_start_time}")
while time.time() - read_start_time < 2.0:
log.debug("waiting for pending s3 read, sleeping")
await asyncio.sleep(1) # sleep for sub-second?
if chunk_id in chunk_cache:
log.info(f"Chunk {chunk_id} has arrived!")
chunk_arr = chunk_cache[chunk_id]
break
if chunk_arr is None:
log.warn(f"s3 read for chunk {chunk_id} timed-out, initiaiting a new read")
if chunk_arr is None:
if chunk_id not in pending_s3_read:
pending_s3_read[chunk_id] = time.time()
log.debug("Reading chunk {} from S3".format(s3key))
deflate_level = getDeflate(app, dset_id, dset_json)
chunk_bytes = await getS3Bytes(app, s3key, deflate_level=deflate_level, s3offset=s3offset, s3size=s3size, bucket=bucket)
if chunk_id in pending_s3_read:
# read complete - remove from pending map
elapsed_time = time.time() - pending_s3_read[chunk_id]
log.info(f"s3 read for {s3key} took {elapsed_time}")
del pending_s3_read[chunk_id]
else:
log.warn(f"expected to find {chunk_id} in pending_s3_read map")
chunk_arr = np.fromstring(chunk_bytes, dtype=dt)
chunk_arr = chunk_arr.reshape(dims)
log.debug("chunk size: {}".format(chunk_arr.size))
elif chunk_init:
log.debug("Initializing chunk {chunk_id}")
fill_value = getFillValue(dset_json)
if fill_value:
# need to convert list to tuples for numpy broadcast
if isinstance(fill_value, list):
fill_value = tuple(fill_value)
chunk_arr = np.empty(dims, dtype=dt, order='C')
chunk_arr[...] = fill_value
else:
chunk_arr = np.zeros(dims, dtype=dt, order='C')
else:
log.debug(f"Chunk {chunk_id} not found")
if chunk_arr is not None:
# check that there's room in the cache before adding it
if chunk_cache.memTarget - chunk_cache.memDirty < chunk_arr.size:
# no room in the cache, wait till space is freed by the s3sync task
wait_start = time.time()
while chunk_cache.memTarget - chunk_cache.memDirty < chunk_arr.size:
log.warn(f"getChunk, cache utilization: {chunk_cache.cacheUtilizationPercent}, sleeping till items are flushed")
if time.time() - wait_start > MAX_WAIT_TIME:
log.error(f"unable to save updated chunk {chunk_id} to cache returning 503 error")
raise HTTPServiceUnavailable()
await asyncio.sleep(1)
chunk_cache[chunk_id] = chunk_arr # store in cache
return chunk_arr
async def POST_Dataset(request):
""" Handler for POST /datasets"""
log.request(request)
app = request.app
if not request.has_body:
msg = "POST_Dataset with no body"
log.error(msg)
raise HTTPBadRequest(reason=msg)
body = await request.json()
log.info("POST_Dataset, body: {}".format(body))
dset_id = get_obj_id(request, body=body)
if not isValidUuid(dset_id, obj_class="dataset"):
log.error("Unexpected dataset_id: {}".format(dset_id))
raise HTTPInternalServerError()
# verify the id doesn't already exist
obj_found = await check_metadata_obj(app, dset_id)
if obj_found:
log.error("Post with existing dset_id: {}".format(dset_id))
raise HTTPInternalServerError()
if "root" not in body:
msg = "POST_Dataset with no root"
log.error(msg)
raise HTTPInternalServerError()
root_id = body["root"]
try:
validateUuid(root_id, "group")
except ValueError:
msg = "Invalid root_id: " + root_id
log.error(msg)
raise HTTPInternalServerError()
if "type" not in body:
msg = "POST_Dataset with no type"
log.error(msg)
raise HTTPInternalServerError()
type_json = body["type"]
if "shape" not in body:
msg = "POST_Dataset with no shape"
log.error(msg)
raise HTTPInternalServerError()
shape_json = body["shape"]
layout = None
if "layout" in body:
layout = body["layout"] # client specified chunk layout
# ok - all set, create committed type obj
now = int(time.time())
log.debug("POST_dataset typejson: {}, shapejson: {}".format(
type_json, shape_json))
dset_json = {
"id": dset_id,
"root": root_id,
"created": now,
"lastModified": now,
"type": type_json,
"shape": shape_json,
"attributes": {}
}
if "creationProperties" in body:
dset_json["creationProperties"] = body["creationProperties"]
if layout is not None:
dset_json["layout"] = layout
await save_metadata_obj(app, dset_id, dset_json, notify=True, flush=True)
resp_json = {}
resp_json["id"] = dset_id
resp_json["root"] = root_id
resp_json["created"] = dset_json["created"]
resp_json["type"] = type_json
resp_json["shape"] = shape_json
resp_json["lastModified"] = dset_json["lastModified"]
resp_json["attributeCount"] = 0
resp = json_response(resp_json, status=201)
log.response(request, resp=resp)
return resp
async def PUT_Link(request):
"""HTTP method to create a new link"""
log.request(request)
app = request.app
group_id = request.match_info.get('id')
if not group_id:
msg = "Missing group id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(group_id, obj_class="Group"):
msg = "Invalid group id: {}".format(group_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
link_title = request.match_info.get('title')
log.info("PUT Link_title: [{}]".format(link_title))
validateLinkName(link_title)
username, pswd = getUserPasswordFromRequest(request)
# write actions need auth
await validateUserPassword(app, username, pswd)
if not request.has_body:
msg = "PUT Link with no body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
body = await request.json()
link_json = {}
if "id" in body:
if not isValidUuid(body["id"]):
msg = "PUT Link with invalid id in body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
link_json["id"] = body["id"]
link_json["class"] = "H5L_TYPE_HARD"
elif "h5path" in body:
link_json["h5path"] = body["h5path"]
# could be hard or soft link
if "h5domain" in body:
link_json["h5domain"] = body["h5domain"]
link_json["class"] = "H5L_TYPE_EXTERNAL"
else:
# soft link
link_json["class"] = "H5L_TYPE_SOFT"
else:
msg = "PUT Link with no id or h5path keys"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
domain = getDomainFromRequest(request)
if not isValidDomain(domain):
msg = "Invalid host value: {}".format(domain)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
await validateAction(app, domain, group_id, username, "create")
# for hard links, verify that the referenced id exists and is in this domain
if "id" in body:
ref_id = body["id"]
ref_json = await getObjectJson(app, ref_id)
group_json = await getObjectJson(app, group_id)
if ref_json["root"] != group_json["root"]:
msg = "Hard link must reference an object in the same domain"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
# ready to add link now
req = getDataNodeUrl(app, group_id)
req += "/groups/" + group_id + "/links/" + link_title
log.debug("PUT link - getting group: " + req)
put_rsp = await http_put(app, req, data=link_json)
log.debug("PUT Link resp: " + str(put_rsp))
hrefs = [] # TBD
req_rsp = {"hrefs": hrefs}
# link creation successful
resp = await jsonResponse(request, req_rsp, status=201)
log.response(request, resp=resp)
return resp
def getSliceQueryParam(request, dim, extent, body=None):
# Get optional query parameters for given dim
log.debug("getSliceQueryParam: " + str(dim) + ", " + str(extent))
params = request.rel_url.query
start = 0
stop = extent
step = 1
if body and "start" in body:
# look for start params in body JSON
start_val = body["start"]
if isinstance(start_val, (list, tuple)):
if len(start_val) < dim:
msg = "Not enough dimensions supplied to body start key"
log.arn(msg)
raise HTTPBadRequest(reason=msg)
start = start_val[dim]
else:
start = start_val
if body and "stop" in body:
stop_val = body["stop"]
if isinstance(stop_val, (list, tuple)):
if len(stop_val) < dim:
msg = "Not enough dimensions supplied to body stop key"
log.arn(msg)
raise HTTPBadRequest(reason=msg)
stop = stop_val[dim]
else:
stop = stop_val
if body and "step" in body:
step_val = body["step"]
if isinstance(step_val, (list, tuple)):
if len(step_val) < dim:
msg = "Not enough dimensions supplied to body step key"
log.arn(msg)
raise HTTPBadRequest(reason=msg)
step = step_val[dim]
else:
step = step_val
if "select" in params:
query = params["select"]
log.debug("select query value:" + query)
if not query.startswith('['):
msg = "Bad Request: selection query missing start bracket"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not query.endswith(']'):
msg = "Bad Request: selection query missing end bracket"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
# now strip out brackets
query = query[1:-1]
query_array = query.split(',')
if dim >= len(query_array):
msg = "Not enough dimensions supplied to query argument"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
dim_query = query_array[dim].strip()
if dim_query.find(':') < 0:
# just a number - return start = stop for this value
try:
start = int(dim_query)
except ValueError:
msg = "Bad Request: invalid selection parameter (can't convert to int) for dimension: " + str(
dim)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
stop = start
elif dim_query == ':':
# select everything
pass
else:
fields = dim_query.split(":")
log.debug("got fields: {}".format(fields))
if len(fields) > 3:
msg = "Bad Request: Too many ':' seperators for dimension: " + str(
dim)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
try:
if fields[0]:
start = int(fields[0])
if fields[1]:
stop = int(fields[1])
if len(fields) > 2 and fields[2]:
step = int(fields[2])
except ValueError:
msg = "Bad Request: invalid selection parameter (can't convert to int) for dimension: " + str(
dim)
log.info(msg)
raise HTTPBadRequest(reason=msg)
log.debug("start: {}, stop: {}, step: {}".format(start, stop, step))
# now, validate whaterver start/stop/step values we got
if start < 0 or start > extent:
msg = "Bad Request: Invalid selection start parameter for dimension: " + str(
dim)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if stop > extent:
msg = "Bad Request: Invalid selection stop parameter for dimension: " + str(
dim)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if step <= 0:
msg = "Bad Request: invalid selection step parameter for dimension: " + str(
dim)
log.debug(msg)
raise HTTPBadRequest(reason=msg)
s = slice(start, stop, step)
log.debug("dim query[" + str(dim) + "] returning: start: " + str(start) +
" stop: " + str(stop) + " step: " + str(step))
return s
async def get_metadata_obj(app, obj_id, bucket=None):
""" Get object from metadata cache (if present).
Otherwise fetch from S3 and add to cache
"""
log.info(f"get_metadata_obj: {obj_id} bucket: {bucket}")
validateObjId(obj_id, bucket) # throws internal server error if invalid
if isValidDomain(obj_id):
bucket = getBucketForDomain(obj_id)
"""
try:
validateInPartition(app, obj_id)
except KeyError:
log.error("Domain not in partition")
raise HTTPInternalServerError()
"""
deleted_ids = app['deleted_ids']
if obj_id in deleted_ids:
msg = f"{obj_id} has been deleted"
log.warn(msg)
raise HTTPGone()
meta_cache = app['meta_cache']
obj_json = None
if obj_id in meta_cache:
log.debug(f"{obj_id} found in meta cache")
obj_json = meta_cache[obj_id]
else:
s3_key = getS3Key(obj_id)
pending_s3_read = app["pending_s3_read"]
if obj_id in pending_s3_read:
# already a read in progress, wait for it to complete
read_start_time = pending_s3_read[obj_id]
log.info(
f"s3 read request for {s3_key} was requested at: {read_start_time}"
)
while time.time() - read_start_time < 2.0:
log.debug("waiting for pending s3 read, sleeping")
await asyncio.sleep(1) # sleep for sub-second?
if obj_id in meta_cache:
log.info(f"object {obj_id} has arrived!")
obj_json = meta_cache[obj_id]
break
if not obj_json:
log.warn(
f"s3 read for object {s3_key} timed-out, initiaiting a new read"
)
# invoke S3 read unless the object has just come in from pending read
if not obj_json:
log.debug(f"getS3JSONObj({s3_key}, bucket={bucket})")
if obj_id not in pending_s3_read:
pending_s3_read[obj_id] = time.time()
# read S3 object as JSON
obj_json = await getS3JSONObj(app, s3_key, bucket=bucket)
if obj_id in pending_s3_read:
# read complete - remove from pending map
elapsed_time = time.time() - pending_s3_read[obj_id]
log.info(f"s3 read for {s3_key} took {elapsed_time}")
del pending_s3_read[obj_id]
meta_cache[obj_id] = obj_json # add to cache
return obj_json
def getS3Client(app):
""" Return s3client handle
"""
if "session" not in app:
# app startup should have set this
raise KeyError("Session not initialized")
session = app["session"]
if "s3" in app:
if "token_expiration" in app:
# check that our token is not about to expire
expiration = app["token_expiration"]
now = datetime.datetime.now()
delta = expiration - now
if delta.total_seconds() > 10:
return app["s3"]
# otherwise, fall through and get a new token
log.info("S3 access token has expired - renewing")
else:
return app["s3"]
# first time setup of s3 client or limited time token has expired
aws_region = config.get("aws_region")
log.info(f"aws_region {aws_region}")
aws_secret_access_key = None
aws_access_key_id = None
aws_session_token = None
aws_iam_role = config.get("aws_iam_role")
aws_secret_access_key = config.get("aws_secret_access_key")
aws_access_key_id = config.get("aws_access_key_id")
if not aws_secret_access_key or aws_secret_access_key == 'xxx':
log.info("aws secret access key not set")
aws_secret_access_key = None
if not aws_access_key_id or aws_access_key_id == 'xxx':
log.info("aws access key id not set")
aws_access_key_id = None
if aws_iam_role and not aws_secret_access_key:
log.info("using iam role: {}".format(aws_iam_role))
log.info("getting EC2 IAM role credentials")
# Use EC2 IAM role to get credentials
# See: https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/iam-roles-for-amazon-ec2.html?icmpid=docs_ec2_console
curl_cmd = ["curl", "http://169.254.169.254/latest/meta-data/iam/security-credentials/{}".format(aws_iam_role)]
p = subprocess.run(curl_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
if p.returncode != 0:
msg = "Error getting IAM role credentials: {}".format(p.stderr)
log.error(msg)
else:
stdout = p.stdout.decode("utf-8")
try:
cred = json.loads(stdout)
aws_secret_access_key = cred["SecretAccessKey"]
aws_access_key_id = cred["AccessKeyId"]
log.info("Got ACCESS_KEY_ID: {} from EC2 metadata".format(aws_access_key_id))
aws_session_token = cred["Token"]
log.info("Got Expiration of: {}".format(cred["Expiration"]))
expiration_str = cred["Expiration"][:-1] + "UTC" # trim off 'Z' and add 'UTC'
# save the expiration
app["token_expiration"] = datetime.datetime.strptime(expiration_str, "%Y-%m-%dT%H:%M:%S%Z")
except json.JSONDecodeError:
msg = "Unexpected error decoding EC2 meta-data response"
log.error(msg)
except KeyError:
msg = "Missing expected key from EC2 meta-data response"
log.error(msg)
s3_gateway = config.get('aws_s3_gateway')
if not s3_gateway:
msg="Invalid aws s3 gateway"
log.error(msg)
raise ValueError(msg)
if s3_gateway[0] == '[' and s3_gateway[-1] == ']':
# convert string to a comma separated list
items = s3_gateway[1:-1].split(',')
s3_gateway = []
for item in items:
s3_gateway.append(item.strip())
if isinstance(s3_gateway, list):
# use the node number to select an item from the list
node_number = 0
if "node_number" in app:
node_number = app["node_number"]
item = s3_gateway[node_number % len(s3_gateway)]
log.debug(f"selecting: {item} from s3_gateway list: {s3_gateway}")
s3_gateway = item
log.info(f"Using S3Gateway: {s3_gateway}")
use_ssl = False
if s3_gateway.startswith("https"):
use_ssl = True
max_pool_connections = config.get('aio_max_pool_connections')
aio_config = AioConfig(max_pool_connections=max_pool_connections)
s3 = session.create_client('s3', region_name=aws_region,
aws_secret_access_key=aws_secret_access_key,
aws_access_key_id=aws_access_key_id,
aws_session_token=aws_session_token,
endpoint_url=s3_gateway,
use_ssl=use_ssl,
config=aio_config)
app['s3'] = s3 # save so same client can be returned in subsequent calls
return s3
