def request(req):
domain = getDomainFromRequest(req, validate=False)
if domain is None:
print("REQ> {}: {}".format(req.method, req.path))
else:
print("REQ> {}: {} [{}]".format(req.method, req.path, domain))
if app:
node_state = app["node_state"]
if node_state != "READY":
print(f"WARN: returning 503 - node_state: {node_state}")
raise HTTPServiceUnavailable()
counter = app["req_count"]
if req.method in ("GET", "POST", "PUT", "DELETE"):
counter[req.method] += 1
num_tasks = len(asyncio.Task.all_tasks())
active_tasks = len(
[task for task in asyncio.Task.all_tasks() if not task.done()])
counter["num_tasks"] = num_tasks
if config.get("log_level") == "DEBUG":
print(
f"DEBUG> num tasks: {num_tasks} active tasks: {active_tasks}")
max_task_count = config.get("max_task_count")
if app["node_type"] == "sn" and max_task_count and active_tasks > max_task_count:
print(f"WARN: more than {max_task_count} tasks, returning 503")
raise HTTPServiceUnavailable()
async def DELETE_Link(request):
"""HTTP method to delete a 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)
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, "delete")
req = getDataNodeUrl(app, group_id)
req += "/groups/" + group_id + "/links/" + link_title
rsp_json = await http_delete(app, req)
resp = await jsonResponse(request, rsp_json)
log.response(request, resp=resp)
return resp
async def DELETE_Group(request):
"""HTTP method to delete a group resource"""
log.request(request)
app = request.app
meta_cache = app['meta_cache']
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, "Group"):
msg = f"Invalid group id: {group_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
username, pswd = getUserPasswordFromRequest(request)
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)
# get domain JSON
domain_json = await getDomainJson(app, domain)
# TBD - verify that the obj_id belongs to the given domain
await validateAction(app, domain, group_id, username, "delete")
if "root" not in domain_json:
log.error(f"Expected root key for domain: {domain}")
raise HTTPBadRequest(reason="Unexpected Error")
if group_id == domain_json["root"]:
msg = "Forbidden - deletion of root group is not allowed - delete domain first"
log.warn(msg)
raise HTTPForbidden()
req = getDataNodeUrl(app, group_id)
req += "/groups/" + group_id
params = {}
if bucket:
params["bucket"] = bucket
log.debug(f"http_delete req: {req} params: {params}")
await http_delete(app, req, params=params)
if group_id in meta_cache:
del meta_cache[group_id] # remove from cache
resp = await jsonResponse(request, {})
log.response(request, resp=resp)
return resp
async def DELETE_Attribute(request):
"""HTTP method to delete a attribute resource"""
log.request(request)
app = request.app
collection = getRequestCollectionName(
request) # returns datasets|groups|datatypes
obj_id = request.match_info.get('id')
if not obj_id:
msg = "Missing object id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(obj_id, obj_class=collection):
msg = f"Invalid object id: {obj_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
attr_name = request.match_info.get('name')
log.debug(f"Attribute name: [{attr_name}]")
validateAttributeName(attr_name)
username, pswd = getUserPasswordFromRequest(request)
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)
# get domain JSON
domain_json = await getDomainJson(app, domain)
if "root" not in domain_json:
log.error(f"Expected root key for domain: {domain}")
raise HTTPBadRequest(reason="Unexpected Error")
# TBD - verify that the obj_id belongs to the given domain
await validateAction(app, domain, obj_id, username, "delete")
req = getDataNodeUrl(app, obj_id)
req += '/' + collection + '/' + obj_id + "/attributes/" + attr_name
log.info("PUT Attribute: " + req)
params = {}
if bucket:
params["bucket"] = bucket
rsp_json = await http_delete(app, req, params=params)
log.info(f"PUT Attribute resp: {rsp_json}")
hrefs = [] # TBD
req_rsp = {"hrefs": hrefs}
resp = await jsonResponse(request, req_rsp)
log.response(request, resp=resp)
return resp
async def PUT_ACL(request):
"""HTTP method to add a new ACL for a domain"""
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)
await validateUserPassword(app, username, pswd)
if not request.has_body:
msg = "PUT ACL with no body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
body = await request.json()
acl_keys = getAclKeys()
for k in body.keys():
if k not in acl_keys:
msg = "Unexpected key in request body: {}".format(k)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if body[k] not in (True, False):
msg = "Unexpected value for key in request body: {}".format(k)
log.warn(k)
raise HTTPBadRequest(reason=msg)
try:
domain = getDomainFromRequest(request)
except ValueError:
msg = "Invalid domain"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
# don't use app["domain_cache"] if a direct domain request is made
# as opposed to an implicit request as with other operations, query
# the domain from the authoritative source (the dn node)
req = getDataNodeUrl(app, domain)
req += "/acls/" + acl_username
log.info("sending dn req: {}".format(req))
body["domain"] = domain
put_rsp = await http_put(app, req, data=body)
log.info("PUT ACL resp: " + str(put_rsp))
# ACL update successful
resp = await jsonResponse(request, put_rsp, status=201)
log.response(request, resp=resp)
return resp
async def GET_DatasetShape(request):
"""HTTP method to return JSON for dataset's shape"""
log.request(request)
app = request.app
dset_id = request.match_info.get('id')
if not dset_id:
msg = "Missing dataset id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(dset_id, "Dataset"):
msg = f"Invalid dataset id: {dset_id}"
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)
domain = getDomainFromRequest(request)
if not isValidDomain(domain):
msg = f"Invalid domain: {domain}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
bucket = getBucketForDomain(domain)
# get authoritative state for dataset from DN (even if it's in the meta_cache).
dset_json = await getObjectJson(app, dset_id, refresh=True, bucket=bucket)
await validateAction(app, domain, dset_id, username, "read")
hrefs = []
dset_uri = '/datasets/' + dset_id
self_uri = dset_uri + "/shape"
hrefs.append({'rel': 'self', 'href': getHref(request, self_uri)})
dset_uri = '/datasets/' + dset_id
hrefs.append({'rel': 'owner', 'href': getHref(request, dset_uri)})
root_uri = '/groups/' + dset_json["root"]
hrefs.append({'rel': 'root', 'href': getHref(request, root_uri)})
resp_json = {}
resp_json["shape"] = dset_json["shape"]
resp_json["hrefs"] = hrefs
resp_json["created"] = dset_json["created"]
resp_json["lastModified"] = dset_json["lastModified"]
resp = await jsonResponse(request, resp_json)
log.response(request, resp=resp)
return resp
async def DELETE_Datatype(request):
"""HTTP method to delete a committed type resource"""
log.request(request)
app = request.app
meta_cache = app['meta_cache']
ctype_id = request.match_info.get('id')
if not ctype_id:
msg = "Missing committed type id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(ctype_id, "Type"):
msg = f"Invalid committed type id: {ctype_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
username, pswd = getUserPasswordFromRequest(request)
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)
params = {}
if bucket:
params["bucket"] = bucket
# get domain JSON
domain_json = await getDomainJson(app, domain)
if "root" not in domain_json:
log.error(f"Expected root key for domain: {domain}")
raise HTTPBadRequest(reason="Unexpected Error")
# TBD - verify that the obj_id belongs to the given domain
await validateAction(app, domain, ctype_id, username, "delete")
req = getDataNodeUrl(app, ctype_id) + "/datatypes/" + ctype_id
await http_delete(app, req, params=params)
if ctype_id in meta_cache:
del meta_cache[ctype_id] # remove from cache
resp = await jsonResponse(request, {})
log.response(request, resp=resp)
return resp
async def DELETE_Dataset(request):
"""HTTP method to delete a dataset resource"""
log.request(request)
app = request.app
meta_cache = app['meta_cache']
dset_id = request.match_info.get('id')
if not dset_id:
msg = "Missing dataset id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(dset_id, "Dataset"):
msg = "Invalid dataset id: {}".format(dset_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
username, pswd = getUserPasswordFromRequest(request)
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)
# get domain JSON
domain_json = await getDomainJson(app, domain)
if "root" not in domain_json:
log.error("Expected root key for domain: {}".format(domain))
raise HTTPBadRequest(reason="Unexpected Error")
# TBD - verify that the obj_id belongs to the given domain
await validateAction(app, domain, dset_id, username, "delete")
req = getDataNodeUrl(app, dset_id) + "/datasets/" + dset_id
await http_delete(app, req)
if dset_id in meta_cache:
del meta_cache[dset_id] # remove from cache
resp = await jsonResponse(request, {})
log.response(request, resp=resp)
return resp
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_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 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 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_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_AttributeValue(request):
"""HTTP method to update an attributes data"""
log.request(request)
log.info("PUT_AttributeValue")
app = request.app
collection = getRequestCollectionName(request) # returns datasets|groups|datatypes
obj_id = request.match_info.get('id')
if not obj_id:
msg = "Missing object id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(obj_id, obj_class=collection):
msg = f"Invalid object id: {obj_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
attr_name = request.match_info.get('name')
log.debug(f"Attribute name: [{attr_name}]")
validateAttributeName(attr_name)
log.info(f"PUT Attribute Value id: {obj_id} name: {attr_name}")
username, pswd = getUserPasswordFromRequest(request)
# write actions need auth
await validateUserPassword(app, username, pswd)
if not request.has_body:
msg = "PUT AttributeValue with no body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
domain = getDomainFromRequest(request)
if not isValidDomain(domain):
msg = f"Invalid domain: {domain}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
bucket = getBucketForDomain(domain)
# get domain JSON
domain_json = await getDomainJson(app, domain)
if "root" not in domain_json:
log.error(f"Expected root key for domain: {domain}")
raise HTTPInternalServerError()
# TBD - verify that the obj_id belongs to the given domain
await validateAction(app, domain, obj_id, username, "update")
req = getDataNodeUrl(app, obj_id)
req += '/' + collection + '/' + obj_id + "/attributes/" + attr_name
log.debug("get Attribute: " + req)
params = {}
if bucket:
params["bucket"] = bucket
dn_json = await http_get(app, req, params=params)
log.debug("got attributes json from dn for obj_id: " + str(obj_id))
log.debug(f"got dn_json: {dn_json}")
attr_shape = dn_json["shape"]
if attr_shape["class"] == 'H5S_NULL':
msg = "Null space attributes can not be updated"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
np_shape = getShapeDims(attr_shape)
type_json = dn_json["type"]
np_dtype = createDataType(type_json) # np datatype
request_type = "json"
if "Content-Type" in request.headers:
# client should use "application/octet-stream" for binary transfer
content_type = request.headers["Content-Type"]
if content_type not in ("application/json", "application/octet-stream"):
msg = f"Unknown content_type: {content_type}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if content_type == "application/octet-stream":
log.debug("PUT AttributeValue - request_type is binary")
request_type = "binary"
else:
log.debug("PUT AttribueValue - request type is json")
binary_data = None
if request_type == "binary":
item_size = getItemSize(type_json)
if item_size == 'H5T_VARIABLE':
msg = "Only JSON is supported for variable length data types"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
# read binary data
binary_data = await request.read()
if len(binary_data) != request.content_length:
msg = f"Read {len(binary_data)} bytes, expecting: {request.content_length}"
log.error(msg)
raise HTTPInternalServerError()
arr = None # np array to hold request data
if binary_data:
npoints = getNumElements(np_shape)
if npoints*item_size != len(binary_data):
msg = "Expected: " + str(npoints*item_size) + " bytes, but got: " + str(len(binary_data))
log.warn(msg)
raise HTTPBadRequest(reason=msg)
arr = np.fromstring(binary_data, dtype=np_dtype)
arr = arr.reshape(np_shape) # conform to selection shape
# convert to JSON for transmission to DN
data = arr.tolist()
value = bytesArrayToList(data)
else:
body = await request.json()
if "value" not in body:
msg = "PUT attribute value with no value in body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
value = body["value"]
# validate that the value agrees with type/shape
try:
arr = jsonToArray(np_shape, np_dtype, value)
except ValueError:
msg = "Bad Request: input data doesn't match selection"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
log.info(f"Got: {arr.size} array elements")
# ready to add attribute now
attr_json = {}
attr_json["type"] = type_json
attr_json["shape"] = attr_shape
attr_json["value"] = value
req = getDataNodeUrl(app, obj_id)
req += '/' + collection + '/' + obj_id + "/attributes/" + attr_name
log.info(f"PUT Attribute Value: {req}")
dn_json["value"] = value
params = {}
params = {"replace": 1} # let the DN know we can overwrite the attribute
if bucket:
params["bucket"] = bucket
put_rsp = await http_put(app, req, params=params, data=attr_json)
log.info(f"PUT Attribute Value resp: {put_rsp}")
hrefs = [] # TBD
req_rsp = { "hrefs": hrefs }
# attribute creation successful
resp = await jsonResponse(request, req_rsp)
log.response(request, resp=resp)
return resp
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 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 POST_Dataset(request):
"""HTTP method to create a new dataset object"""
log.request(request)
app = request.app
username, pswd = getUserPasswordFromRequest(request)
# write actions need auth
await validateUserPassword(app, username, pswd)
if not request.has_body:
msg = "POST Datasets with no body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
body = await request.json()
# get domain, check authorization
domain = getDomainFromRequest(request)
if not isValidDomain(domain):
msg = "Invalid host value: {}".format(domain)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
domain_json = await getDomainJson(app, domain, reload=True)
root_id = domain_json["root"]
aclCheck(domain_json, "create",
username) # throws exception if not allowed
if "root" not in domain_json:
msg = "Expected root key for domain: {}".format(domain)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
#
# validate type input
#
if "type" not in body:
msg = "POST Dataset has no type key in body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
datatype = body["type"]
if isinstance(datatype, str) and datatype.startswith("t-"):
# Committed type - fetch type json from DN
ctype_id = datatype
log.debug("got ctypeid: {}".format(ctype_id))
ctype_json = await getObjectJson(app, ctype_id)
log.debug("ctype: {}".format(ctype_json))
if ctype_json["root"] != root_id:
msg = "Referenced committed datatype must belong in same domain"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
datatype = ctype_json["type"]
# add the ctype_id to type type
datatype["id"] = ctype_id
elif isinstance(datatype, str):
try:
# convert predefined type string (e.g. "H5T_STD_I32LE") to
# corresponding json representation
datatype = getBaseTypeJson(datatype)
log.debug("got datatype: {}".format(datatype))
except TypeError:
msg = "POST Dataset with invalid predefined type"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
validateTypeItem(datatype)
item_size = getItemSize(datatype)
#
# Validate shape input
#
dims = None
shape_json = {}
if "shape" not in body:
shape_json["class"] = "H5S_SCALAR"
else:
shape = body["shape"]
if isinstance(shape, int):
shape_json["class"] = "H5S_SIMPLE"
dims = [
shape,
]
shape_json["dims"] = dims
elif isinstance(shape, str):
# only valid string value is H5S_NULL
if shape != "H5S_NULL":
msg = "POST Datset with invalid shape value"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
shape_json["class"] = "H5S_NULL"
elif isinstance(shape, list):
if len(shape) == 0:
shape_json["class"] = "H5S_SCALAR"
else:
shape_json["class"] = "H5S_SIMPLE"
shape_json["dims"] = shape
dims = shape
else:
msg = "Bad Request: shape is invalid"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if dims is not None:
for i in range(len(dims)):
extent = dims[i]
if not isinstance(extent, int):
msg = "Invalid shape type"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if extent < 0:
msg = "shape dimension is negative"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
maxdims = None
if "maxdims" in body:
if dims is None:
msg = "Maxdims cannot be supplied if space is NULL"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
maxdims = body["maxdims"]
if isinstance(maxdims, int):
dim1 = maxdims
maxdims = [dim1]
elif isinstance(maxdims, list):
pass # can use as is
else:
msg = "Bad Request: maxdims is invalid"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if len(dims) != len(maxdims):
msg = "Maxdims rank doesn't match Shape"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if maxdims is not None:
for extent in maxdims:
if not isinstance(extent, int):
msg = "Invalid maxdims type"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if extent < 0:
msg = "maxdims dimension is negative"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if len(maxdims) != len(dims):
msg = "Bad Request: maxdims array length must equal shape array length"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
shape_json["maxdims"] = []
for i in range(len(dims)):
maxextent = maxdims[i]
if not isinstance(maxextent, int):
msg = "Bad Request: maxdims must be integer type"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
elif maxextent == 0:
# unlimited dimension
shape_json["maxdims"].append(0)
elif maxextent < dims[i]:
msg = "Bad Request: maxdims extent can't be smaller than shape extent"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
else:
shape_json["maxdims"].append(maxextent)
layout = None
min_chunk_size = int(config.get("min_chunk_size"))
max_chunk_size = int(config.get("max_chunk_size"))
if 'creationProperties' in body:
creationProperties = body["creationProperties"]
if 'layout' in creationProperties:
layout = creationProperties["layout"]
validateChunkLayout(shape_json, item_size, layout)
if layout is None and shape_json["class"] != "H5S_NULL":
# default to chunked layout
layout = {"class": "H5D_CHUNKED"}
if layout and layout["class"] == 'H5D_CONTIGUOUS_REF':
chunk_dims = getContiguousLayout(shape_json,
item_size,
chunk_min=min_chunk_size,
chunk_max=max_chunk_size)
layout["dims"] = chunk_dims
log.debug(f"autoContiguous layout: {layout}")
if layout and layout["class"] == 'H5D_CHUNKED' and "dims" not in layout:
# do autochunking
chunk_dims = guessChunk(shape_json, item_size)
layout["dims"] = chunk_dims
log.debug(f"initial autochunk layout: {layout}")
if layout and layout["class"] == 'H5D_CHUNKED':
chunk_dims = layout["dims"]
chunk_size = getChunkSize(chunk_dims, item_size)
log.debug("chunk_size: {}, min: {}, max: {}".format(
chunk_size, min_chunk_size, max_chunk_size))
# adjust the chunk shape if chunk size is too small or too big
adjusted_chunk_dims = None
if chunk_size < min_chunk_size:
log.debug(
"chunk size: {} less than min size: {}, expanding".format(
chunk_size, min_chunk_size))
adjusted_chunk_dims = expandChunk(chunk_dims,
item_size,
shape_json,
chunk_min=min_chunk_size,
layout_class=layout["class"])
elif chunk_size > max_chunk_size:
log.debug(
"chunk size: {} greater than max size: {}, expanding".format(
chunk_size, max_chunk_size, layout_class=layout["class"]))
adjusted_chunk_dims = shrinkChunk(chunk_dims,
item_size,
chunk_max=max_chunk_size)
if adjusted_chunk_dims:
log.debug(
f"requested chunk_dimensions: {chunk_dims} modified dimensions: {adjusted_chunk_dims}"
)
layout["dims"] = adjusted_chunk_dims
if layout and layout["class"] in ('H5D_CHUNKED_REF',
'H5D_CHUNKED_REF_INDIRECT'):
chunk_dims = layout["dims"]
chunk_size = getChunkSize(chunk_dims, item_size)
log.debug("chunk_size: {}, min: {}, max: {}".format(
chunk_size, min_chunk_size, max_chunk_size))
# adjust the chunk shape if chunk size is too small or too big
if chunk_size < min_chunk_size:
log.warn(
"chunk size: {} less than min size: {} for H5D_CHUNKED_REF dataset"
.format(chunk_size, min_chunk_size))
elif chunk_size > max_chunk_size:
log.warn(
"chunk size: {} greater than max size: {}, for H5D_CHUNKED_REF dataset"
.format(chunk_size,
max_chunk_size,
layout_class=layout["class"]))
link_id = None
link_title = None
if "link" in body:
link_body = body["link"]
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.info("link id: {}".format(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")
dset_id = createObjId("datasets", rootid=root_id)
log.info("new dataset id: {}".format(dset_id))
dataset_json = {
"id": dset_id,
"root": root_id,
"type": datatype,
"shape": shape_json
}
if "creationProperties" in body:
# TBD - validate all creationProperties
creationProperties = body["creationProperties"]
if "fillValue" in creationProperties:
# validate fill value compatible with type
dt = createDataType(datatype)
fill_value = creationProperties["fillValue"]
if isinstance(fill_value, list):
fill_value = tuple(fill_value)
try:
np.asarray(fill_value, dtype=dt)
except (TypeError, ValueError):
msg = "Fill value {} not compatible with dataset type: {}".format(
fill_value, datatype)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
dataset_json["creationProperties"] = creationProperties
if layout is not None:
dataset_json["layout"] = layout
log.debug("create dataset: " + json.dumps(dataset_json))
req = getDataNodeUrl(app, dset_id) + "/datasets"
post_json = await http_post(app, req, data=dataset_json)
# create link if requested
if link_id and link_title:
link_json = {}
link_json["id"] = dset_id
link_json["class"] = "H5L_TYPE_HARD"
link_req = getDataNodeUrl(app, link_id)
link_req += "/groups/" + link_id + "/links/" + link_title
log.info("PUT link - : " + link_req)
put_rsp = await http_put(app, link_req, data=link_json)
log.debug("PUT Link resp: {}".format(put_rsp))
# dataset creation successful
resp = await jsonResponse(request, post_json, status=201)
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 PUT_DatasetShape(request):
"""HTTP method to update dataset's shape"""
log.request(request)
app = request.app
shape_update = None
extend = 0
extend_dim = 0
dset_id = request.match_info.get('id')
if not dset_id:
msg = "Missing dataset id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(dset_id, "Dataset"):
msg = "Invalid dataset id: {}".format(dset_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
username, pswd = getUserPasswordFromRequest(request)
await validateUserPassword(app, username, pswd)
# validate request
if not request.has_body:
msg = "PUT shape with no body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
data = await request.json()
if "shape" not in data and "extend" not in data:
msg = "PUT shape has no shape or extend key in body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "shape" in data:
shape_update = data["shape"]
if isinstance(shape_update, int):
# convert to a list
shape_update = [
shape_update,
]
log.debug("shape_update: {}".format(shape_update))
if "extend" in data:
try:
extend = int(data["extend"])
except ValueError:
msg = "extend value must be integer"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if extend <= 0:
msg = "extend value must be positive"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "extend_dim" in data:
try:
extend_dim = int(data["extend_dim"])
except ValueError:
msg = "extend_dim value must be integer"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if extend_dim < 0:
msg = "extend_dim value must be non-negative"
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)
# verify the user has permission to update shape
await validateAction(app, domain, dset_id, username, "update")
# get authoritative state for dataset from DN (even if it's in the meta_cache).
dset_json = await getObjectJson(app, dset_id, refresh=True)
shape_orig = dset_json["shape"]
log.debug("shape_orig: {}".format(shape_orig))
# verify that the extend request is valid
if shape_orig["class"] != "H5S_SIMPLE":
msg = "Unable to extend shape of datasets who are not H5S_SIMPLE"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "maxdims" not in shape_orig:
msg = "Dataset is not extensible"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
dims = shape_orig["dims"]
rank = len(dims)
maxdims = shape_orig["maxdims"]
if shape_update and len(shape_update) != rank:
msg = "Extent of update shape request does not match dataset sahpe"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
for i in range(rank):
if shape_update and shape_update[i] < dims[i]:
msg = "Dataspace can not be made smaller"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if shape_update and maxdims[i] != 0 and shape_update[i] > maxdims[i]:
msg = "Database can not be extended past max extent"
log.warn(msg)
raise HTTPConflict()
if extend_dim < 0 or extend_dim >= rank:
msg = "Extension dimension must be less than rank and non-negative"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
# send request onto DN
req = getDataNodeUrl(app, dset_id) + "/datasets/" + dset_id + "/shape"
json_resp = {"hrefs": []}
if extend:
data = {"extend": extend, "extend_dim": extend_dim}
else:
data = {"shape": shape_update}
try:
put_rsp = await http_put(app, req, data=data)
log.info(f"got shape put rsp: {put_rsp}")
if "selection" in put_rsp:
json_resp["selection"] = put_rsp["selection"]
except HTTPConflict:
log.warn("got 409 extending dataspace")
raise
resp = await jsonResponse(request, json_resp, status=201)
log.response(request, resp=resp)
return resp
async def GET_Dataset(request):
"""HTTP method to return JSON description of a dataset"""
log.request(request)
app = request.app
params = request.rel_url.query
h5path = None
getAlias = False
dset_id = request.match_info.get('id')
if not dset_id and "h5path" not in params:
msg = "Missing dataset id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if dset_id:
if not isValidUuid(dset_id, "Dataset"):
msg = "Invalid dataset id: {}".format(dset_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "getalias" in params:
if params["getalias"]:
getAlias = True
else:
group_id = None
if "grpid" in params:
group_id = params["grpid"]
if not isValidUuid(group_id, "Group"):
msg = "Invalid parent group id: {}".format(group_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "h5path" not in params:
msg = "Expecting either ctype id or h5path url param"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
h5path = params["h5path"]
if not group_id and h5path[0] != '/':
msg = "h5paths must be absolute"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
log.info("GET_Dataset, h5path: {}".format(h5path))
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)
verbose = False
if "verbose" in params and params["verbose"]:
verbose = True
if h5path:
if group_id is None:
domain_json = await getDomainJson(app, domain)
if "root" not in domain_json:
msg = "Expected root key for domain: {}".format(domain)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
group_id = domain_json["root"]
dset_id = await getObjectIdByPath(app, group_id,
h5path) # throws 404 if not found
if not isValidUuid(dset_id, "Dataset"):
msg = "No dataset exist with the path: {}".format(h5path)
log.warn(msg)
raise HTTPNotFound()
log.info("get dataset_id: {} from h5path: {}".format(dset_id, h5path))
# get authoritative state for dataset from DN (even if it's in the meta_cache).
dset_json = await getObjectJson(app, dset_id, refresh=True)
# check that we have permissions to read the object
await validateAction(app, domain, dset_id, username, "read")
log.debug("got dset_json: {}".format(dset_json))
resp_json = {}
resp_json["id"] = dset_json["id"]
resp_json["root"] = dset_json["root"]
resp_json["shape"] = dset_json["shape"]
resp_json["type"] = dset_json["type"]
if "creationProperties" in dset_json:
resp_json["creationProperties"] = dset_json["creationProperties"]
else:
resp_json["creationProperties"] = {}
if "layout" in dset_json:
resp_json["layout"] = dset_json["layout"]
resp_json["attributeCount"] = dset_json["attributeCount"]
resp_json["created"] = dset_json["created"]
resp_json["lastModified"] = dset_json["lastModified"]
resp_json["domain"] = domain
if getAlias:
root_id = dset_json["root"]
alias = []
idpath_map = {root_id: '/'}
h5path = await getPathForObjectId(app,
root_id,
idpath_map,
tgt_id=dset_id)
if h5path:
alias.append(h5path)
resp_json["alias"] = alias
hrefs = []
dset_uri = '/datasets/' + dset_id
hrefs.append({'rel': 'self', 'href': getHref(request, dset_uri)})
root_uri = '/groups/' + dset_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, dset_uri + '/attributes')
})
# provide a value link if the dataset is relatively small,
# otherwise create a preview link that shows a limited number of data values
dset_shape = dset_json["shape"]
if dset_shape["class"] != 'H5S_NULL':
count = 1
if dset_shape["class"] == 'H5S_SIMPLE':
dims = dset_shape["dims"]
count = getNumElements(dims)
if count <= 100:
# small number of values, provide link to entire dataset
hrefs.append({
'rel': 'data',
'href': getHref(request, dset_uri + '/value')
})
else:
# large number of values, create preview link
previewQuery = getPreviewQuery(dset_shape["dims"])
hrefs.append({
'rel':
'preview',
'href':
getHref(request, dset_uri + '/value', query=previewQuery)
})
resp_json["hrefs"] = hrefs
if verbose:
# get allocated size and num_chunks for the dataset if available
dset_detail = await getDatasetDetails(app, dset_id, dset_json["root"])
if dset_detail is not None:
if "num_chunks" in dset_detail:
resp_json["num_chunks"] = dset_detail["num_chunks"]
if "allocated_bytes" in dset_detail:
resp_json["allocated_size"] = dset_detail["allocated_bytes"]
if "lastModified" in dset_detail:
resp_json["lastModified"] = dset_detail["lastModified"]
resp = await jsonResponse(request, resp_json)
log.response(request, resp=resp)
return resp
async def GET_Datatype(request):
"""HTTP method to return JSON for committed datatype"""
log.request(request)
app = request.app
params = request.rel_url.query
include_attrs = False
h5path = None
getAlias = False
ctype_id = request.match_info.get('id')
if not ctype_id and "h5path" not in params:
msg = "Missing type id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "include_attrs" in params and params["include_attrs"]:
include_attrs = True
if ctype_id:
if not isValidUuid(ctype_id, "Type"):
msg = f"Invalid type id: {ctype_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "getalias" in params:
if params["getalias"]:
getAlias = True
else:
group_id = None
if "grpid" in params:
group_id = params["grpid"]
if not isValidUuid(group_id, "Group"):
msg = f"Invalid parent group id: {group_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if "h5path" not in params:
msg = "Expecting either ctype id or h5path url param"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
h5path = params["h5path"]
if h5path[0] != '/' and group_id is None:
msg = "h5paths must be absolute"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
log.info(f"GET_Datatype, h5path: {h5path}")
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:
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)
if group_id is None:
group_id = domain_json["root"]
ctype_id = await getObjectIdByPath(app,
group_id,
h5path,
bucket=bucket
) # throws 404 if not found
if not isValidUuid(ctype_id, "Datatype"):
msg = f"No datatype exist with the path: {h5path}"
log.warn(msg)
raise HTTPGone()
log.info(f"got ctype_id: {ctype_id} from h5path: {h5path}")
await validateAction(app, domain, ctype_id, username, "read")
# get authoritative state for ctype from DN (even if it's in the meta_cache).
type_json = await getObjectJson(app,
ctype_id,
bucket=bucket,
refresh=True,
include_attrs=include_attrs)
type_json["domain"] = domain
if getAlias:
root_id = type_json["root"]
alias = []
idpath_map = {root_id: '/'}
h5path = await getPathForObjectId(app,
root_id,
idpath_map,
tgt_id=ctype_id,
bucket=bucket)
if h5path:
alias.append(h5path)
type_json["alias"] = alias
hrefs = []
ctype_uri = '/datatypes/' + ctype_id
hrefs.append({'rel': 'self', 'href': getHref(request, ctype_uri)})
root_uri = '/groups/' + type_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, ctype_uri + '/attributes')
})
type_json["hrefs"] = hrefs
resp = await jsonResponse(request, type_json)
log.response(request, resp=resp)
return resp
async def GET_Attributes(request):
"""HTTP method to return JSON for attribute collection"""
log.request(request)
app = request.app
params = request.rel_url.query
collection = getRequestCollectionName(request) # returns datasets|groups|datatypes
obj_id = request.match_info.get('id')
if not obj_id:
msg = "Missing object id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(obj_id, obj_class=collection):
msg = "Invalid obj id: {}".format(obj_id)
log.warn(msg)
raise HTTPBadRequest(reason=msg)
include_data = False
if "IncludeData" in params and params["IncludeData"]:
include_data = True
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 = f"Invalid domain: {domain}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
bucket = getBucketForDomain(domain)
# TBD - verify that the obj_id belongs to the given domain
await validateAction(app, domain, obj_id, username, "read")
req = getDataNodeUrl(app, obj_id)
req += '/' + collection + '/' + obj_id + "/attributes"
params = {}
if limit is not None:
params["Limit"] = str(limit)
if marker is not None:
params["Marker"] = marker
if include_data:
params["IncludeData"] = '1'
if bucket:
params["bucket"] = bucket
log.debug(f"get attributes: {req}")
dn_json = await http_get(app, req, params=params)
log.debug(f"got attributes json from dn for obj_id: {obj_id}")
attributes = dn_json["attributes"]
# mixin hrefs
for attribute in attributes:
attr_name = attribute["name"]
attr_href = '/' + collection + '/' + obj_id + '/attributes/' + attr_name
attribute["href"] = getHref(request, attr_href)
resp_json = {}
resp_json["attributes"] = attributes
hrefs = []
obj_uri = '/' + collection + '/' + obj_id
hrefs.append({'rel': 'self', 'href': getHref(request, obj_uri + '/attributes')})
hrefs.append({'rel': 'home', 'href': getHref(request, '/')})
hrefs.append({'rel': 'owner', 'href': getHref(request, obj_uri)})
resp_json["hrefs"] = hrefs
resp = await jsonResponse(request, resp_json)
log.response(request, resp=resp)
return resp
async def POST_Datatype(request):
"""HTTP method to create new committed datatype object"""
log.request(request)
app = request.app
username, pswd = getUserPasswordFromRequest(request)
# write actions need auth
await validateUserPassword(app, username, pswd)
if not request.has_body:
msg = "POST Datatype with no body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
body = await request.json()
if "type" not in body:
msg = "POST Datatype has no type key in body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
datatype = body["type"]
if isinstance(datatype, str):
try:
# convert predefined type string (e.g. "H5T_STD_I32LE") to
# corresponding json representation
datatype = getBaseTypeJson(datatype)
log.debug(f"got datatype: {datatype}")
except TypeError:
msg = "POST Dataset with invalid predefined type"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
validateTypeItem(datatype)
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 "link" in body:
link_body = body["link"]
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")
root_id = domain_json["root"]
ctype_id = createObjId("datatypes", rootid=root_id)
log.debug(f"new type id: {ctype_id}")
ctype_json = {"id": ctype_id, "root": root_id, "type": datatype}
log.debug("create named type, body: " + json.dumps(ctype_json))
req = getDataNodeUrl(app, ctype_id) + "/datatypes"
params = {}
if bucket:
params["bucket"] = bucket
type_json = await http_post(app, req, data=ctype_json, params=params)
# create link if requested
if link_id and link_title:
link_json = {}
link_json["id"] = ctype_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_rsp = await http_put(app, link_req, data=link_json, params=params)
log.debug(f"PUT Link resp: {put_rsp}")
# datatype creation successful
resp = await jsonResponse(request, type_json, status=201)
log.response(request, resp=resp)
return resp
async def GET_Attribute(request):
"""HTTP method to return JSON for an attribute"""
log.request(request)
app = request.app
collection = getRequestCollectionName(request) # returns datasets|groups|datatypes
obj_id = request.match_info.get('id')
if not obj_id:
msg = "Missing object id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(obj_id, obj_class=collection):
msg = f"Invalid object id: {obj_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
attr_name = request.match_info.get('name')
validateAttributeName(attr_name)
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)
# TBD - verify that the obj_id belongs to the given domain
await validateAction(app, domain, obj_id, username, "read")
req = getDataNodeUrl(app, obj_id)
req += '/' + collection + '/' + obj_id + "/attributes/" + attr_name
log.debug("get Attribute: " + req)
params = {}
if bucket:
params["bucket"] = bucket
dn_json = await http_get(app, req, params=params)
log.debug("got attributes json from dn for obj_id: " + str(obj_id))
resp_json = {}
resp_json["name"] = attr_name
resp_json["type"] = dn_json["type"]
resp_json["shape"] = dn_json["shape"]
if "value" in dn_json:
resp_json["value"] = dn_json["value"]
resp_json["created"] = dn_json["created"]
# attributes don't get modified, so use created timestamp as lastModified
resp_json["lastModified"] = dn_json["created"]
hrefs = []
obj_uri = '/' + collection + '/' + obj_id
attr_uri = obj_uri + '/attributes/' + attr_name
hrefs.append({'rel': 'self', 'href': getHref(request, attr_uri)})
hrefs.append({'rel': 'home', 'href': getHref(request, '/')})
hrefs.append({'rel': 'owner', 'href': getHref(request, obj_uri)})
resp_json["hrefs"] = hrefs
resp = await jsonResponse(request, resp_json)
log.response(request, resp=resp)
return resp
async def PUT_Attribute(request):
"""HTTP method to create a new attribute"""
log.request(request)
app = request.app
collection = getRequestCollectionName(request) # returns datasets|groups|datatypes
obj_id = request.match_info.get('id')
if not obj_id:
msg = "Missing object id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(obj_id, obj_class=collection):
msg = f"Invalid object id: {obj_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
attr_name = request.match_info.get('name')
log.debug(f"Attribute name: [{attr_name}]")
validateAttributeName(attr_name)
log.info(f"PUT Attribute id: {obj_id} name: {attr_name}")
username, pswd = getUserPasswordFromRequest(request)
# write actions need auth
await validateUserPassword(app, username, pswd)
if not request.has_body:
msg = "PUT Attribute with no body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
body = await request.json()
domain = getDomainFromRequest(request)
if not isValidDomain(domain):
msg = f"Invalid domain: {domain}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
bucket = getBucketForDomain(domain)
# get domain JSON
domain_json = await getDomainJson(app, domain)
if "root" not in domain_json:
log.error(f"Expected root key for domain: {domain}")
raise HTTPBadRequest(reason="Unexpected Error")
root_id = domain_json["root"]
# TBD - verify that the obj_id belongs to the given domain
await validateAction(app, domain, obj_id, username, "create")
if "type" not in body:
msg = "PUT attribute with no type in body"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
datatype = body["type"]
if isinstance(datatype, str) and datatype.startswith("t-"):
# Committed type - fetch type json from DN
ctype_id = datatype
log.debug(f"got ctypeid: {ctype_id}")
ctype_json = await getObjectJson(app, ctype_id, bucket=bucket)
log.debug(f"ctype {ctype_id}: {ctype_json}")
if ctype_json["root"] != root_id:
msg = "Referenced committed datatype must belong in same domain"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
datatype = ctype_json["type"]
# add the ctype_id to type type
datatype["id"] = ctype_id
elif isinstance(datatype, str):
try:
# convert predefined type string (e.g. "H5T_STD_I32LE") to
# corresponding json representation
datatype = getBaseTypeJson(datatype)
log.debug(f"got datatype: {datatype}")
except TypeError:
msg = "PUT attribute with invalid predefined type"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
validateTypeItem(datatype)
dims = None
shape_json = {}
if "shape" in body:
shape_body = body["shape"]
shape_class = None
if isinstance(shape_body, dict) and "class" in shape_body:
shape_class = shape_body["class"]
elif isinstance(shape_body, str):
shape_class = shape_body
if shape_class:
if shape_class == "H5S_NULL":
shape_json["class"] = "H5S_NULL"
if isinstance(shape_body, dict) and "dims" in shape_body:
msg = "can't include dims with null shape"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if isinstance(shape_body, dict) and "value" in body:
msg = "can't have H5S_NULL shape with value"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
elif shape_class == "H5S_SCALAR":
shape_json["class"] = "H5S_SCALAR"
dims = getShapeDims(shape_body)
if len(dims) != 1 or dims[0] != 1:
msg = "dimensions aren't valid for scalar attribute"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
elif shape_class == "H5S_SIMPLE":
shape_json["class"] = "H5S_SIMPLE"
dims = getShapeDims(shape_body)
shape_json["dims"] = dims
else:
msg = f"Unknown shape class: {shape_class}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
else:
# no class, interpet shape value as dimensions and
# use H5S_SIMPLE as class
if isinstance(shape_body, list) and len(shape_body) == 0:
shape_json["class"] = "H5S_SCALAR"
dims = [1,]
else:
shape_json["class"] = "H5S_SIMPLE"
dims = getShapeDims(shape_body)
shape_json["dims"] = dims
else:
shape_json["class"] = "H5S_SCALAR"
dims = [1,]
if "value" in body:
if dims is None:
msg = "Bad Request: data can not be included with H5S_NULL space"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
value = body["value"]
# validate that the value agrees with type/shape
arr_dtype = createDataType(datatype) # np datatype
if len(dims) == 0:
np_dims = [1,]
else:
np_dims = dims
log.debug(f"attribute dims: {np_dims}")
log.debug(f"attribute value: {value}")
try:
arr = jsonToArray(np_dims, arr_dtype, value)
except ValueError:
msg = "Bad Request: input data doesn't match selection"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
log.info(f"Got: {arr.size} array elements")
else:
value = None
# ready to add attribute now
req = getDataNodeUrl(app, obj_id)
req += '/' + collection + '/' + obj_id + "/attributes/" + attr_name
log.info("PUT Attribute: " + req)
attr_json = {}
attr_json["type"] = datatype
attr_json["shape"] = shape_json
if value is not None:
attr_json["value"] = value
params = {}
if bucket:
params["bucket"] = bucket
put_rsp = await http_put(app, req, params=params, data=attr_json)
log.info(f"PUT Attribute resp: {put_rsp}")
hrefs = [] # TBD
req_rsp = { "hrefs": hrefs }
# attribute creation successful
resp = await jsonResponse(request, req_rsp, 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
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
async def DELETE_Domain(request):
"""HTTP method to delete a domain resource"""
log.request(request)
app = request.app
params = request.rel_url.query
meta_only = False # if True, just delete the meta cache value
keep_root = False
if request.has_body:
body = await request.json()
if "meta_only" in body:
meta_only = body["meta_only"]
if "keep_root" in body:
keep_root = body["keep_root"]
else:
if "meta_only" in params:
meta_only = params["meta_only"]
if "keep_root" in params:
keep_root = params["keep_root"]
domain = None
try:
domain = getDomainFromRequest(request)
except ValueError:
log.warn(f"Invalid domain: {domain}")
raise HTTPBadRequest(reason="Invalid domain name")
bucket = getBucketForDomain(domain)
log.debug(f"GET_Domain domain: {domain}")
if not domain:
msg = "No domain given"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
log.info(f"meta_only domain delete: {meta_only}")
if meta_only:
# remove from domain cache if present
domain_cache = app["domain_cache"]
if domain in domain_cache:
log.info(f"deleting {domain} from domain_cache")
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 getPathForDomain(parent_domain) == '/':
is_toplevel = True
else:
is_toplevel = False
if is_toplevel 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:
index = domain.find('/')
s3prefix = domain[(index + 1):] + '/'
log.info(f"checking s3key with prefix: {s3prefix} in bucket: {bucket}")
s3keys = await getS3Keys(app,
include_stats=False,
prefix=s3prefix,
deliminator='/',
bucket=bucket)
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"
params = {} # for http_delete requests to DN nodes
params["domain"] = domain
rsp_json = await http_delete(app, req, params=params)
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, params=params)
# 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"]
params = {}
params["domain"] = getPathForDomain(domain)
params["bucket"] = getBucketForDomain(domain)
params[
"meta_only"] = 1 # can't pass booleans as params, so use 1 instead of 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(f"sending sn request: {req}")
try:
sn_rsp = await http_delete(app, req, params=params)
log.info(f"{req} response: {sn_rsp}")
except ClientResponseError as ce:
log.warn(f"got error for sn_delete: {ce}")
resp = await jsonResponse(request, rsp_json)
log.response(request, resp=resp)
return resp
async def GET_AttributeValue(request):
"""HTTP method to return an attribute value"""
log.request(request)
app = request.app
log.info("GET_AttributeValue")
collection = getRequestCollectionName(request) # returns datasets|groups|datatypes
obj_id = request.match_info.get('id')
if not obj_id:
msg = "Missing object id"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
if not isValidUuid(obj_id, obj_class=collection):
msg = f"Invalid object id: {obj_id}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
attr_name = request.match_info.get('name')
validateAttributeName(attr_name)
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 value: {domain}"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
bucket = getBucketForDomain(domain)
# get domain JSON
domain_json = await getDomainJson(app, domain)
if "root" not in domain_json:
log.error(f"Expected root key for domain: {domain}")
raise HTTPBadRequest(reason="Unexpected Error")
# TBD - verify that the obj_id belongs to the given domain
await validateAction(app, domain, obj_id, username, "read")
req = getDataNodeUrl(app, obj_id)
req += '/' + collection + '/' + obj_id + "/attributes/" + attr_name
log.debug("get Attribute: " + req)
params = {}
if bucket:
params["bucket"] = bucket
dn_json = await http_get(app, req, params=params)
log.debug("got attributes json from dn for obj_id: " + str(dn_json))
attr_shape = dn_json["shape"]
log.debug(f"attribute shape: {attr_shape}")
if attr_shape["class"] == 'H5S_NULL':
msg = "Null space attributes can not be read"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
accept_type = getAcceptType(request)
response_type = accept_type # will adjust later if binary not possible
type_json = dn_json["type"]
shape_json = dn_json["shape"]
item_size = getItemSize(type_json)
if item_size == 'H5T_VARIABLE' and accept_type != "json":
msg = "Client requested binary, but only JSON is supported for variable length data types"
log.info(msg)
response_type = "json"
if response_type == "binary":
arr_dtype = createDataType(type_json) # np datatype
np_shape = getShapeDims(shape_json)
try:
arr = jsonToArray(np_shape, arr_dtype, dn_json["value"])
except ValueError:
msg = "Bad Request: input data doesn't match selection"
log.warn(msg)
raise HTTPBadRequest(reason=msg)
output_data = arr.tobytes()
log.debug(f"GET AttributeValue - returning {len(output_data)} bytes binary data")
# write response
try:
resp = StreamResponse()
resp.content_type = "application/octet-stream"
resp.content_length = len(output_data)
# allow CORS
resp.headers['Access-Control-Allow-Origin'] = '*'
resp.headers['Access-Control-Allow-Methods'] = "GET, POST, DELETE, PUT, OPTIONS"
resp.headers['Access-Control-Allow-Headers'] = "Content-Type, api_key, Authorization"
await resp.prepare(request)
await resp.write(output_data)
except Exception as e:
log.error(f"Got exception: {e}")
raise HTTPInternalServerError()
finally:
await resp.write_eof()
else:
resp_json = {}
if "value" in dn_json:
resp_json["value"] = dn_json["value"]
hrefs = []
obj_uri = '/' + collection + '/' + obj_id
attr_uri = obj_uri + '/attributes/' + attr_name
hrefs.append({'rel': 'self', 'href': getHref(request, attr_uri)})
hrefs.append({'rel': 'home', 'href': getHref(request, '/')})
hrefs.append({'rel': 'owner', 'href': getHref(request, obj_uri)})
resp_json["hrefs"] = hrefs
resp = await jsonResponse(request, resp_json)
log.response(request, resp=resp)
return resp