"Description for the pipeline instance.",
:short => :none,
:type => :string)
+ opt(:project_uuid,
+ "UUID of the project for the pipeline instance.",
+ short: :none,
+ type: :string)
stop_on [:'--']
end
$options = Trollop::with_standard_exception_handling p do
end
end
else
- description = $options[:description]
- description = ("Created at #{Time.now.localtime}" + (@template[:name].andand.size.andand>0 ? " using the pipeline template *#{@template[:name]}*" : "")) if !description
- @instance = PipelineInstance.
- create(components: @components,
- properties: {
- run_options: {
- enable_job_reuse: !@options[:no_reuse]
- }
- },
- pipeline_template_uuid: @template[:uuid],
- description: description,
- state: ($options[:submit] ? 'RunningOnServer' : 'RunningOnClient'))
+ description = $options[:description] ||
+ ("Created at #{Time.now.localtime}" + (@template[:name].andand.size.andand>0 ? " using the pipeline template *#{@template[:name]}*" : ""))
+ instance_body = {
+ components: @components,
+ properties: {
+ run_options: {
+ enable_job_reuse: !@options[:no_reuse]
+ }
+ },
+ pipeline_template_uuid: @template[:uuid],
+ description: description,
+ state: ($options[:submit] ? 'RunningOnServer' : 'RunningOnClient')
+ }
+ if @options[:project_uuid]
+ instance_body[:owner_uuid] = @options[:project_uuid]
+ end
+ @instance = PipelineInstance.create(instance_body)
end
self
end
.q{&& SWAP=$(awk '($1 == "SwapTotal:"){print $2}' </proc/meminfo) }
."&& MEMLIMIT=\$(( (\$MEM * 95) / ($ENV{CRUNCH_NODE_SLOTS} * 100) )) "
."&& let SWAPLIMIT=\$MEMLIMIT+\$SWAP ";
- $command .= "&& exec arv-mount --by-id --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
+ $command .= "&& exec arv-mount --by-pdh --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
if ($docker_hash)
{
my $containername = "$Jobstep->{arvados_task}->{uuid}-$Jobstep->{failures}";
// such failures by always using a new or recently active socket.
var MaxIdleConnectionDuration = 30 * time.Second
+var RetryDelay = 2 * time.Second
+
// Indicates an error that was returned by the API server.
type APIServerError struct {
// Address of server returning error, of the form "host:port".
// Information about how to contact the Arvados server
type ArvadosClient struct {
+ // https
+ Scheme string
+
// Arvados API server, form "host:port"
ApiServer string
DiscoveryDoc Dict
lastClosedIdlesAt time.Time
+
+ // Number of retries
+ Retries int
}
// Create a new ArvadosClient, initialized with standard Arvados environment
external := matchTrue.MatchString(os.Getenv("ARVADOS_EXTERNAL_CLIENT"))
ac = ArvadosClient{
+ Scheme: "https",
ApiServer: os.Getenv("ARVADOS_API_HOST"),
ApiToken: os.Getenv("ARVADOS_API_TOKEN"),
ApiInsecure: insecure,
Client: &http.Client{Transport: &http.Transport{
TLSClientConfig: &tls.Config{InsecureSkipVerify: insecure}}},
- External: external}
+ External: external,
+ Retries: 2}
if ac.ApiServer == "" {
return ac, MissingArvadosApiHost
// CallRaw is the same as Call() but returns a Reader that reads the
// response body, instead of taking an output object.
func (c ArvadosClient) CallRaw(method string, resourceType string, uuid string, action string, parameters Dict) (reader io.ReadCloser, err error) {
- var req *http.Request
-
+ scheme := c.Scheme
+ if scheme == "" {
+ scheme = "https"
+ }
u := url.URL{
- Scheme: "https",
+ Scheme: scheme,
Host: c.ApiServer}
if resourceType != API_DISCOVERY_RESOURCE {
}
}
- if method == "GET" || method == "HEAD" {
- u.RawQuery = vals.Encode()
- if req, err = http.NewRequest(method, u.String(), nil); err != nil {
- return nil, err
- }
- } else {
- if req, err = http.NewRequest(method, u.String(), bytes.NewBufferString(vals.Encode())); err != nil {
- return nil, err
- }
- req.Header.Add("Content-Type", "application/x-www-form-urlencoded")
+ retryable := false
+ switch method {
+ case "GET", "HEAD", "PUT", "OPTIONS", "DELETE":
+ retryable = true
}
- // Add api token header
- req.Header.Add("Authorization", fmt.Sprintf("OAuth2 %s", c.ApiToken))
- if c.External {
- req.Header.Add("X-External-Client", "1")
- }
-
- // POST and DELETE are not safe to retry automatically, so we minimize
- // such failures by always using a new or recently active socket
- if method == "POST" || method == "DELETE" {
+ // Non-retryable methods such as POST are not safe to retry automatically,
+ // so we minimize such failures by always using a new or recently active socket
+ if !retryable {
if time.Since(c.lastClosedIdlesAt) > MaxIdleConnectionDuration {
c.lastClosedIdlesAt = time.Now()
c.Client.Transport.(*http.Transport).CloseIdleConnections()
}
// Make the request
+ var req *http.Request
var resp *http.Response
- if resp, err = c.Client.Do(req); err != nil {
- return nil, err
- }
- if resp.StatusCode == http.StatusOK {
- return resp.Body, nil
+ for attempt := 0; attempt <= c.Retries; attempt++ {
+ if method == "GET" || method == "HEAD" {
+ u.RawQuery = vals.Encode()
+ if req, err = http.NewRequest(method, u.String(), nil); err != nil {
+ return nil, err
+ }
+ } else {
+ if req, err = http.NewRequest(method, u.String(), bytes.NewBufferString(vals.Encode())); err != nil {
+ return nil, err
+ }
+ req.Header.Add("Content-Type", "application/x-www-form-urlencoded")
+ }
+
+ // Add api token header
+ req.Header.Add("Authorization", fmt.Sprintf("OAuth2 %s", c.ApiToken))
+ if c.External {
+ req.Header.Add("X-External-Client", "1")
+ }
+
+ resp, err = c.Client.Do(req)
+ if err != nil {
+ if retryable {
+ time.Sleep(RetryDelay)
+ continue
+ } else {
+ return nil, err
+ }
+ }
+
+ if resp.StatusCode == http.StatusOK {
+ return resp.Body, nil
+ }
+
+ defer resp.Body.Close()
+
+ switch resp.StatusCode {
+ case 408, 409, 422, 423, 500, 502, 503, 504:
+ time.Sleep(RetryDelay)
+ continue
+ default:
+ return nil, newAPIServerError(c.ApiServer, resp)
+ }
}
- defer resp.Body.Close()
- return nil, newAPIServerError(c.ApiServer, resp)
+ if resp != nil {
+ return nil, newAPIServerError(c.ApiServer, resp)
+ }
+ return nil, err
}
func newAPIServerError(ServerAddress string, resp *http.Response) APIServerError {
package arvadosclient
import (
+ "fmt"
"git.curoverse.com/arvados.git/sdk/go/arvadostest"
. "gopkg.in/check.v1"
+ "net"
"net/http"
"os"
"testing"
var _ = Suite(&ServerRequiredSuite{})
var _ = Suite(&UnitSuite{})
+var _ = Suite(&MockArvadosServerSuite{})
// Tests that require the Keep server running
type ServerRequiredSuite struct{}
func (s *ServerRequiredSuite) SetUpSuite(c *C) {
arvadostest.StartAPI()
arvadostest.StartKeep(2, false)
+ RetryDelay = 0
}
func (s *ServerRequiredSuite) TearDownSuite(c *C) {
c.Assert(PDHMatch("+12345"), Equals, false)
c.Assert(PDHMatch(""), Equals, false)
}
+
+// Tests that use mock arvados server
+type MockArvadosServerSuite struct{}
+
+func (s *MockArvadosServerSuite) SetUpSuite(c *C) {
+ RetryDelay = 0
+}
+
+func (s *MockArvadosServerSuite) SetUpTest(c *C) {
+ arvadostest.ResetEnv()
+}
+
+type APIServer struct {
+ listener net.Listener
+ url string
+}
+
+func RunFakeArvadosServer(st http.Handler) (api APIServer, err error) {
+ api.listener, err = net.ListenTCP("tcp", &net.TCPAddr{Port: 0})
+ if err != nil {
+ return
+ }
+ api.url = api.listener.Addr().String()
+ go http.Serve(api.listener, st)
+ return
+}
+
+type APIStub struct {
+ method string
+ retryAttempts int
+ expected int
+ respStatus []int
+ responseBody []string
+}
+
+func (h *APIStub) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ if req.URL.Path == "/redirect-loop" {
+ http.Redirect(resp, req, "/redirect-loop", http.StatusFound)
+ return
+ }
+ if h.respStatus[h.retryAttempts] < 0 {
+ // Fail the client's Do() by starting a redirect loop
+ http.Redirect(resp, req, "/redirect-loop", http.StatusFound)
+ } else {
+ resp.WriteHeader(h.respStatus[h.retryAttempts])
+ resp.Write([]byte(h.responseBody[h.retryAttempts]))
+ }
+ h.retryAttempts++
+}
+
+func (s *MockArvadosServerSuite) TestWithRetries(c *C) {
+ for _, stub := range []APIStub{
+ {
+ "get", 0, 200, []int{200, 500}, []string{`{"ok":"ok"}`, ``},
+ },
+ {
+ "create", 0, 200, []int{200, 500}, []string{`{"ok":"ok"}`, ``},
+ },
+ {
+ "get", 0, 500, []int{500, 500, 500, 200}, []string{``, ``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "create", 0, 500, []int{500, 500, 500, 200}, []string{``, ``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "update", 0, 500, []int{500, 500, 500, 200}, []string{``, ``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "delete", 0, 500, []int{500, 500, 500, 200}, []string{``, ``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "get", 0, 502, []int{500, 500, 502, 200}, []string{``, ``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "create", 0, 502, []int{500, 500, 502, 200}, []string{``, ``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "get", 0, 200, []int{500, 500, 200}, []string{``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "create", 0, 200, []int{500, 500, 200}, []string{``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "delete", 0, 200, []int{500, 500, 200}, []string{``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "update", 0, 200, []int{500, 500, 200}, []string{``, ``, `{"ok":"ok"}`},
+ },
+ {
+ "get", 0, 401, []int{401, 200}, []string{``, `{"ok":"ok"}`},
+ },
+ {
+ "create", 0, 401, []int{401, 200}, []string{``, `{"ok":"ok"}`},
+ },
+ {
+ "get", 0, 404, []int{404, 200}, []string{``, `{"ok":"ok"}`},
+ },
+ {
+ "get", 0, 401, []int{500, 401, 200}, []string{``, ``, `{"ok":"ok"}`},
+ },
+
+ // Response code -1 simulates an HTTP/network error
+ // (i.e., Do() returns an error; there is no HTTP
+ // response status code).
+
+ // Succeed on second retry
+ {
+ "get", 0, 200, []int{-1, -1, 200}, []string{``, ``, `{"ok":"ok"}`},
+ },
+ // "POST" is not safe to retry: fail after one error
+ {
+ "create", 0, -1, []int{-1, 200}, []string{``, `{"ok":"ok"}`},
+ },
+ } {
+ api, err := RunFakeArvadosServer(&stub)
+ c.Check(err, IsNil)
+
+ defer api.listener.Close()
+
+ arv := ArvadosClient{
+ Scheme: "http",
+ ApiServer: api.url,
+ ApiToken: "abc123",
+ ApiInsecure: true,
+ Client: &http.Client{Transport: &http.Transport{}},
+ Retries: 2}
+
+ getback := make(Dict)
+ switch stub.method {
+ case "get":
+ err = arv.Get("collections", "zzzzz-4zz18-znfnqtbbv4spc3w", nil, &getback)
+ case "create":
+ err = arv.Create("collections",
+ Dict{"collection": Dict{"name": "testing"}},
+ &getback)
+ case "update":
+ err = arv.Update("collections", "zzzzz-4zz18-znfnqtbbv4spc3w",
+ Dict{"collection": Dict{"name": "testing"}},
+ &getback)
+ case "delete":
+ err = arv.Delete("pipeline_templates", "zzzzz-4zz18-znfnqtbbv4spc3w", nil, &getback)
+ }
+
+ switch stub.expected {
+ case 200:
+ c.Check(err, IsNil)
+ c.Check(getback["ok"], Equals, "ok")
+ case -1:
+ c.Check(err, NotNil)
+ c.Check(err, ErrorMatches, `.*stopped after \d+ redirects`)
+ default:
+ c.Check(err, NotNil)
+ c.Check(err, ErrorMatches, fmt.Sprintf("arvados API server error: %d.*", stub.expected))
+ c.Check(err.(APIServerError).HttpStatusCode, Equals, stub.expected)
+ }
+ }
+}
will appear if it exists.
""".lstrip()
- def __init__(self, parent_inode, inodes, api, num_retries):
+ def __init__(self, parent_inode, inodes, api, num_retries, pdh_only=False):
super(MagicDirectory, self).__init__(parent_inode, inodes)
self.api = api
self.num_retries = num_retries
+ self.pdh_only = pdh_only
def __setattr__(self, name, value):
super(MagicDirectory, self).__setattr__(name, value)
# If we're the root directory, add an identical by_id subdirectory.
if self.inode == llfuse.ROOT_INODE:
self._entries['by_id'] = self.inodes.add_entry(MagicDirectory(
- self.inode, self.inodes, self.api, self.num_retries))
+ self.inode, self.inodes, self.api, self.num_retries, self.pdh_only))
def __contains__(self, k):
if k in self._entries:
return True
- if not portable_data_hash_pattern.match(k) and not uuid_pattern.match(k):
+ if not portable_data_hash_pattern.match(k) and (self.pdh_only or not uuid_pattern.match(k)):
return False
try:
help="""Mount subdirectories listed by tag.""")
mount_mode.add_argument('--by-id', action='store_true',
help="""Mount subdirectories listed by portable data hash or uuid.""")
+ mount_mode.add_argument('--by-pdh', action='store_true',
+ help="""Mount subdirectories listed by portable data hash.""")
mount_mode.add_argument('--project', type=str, help="""Mount a specific project.""")
mount_mode.add_argument('--collection', type=str, help="""Mount only the specified collection.""")
now = time.time()
dir_class = None
dir_args = [llfuse.ROOT_INODE, operations.inodes, api, args.retries]
- if args.by_id:
+ if args.by_id or args.by_pdh:
# Set up the request handler with the 'magic directory' at the root
dir_class = MagicDirectory
+ dir_args.append(args.by_pdh)
elif args.by_tag:
dir_class = TagsDirectory
elif args.shared:
dir_args[0] = e.inode
e._entries['by_id'] = operations.inodes.add_entry(MagicDirectory(*dir_args))
+
e._entries['by_tag'] = operations.inodes.add_entry(TagsDirectory(*dir_args))
dir_args.append(usr)
llfuse.init(operations, args.mountpoint, opts)
# Subscribe to change events from API server
- operations.listen_for_events(api)
+ if not args.by_pdh:
+ operations.listen_for_events(api)
t = threading.Thread(None, lambda: llfuse.main())
t.start()
self.assertEqual("_", fuse.sanitize_filename(""))
self.assertEqual("_", fuse.sanitize_filename("."))
self.assertEqual("__", fuse.sanitize_filename(".."))
+
+
+class FuseMagicTestPDHOnly(MountTestBase):
+ def setUp(self, api=None):
+ super(FuseMagicTestPDHOnly, self).setUp(api=api)
+
+ cw = arvados.CollectionWriter()
+
+ cw.start_new_file('thing1.txt')
+ cw.write("data 1")
+
+ self.testcollection = cw.finish()
+ self.test_manifest = cw.manifest_text()
+ created = self.api.collections().create(body={"manifest_text":self.test_manifest}).execute()
+ self.testcollectionuuid = str(created['uuid'])
+
+ def verify_pdh_only(self, pdh_only=False, skip_pdh_only=False):
+ if skip_pdh_only is True:
+ self.make_mount(fuse.MagicDirectory) # in this case, the default by_id applies
+ else:
+ self.make_mount(fuse.MagicDirectory, pdh_only=pdh_only)
+
+ mount_ls = llfuse.listdir(self.mounttmp)
+ self.assertIn('README', mount_ls)
+ self.assertFalse(any(arvados.util.keep_locator_pattern.match(fn) or
+ arvados.util.uuid_pattern.match(fn)
+ for fn in mount_ls),
+ "new FUSE MagicDirectory lists Collection")
+
+ # look up using pdh should succeed in all cases
+ self.assertDirContents(self.testcollection, ['thing1.txt'])
+ self.assertDirContents(os.path.join('by_id', self.testcollection),
+ ['thing1.txt'])
+ mount_ls = llfuse.listdir(self.mounttmp)
+ self.assertIn('README', mount_ls)
+ self.assertIn(self.testcollection, mount_ls)
+ self.assertIn(self.testcollection,
+ llfuse.listdir(os.path.join(self.mounttmp, 'by_id')))
+
+ files = {}
+ files[os.path.join(self.mounttmp, self.testcollection, 'thing1.txt')] = 'data 1'
+
+ for k, v in files.items():
+ with open(os.path.join(self.mounttmp, k)) as f:
+ self.assertEqual(v, f.read())
+
+ # look up using uuid should fail when pdh_only is set
+ if pdh_only is True:
+ with self.assertRaises(OSError):
+ self.assertDirContents(os.path.join('by_id', self.testcollectionuuid),
+ ['thing1.txt'])
+ else:
+ self.assertDirContents(os.path.join('by_id', self.testcollectionuuid),
+ ['thing1.txt'])
+
+ def test_with_pdh_only_true(self):
+ self.verify_pdh_only(pdh_only=True)
+
+ def test_with_pdh_only_false(self):
+ self.verify_pdh_only(pdh_only=False)
+
+ def test_with_default_by_id(self):
+ self.verify_pdh_only(skip_pdh_only=True)
projects / arvados.git / commitdiff