[ARVADOS] updated: b9d2799dfebae724dda3b3e28641116ca5daf5c7
Git user
git at public.curoverse.com
Mon Oct 17 04:36:37 EDT 2016
Summary of changes:
.../app/controllers/application_controller.rb | 39 ++++--
apps/workbench/app/helpers/application_helper.rb | 6 +-
apps/workbench/app/models/proxy_work_unit.rb | 25 ----
apps/workbench/app/models/work_unit.rb | 8 --
.../app/views/projects/_show_dashboard.html.erb | 43 +++++--
.../views/work_units/_component_detail.html.erb | 11 +-
.../app/views/work_units/_show_child.html.erb | 2 +-
.../app/views/work_units/_show_component.html.erb | 32 ++++-
.../app/views/work_units/_show_log_link.html.erb | 14 ++
apps/workbench/config/application.default.yml | 6 +
.../test/controllers/work_units_controller_test.rb | 23 ++++
apps/workbench/test/diagnostics/pipeline_test.rb | 2 +-
apps/workbench/test/diagnostics_test_helper.rb | 7 +-
apps/workbench/test/helpers/share_object_helper.rb | 8 +-
.../test/integration/application_layout_test.rb | 5 +-
.../test/integration/pipeline_instances_test.rb | 8 +-
apps/workbench/test/integration/users_test.rb | 3 +-
apps/workbench/test/integration/work_units_test.rb | 6 +-
apps/workbench/test/integration_helper.rb | 18 ++-
apps/workbench/test/unit/work_unit_test.rb | 28 +---
build/run-build-packages.sh | 8 +-
crunch_scripts/cwl-runner | 40 ++----
.../_container_runtime_constraints.liquid | 1 +
.../install-dispatch.html.textile.liquid | 33 ++++-
.../install-arv-git-httpd.html.textile.liquid | 52 +++-----
sdk/cli/test/test_arv-keep-get.rb | 4 +-
sdk/cwl/arvados_cwl/__init__.py | 118 +++++++++++++++--
sdk/cwl/arvados_cwl/arv-cwl-schema.yml | 38 ++++++
sdk/cwl/arvados_cwl/arvcontainer.py | 16 ++-
sdk/cwl/arvados_cwl/arvjob.py | 133 ++++++++++++-------
sdk/cwl/arvados_cwl/arvworkflow.py | 75 +++++------
sdk/cwl/arvados_cwl/fsaccess.py | 6 +-
sdk/cwl/arvados_cwl/pathmapper.py | 40 ++++--
sdk/cwl/arvados_cwl/perf.py | 2 +-
sdk/cwl/arvados_cwl/runner.py | 61 +++++----
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/hw.py | 1 +
sdk/cwl/tests/test_container.py | 10 +-
sdk/cwl/tests/test_job.py | 125 +++++++++---------
sdk/cwl/tests/test_make_output.py | 58 +++++++++
sdk/cwl/tests/test_pathmapper.py | 91 +++++++++++++
sdk/cwl/tests/test_submit.py | 90 +++++++++----
sdk/go/arvados/container.go | 7 +-
sdk/go/crunchrunner/crunchrunner.go | 69 ++++++++--
sdk/go/crunchrunner/crunchrunner_test.go | 28 ++++
sdk/python/arvados/arvfile.py | 84 +++++++++++-
sdk/python/tests/test_collections.py | 21 ++-
services/api/app/models/container.rb | 35 ++++-
services/api/app/models/container_request.rb | 26 +++-
services/api/config/application.default.yml | 7 +
.../migrate/20160926194129_add_container_count.rb | 9 ++
services/api/db/structure.sql | 7 +-
services/api/test/fixtures/container_requests.yml | 20 +++
services/api/test/unit/container_request_test.rb | 71 ++++++++++-
...git-httpd.service => arvados-git-httpd.service} | 2 +-
services/arv-git-httpd/doc.go | 35 -----
services/arv-git-httpd/git_handler.go | 31 +++--
services/arv-git-httpd/git_handler_test.go | 10 +-
services/arv-git-httpd/gitolite_test.go | 10 +-
services/arv-git-httpd/integration_test.go | 2 +
services/arv-git-httpd/main.go | 21 ++-
services/arv-git-httpd/usage.go | 39 ++++--
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 5 +-
.../crunch-dispatch-slurm_test.go | 16 ++-
services/crunch-dispatch-slurm/squeue.go | 2 +-
services/crunch-dispatch-slurm/usage.go | 1 +
services/fuse/arvados_fuse/command.py | 6 +-
services/fuse/tests/test_command_args.py | 14 ++
services/fuse/tests/test_mount.py | 1 +
services/keepstore/azure_blob_volume.go | 2 +-
services/keepstore/deprecated.go | 43 +++++++
services/keepstore/keepstore.go | 28 +---
services/keepstore/s3_volume.go | 4 +-
services/keepstore/usage.go | 18 ++-
services/keepstore/volume_unix.go | 10 +-
services/login-sync/bin/arvados-login-sync | 2 +-
.../docker/service/arv-git-httpd/run-service | 9 +-
.../crunchstat_summary/summarizer.py | 141 +++++++++++----------
78 files changed, 1502 insertions(+), 632 deletions(-)
create mode 100644 apps/workbench/app/views/work_units/_show_log_link.html.erb
create mode 100644 sdk/cwl/tests/hw.py
create mode 100644 sdk/cwl/tests/test_make_output.py
create mode 100644 sdk/cwl/tests/test_pathmapper.py
create mode 100644 services/api/db/migrate/20160926194129_add_container_count.rb
rename services/arv-git-httpd/{arv-git-httpd.service => arvados-git-httpd.service} (75%)
delete mode 100644 services/arv-git-httpd/doc.go
create mode 100644 services/keepstore/deprecated.go
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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit b9d2799dfebae724dda3b3e28641116ca5daf5c7
Merge: 82cc494 8b03f0b
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Oct 17 04:32:37 2016 -0400
Merge branch 'master' into 9956-keepstore-config
Conflicts:
services/keepstore/keepstore.go
commit 82cc494a64aaac576dfefe0487faafdda82482bc
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Oct 17 04:27:55 2016 -0400
9956: Show list of supported volume types.
diff --git a/services/keepstore/usage.go b/services/keepstore/usage.go
index c067ec0..29f89f5 100644
--- a/services/keepstore/usage.go
+++ b/services/keepstore/usage.go
@@ -4,19 +4,25 @@ import (
"flag"
"fmt"
"os"
+ "sort"
+ "strings"
"github.com/ghodss/yaml"
)
func usage() {
c := DefaultConfig()
+ knownTypes := []string{}
for _, vt := range VolumeTypes {
c.Volumes = append(c.Volumes, vt().Examples()...)
+ knownTypes = append(knownTypes, vt().Type())
}
exampleConfigFile, err := yaml.Marshal(c)
if err != nil {
panic(err)
}
+ sort.Strings(knownTypes)
+ knownTypeList := strings.Join(knownTypes, ", ")
fmt.Fprintf(os.Stderr, `
keepstore provides a content-addressed data store backed by a local filesystem or networked storage.
@@ -110,5 +116,9 @@ Volumes:
use all directories named "keep" that exist in the top level
directory of a mount point at startup time.
-`, exampleConfigFile)
+ Volume types: %s
+
+ (See volume configuration examples above.)
+
+`, exampleConfigFile, knownTypeList)
}
commit f935965259f9c0476a9c5ffa79e5c27ce9da4800
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Oct 17 04:12:14 2016 -0400
9956: Remove obsolete TODO comment.
diff --git a/services/keepstore/keepstore.go b/services/keepstore/keepstore.go
index 8267fd7..69ff565 100644
--- a/services/keepstore/keepstore.go
+++ b/services/keepstore/keepstore.go
@@ -104,7 +104,6 @@ func main() {
deprecated.afterFlagParse(theConfig)
- // TODO: Load config
err := config.LoadFile(theConfig, configPath)
if err != nil && (!os.IsNotExist(err) || configPath != defaultConfigPath) {
log.Fatal(err)
commit e5b9158fc357495fba2d110bf6eafa72b1ebe145
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Oct 17 04:09:41 2016 -0400
9956: Move deprecated options out to a separate file.
diff --git a/services/keepstore/azure_blob_volume.go b/services/keepstore/azure_blob_volume.go
index 41b6c69..d2163f6 100644
--- a/services/keepstore/azure_blob_volume.go
+++ b/services/keepstore/azure_blob_volume.go
@@ -54,7 +54,7 @@ func (s *azureVolumeAdder) Set(containerName string) error {
StorageAccountName: azureStorageAccountName,
StorageAccountKeyFile: azureStorageAccountKeyFile,
AzureReplication: azureStorageReplication,
- ReadOnly: flagReadonly,
+ ReadOnly: deprecated.flagReadonly,
})
return nil
}
diff --git a/services/keepstore/deprecated.go b/services/keepstore/deprecated.go
new file mode 100644
index 0000000..7caa6b5
--- /dev/null
+++ b/services/keepstore/deprecated.go
@@ -0,0 +1,43 @@
+package main
+
+import (
+ "flag"
+ "time"
+
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
+)
+
+type deprecatedOptions struct {
+ flagSerializeIO bool
+ flagReadonly bool
+ neverDelete bool
+ signatureTTLSeconds int
+}
+
+var deprecated = deprecatedOptions{
+ neverDelete: !theConfig.EnableDelete,
+ signatureTTLSeconds: int(theConfig.BlobSignatureTTL.Duration() / time.Second),
+}
+
+func (depr *deprecatedOptions) beforeFlagParse(cfg *Config) {
+ flag.StringVar(&cfg.Listen, "listen", cfg.Listen, "see Listen configuration")
+ flag.IntVar(&cfg.MaxBuffers, "max-buffers", cfg.MaxBuffers, "see MaxBuffers configuration")
+ flag.IntVar(&cfg.MaxRequests, "max-requests", cfg.MaxRequests, "see MaxRequests configuration")
+ flag.BoolVar(&depr.neverDelete, "never-delete", depr.neverDelete, "see EnableDelete configuration")
+ flag.BoolVar(&cfg.RequireSignatures, "enforce-permissions", cfg.RequireSignatures, "see RequireSignatures configuration")
+ flag.StringVar(&cfg.BlobSigningKeyFile, "permission-key-file", cfg.BlobSigningKeyFile, "see BlobSigningKey`File` configuration")
+ flag.StringVar(&cfg.BlobSigningKeyFile, "blob-signing-key-file", cfg.BlobSigningKeyFile, "see BlobSigningKey`File` configuration")
+ flag.StringVar(&cfg.SystemAuthTokenFile, "data-manager-token-file", cfg.SystemAuthTokenFile, "see SystemAuthToken`File` configuration")
+ flag.IntVar(&depr.signatureTTLSeconds, "permission-ttl", depr.signatureTTLSeconds, "signature TTL in seconds; see BlobSignatureTTL configuration")
+ flag.IntVar(&depr.signatureTTLSeconds, "blob-signature-ttl", depr.signatureTTLSeconds, "signature TTL in seconds; see BlobSignatureTTL configuration")
+ flag.Var(&cfg.TrashLifetime, "trash-lifetime", "see TrashLifetime configuration")
+ flag.BoolVar(&depr.flagSerializeIO, "serialize", depr.flagSerializeIO, "serialize read and write operations on the following volumes.")
+ flag.BoolVar(&depr.flagReadonly, "readonly", depr.flagReadonly, "do not write, delete, or touch anything on the following volumes.")
+ flag.StringVar(&cfg.PIDFile, "pid", cfg.PIDFile, "see `PIDFile` configuration")
+ flag.Var(&cfg.TrashCheckInterval, "trash-check-interval", "see TrashCheckInterval configuration")
+}
+
+func (depr *deprecatedOptions) afterFlagParse(cfg *Config) {
+ cfg.BlobSignatureTTL = arvados.Duration(depr.signatureTTLSeconds) * arvados.Duration(time.Second)
+ cfg.EnableDelete = !depr.neverDelete
+}
diff --git a/services/keepstore/keepstore.go b/services/keepstore/keepstore.go
index 7a9cec0..8267fd7 100644
--- a/services/keepstore/keepstore.go
+++ b/services/keepstore/keepstore.go
@@ -11,7 +11,6 @@ import (
"syscall"
"time"
- "git.curoverse.com/arvados.git/sdk/go/arvados"
"git.curoverse.com/arvados.git/sdk/go/arvadosclient"
"git.curoverse.com/arvados.git/sdk/go/config"
"git.curoverse.com/arvados.git/sdk/go/httpserver"
@@ -83,34 +82,13 @@ var KeepVM VolumeManager
var pullq *WorkQueue
var trashq *WorkQueue
-var (
- flagSerializeIO bool
- flagReadonly bool
-)
-
// TODO(twp): continue moving as much code as possible out of main
// so it can be effectively tested. Esp. handling and postprocessing
// of command line flags (identifying Keep volumes and initializing
// permission arguments).
func main() {
- neverDelete := !theConfig.EnableDelete
- signatureTTLSeconds := int(theConfig.BlobSignatureTTL.Duration() / time.Second)
- flag.StringVar(&theConfig.Listen, "listen", theConfig.Listen, "see Listen configuration")
- flag.IntVar(&theConfig.MaxBuffers, "max-buffers", theConfig.MaxBuffers, "see MaxBuffers configuration")
- flag.IntVar(&theConfig.MaxRequests, "max-requests", theConfig.MaxRequests, "see MaxRequests configuration")
- flag.BoolVar(&neverDelete, "never-delete", neverDelete, "see EnableDelete configuration")
- flag.BoolVar(&theConfig.RequireSignatures, "enforce-permissions", theConfig.RequireSignatures, "see RequireSignatures configuration")
- flag.StringVar(&theConfig.BlobSigningKeyFile, "permission-key-file", theConfig.BlobSigningKeyFile, "see BlobSigningKey`File` configuration")
- flag.StringVar(&theConfig.BlobSigningKeyFile, "blob-signing-key-file", theConfig.BlobSigningKeyFile, "see BlobSigningKey`File` configuration")
- flag.StringVar(&theConfig.SystemAuthTokenFile, "data-manager-token-file", theConfig.SystemAuthTokenFile, "see SystemAuthToken`File` configuration")
- flag.IntVar(&signatureTTLSeconds, "permission-ttl", signatureTTLSeconds, "signature TTL in seconds; see BlobSignatureTTL configuration")
- flag.IntVar(&signatureTTLSeconds, "blob-signature-ttl", signatureTTLSeconds, "signature TTL in seconds; see BlobSignatureTTL configuration")
- flag.Var(&theConfig.TrashLifetime, "trash-lifetime", "see TrashLifetime configuration")
- flag.BoolVar(&flagSerializeIO, "serialize", false, "serialize read and write operations on the following volumes.")
- flag.BoolVar(&flagReadonly, "readonly", false, "do not write, delete, or touch anything on the following volumes.")
- flag.StringVar(&theConfig.PIDFile, "pid", theConfig.PIDFile, "see `PIDFile` configuration")
- flag.Var(&theConfig.TrashCheckInterval, "trash-check-interval", "see TrashCheckInterval configuration")
+ deprecated.beforeFlagParse(theConfig)
dumpConfig := flag.Bool("dump-config", false, "write current configuration to stdout and exit (useful for migrating from command line flags to config file)")
@@ -124,8 +102,7 @@ func main() {
flag.Usage = usage
flag.Parse()
- theConfig.BlobSignatureTTL = arvados.Duration(signatureTTLSeconds) * arvados.Duration(time.Second)
- theConfig.EnableDelete = !neverDelete
+ deprecated.afterFlagParse(theConfig)
// TODO: Load config
err := config.LoadFile(theConfig, configPath)
diff --git a/services/keepstore/s3_volume.go b/services/keepstore/s3_volume.go
index 7f2c3f0..caed35b 100644
--- a/services/keepstore/s3_volume.go
+++ b/services/keepstore/s3_volume.go
@@ -56,7 +56,7 @@ func (s *s3VolumeAdder) Set(bucketName string) error {
if s3AccessKeyFile == "" || s3SecretKeyFile == "" {
return fmt.Errorf("-s3-access-key-file and -s3-secret-key-file arguments must given before -s3-bucket-volume")
}
- if flagSerializeIO {
+ if deprecated.flagSerializeIO {
log.Print("Notice: -serialize is not supported by s3-bucket volumes.")
}
s.Config.Volumes = append(s.Config.Volumes, &S3Volume{
@@ -68,7 +68,7 @@ func (s *s3VolumeAdder) Set(bucketName string) error {
RaceWindow: arvados.Duration(s3RaceWindow),
S3Replication: s3Replication,
UnsafeDelete: s3UnsafeDelete,
- ReadOnly: flagReadonly,
+ ReadOnly: deprecated.flagReadonly,
IndexPageSize: 1000,
})
return nil
diff --git a/services/keepstore/volume_unix.go b/services/keepstore/volume_unix.go
index 1866c7b..92c897e 100644
--- a/services/keepstore/volume_unix.go
+++ b/services/keepstore/volume_unix.go
@@ -38,8 +38,8 @@ func (vs *unixVolumeAdder) Set(path string) error {
}
vs.Config.Volumes = append(vs.Config.Volumes, &UnixVolume{
Root: path,
- ReadOnly: flagReadonly,
- Serialize: flagSerializeIO,
+ ReadOnly: deprecated.flagReadonly,
+ Serialize: deprecated.flagSerializeIO,
})
return nil
}
@@ -79,10 +79,10 @@ func (vs *unixVolumeAdder) Discover() int {
}
// Set the -readonly flag (but only for this volume)
// if the filesystem is mounted readonly.
- flagReadonlyWas := flagReadonly
+ flagReadonlyWas := deprecated.flagReadonly
for _, fsopt := range strings.Split(args[3], ",") {
if fsopt == "ro" {
- flagReadonly = true
+ deprecated.flagReadonly = true
break
}
if fsopt == "rw" {
@@ -94,7 +94,7 @@ func (vs *unixVolumeAdder) Discover() int {
} else {
added++
}
- flagReadonly = flagReadonlyWas
+ deprecated.flagReadonly = flagReadonlyWas
}
return added
}
commit d3b56f18947c3ccb42fee52ff33b3b00db0dffd9
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Oct 17 04:08:43 2016 -0400
9956: Remove "listen on address with no port" in help message.
diff --git a/services/keepstore/usage.go b/services/keepstore/usage.go
index 748ef38..c067ec0 100644
--- a/services/keepstore/usage.go
+++ b/services/keepstore/usage.go
@@ -38,9 +38,9 @@ Example config file:
Listen:
- Local port to listen on. Can be "address", "address:port", or
- ":port", where "address" is a host IP address or name and "port"
- is a port number or name.
+ Local port to listen on. Can be "address:port" or ":port", where
+ "address" is a host IP address or name and "port" is a port number
+ or name.
PIDFile:
-----------------------------------------------------------------------
hooks/post-receive
--
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