[ARVADOS] updated: 1.1.2-141-g0e3c1f9
Git user
git at public.curoverse.com
Fri Feb 2 09:55:42 EST 2018
Summary of changes:
.../app/assets/javascripts/components/search.js | 4 +-
.../app/assets/javascripts/components/sessions.js | 12 +-
.../app/assets/javascripts/models/session_db.js | 96 +++++++--
.../views/search/{index.html.erb => index.html} | 3 +-
apps/workbench/config/application.default.yml | 5 -
sdk/cwl/tests/arvados-tests.sh | 3 +
sdk/cwl/tests/{secondary/dir => hg19}/hg19.fa | 0
sdk/cwl/tests/{secondary/dir => hg19}/hg19.fa.amb | 0
sdk/cwl/tests/{secondary/dir => hg19}/hg19.fa.ann | 0
sdk/cwl/tests/{secondary/dir => hg19}/hg19.fa.fai | 0
sdk/go/arvadostest/fixtures.go | 1 +
.../controllers/arvados/v1/schema_controller.rb | 1 +
services/api/test/fixtures/users.yml | 16 ++
.../arvados/v1/schema_controller_test.rb | 1 +
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 91 +++-----
.../crunch-dispatch-slurm_test.go | 195 ++++++-----------
services/crunch-dispatch-slurm/slurm.go | 73 +++++++
services/crunch-dispatch-slurm/squeue.go | 9 +-
services/crunch-run/crunchrun.go | 239 +++++++++------------
services/crunch-run/crunchrun_test.go | 143 ++++++------
services/fuse/arvados_fuse/fusedir.py | 105 ++++-----
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 1 +
tools/arvbox/lib/arvbox/docker/Dockerfile.demo | 5 +-
tools/arvbox/lib/arvbox/docker/crunch-setup.sh | 9 +-
tools/arvbox/lib/arvbox/docker/go-setup.sh | 16 ++
tools/arvbox/lib/arvbox/docker/keep-setup.sh | 9 +-
.../docker/service/arv-git-httpd/run-service | 9 +-
.../lib/arvbox/docker/service/composer/run-service | 12 +-
.../service/crunch-dispatch-local/run-service | 15 +-
.../lib/arvbox/docker/service/keep-web/run-service | 9 +-
.../arvbox/docker/service/keepproxy/run-service | 9 +-
.../arvbox/lib/arvbox/docker/service/postgres/run | 2 +
.../arvbox/docker/service/websockets/run-service | 8 +-
tools/sync-groups/sync-groups.go | 21 +-
tools/sync-groups/sync-groups_test.go | 33 +--
35 files changed, 586 insertions(+), 569 deletions(-)
rename apps/workbench/app/views/search/{index.html.erb => index.html} (52%)
copy sdk/cwl/tests/{secondary/dir => hg19}/hg19.fa (100%)
copy sdk/cwl/tests/{secondary/dir => hg19}/hg19.fa.amb (100%)
copy sdk/cwl/tests/{secondary/dir => hg19}/hg19.fa.ann (100%)
copy sdk/cwl/tests/{secondary/dir => hg19}/hg19.fa.fai (100%)
create mode 100644 services/crunch-dispatch-slurm/slurm.go
create mode 100644 tools/arvbox/lib/arvbox/docker/go-setup.sh
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commit 0e3c1f9c71f537d000459cbd3159ca6c198461c8
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date: Fri Feb 2 11:53:48 2018 -0300
11454: Removed unnecessary call on migrateNonFederatedSessions()
Added auto loading of remote hosts listed on home cluster's api discovery doc. (WIP)
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>
diff --git a/apps/workbench/app/assets/javascripts/components/search.js b/apps/workbench/app/assets/javascripts/components/search.js
index 0839491..17055b3 100644
--- a/apps/workbench/app/assets/javascripts/components/search.js
+++ b/apps/workbench/app/assets/javascripts/components/search.js
@@ -2,11 +2,6 @@
//
// SPDX-License-Identifier: AGPL-3.0
-$(document).on('ready', function() {
- var db = new SessionDB()
- db.migrateNonFederatedSessions()
-})
-
window.SearchResultsTable = {
maybeLoadMore: function(dom) {
var loader = this.loader
diff --git a/apps/workbench/app/assets/javascripts/components/sessions.js b/apps/workbench/app/assets/javascripts/components/sessions.js
index 6a20342..12015b0 100644
--- a/apps/workbench/app/assets/javascripts/components/sessions.js
+++ b/apps/workbench/app/assets/javascripts/components/sessions.js
@@ -7,6 +7,7 @@ $(document).on('ready', function() {
db.checkForNewToken()
db.fillMissingUUIDs()
db.migrateNonFederatedSessions()
+ db.autoLoadRemoteHosts()
})
window.SessionsTable = {
diff --git a/apps/workbench/app/assets/javascripts/models/session_db.js b/apps/workbench/app/assets/javascripts/models/session_db.js
index 26306b8..2d22a98 100644
--- a/apps/workbench/app/assets/javascripts/models/session_db.js
+++ b/apps/workbench/app/assets/javascripts/models/session_db.js
@@ -238,5 +238,23 @@ window.SessionDB = function() {
}
})
},
+ // If remoteHosts is listed on the local API discovery doc, try to add any
+ // listed remote without an active session.
+ autoLoadRemoteHosts: function() {
+ var activeSessions = db.loadActive()
+ var doc = db.discoveryDoc(db.loadLocal())
+ doc.map(function(d) {
+ // NOTE: the below line is to simulate that 9tee4 is included as a remote host
+ // the current test cluster
+ // d.remoteHosts = {"9tee4":"9tee4.arvadosapi.com"}
+ Object.keys(d.remoteHosts).map(function(uuidPrefix) {
+ if (!(uuidPrefix in Object.keys(activeSessions))) {
+ db.findAPI(d.remoteHosts[uuidPrefix]).then(function(baseURL) {
+ db.login(baseURL, false)
+ })
+ }
+ })
+ })
+ },
})
}
commit 75fd99e49f880aac55ae568c76c5151857e6beff
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date: Thu Feb 1 13:40:17 2018 -0300
11454: Show a link to the remote workbench on the sessions page.
On page load, detect those non-federated active sessions and try to
migrate them to federated logins just in case they're stale sessions.
If the federated login doesn't succeed, keep the session's previous state.
Removed workbench remote_hosts config.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>
diff --git a/apps/workbench/app/assets/javascripts/components/search.js b/apps/workbench/app/assets/javascripts/components/search.js
index 9a23648..0839491 100644
--- a/apps/workbench/app/assets/javascripts/components/search.js
+++ b/apps/workbench/app/assets/javascripts/components/search.js
@@ -2,6 +2,11 @@
//
// SPDX-License-Identifier: AGPL-3.0
+$(document).on('ready', function() {
+ var db = new SessionDB()
+ db.migrateNonFederatedSessions()
+})
+
window.SearchResultsTable = {
maybeLoadMore: function(dom) {
var loader = this.loader
@@ -90,7 +95,7 @@ window.SearchResultsTable = {
window.Search = {
oninit: function(vnode) {
- vnode.state.sessionDB = new SessionDB(vnode.attrs.remoteHosts)
+ vnode.state.sessionDB = new SessionDB()
vnode.state.searchEntered = m.stream()
vnode.state.searchActive = m.stream()
// When searchActive changes (e.g., when restoring state
diff --git a/apps/workbench/app/assets/javascripts/components/sessions.js b/apps/workbench/app/assets/javascripts/components/sessions.js
index 964f89a..6a20342 100644
--- a/apps/workbench/app/assets/javascripts/components/sessions.js
+++ b/apps/workbench/app/assets/javascripts/components/sessions.js
@@ -6,6 +6,7 @@ $(document).on('ready', function() {
var db = new SessionDB()
db.checkForNewToken()
db.fillMissingUUIDs()
+ db.migrateNonFederatedSessions()
})
window.SessionsTable = {
@@ -41,7 +42,11 @@ window.SessionsTable = {
m('td', session.user.is_active ?
m('span.label.label-success', 'logged in') :
m('span.label.label-warning', 'inactive')),
- m('td', {title: session.baseURL}, uuidPrefix),
+ m('td', {title: session.baseURL}, [
+ m('a', {
+ href: db.workbenchBaseURL(session) + '?api_token=' + session.token
+ }, uuidPrefix),
+ ]),
m('td', session.user.username),
m('td', session.user.email),
m('td', session.isFromRails ? null : m('button.btn.btn-xs.btn-default', {
diff --git a/apps/workbench/app/assets/javascripts/models/session_db.js b/apps/workbench/app/assets/javascripts/models/session_db.js
index 52d8930..26306b8 100644
--- a/apps/workbench/app/assets/javascripts/models/session_db.js
+++ b/apps/workbench/app/assets/javascripts/models/session_db.js
@@ -2,10 +2,9 @@
//
// SPDX-License-Identifier: AGPL-3.0
-window.SessionDB = function(rhosts) {
+window.SessionDB = function() {
var db = this
Object.assign(db, {
- remoteHosts: rhosts || [],
discoveryCache: {},
tokenUUIDCache: null,
loadFromLocalStorage: function() {
@@ -75,7 +74,7 @@ window.SessionDB = function(rhosts) {
})
})
},
- login: function(baseURL) {
+ login: function(baseURL, fallbackLogin = true) {
// Initiate login procedure with given API base URL (e.g.,
// "http://api.example/").
//
@@ -104,7 +103,7 @@ window.SessionDB = function(rhosts) {
db.save(user.owner_uuid.slice(0, 5), remoteSession)
})
})
- } else {
+ } else if (fallbackLogin) {
// Classic login
document.location = baseURL + 'login?return_to=' + encodeURIComponent(document.location.href.replace(/\?.*/, '')+'?baseURL='+encodeURIComponent(baseURL))
}
@@ -227,5 +226,17 @@ window.SessionDB = function(rhosts) {
opts.headers.authorization = 'OAuth2 '+ session.token
return m.request(session.baseURL + path, opts)
},
+ // Check non-federated remote active sessions if they should be migrated to
+ // a salted token.
+ migrateNonFederatedSessions: function() {
+ var sessions = db.loadActive()
+ Object.keys(sessions).map(function(uuidPrefix) {
+ session = sessions[uuidPrefix]
+ if (!session.isFromRails && session.token && session.token.indexOf('v2/') < 0) {
+ // Only try the federated login
+ db.login(session.baseURL, false)
+ }
+ })
+ },
})
}
diff --git a/apps/workbench/app/views/search/index.html.erb b/apps/workbench/app/views/search/index.html
similarity index 52%
rename from apps/workbench/app/views/search/index.html.erb
rename to apps/workbench/app/views/search/index.html
index ff3e190..d2a83864 100644
--- a/apps/workbench/app/views/search/index.html.erb
+++ b/apps/workbench/app/views/search/index.html
@@ -2,6 +2,5 @@
SPDX-License-Identifier: AGPL-3.0 -->
-<div data-mount-mithril="Search"
- data-remote-hosts="<%= Rails.configuration.remote_hosts %>">
+<div data-mount-mithril="Search">
</div>
diff --git a/apps/workbench/config/application.default.yml b/apps/workbench/config/application.default.yml
index 4cf7b5e..76f7a30 100644
--- a/apps/workbench/config/application.default.yml
+++ b/apps/workbench/config/application.default.yml
@@ -314,8 +314,3 @@ common:
# Link to use for Arvados Workflow Composer app, or false if not available.
#
composer_url: false
-
- # Multi site search federation feature:
- # * remote_hosts: List of API servers that allow logins from accounts on this
- # workbench's cluster.
- remote_hosts: []
commit dac01e1015f4d769a929651a74096e8a13592cf7
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date: Wed Jan 31 16:37:15 2018 -0300
11454: Do federated logins by requesting the current user object
instead of the classic login flow.
When the user is inactive on the remote cluster, label the session
properly and exclude it from SessionDB.loadActive()'s results.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>
diff --git a/apps/workbench/app/assets/javascripts/components/search.js b/apps/workbench/app/assets/javascripts/components/search.js
index 5cb292b..9a23648 100644
--- a/apps/workbench/app/assets/javascripts/components/search.js
+++ b/apps/workbench/app/assets/javascripts/components/search.js
@@ -154,8 +154,6 @@ window.Search = {
})
},
view: function(vnode) {
- // FIXME: The line below seems superfluous
- // var sessions = vnode.state.sessionDB.loadAll()
return m('form', {
onsubmit: function() {
vnode.state.searchActive(vnode.state.searchEntered())
diff --git a/apps/workbench/app/assets/javascripts/components/sessions.js b/apps/workbench/app/assets/javascripts/components/sessions.js
index e7cc505..964f89a 100644
--- a/apps/workbench/app/assets/javascripts/components/sessions.js
+++ b/apps/workbench/app/assets/javascripts/components/sessions.js
@@ -38,7 +38,9 @@ window.SessionsTable = {
var session = sessions[uuidPrefix]
return m('tr', [
session.token && session.user ? [
- m('td', m('span.label.label-success', 'logged in')),
+ m('td', session.user.is_active ?
+ m('span.label.label-success', 'logged in') :
+ m('span.label.label-warning', 'inactive')),
m('td', {title: session.baseURL}, uuidPrefix),
m('td', session.user.username),
m('td', session.user.email),
diff --git a/apps/workbench/app/assets/javascripts/models/session_db.js b/apps/workbench/app/assets/javascripts/models/session_db.js
index 77fddcb..52d8930 100644
--- a/apps/workbench/app/assets/javascripts/models/session_db.js
+++ b/apps/workbench/app/assets/javascripts/models/session_db.js
@@ -25,7 +25,7 @@ window.SessionDB = function(rhosts) {
loadActive: function() {
var sessions = db.loadAll()
Object.keys(sessions).forEach(function(key) {
- if (!sessions[key].token)
+ if (!sessions[key].token || !sessions[key].user.is_active)
delete sessions[key]
})
return sessions
@@ -91,7 +91,18 @@ window.SessionDB = function(rhosts) {
(dd.remoteHostsViaDNS && apiHostname.indexOf('arvadosapi.com') >= 0)) {
// Federated identity login via salted token
db.saltedToken(dd.uuidPrefix).then(function(token) {
- document.location = baseURL + 'login?return_to=' + encodeURIComponent(document.location.href.replace(/\?.*/, '')+'?baseURL='+encodeURIComponent(baseURL)) + '&api_token='+encodeURIComponent(token)
+ m.request(baseURL+'arvados/v1/users/current', {
+ headers: {
+ authorization: 'Bearer '+token,
+ },
+ }).then(function(user) {
+ var remoteSession = {
+ user: user,
+ baseURL: baseURL,
+ token: token
+ }
+ db.save(user.owner_uuid.slice(0, 5), remoteSession)
+ })
})
} else {
// Classic login
commit 29e4cf39674f54e5607d84d612ff867a4add0347
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date: Tue Jan 30 20:43:44 2018 -0300
11454: Cache the local session token's uuid after being requested from the API.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>
diff --git a/apps/workbench/app/assets/javascripts/models/session_db.js b/apps/workbench/app/assets/javascripts/models/session_db.js
index 79e98ca..77fddcb 100644
--- a/apps/workbench/app/assets/javascripts/models/session_db.js
+++ b/apps/workbench/app/assets/javascripts/models/session_db.js
@@ -7,6 +7,7 @@ window.SessionDB = function(rhosts) {
Object.assign(db, {
remoteHosts: rhosts || [],
discoveryCache: {},
+ tokenUUIDCache: null,
loadFromLocalStorage: function() {
try {
return JSON.parse(window.localStorage.getItem('sessions')) || {}
@@ -111,22 +112,13 @@ window.SessionDB = function(rhosts) {
// Takes a cluster UUID prefix and returns a salted token to allow
// log into said cluster using federated identity.
var session = db.loadLocal()
- return db.request(session, '/arvados/v1/api_client_authorizations', {
- data: {
- filters: JSON.stringify([['api_token', '=', session.token]]),
- }
- }).then(function(resp) {
- if (resp.items.length == 1) {
- var token_uuid = resp.items[0].uuid
- if (token_uuid.length !== '') {
- var shaObj = new jsSHA("SHA-1", "TEXT")
- shaObj.setHMACKey(session.token, "TEXT")
- shaObj.update(uuid_prefix)
- var hmac = shaObj.getHMAC("HEX")
- return 'v2/' + token_uuid + '/' + hmac
- } else { return null }
- }
- }).catch(function(err) { return null })
+ return db.tokenUUID().then(function(token_uuid){
+ var shaObj = new jsSHA("SHA-1", "TEXT")
+ shaObj.setHMACKey(session.token, "TEXT")
+ shaObj.update(uuid_prefix)
+ var hmac = shaObj.getHMAC("HEX")
+ return 'v2/' + token_uuid + '/' + hmac
+ })
},
checkForNewToken: function() {
// If there's a token and baseURL in the location bar (i.e.,
@@ -198,6 +190,26 @@ window.SessionDB = function(rhosts) {
}
return cache
},
+ // Return a promise with the local session token's UUID from the API server.
+ tokenUUID: function() {
+ var cache = db.tokenUUIDCache
+ if (!cache) {
+ var session = db.loadLocal()
+ return db.request(session, '/arvados/v1/api_client_authorizations', {
+ data: {
+ filters: JSON.stringify([['api_token', '=', session.token]]),
+ }
+ }).then(function(resp) {
+ var uuid = resp.items[0].uuid
+ db.tokenUUIDCache = uuid
+ return uuid
+ })
+ } else {
+ return new Promise(function(resolve, reject) {
+ resolve(cache)
+ })
+ }
+ },
request: function(session, path, opts) {
opts = opts || {}
opts.headers = opts.headers || {}
commit ef2889f20ad25c30abb05c53cc5e08e2c2ed97d3
Merge: 95c228e 9482a91
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date: Tue Jan 30 15:29:50 2018 -0300
Merge branch 'master' into 11454-wb-federated-search
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>
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