[ARVADOS] updated: 1.3.0-9-ge48387b53

Git user git at public.curoverse.com
Tue Feb 12 10:58:01 EST 2019


Summary of changes:
 services/api/app/models/api_client_authorization.rb | 6 ++++++
 1 file changed, 6 insertions(+)

  discards  4b7d1eb1093a4b5a62e1617808d3db92c7a2e6a9 (commit)
  discards  bd7cd13953c10de3c35fa1310848ae89ace3f765 (commit)
  discards  8847e85d63499f777c4b2884b7d51d276d6a10fe (commit)
       via  e48387b530d01be0f92f70390570169ddf3b9111 (commit)
       via  90a6b5c117d244f6683ed468ec06df4e28dcaf12 (commit)
       via  90d404ddaeeaef949b72d52abb073e25a35853c6 (commit)
       via  500e77f07a46a6dd0c85e445ecf90007435b8349 (commit)
       via  08fbaa7e7b6aedd2403bf60cc8f9d1e5c891fd02 (commit)
       via  5b640d0c44e583a38233cb4eea64f76a349816bd (commit)
       via  698be629fb986fd1b652927b7281feaeba01ee07 (commit)
       via  5eb625a15defc30fd6ecfd0e40bc29dd0b97656d (commit)
       via  13ee649240ee4424bc33cc93bdbfcca9d31b05c4 (commit)

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commit e48387b530d01be0f92f70390570169ddf3b9111
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Feb 11 13:05:34 2019 -0500

    14826: Fix copy and paste error
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/services/api/app/models/api_client_authorization.rb b/services/api/app/models/api_client_authorization.rb
index b93d06f9f..5f495d1b9 100644
--- a/services/api/app/models/api_client_authorization.rb
+++ b/services/api/app/models/api_client_authorization.rb
@@ -160,7 +160,7 @@ class ApiClientAuthorization < ArvadosModel
           ["/etc/ssl/certs/ca-certificates.crt",
            "/etc/pki/tls/certs/ca-bundle.crt"]
             .select { |ca_path| File.readable?(ca_path) }
-            .each { |ca_path| @api_client.ssl_config.add_trust_ca(ca_path) }
+            .each { |ca_path| clnt.ssl_config.add_trust_ca(ca_path) }
         end
         remote_user = SafeJSON.load(
           clnt.get_content('https://' + host + '/arvados/v1/users/current',

commit 90a6b5c117d244f6683ed468ec06df4e28dcaf12
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Feb 11 10:57:45 2019 -0500

    14826: API server looks in CA cert path that works on CentOS
    
    API server makes callbacks to remote clusters to validate remote
    users, ensure it has the right system CA cert path to validate TLS
    certs of remote clusters.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/services/api/app/models/api_client_authorization.rb b/services/api/app/models/api_client_authorization.rb
index 53ae6af46..b93d06f9f 100644
--- a/services/api/app/models/api_client_authorization.rb
+++ b/services/api/app/models/api_client_authorization.rb
@@ -155,6 +155,12 @@ class ApiClientAuthorization < ArvadosModel
         clnt = HTTPClient.new
         if Rails.configuration.sso_insecure
           clnt.ssl_config.verify_mode = OpenSSL::SSL::VERIFY_NONE
+        else
+          # Use system CA certificates
+          ["/etc/ssl/certs/ca-certificates.crt",
+           "/etc/pki/tls/certs/ca-bundle.crt"]
+            .select { |ca_path| File.readable?(ca_path) }
+            .each { |ca_path| @api_client.ssl_config.add_trust_ca(ca_path) }
         end
         remote_user = SafeJSON.load(
           clnt.get_content('https://' + host + '/arvados/v1/users/current',

commit 90d404ddaeeaef949b72d52abb073e25a35853c6
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Tue Jan 29 19:48:15 2019 -0300

    14738: Replaces double with single quotes for code style.
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/apps/workbench/app/assets/javascripts/components/edit_tags.js b/apps/workbench/app/assets/javascripts/components/edit_tags.js
index e7083b145..1fddb2651 100644
--- a/apps/workbench/app/assets/javascripts/components/edit_tags.js
+++ b/apps/workbench/app/assets/javascripts/components/edit_tags.js
@@ -4,7 +4,7 @@
 
 window.SimpleInput = {
     view: function(vnode) {
-        return m("input.form-control", {
+        return m('input.form-control', {
             style: {
                 width: '100%',
             },
@@ -22,7 +22,7 @@ window.SimpleInput = {
 
 window.SelectOrAutocomplete = {
     view: function(vnode) {
-        return m("input.form-control", {
+        return m('input.form-control', {
             style: {
                 width: '100%'
             },
@@ -87,9 +87,9 @@ window.TagEditorRow = {
                     valueOpts = vnode.attrs.vocabulary().tags[vnode.attrs.name()].values
             }
         }
-        return m("tr", [
+        return m('tr', [
             // Erase tag
-            m("td", [
+            m('td', [
                 vnode.attrs.editMode &&
                 m('div.text-center', m('a.btn.btn-default.btn-sm', {
                     style: {
@@ -99,13 +99,13 @@ window.TagEditorRow = {
                 }, m('i.fa.fa-fw.fa-trash-o')))
             ]),
             // Tag key
-            m("td", [
+            m('td', [
                 vnode.attrs.editMode ?
-                m("div", {key: 'key'}, [
+                m('div', {key: 'key'}, [
                     m(inputComponent, {
                         options: nameOpts,
                         value: vnode.attrs.name,
-                        // Allow any tag name unless "strict" is set to true.
+                        // Allow any tag name unless 'strict' is set to true.
                         create: !vnode.attrs.vocabulary().strict,
                         placeholder: 'key',
                     })
@@ -113,9 +113,9 @@ window.TagEditorRow = {
                 : vnode.attrs.name
             ]),
             // Tag value
-            m("td", [
+            m('td', [
                 vnode.attrs.editMode ?
-                m("div", {key: 'value'}, [
+                m('div', {key: 'value'}, [
                     m(inputComponent, {
                         options: valueOpts,
                         value: vnode.attrs.value,
@@ -137,20 +137,20 @@ window.TagEditorRow = {
 
 window.TagEditorTable = {
     view: function(vnode) {
-        return m("table.table.table-condensed.table-justforlayout", [
-            m("colgroup", [
-                m("col", {width:"5%"}),
-                m("col", {width:"25%"}),
-                m("col", {width:"70%"}),
+        return m('table.table.table-condensed.table-justforlayout', [
+            m('colgroup', [
+                m('col', {width:'5%'}),
+                m('col', {width:'25%'}),
+                m('col', {width:'70%'}),
             ]),
-            m("thead", [
-                m("tr", [
-                    m("th"),
-                    m("th", "Key"),
-                    m("th", "Value"),
+            m('thead', [
+                m('tr', [
+                    m('th'),
+                    m('th', 'Key'),
+                    m('th', 'Value'),
                 ])
             ]),
-            m("tbody", [
+            m('tbody', [
                 vnode.attrs.tags.length > 0
                 ? vnode.attrs.tags.map(function(tag, idx) {
                     return m(TagEditorRow, {
@@ -165,7 +165,7 @@ window.TagEditorTable = {
                         vocabulary: vnode.attrs.vocabulary
                     })
                 })
-                : m("tr", m("td[colspan=3]", m("center", "Loading tags...")))
+                : m('tr', m('td[colspan=3]', m('center', 'Loading tags...')))
             ]),
         ])
     }
@@ -185,7 +185,7 @@ window.TagEditorApp = {
     oninit: function(vnode) {
         vnode.state.sessionDB = new SessionDB()
         // Get vocabulary
-        vnode.state.vocabulary = m.stream({"strict":false, "tags":{}})
+        vnode.state.vocabulary = m.stream({'strict':false, 'tags':{}})
         var vocabularyTimestamp = parseInt(Date.now() / 300000) // Bust cache every 5 minutes
         m.request('/vocabulary.json?v=' + vocabularyTimestamp).then(vnode.state.vocabulary)
         vnode.state.editMode = vnode.attrs.targetEditable
@@ -228,8 +228,8 @@ window.TagEditorApp = {
     view: function(vnode) {
         return [
             vnode.state.editMode &&
-            m("div.pull-left", [
-                m("a.btn.btn-primary.btn-sm" + (vnode.state.dirty() ? '' : '.disabled'), {
+            m('div.pull-left', [
+                m('a.btn.btn-primary.btn-sm' + (vnode.state.dirty() ? '' : '.disabled'), {
                     style: {
                         margin: '10px 0px'
                     },
@@ -244,7 +244,7 @@ window.TagEditorApp = {
                         vnode.state.sessionDB.request(
                             vnode.state.sessionDB.loadLocal(),
                             vnode.state.objPath, {
-                                method: "PUT",
+                                method: 'PUT',
                                 data: {properties: JSON.stringify(tags)}
                             }
                         ).then(function(v) {

commit 500e77f07a46a6dd0c85e445ecf90007435b8349
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Tue Jan 29 17:39:26 2019 -0300

    14738: Enhances code readability when concatenating strings.
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/apps/workbench/app/assets/javascripts/components/edit_tags.js b/apps/workbench/app/assets/javascripts/components/edit_tags.js
index 946344a2c..e7083b145 100644
--- a/apps/workbench/app/assets/javascripts/components/edit_tags.js
+++ b/apps/workbench/app/assets/javascripts/components/edit_tags.js
@@ -192,11 +192,11 @@ window.TagEditorApp = {
         vnode.state.tags = []
         vnode.state.dirty = m.stream(false)
         vnode.state.dirty.map(m.redraw)
-        vnode.state.objPath = 'arvados/v1/'+vnode.attrs.targetController+'/'+vnode.attrs.targetUuid
+        vnode.state.objPath = 'arvados/v1/' + vnode.attrs.targetController + '/' + vnode.attrs.targetUuid
         // Get tags
         vnode.state.sessionDB.request(
             vnode.state.sessionDB.loadLocal(),
-            'arvados/v1/'+vnode.attrs.targetController,
+            'arvados/v1/' + vnode.attrs.targetController,
             {
                 data: {
                     filters: JSON.stringify([['uuid', '=', vnode.attrs.targetUuid]]),
@@ -229,7 +229,7 @@ window.TagEditorApp = {
         return [
             vnode.state.editMode &&
             m("div.pull-left", [
-                m("a.btn.btn-primary.btn-sm"+(vnode.state.dirty() ? '' : '.disabled'), {
+                m("a.btn.btn-primary.btn-sm" + (vnode.state.dirty() ? '' : '.disabled'), {
                     style: {
                         margin: '10px 0px'
                     },

commit 08fbaa7e7b6aedd2403bf60cc8f9d1e5c891fd02
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Tue Jan 29 16:25:02 2019 -0300

    14738: Fixes the double-slash usage on requests to prevent 301 from controller
    
    When a request is made to controller using double slashes, for example to
    http://apiserver//arvados/v1/collections, arvados controller returns a 301
    that breaks CORS.
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/apps/workbench/app/assets/javascripts/components/edit_tags.js b/apps/workbench/app/assets/javascripts/components/edit_tags.js
index ac4d2df7b..946344a2c 100644
--- a/apps/workbench/app/assets/javascripts/components/edit_tags.js
+++ b/apps/workbench/app/assets/javascripts/components/edit_tags.js
@@ -192,11 +192,11 @@ window.TagEditorApp = {
         vnode.state.tags = []
         vnode.state.dirty = m.stream(false)
         vnode.state.dirty.map(m.redraw)
-        vnode.state.objPath = '/arvados/v1/'+vnode.attrs.targetController+'/'+vnode.attrs.targetUuid
+        vnode.state.objPath = 'arvados/v1/'+vnode.attrs.targetController+'/'+vnode.attrs.targetUuid
         // Get tags
         vnode.state.sessionDB.request(
             vnode.state.sessionDB.loadLocal(),
-            '/arvados/v1/'+vnode.attrs.targetController,
+            'arvados/v1/'+vnode.attrs.targetController,
             {
                 data: {
                     filters: JSON.stringify([['uuid', '=', vnode.attrs.targetUuid]]),

commit 5b640d0c44e583a38233cb4eea64f76a349816bd
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Thu Jan 24 15:48:54 2019 -0300

    14770: Fixes parameter on acr call.
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/apps/workbench/app/controllers/work_units_controller.rb b/apps/workbench/app/controllers/work_units_controller.rb
index 767762c81..d3ded867c 100644
--- a/apps/workbench/app/controllers/work_units_controller.rb
+++ b/apps/workbench/app/controllers/work_units_controller.rb
@@ -126,7 +126,7 @@ class WorkUnitsController < ApplicationController
                           "--local",
                           "--api=containers",
                           "--project-uuid=#{params['work_unit']['owner_uuid']}",
-                          "--collection-keep-cache=#{keep_cache}",
+                          "--collection-cache-size=#{keep_cache}",
                           "/var/lib/cwl/workflow.json#main",
                           "/var/lib/cwl/cwl.input.json"]
 

commit 698be629fb986fd1b652927b7281feaeba01ee07
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Dec 7 15:57:45 2018 -0500

    14593: Fix typo.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index 4ebb62544..6a3e000ca 100644
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -36,7 +36,7 @@ This release includes several database migrations, which will be executed automa
 
 The @arvados-controller@ component now requires the /etc/arvados/config.yml file to be present. See <a href="{{ site.baseurl }}/install/install-controller.html#configuration">the @arvados-controller@ installation instructions</a>.
 
-Support for the deprecated "jobs" API is broken in this release.  Users who rely on it should not upgrade.  This will be fixed in in an upcoming 1.3.1 patch release, however users are "encouraged to migrate":upgrade-crunch2.html as support for the "jobs" API will be dropped in an upcoming release.  Users who are already using the "containers" API are not affected.
+Support for the deprecated "jobs" API is broken in this release.  Users who rely on it should not upgrade.  This will be fixed in an upcoming 1.3.1 patch release, however users are "encouraged to migrate":upgrade-crunch2.html as support for the "jobs" API will be dropped in an upcoming release.  Users who are already using the "containers" API are not affected.
 
 h3. v1.2.1 (2018-11-26)
 

commit 5eb625a15defc30fd6ecfd0e40bc29dd0b97656d
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Dec 7 15:43:16 2018 -0500

    14593: Add note about broken crunch1 to upgrade docs.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index 0941fef33..4ebb62544 100644
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -30,6 +30,14 @@ Note to developers: Add new items at the top. Include the date, issue number, co
 TODO: extract this information based on git commit messages and generate changelogs / release notes automatically.
 {% endcomment %}
 
+h3. v1.3.0 (2018-12-05)
+
+This release includes several database migrations, which will be executed automatically as part of the API server upgrade. On large Arvados installations, these migrations will take a while. We've seen the upgrade take 30 minutes or more on installations with a lot of collections.
+
+The @arvados-controller@ component now requires the /etc/arvados/config.yml file to be present. See <a href="{{ site.baseurl }}/install/install-controller.html#configuration">the @arvados-controller@ installation instructions</a>.
+
+Support for the deprecated "jobs" API is broken in this release.  Users who rely on it should not upgrade.  This will be fixed in in an upcoming 1.3.1 patch release, however users are "encouraged to migrate":upgrade-crunch2.html as support for the "jobs" API will be dropped in an upcoming release.  Users who are already using the "containers" API are not affected.
+
 h3. v1.2.1 (2018-11-26)
 
 There are no special upgrade notes for this release.

commit 13ee649240ee4424bc33cc93bdbfcca9d31b05c4
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Dec 7 15:03:04 2018 -0500

    14593: Fix a-c-r when running on the "jobs" API
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index 7512d5bef..61f9cbbe0 100644
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -103,6 +103,7 @@ def run():
         arvargs.output_name = output_name
         arvargs.output_tags = output_tags
         arvargs.thread_count = 1
+        arvargs.collection_cache_size = None
 
         runner = arvados_cwl.ArvCwlExecutor(api_client=arvados.safeapi.ThreadSafeApiCache(
             api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),

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