[ARVADOS] updated: 1e8f93a86465bce9bf6b32245ef99932c3cbfe08
git at public.curoverse.com
git at public.curoverse.com
Mon Dec 30 15:08:16 EST 2013
Summary of changes:
apps/workbench/app/controllers/users_controller.rb | 2 +
.../app/views/layouts/application.html.erb | 8 +-
.../app/views/users/_notifications.html.erb | 101 +++++++++
apps/workbench/app/views/users/_tables.html.erb | 182 +++++++++++++++
apps/workbench/app/views/users/home.html.erb | 236 +++-----------------
doc/api/crunch-scripts.textile | 4 +-
doc/api/index.textile | 44 ++--
.../{ApiClients.textile => ApiClient.textile} | 10 +-
doc/api/schema/ApiClientAuthorization.textile | 6 +-
doc/api/schema/AuthorizedKey.textile | 8 +-
.../{Collections.textile => Collection.textile} | 12 +-
doc/api/schema/Commit.textile | 8 +-
doc/api/schema/CommitAncestor.textile | 8 +-
doc/api/schema/Group.textile | 8 +-
doc/api/schema/Human.textile | 8 +-
doc/api/schema/{Jobs.textile => Job.textile} | 16 +-
.../schema/{JobTasks.textile => JobTask.textile} | 14 +-
doc/api/schema/KeepDisk.textile | 8 +-
doc/api/schema/Link.textile | 62 ++++--
doc/api/schema/Links.textile | 58 -----
doc/api/schema/Log.textile | 8 +-
doc/api/schema/Node.textile | 8 +-
doc/api/schema/PipelineInstance.textile | 8 +-
doc/api/schema/PipelineTemplate.textile | 8 +-
doc/api/schema/Repository.textile | 8 +-
doc/api/schema/Specimen.textile | 8 +-
doc/api/schema/Trait.textile | 8 +-
doc/api/schema/User.textile | 8 +-
doc/api/schema/VirtualMachine.textile | 8 +-
docker/run.sh | 2 +-
sdk/cli/Gemfile | 8 +
sdk/cli/Gemfile.lock | 46 ++++
sdk/python/requirements.txt | 4 +
33 files changed, 526 insertions(+), 409 deletions(-)
create mode 100644 apps/workbench/app/views/users/_notifications.html.erb
create mode 100644 apps/workbench/app/views/users/_tables.html.erb
rename doc/api/schema/{ApiClients.textile => ApiClient.textile} (75%)
rename doc/api/schema/{Collections.textile => Collection.textile} (81%)
rename doc/api/schema/{Jobs.textile => Job.textile} (86%)
rename doc/api/schema/{JobTasks.textile => JobTask.textile} (88%)
delete mode 100644 doc/api/schema/Links.textile
create mode 100644 sdk/python/requirements.txt
via 1e8f93a86465bce9bf6b32245ef99932c3cbfe08 (commit)
via 0be3297ce7c76d312b429532541bf94a7da2b83c (commit)
via 8c8391fa8c763032742bdc0d6fa0c02ca336a82a (commit)
via 10be0dd7536aeb8909cb21573f9c47bfdc4cfbea (commit)
via 0b7ddcd0f4d867b1794bf0a0b67a6120d3345fbd (commit)
via f26e2be2691915e1db2b384bb7b90260ca4f121f (commit)
via cb2aec9c9a0fb6c4d15b9b3db25e59f3c531df42 (commit)
via c5293d314b5ac46ef712ffbee0c2fa64e8baba52 (commit)
from 8fe9c3a7c28ecc4a8b4f9fd788d5554dd391f725 (commit)
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commit 1e8f93a86465bce9bf6b32245ef99932c3cbfe08
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Dec 30 15:08:42 2013 -0500
Account status is now part of the "notifications" area
diff --git a/apps/workbench/app/controllers/users_controller.rb b/apps/workbench/app/controllers/users_controller.rb
index 002ea62..89d336f 100644
--- a/apps/workbench/app/controllers/users_controller.rb
+++ b/apps/workbench/app/controllers/users_controller.rb
@@ -10,9 +10,11 @@ class UsersController < ApplicationController
end
def home
+ @showallalerts = false
@my_ssh_keys = AuthorizedKey.where(authorized_user_uuid: current_user.uuid)
# @my_vm_perms = Link.where(tail_uuid: current_user.uuid, head_kind: 'arvados#virtual_machine', link_class: 'permission', name: 'can_login')
# @my_repo_perms = Link.where(tail_uuid: current_user.uuid, head_kind: 'arvados#repository', link_class: 'permission', name: 'can_write')
+
@my_jobs = Job.
limit(10).
order('created_at desc').
diff --git a/apps/workbench/app/views/users/_notifications.html.erb b/apps/workbench/app/views/users/_notifications.html.erb
new file mode 100644
index 0000000..37636c6
--- /dev/null
+++ b/apps/workbench/app/views/users/_notifications.html.erb
@@ -0,0 +1,101 @@
+<% if current_user.andand.is_active %>
+
+<% if @my_ssh_keys.count == 0 || @showallalerts %>
+ <div class="alert alert-info daxalert">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <%= image_tag "dax.png", class: "dax" %>
+ <div>
+ Hi, I noticed that you have not yet set up an SSH public key for use with Arvados.
+ <%= link_to "Click here to learn about SSH keys in Arvados.",
+ "http://doc.arvados.org/user/getting_started/ssh-access.html",
+ style: "font-weight: bold",
+ target: "_blank" %>
+ When you have an SSH key you would like to use, paste the SSH public key
+ in the text box.
+ </div>
+ <%= form_for AuthorizedKey.new do |f| %>
+ <%= hidden_field_tag :return_to, request.original_url %>
+ <%= f.text_area :public_key, cols: 50, rows: 4, placeholder: "Paste your public key here", style: "width: 100%" %>
+ <%= f.submit :Save, value: raw("✓"), class: "btn btn-primary pull-right" %>
+ <% end %>
+ </div>
+<% end %>
+
+<% if @my_collections.count == 0 || @showallalerts %>
+<div class="alert alert-info daxalert">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <%= image_tag "dax.png", class: "dax" %>
+ <p>
+ Hi, I noticed you haven't uploaded a new collection yet.
+ <%= link_to "Click here to learn how to upload data to Arvados Keep.",
+ "http://doc.arvados.org/user/tutorials/tutorial-keep.html",
+ style: "font-weight: bold", target: "_blank" %>
+ </p>
+</div>
+
+<% end %>
+
+<% if @my_jobs.count == 0 || @showallalerts %>
+<div class="alert alert-info daxalert">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <p><%= image_tag "dax.png", class: "dax" %>
+ Hi, I noticed you haven't run a job yet.
+ <%= link_to "Click here to learn how to run an Arvados Crunch job.",
+ "http://doc.arvados.org/user/tutorials/tutorial-job1.html",
+ style: "font-weight: bold",
+ target: "_blank" %>
+ </p>
+</div>
+<% end %>
+
+<% if @my_pipelines.count == 0 || @showallalerts %>
+<div class="alert alert-info daxalert">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <p><%= image_tag "dax.png", class: "dax" %>
+ Hi, I noticed you haven't run a pipeline yet.
+ <%= link_to "Click here to learn how to run an Arvados Crunch pipeline.",
+ "http://doc.arvados.org/user/tutorials/tutorial-new-pipeline.html",
+ style: "font-weight: bold",
+ target: "_blank" %>
+ </p>
+</div>
+<% end %>
+
+<% end %>
+
+<div class="well">
+ <p><strong>Useful links</strong></p>
+ <p><ul>
+ <li><%= link_to "Arvados project page", "http://arvados.org", target: "_blank" %></li>
+ <li><%= link_to "Tutorials and user guide",
+ "http://doc.arvados.org/user/", target: "_blank" %></li>
+ </ul>
+ </p>
+</div>
+
+<% if current_user.andand.is_active %>
+<div class="well">
+ <p><strong>System status</strong></p>
+ <table>
+ <% [Human, Trait, Collection, PipelineTemplate,
+ PipelineInstance].each do |aclass| %>
+ <tr>
+ <td>
+ <span style="margin-right: 2em">
+ <a href="/<%= raw(aclass.to_s.pluralize.underscore) %>">
+ <%= raw(aclass.to_s.pluralize.underscore.capitalize.gsub '_', ' ') %>
+ </a>
+ </span>
+ </td>
+ <td>
+ <% if aclass == 'File' %>
+ <%= Collection.limit(4000).where({}).collect(&:files).flatten(1).count %>
+ <% else %>
+ <%= aclass.limit(4000).where({}).count %>
+ <% end %>
+ </td>
+ </tr>
+ <% end %>
+ </table>
+</div>
+<% end %>
diff --git a/apps/workbench/app/views/users/_tables.html.erb b/apps/workbench/app/views/users/_tables.html.erb
new file mode 100644
index 0000000..c52057c
--- /dev/null
+++ b/apps/workbench/app/views/users/_tables.html.erb
@@ -0,0 +1,182 @@
+<% if current_user.andand.is_active %>
+ <div>
+ <strong>Recent jobs</strong>
+ <%= link_to raw("Show all jobs →"), jobs_path, class: 'pull-right' %>
+ <% if not current_user.andand.is_active or @my_jobs.empty? %>
+ <br/>(None)
+ <% else %>
+ <table class="table table-bordered table-condensed job-table">
+ <colgroup>
+ <col width="28%" />
+ <col width="38%" />
+ <col width="7%" />
+ <col width="15%" />
+ <col width="12%" />
+ </colgroup>
+
+ <tr>
+ <th>Script</th>
+ <th>Output</th>
+ <th>Log</th>
+ <th>Status</th>
+ <th>Age</th>
+ </tr>
+
+ <% @my_jobs[0..6].each do |j| %>
+ <tr>
+ <td>
+ <small>
+ <%= link_to j.script[0..31], job_path(j.uuid) %>
+ </small>
+ </td>
+
+ <td>
+ <small>
+ <% if j.success %>
+
+ <a href="<%= collection_path(j.output) %>">
+ <% Collection.limit(1).where(uuid: j.output).each do |c|
+ c.files.each do |file| %>
+ <%= "#{file[0]}/#{file[1]}" %>
+ <% end %>
+ <% end %>
+ </a>
+
+ <% end %>
+ </small>
+</td>
+
+<td>
+ <small>
+ <% if j.success %>
+ <a href="<%= collection_path(j.log) %>">Log</a>
+ <% end %>
+ </small>
+</td>
+
+<td>
+ <small>
+ <%= raw(distance_of_time_in_words(j[:created_at], Time.now).sub('about
+','~').sub(' ',' ')) if j[:created_at] %> ago
+ </small>
+</td>
+
+<td>
+ <% if j.success %>
+ <span class="label label-success">finished</span>
+ <% elsif j.success == false %>
+ <span class="label label-danger">failed</span>
+ <% elsif j.running and j.started_at and not j.finished_at %>
+ <% percent_total_tasks = 100 / (j.tasks_summary[:running] + j.tasks_summary[:done] + j.tasks_summary[:todo]) rescue 0 %>
+ <div class="progress" style="margin-bottom: 0">
+ <div class="bar bar-success" style="width: <%= j.tasks_summary[:done] * percent_total_tasks rescue 0 %>%;"></div>
+ <div class="bar" style="width: <%= j.tasks_summary[:running] * percent_total_tasks rescue 0 %>%; opacity: 0.3"></div>
+ </div>
+ <% else %>
+ <span class="label">queued</span>
+ <% end %>
+</td>
+
+</tr>
+<% end %>
+</table>
+<% end %>
+</div>
+
+<div>
+ <strong>Recent pipeline instances</strong>
+ <%= link_to raw("Show all pipeline instances →"), jobs_path, class: 'pull-right' %>
+ <% if not current_user.andand.is_active or @my_pipelines.empty? %>
+ <br/>(None)
+ <% else %>
+ <table class="table table-bordered table-condensed job-table">
+ <colgroup>
+ <col width="73%" />
+ <col width="15%" />
+ <col width="12%" />
+ </colgroup>
+
+ <tr>
+ <th>Pipeline template</th>
+ <th>Age</th>
+ <th>Status</th>
+ </tr>
+
+ <% @my_pipelines[0..6].each do |p| %>
+ <tr>
+ <td>
+ <small>
+ <% PipelineTemplate.limit(1).where(uuid: p.pipeline_template_uuid).each do |i| %>
+ <%= link_to i.name, pipeline_instance_path(p.uuid) %>
+ <% end %>
+ </small>
+ </td>
+
+ <td>
+ <small>
+ <%= raw(distance_of_time_in_words(p[:created_at], Time.now).sub('about
+','~').sub(' ',' ')) if p[:created_at] %> ago
+ </small>
+ </td>
+
+ <td>
+ <% if p.success %>
+ <span class="label label-success">finished</span>
+ <% elsif p.success == false %>
+ <span class="label label-danger">failed</span>
+ <% elsif p.active %>
+ <span class="label label-info">running</span>
+ <% else %>
+ <span class="label">queued</span>
+ <% end %>
+ </td>
+
+ </tr>
+ <% end %>
+ </table>
+ <% end %>
+</div>
+
+<div>
+ <strong>Recent collections</strong>
+ <%= link_to raw("Show all collections →"), collections_path, class: 'pull-right' %>
+ <% if not current_user.andand.is_active or @my_collections.empty? %>
+ <br/>(None)
+ <% else %>
+ <table class="table table-bordered table-condensed job-table">
+ <colgroup>
+ <col width="73%" />
+ <col width="27%" />
+ </colgroup>
+
+ <tr>
+ <th>Contents</th>
+ <th>Age</th>
+ </tr>
+
+ <% @my_collections[0..6].each do |c| %>
+ <tr>
+ <td>
+ <small>
+ <a href="<%= collection_path(c.uuid) %>">
+ <% c.files.each do |file| %>
+ <%= "#{file[0]}/#{file[1]}" %>
+ <% end %>
+ </a>
+ </small>
+ </td>
+ <td>
+ <small>
+ <%= raw(distance_of_time_in_words(c[:created_at], Time.now).sub('about
+','~').sub(' ',' ')) if c[:created_at] %> ago
+ </small>
+ </td>
+ </tr>
+ <% end %>
+ </table>
+ <% end %>
+</div>
+
+<% else %>
+ <%= image_tag "dax.png", style: "max-width=40%" %>
+<% end %>
diff --git a/apps/workbench/app/views/users/home.html.erb b/apps/workbench/app/views/users/home.html.erb
index 89fab32..d221db9 100644
--- a/apps/workbench/app/views/users/home.html.erb
+++ b/apps/workbench/app/views/users/home.html.erb
@@ -37,315 +37,37 @@
</style>
<% end %>
-<% if current_user.andand.is_active %>
-
<div class="container-fluid">
-
- <div class="span7">
-
- <div>
- <strong>Recent jobs</strong>
- <%= link_to raw("Show all jobs →"), jobs_path, class: 'pull-right' %>
- <% if not current_user.andand.is_active or @my_jobs.empty? %>
- (None)
- <% else %>
- <table class="table table-bordered table-condensed job-table">
- <colgroup>
- <col width="28%" />
- <col width="38%" />
- <col width="7%" />
- <col width="15%" />
- <col width="12%" />
- </colgroup>
-
- <tr>
- <th>Script</th>
- <th>Output</th>
- <th>Log</th>
- <th>Status</th>
- <th>Age</th>
- </tr>
-
- <% @my_jobs[0..6].each do |j| %>
- <tr>
- <td>
- <small>
- <%= link_to j.script[0..31], job_path(j.uuid) %>
- </small>
- </td>
-
- <td>
- <small>
- <% if j.success %>
- <a href="<%= collection_path(j.output) %>">
- <% Collection.limit(1).where(uuid: j.output).each do |c|
- c.files.each do |file| %>
- <%= "#{file[0]}/#{file[1]}" %>
- <% end %>
- <% end %>
- </a>
-
- <% end %>
- </small>
- </td>
-
- <td>
- <small>
- <% if j.success %>
- <a href="<%= collection_path(j.log) %>">Log</a>
- <% end %>
- </small>
- </td>
-
- <td>
- <small>
-<%= raw(distance_of_time_in_words(j[:created_at], Time.now).sub('about
-','~').sub(' ',' ')) if j[:created_at] %> ago
- </small>
- </td>
-
- <td>
- <% if j.success %>
- <span class="label label-success">finished</span>
- <% elsif j.success == false %>
- <span class="label label-danger">failed</span>
- <% elsif j.running and j.started_at and not j.finished_at %>
- <% percent_total_tasks = 100 / (j.tasks_summary[:running] + j.tasks_summary[:done] + j.tasks_summary[:todo]) rescue 0 %>
- <div class="progress" style="margin-bottom: 0">
- <div class="bar bar-success" style="width: <%= j.tasks_summary[:done] * percent_total_tasks rescue 0 %>%;"></div>
- <div class="bar" style="width: <%= j.tasks_summary[:running] * percent_total_tasks rescue 0 %>%; opacity: 0.3"></div>
- </div>
- <% else %>
- <span class="label">queued</span>
- <% end %>
- </td>
-
- </tr>
- <% end %>
- </table>
- <% end %>
- </div>
+ <div class="span3 pull-right">
+ <br/>
- <div>
- <strong>Recent pipeline instances</strong>
- <%= link_to raw("Show all pipeline instances →"), jobs_path, class: 'pull-right' %>
- <% if not current_user.andand.is_active or @my_pipelines.empty? %>
- (None)
- <% else %>
- <table class="table table-bordered table-condensed job-table">
- <colgroup>
- <col width="73%" />
- <col width="15%" />
- <col width="12%" />
- </colgroup>
-
- <tr>
- <th>Pipeline template</th>
- <th>Age</th>
- <th>Status</th>
- </tr>
-
- <% @my_pipelines[0..6].each do |p| %>
- <tr>
- <td>
- <small>
- <% PipelineTemplate.limit(1).where(uuid: p.pipeline_template_uuid).each do |i| %>
- <%= link_to i.name, pipeline_instance_path(p.uuid) %>
- <% end %>
- </small>
- </td>
-
- <td>
- <small>
-<%= raw(distance_of_time_in_words(p[:created_at], Time.now).sub('about
-','~').sub(' ',' ')) if p[:created_at] %> ago
- </small>
- </td>
-
- <td>
- <% if p.success %>
- <span class="label label-success">finished</span>
- <% elsif p.success == false %>
- <span class="label label-danger">failed</span>
- <% elsif p.active %>
- <span class="label label-info">running</span>
- <% else %>
- <span class="label">queued</span>
- <% end %>
- </td>
-
- </tr>
- <% end %>
- </table>
- <% end %>
+ <div class="well">
+<% if current_user.andand.is_active %>
+ <p>Your account status:<br/>
+ <strong>Active</strong></p>
+<% elsif current_user %>
+ <p>Your account status:<br/>
+ <strong>New / inactive</strong></p>
+ <p>
+ Your account must be activated by an Arvados administrator. If this
+ is your first time accessing Arvados and would like to request
+ access, or you believe you are seeing the page in error, please
+ <%= link_to "contact us", Rails.configuration.activation_contact_link %>.
+ You should receive an email at the address you used to log in when
+ your account is activated.
+ </p>
+ <p>
+ <%= link_to raw('Contact us ✉'),
+ Rails.configuration.activation_contact_link, class: "btn btn-primary" %></p>
+<% end %>
</div>
- <div>
- <strong>Recent collections</strong>
- <%= link_to raw("Show all collections →"), collections_path, class: 'pull-right' %>
- <% if not current_user.andand.is_active or @my_collections.empty? %>
- (None)
- <% else %>
- <table class="table table-bordered table-condensed job-table">
- <colgroup>
- <col width="73%" />
- <col width="27%" />
- </colgroup>
-
- <tr>
- <th>Contents</th>
- <th>Age</th>
- </tr>
-
- <% @my_collections[0..6].each do |c| %>
- <tr>
- <td>
- <small>
- <a href="<%= collection_path(c.uuid) %>">
- <% c.files.each do |file| %>
- <%= "#{file[0]}/#{file[1]}" %>
- <% end %>
- </a>
- </small>
- </td>
- <td>
- <small>
-<%= raw(distance_of_time_in_words(c[:created_at], Time.now).sub('about
-','~').sub(' ',' ')) if c[:created_at] %> ago
- </small>
- </td>
- </tr>
- <% end %>
- </table>
- <% end %>
- </div>
+ <%= render :partial => 'notifications' %>
</div>
-
-<div class="span4">
-<br/>
-
-<% if @my_ssh_keys.count == 0%>
- <div class="alert alert-info daxalert">
- <button type="button" class="close" data-dismiss="alert">×</button>
- <%= image_tag "dax.png", class: "dax" %>
- <div>
- Hi, I noticed that you have not yet set up an SSH public key for use with Arvados.
- <%= link_to "Click here to learn about SSH keys in Arvados.",
- "http://doc.arvados.org/user/getting_started/ssh-access.html",
- style: "font-weight: bold",
- target: "_blank" %>
- When you have an SSH key you would like to use, paste the SSH public key
- in the text box.
- </div>
- <%= form_for AuthorizedKey.new do |f| %>
- <%= hidden_field_tag :return_to, request.original_url %>
- <%= f.text_area :public_key, cols: 50, rows: 4, placeholder: "Paste your public key here", style: "width: 100%" %>
- <%= f.submit :Save, value: raw("✓"), class: "btn btn-primary pull-right" %>
- <% end %>
+
+ <div class="span8">
+ <%= render :partial => 'tables' %>
</div>
-<% end %>
-
-<% if @my_collections.count == 0 %>
-<div class="alert alert-info daxalert">
- <button type="button" class="close" data-dismiss="alert">×</button>
- <%= image_tag "dax.png", class: "dax" %>
- <p>
- Hi, I noticed you haven't uploaded a new collection yet.
- <%= link_to "Click here to learn how to upload data to Arvados Keep.",
- "http://doc.arvados.org/user/tutorials/tutorial-keep.html",
- style: "font-weight: bold", target: "_blank" %>
- </p>
-</div>
-
-<% end %>
-
-<% if @my_jobs.count == 0 %>
-<div class="alert alert-info daxalert">
- <button type="button" class="close" data-dismiss="alert">×</button>
- <p><%= image_tag "dax.png", class: "dax" %>
- Hi, I noticed you haven't run a job yet.
- <%= link_to "Click here to learn how to run an Arvados Crunch job.",
- "http://doc.arvados.org/user/tutorials/tutorial-job1.html",
- style: "font-weight: bold",
- target: "_blank" %>
- </p>
-</div>
-<% end %>
-
-<% if @my_pipelines.count == 0 %>
-<div class="alert alert-info daxalert">
- <button type="button" class="close" data-dismiss="alert">×</button>
- <p><%= image_tag "dax.png", class: "dax" %>
- Hi, I noticed you haven't run a pipeline yet.
- <%= link_to "Click here to learn how to run an Arvados Crunch pipeline.",
- "http://doc.arvados.org/user/tutorials/tutorial-new-pipeline.html",
- style: "font-weight: bold",
- target: "_blank" %>
- </p>
-</div>
-<% end %>
-
-<div class="well">
- <p><strong>Useful links</strong></p>
- <p><ul>
- <li><%= link_to "Arvados project page", "http://arvados.org", target: "_blank" %></li>
- <li><%= link_to "Tutorials and user guide",
- "http://doc.arvados.org/user/", target: "_blank" %></li>
- </ul>
- </p>
-</div>
-
-<div class="well">
- <p><strong>System status</strong></p>
- <table>
- <% [Human, Trait, Collection, PipelineTemplate,
- PipelineInstance].each do |aclass| %>
- <tr>
- <td>
- <span style="margin-right: 2em">
- <a href="/<%= raw(aclass.to_s.pluralize.underscore) %>">
- <%= raw(aclass.to_s.pluralize.underscore.capitalize.gsub '_', ' ') %>
- </a>
- </span>
- </td>
- <td>
- <% if aclass == 'File' %>
- <%= Collection.limit(4000).where({}).collect(&:files).flatten(1).count %>
- <% else %>
- <%= aclass.limit(4000).where({}).count %>
- <% end %>
- </td>
- </tr>
- <% end %>
- </table>
-</div>
</div>
-</div>
-
-<% elsif current_user %>
- <%= image_tag "dax.png", style: "float: left; max-width: 25%; margin-right: 2em" %>
- <h1>Welcome to Arvados, <%= current_user.first_name %>!</h1>
- <div class="row-fluid">
- <div class="col span8">
- <h4>Your account status</h4>
- <div class="well clearfix">
- <p><strong>New / inactive</strong></p>
- <p>
- Your account must be activated by an Arvados administrator. If this
- is your first time accessing Arvados and would like to request
- access, or you believe you are seeing the page in error, please
- <%= link_to "contact us", Rails.configuration.activation_contact_link %>.
- You should receive an email at the address you used to log in when
- your account is activated. In the mean time, you can
- <%= link_to "learn more about Arvados", "https://arvados.org/projects/arvados/wiki/Introduction_to_Arvados" %>,
- and <%= link_to "read the Arvados user guide", "http://doc.arvados.org/user" %>.
- </p>
- <p>
- <%= link_to raw('Contact us ✉'),
- Rails.configuration.activation_contact_link, class: "pull-right btn btn-primary" %></p>
- </div>
- </div>
- </div>
-<% end %>
commit 0be3297ce7c76d312b429532541bf94a7da2b83c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Dec 30 12:19:22 2013 -0500
Added system status box
diff --git a/apps/workbench/app/views/users/home.html.erb b/apps/workbench/app/views/users/home.html.erb
index bf14fdd..89fab32 100644
--- a/apps/workbench/app/views/users/home.html.erb
+++ b/apps/workbench/app/views/users/home.html.erb
@@ -223,6 +223,8 @@
</div>
<div class="span4">
+<br/>
+
<% if @my_ssh_keys.count == 0%>
<div class="alert alert-info daxalert">
<button type="button" class="close" data-dismiss="alert">×</button>
@@ -294,6 +296,31 @@
</p>
</div>
+<div class="well">
+ <p><strong>System status</strong></p>
+ <table>
+ <% [Human, Trait, Collection, PipelineTemplate,
+ PipelineInstance].each do |aclass| %>
+ <tr>
+ <td>
+ <span style="margin-right: 2em">
+ <a href="/<%= raw(aclass.to_s.pluralize.underscore) %>">
+ <%= raw(aclass.to_s.pluralize.underscore.capitalize.gsub '_', ' ') %>
+ </a>
+ </span>
+ </td>
+ <td>
+ <% if aclass == 'File' %>
+ <%= Collection.limit(4000).where({}).collect(&:files).flatten(1).count %>
+ <% else %>
+ <%= aclass.limit(4000).where({}).count %>
+ <% end %>
+ </td>
+ </tr>
+ <% end %>
+ </table>
+</div>
+
</div>
</div>
commit 8c8391fa8c763032742bdc0d6fa0c02ca336a82a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Dec 30 11:54:28 2013 -0500
New two-column dashboard layout suggested by Adam
diff --git a/apps/workbench/app/views/layouts/application.html.erb b/apps/workbench/app/views/layouts/application.html.erb
index c295dc3..e7c7d5d 100644
--- a/apps/workbench/app/views/layouts/application.html.erb
+++ b/apps/workbench/app/views/layouts/application.html.erb
@@ -93,10 +93,10 @@
Docs <b class="caret"></b>
</a>
<ul class="dropdown-menu">
- <li><%= link_to 'Tutorials and User guide', "http://doc.arvados.org/user" %></li>
- <li><%= link_to 'API Reference', "http://doc.arvados.org/api" %></li>
- <li><%= link_to 'Admin guide', "http://doc.arvados.org/admin" %></li>
- <li><%= link_to 'Install guide', "http://doc.arvados.org/install" %></li>
+ <li><%= link_to 'Tutorials and User guide', "http://doc.arvados.org/user", target: "_blank" %></li>
+ <li><%= link_to 'API Reference', "http://doc.arvados.org/api", target: "_blank" %></li>
+ <li><%= link_to 'Admin guide', "http://doc.arvados.org/admin", target: "_blank" %></li>
+ <li><%= link_to 'Install guide', "http://doc.arvados.org/install", target: "_blank" %></li>
</ul>
</li>
diff --git a/apps/workbench/app/views/users/home.html.erb b/apps/workbench/app/views/users/home.html.erb
index d99b29a..bf14fdd 100644
--- a/apps/workbench/app/views/users/home.html.erb
+++ b/apps/workbench/app/views/users/home.html.erb
@@ -27,7 +27,7 @@
font-weight: bold;
}
.dax {
- max-width: 5%;
+ max-width: 10%;
margin-right: 1em;
float: left
}
@@ -39,116 +39,72 @@
<% if current_user.andand.is_active %>
+<div class="container-fluid">
+
+ <div class="span7">
-<% if @my_ssh_keys.count == 0%>
- <div class="alert alert-info daxalert">
- <button type="button" class="close" data-dismiss="alert">×</button>
- <%= image_tag "dax.png", class: "dax" %>
- <div class="span5" style="margin-right: 1em">
- Hi, I noticed that you have not yet set up an SSH public key for use with Arvados.
- <%= link_to "Click here to learn about SSH keys in Arvados.",
- "http://doc.arvados.org/user/getting_started/ssh-access.html", style: "font-weight: bold" %>
- Once have an SSH key you would like to use, paste your SSH public key
- in the text box.
- </div>
- <%= form_for AuthorizedKey.new do |f| %>
- <%= hidden_field_tag :return_to, request.original_url %>
- <%= f.text_area :public_key, cols: 50, rows: 4, placeholder: "Paste your public key here", style: "width: 40%" %>
- <%= f.submit :Save, value: raw("✓"), class: "btn btn-primary", style: "vertical-align: top" %>
- <% end %>
- </div>
-<% end %>
-
-<% if @my_collections.count == 0 %>
-<div class="alert alert-info daxalert">
- <button type="button" class="close" data-dismiss="alert">×</button>
- <%= image_tag "dax.png", class: "dax" %>
- <p>
- Hi, I noticed you haven't uploaded a new collection yet.
- <%= link_to "Click here to learn how to upload data to Arvados Keep.", "http://doc.arvados.org/user/tutorials/tutorial-keep.html", style: "font-weight: bold" %>
- </p>
-</div>
-
-<% end %>
-
-<% if @my_jobs.count == 0 %>
-<div class="alert alert-info daxalert">
- <button type="button" class="close" data-dismiss="alert">×</button>
- <p><%= image_tag "dax.png", class: "dax" %>
- Hi, I noticed you haven't run a job yet.
- <%= link_to "Click here to learn how to run an Arvados Crunch job.", "http://doc.arvados.org/user/tutorials/tutorial-job1.html", style: "font-weight: bold" %>
- </p>
-</div>
-<% end %>
-
-<% if @my_pipelines.count == 0 %>
-<div class="alert alert-info daxalert">
- <button type="button" class="close" data-dismiss="alert">×</button>
- <p><%= image_tag "dax.png", class: "dax" %>
- Hi, I noticed you haven't run a pipeline yet.
- <%= link_to "Click here to learn how to run an Arvados Crunch pipeline.", "http://doc.arvados.org/user/tutorials/tutorial-new-pipeline.html", style: "font-weight: bold" %>
- </p>
-</div>
-<% end %>
-
-<div class="row-fluid">
-
- <div class="col span4">
- <div class="clearfix">
- <h4>Recent collections</h4>
- <% if not current_user.andand.is_active or @my_collections.empty? %>
+ <div>
+ <strong>Recent jobs</strong>
+ <%= link_to raw("Show all jobs →"), jobs_path, class: 'pull-right' %>
+ <% if not current_user.andand.is_active or @my_jobs.empty? %>
(None)
<% else %>
<table class="table table-bordered table-condensed job-table">
<colgroup>
- <col width="70%" />
- <col width="30%" />
+ <col width="28%" />
+ <col width="38%" />
+ <col width="7%" />
+ <col width="15%" />
+ <col width="12%" />
</colgroup>
- <% @my_collections[0..8].each do |c| %>
+
+ <tr>
+ <th>Script</th>
+ <th>Output</th>
+ <th>Log</th>
+ <th>Status</th>
+ <th>Age</th>
+ </tr>
+
+ <% @my_jobs[0..6].each do |j| %>
<tr>
<td>
<small>
- <a href="<%= collection_path(c.uuid) %>">
- <% c.files.each do |file| %>
- <%= "#{file[0]}/#{file[1]}" %>
- <% end %>
- </a>
- </small>
- </td>
- <td>
- <small>
-<%= raw(distance_of_time_in_words(c[:created_at], Time.now).sub('about
-','~').sub(' ',' ')) if c[:created_at] %> ago
+ <%= link_to j.script[0..31], job_path(j.uuid) %>
</small>
</td>
- </tr>
- <% end %>
- </table>
- <%= link_to raw("Show all collections →"), collections_path, class: 'pull-right' %>
- <% end %>
- </div>
- </div>
- <div class="col span4">
- <div class="clearfix">
- <h4>Recent jobs</h4>
- <% if not current_user.andand.is_active or @my_jobs.empty? %>
- (None)
- <% else %>
- <table class="table table-bordered table-condensed job-table">
- <colgroup>
- <col width="40%" />
- <col width="20%" />
- <col width="40%" />
- </colgroup>
+ <td>
+ <small>
+ <% if j.success %>
+
+ <a href="<%= collection_path(j.output) %>">
+ <% Collection.limit(1).where(uuid: j.output).each do |c|
+ c.files.each do |file| %>
+ <%= "#{file[0]}/#{file[1]}" %>
+ <% end %>
+ <% end %>
+ </a>
+
+ <% end %>
+ </small>
+ </td>
+
+ <td>
+ <small>
+ <% if j.success %>
+ <a href="<%= collection_path(j.log) %>">Log</a>
+ <% end %>
+ </small>
+ </td>
- <% @my_jobs[0..8].each do |j| %>
- <tr>
<td>
<small>
- <%= link_to j.script[0..31], job_path(j.uuid) %>
+<%= raw(distance_of_time_in_words(j[:created_at], Time.now).sub('about
+','~').sub(' ',' ')) if j[:created_at] %> ago
</small>
</td>
+
<td>
<% if j.success %>
<span class="label label-success">finished</span>
@@ -164,42 +120,33 @@
<span class="label">queued</span>
<% end %>
</td>
- <td>
- <small>
- <% if j.success %>
- <a href="<%= collection_path(j.output) %>">
- <% Collection.limit(1).where(uuid: j.output).each do |c|
- c.files.each do |file| %>
- <%= "#{file[0]}/#{file[1]}" %>
- <% end %>
- <% end %>
- </a>
-
- <% end %>
- </small>
- </td>
</tr>
<% end %>
</table>
- <%= link_to raw("Show all jobs →"), jobs_path, class: 'pull-right' %>
<% end %>
</div>
- </div>
- <div class="col span4">
- <div class="clearfix">
- <h4>Recent pipeline instances</h4>
+ <div>
+ <strong>Recent pipeline instances</strong>
+ <%= link_to raw("Show all pipeline instances →"), jobs_path, class: 'pull-right' %>
<% if not current_user.andand.is_active or @my_pipelines.empty? %>
(None)
<% else %>
<table class="table table-bordered table-condensed job-table">
<colgroup>
- <col width="80%" />
- <col width="20%" />
+ <col width="73%" />
+ <col width="15%" />
+ <col width="12%" />
</colgroup>
- <% @my_pipelines[0..8].each do |p| %>
+ <tr>
+ <th>Pipeline template</th>
+ <th>Age</th>
+ <th>Status</th>
+ </tr>
+
+ <% @my_pipelines[0..6].each do |p| %>
<tr>
<td>
<small>
@@ -208,6 +155,14 @@
<% end %>
</small>
</td>
+
+ <td>
+ <small>
+<%= raw(distance_of_time_in_words(p[:created_at], Time.now).sub('about
+','~').sub(' ',' ')) if p[:created_at] %> ago
+ </small>
+ </td>
+
<td>
<% if p.success %>
<span class="label label-success">finished</span>
@@ -219,15 +174,127 @@
<span class="label">queued</span>
<% end %>
</td>
+
+ </tr>
+ <% end %>
+ </table>
+ <% end %>
+ </div>
+
+ <div>
+ <strong>Recent collections</strong>
+ <%= link_to raw("Show all collections →"), collections_path, class: 'pull-right' %>
+ <% if not current_user.andand.is_active or @my_collections.empty? %>
+ (None)
+ <% else %>
+ <table class="table table-bordered table-condensed job-table">
+ <colgroup>
+ <col width="73%" />
+ <col width="27%" />
+ </colgroup>
+
+ <tr>
+ <th>Contents</th>
+ <th>Age</th>
+ </tr>
+
+ <% @my_collections[0..6].each do |c| %>
+ <tr>
+ <td>
+ <small>
+ <a href="<%= collection_path(c.uuid) %>">
+ <% c.files.each do |file| %>
+ <%= "#{file[0]}/#{file[1]}" %>
+ <% end %>
+ </a>
+ </small>
+ </td>
+ <td>
+ <small>
+<%= raw(distance_of_time_in_words(c[:created_at], Time.now).sub('about
+','~').sub(' ',' ')) if c[:created_at] %> ago
+ </small>
+ </td>
</tr>
<% end %>
</table>
- <%= link_to raw("Show all pipeline instances →"), jobs_path, class: 'pull-right' %>
<% end %>
</div>
</div>
+<div class="span4">
+<% if @my_ssh_keys.count == 0%>
+ <div class="alert alert-info daxalert">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <%= image_tag "dax.png", class: "dax" %>
+ <div>
+ Hi, I noticed that you have not yet set up an SSH public key for use with Arvados.
+ <%= link_to "Click here to learn about SSH keys in Arvados.",
+ "http://doc.arvados.org/user/getting_started/ssh-access.html",
+ style: "font-weight: bold",
+ target: "_blank" %>
+ When you have an SSH key you would like to use, paste the SSH public key
+ in the text box.
+ </div>
+ <%= form_for AuthorizedKey.new do |f| %>
+ <%= hidden_field_tag :return_to, request.original_url %>
+ <%= f.text_area :public_key, cols: 50, rows: 4, placeholder: "Paste your public key here", style: "width: 100%" %>
+ <%= f.submit :Save, value: raw("✓"), class: "btn btn-primary pull-right" %>
+ <% end %>
+ </div>
+<% end %>
+<% if @my_collections.count == 0 %>
+<div class="alert alert-info daxalert">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <%= image_tag "dax.png", class: "dax" %>
+ <p>
+ Hi, I noticed you haven't uploaded a new collection yet.
+ <%= link_to "Click here to learn how to upload data to Arvados Keep.",
+ "http://doc.arvados.org/user/tutorials/tutorial-keep.html",
+ style: "font-weight: bold", target: "_blank" %>
+ </p>
+</div>
+
+<% end %>
+
+<% if @my_jobs.count == 0 %>
+<div class="alert alert-info daxalert">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <p><%= image_tag "dax.png", class: "dax" %>
+ Hi, I noticed you haven't run a job yet.
+ <%= link_to "Click here to learn how to run an Arvados Crunch job.",
+ "http://doc.arvados.org/user/tutorials/tutorial-job1.html",
+ style: "font-weight: bold",
+ target: "_blank" %>
+ </p>
+</div>
+<% end %>
+
+<% if @my_pipelines.count == 0 %>
+<div class="alert alert-info daxalert">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <p><%= image_tag "dax.png", class: "dax" %>
+ Hi, I noticed you haven't run a pipeline yet.
+ <%= link_to "Click here to learn how to run an Arvados Crunch pipeline.",
+ "http://doc.arvados.org/user/tutorials/tutorial-new-pipeline.html",
+ style: "font-weight: bold",
+ target: "_blank" %>
+ </p>
+</div>
+<% end %>
+
+<div class="well">
+ <p><strong>Useful links</strong></p>
+ <p><ul>
+ <li><%= link_to "Arvados project page", "http://arvados.org", target: "_blank" %></li>
+ <li><%= link_to "Tutorials and user guide",
+ "http://doc.arvados.org/user/", target: "_blank" %></li>
+ </ul>
+ </p>
+</div>
+
+</div>
</div>
<% elsif current_user %>
diff --git a/sdk/cli/Gemfile.lock b/sdk/cli/Gemfile.lock
index afbc573..b14404a 100644
--- a/sdk/cli/Gemfile.lock
+++ b/sdk/cli/Gemfile.lock
@@ -1,12 +1,58 @@
GEM
remote: https://rubygems.org/
specs:
+ activesupport (3.2.16)
+ i18n (~> 0.6, >= 0.6.4)
+ multi_json (~> 1.0)
+ addressable (2.3.5)
+ andand (1.3.3)
+ autoparse (0.3.3)
+ addressable (>= 2.3.1)
+ extlib (>= 0.9.15)
+ multi_json (>= 1.0.0)
+ curb (0.8.5)
+ extlib (0.9.16)
+ faraday (0.8.8)
+ multipart-post (~> 1.2.0)
+ google-api-client (0.6.4)
+ addressable (>= 2.3.2)
+ autoparse (>= 0.3.3)
+ extlib (>= 0.9.15)
+ faraday (~> 0.8.4)
+ jwt (>= 0.1.5)
+ launchy (>= 2.1.1)
+ multi_json (>= 1.0.0)
+ signet (~> 0.4.5)
+ uuidtools (>= 2.1.0)
+ i18n (0.6.9)
+ json (1.8.1)
+ jwt (0.1.8)
+ multi_json (>= 1.5)
+ launchy (2.4.2)
+ addressable (~> 2.3)
minitest (5.0.8)
+ multi_json (1.8.2)
+ multipart-post (1.2.0)
+ oj (2.5.1)
rake (10.1.0)
+ signet (0.4.5)
+ addressable (>= 2.2.3)
+ faraday (~> 0.8.1)
+ jwt (>= 0.1.5)
+ multi_json (>= 1.0.0)
+ trollop (2.0)
+ uuidtools (2.1.4)
PLATFORMS
ruby
DEPENDENCIES
+ activesupport (>= 3.2.13)
+ andand (>= 1.3.3)
+ curb (~> 0.8)
+ google-api-client (>= 0.6.3)
+ json (>= 1.7.7)
minitest
+ oj (>= 2.0.3)
rake
+ trollop (>= 2.0)
commit 10be0dd7536aeb8909cb21573f9c47bfdc4cfbea
Merge: 8fe9c3a 0b7ddcd
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Dec 30 09:05:05 2013 -0500
Merge branch 'master' of git.clinicalfuture.com:arvados into 1692-redesign-dashboard
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