[ARVADOS] updated: ebd7d57174dd06515a9938e227d2aa5d5dc00908
git at public.curoverse.com
git at public.curoverse.com
Tue Jul 8 09:57:34 EDT 2014
Summary of changes:
.../app/controllers/projects_controller.rb | 2 +-
.../app/views/collections/_show_recent.html.erb | 22 ++-
.../pipeline_instances/_show_components.html.erb | 10 +-
.../app/views/projects/_show_contents.html.erb | 122 +++++++++++++++++
crunch_scripts/arvados-bcbio-nextgen.py | 4 +
doc/_includes/_ssh_addkey.liquid | 26 ++++
doc/_includes/_ssh_intro.liquid | 7 +
doc/images/ssh-adding-public-key.png | Bin 38943 -> 17463 bytes
.../ssh-access-unix.html.textile.liquid | 32 +----
.../ssh-access-windows.html.textile.liquid | 32 +----
sdk/cli/bin/arv-run-pipeline-instance | 35 +++--
sdk/cli/bin/crunch-job | 19 +--
sdk/python/arvados/commands/put.py | 100 +++++++++++---
sdk/python/tests/test_arv_put.py | 151 ++++++++++++++++++++-
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 6 +-
16 files changed, 442 insertions(+), 128 deletions(-)
create mode 100644 apps/workbench/app/views/projects/_show_contents.html.erb
create mode 100644 doc/_includes/_ssh_addkey.liquid
create mode 100644 doc/_includes/_ssh_intro.liquid
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commit ebd7d57174dd06515a9938e227d2aa5d5dc00908
Merge: d61435c dc680bd
Author: radhika <radhika at curoverse.com>
Date: Tue Jul 8 09:40:55 2014 -0400
Merge branch 'master' into 2380-ssh-doc
commit d61435c10c5fc3b6e346a7668bd9b44a7b12c67e
Author: radhika <radhika at curoverse.com>
Date: Tue Jul 8 09:40:27 2014 -0400
2380: update the add key image and text
diff --git a/doc/_includes/_ssh_addkey.liquid b/doc/_includes/_ssh_addkey.liquid
index aa6b72d..8f2a233 100644
--- a/doc/_includes/_ssh_addkey.liquid
+++ b/doc/_includes/_ssh_addkey.liquid
@@ -13,11 +13,11 @@ If you want to add more SSH keys, click on the link with your _email address_ in
On the *Authorized keys* page, the click on the button <span class="btn btn-primary disabled">Add a new authorized key</span> in the upper right corner.
-The page will reload with a new row of information. Under the *public_key* column heading, click on the cell +New authorized key+. This will open an editing popup as shown in this screenshot:
+A new authorized key will be added and you will be taken to the key's page. Towards the bottom of this page you will see the *public_key* attribute. Click on the cell +New authorized key+. This will open an editing popup as shown in this screenshot:
!{{ site.baseurl }}/images/ssh-adding-public-key.png!
-Paste the public key that you copied to the cliboard in the previous section into the popup text box, then click on the check mark to save it. This should refresh the page with the public key that you just added now listed under the *public_key* column. You are now ready to "log into an Arvados VM":#login.
+Paste the public key that you copied to the cliboard in the previous section into the popup text box, then click on the check mark to save it. This should refresh the page with the public key that you just added as the *public_key* attribute value. You are now ready to "log into an Arvados VM":#login.
h1(#login). Using SSH to log into an Arvados VM
diff --git a/doc/images/ssh-adding-public-key.png b/doc/images/ssh-adding-public-key.png
index e7262bb..aab2955 100644
Binary files a/doc/images/ssh-adding-public-key.png and b/doc/images/ssh-adding-public-key.png differ
commit 1e8b1d0e816e09bee9a819277fd91da1dea6fa35
Author: radhika <radhika at curoverse.com>
Date: Tue Jul 8 09:09:02 2014 -0400
2380: more updates
diff --git a/doc/_includes/_ssh_addkey.liquid b/doc/_includes/_ssh_addkey.liquid
index 830bcfb..aa6b72d 100644
--- a/doc/_includes/_ssh_addkey.liquid
+++ b/doc/_includes/_ssh_addkey.liquid
@@ -21,6 +21,6 @@ Paste the public key that you copied to the cliboard in the previous section int
h1(#login). Using SSH to log into an Arvados VM
-To see a list of virtual machines that you have access to and determine the name and login information, click on *Settings* menu in the top navigation bar and click on *Virtual machines*. Once on the *Virtual machines* page, The *hostname* columns lists the name of each available VM. The *logins* column will have a value in the form of @["you"]@. Your login name is the text inside the quotes. In this guide the hostname will be *_shell_* and the login will be *_you_*. Replace these with your hostname and login name as appropriate.
+To see a list of virtual machines that you have access to and determine the name and login information, click on *Settings* menu in the top navigation bar and click on *Virtual machines*. Once on the *Virtual machines* page, The *hostname* column lists the name of each available VM. The *logins* column will have a value in the form of @["you"]@. Your login name is the text inside the quotes. In this guide the hostname will be *_shell_* and the login will be *_you_*. Replace these with your hostname and login name as appropriate.
diff --git a/doc/user/getting_started/ssh-access-unix.html.textile.liquid b/doc/user/getting_started/ssh-access-unix.html.textile.liquid
index fa7e3c2..83513b8 100644
--- a/doc/user/getting_started/ssh-access-unix.html.textile.liquid
+++ b/doc/user/getting_started/ssh-access-unix.html.textile.liquid
@@ -16,7 +16,7 @@ Start by opening a terminal window. Check if you have an existing public key:
notextile. <pre><code>$ <span class="userinput">ls ~/.ssh/id_rsa.pub</span></code></pre>
-If the file @id_rsa.pub@ exists, then you may use your existing key. Copy the contents of @~/.ssh/id_rsa.pub@ onto the clipboard (this is your public key). You can skip this step and proceed by "adding your key to the Arvados Workbench.":#workbench
+If the file @id_rsa.pub@ exists, then you may use your existing key. Copy the contents of @~/.ssh/id_rsa.pub@ onto the clipboard (this is your public key). You can skip the rest of this section and proceed by "adding your key to the Arvados Workbench.":#workbench
If there is no file @~/.ssh/id_rsa.pub@, you must generate a new key. Use @ssh-keygen@ to do this:
commit 9a41032ed98c3cf5869a0a793380d673b16f1293
Author: radhika <radhika at curoverse.com>
Date: Tue Jul 8 08:51:30 2014 -0400
2380: Extract common documentation items from Unix and Windows environments into include files.
diff --git a/doc/_includes/_ssh_addkey.liquid b/doc/_includes/_ssh_addkey.liquid
new file mode 100644
index 0000000..830bcfb
--- /dev/null
+++ b/doc/_includes/_ssh_addkey.liquid
@@ -0,0 +1,26 @@
+
+You may now proceed to "adding your key to the Arvados Workbench.":#workbench
+
+h1(#workbench). Adding your key to Arvados Workbench
+
+h3. From the Workbench dashboard
+
+If you have no SSH keys registered, there should be a notification asking you to provide your SSH public key. In the Workbench top navigation menu, look for a dropdown menu with your email address in upper right corner. It will have an icon such as <span class="badge badge-alert">1</span> (the number indicates there are new notifications). Click on this icon and a dropdown menu should appear with a message asking you to add your public key. Paste your public key into the text area provided and click on the check button to submit the key. You are now ready to "log into an Arvados VM":#login.
+
+h3. Alternate way to add SSH keys
+
+If you want to add more SSH keys, click on the link with your _email address_ in the upper right corner to access the user settings menu, and click on the menu item *Manage ssh keys* to go to the Authorized keys page.
+
+On the *Authorized keys* page, the click on the button <span class="btn btn-primary disabled">Add a new authorized key</span> in the upper right corner.
+
+The page will reload with a new row of information. Under the *public_key* column heading, click on the cell +New authorized key+. This will open an editing popup as shown in this screenshot:
+
+!{{ site.baseurl }}/images/ssh-adding-public-key.png!
+
+Paste the public key that you copied to the cliboard in the previous section into the popup text box, then click on the check mark to save it. This should refresh the page with the public key that you just added now listed under the *public_key* column. You are now ready to "log into an Arvados VM":#login.
+
+h1(#login). Using SSH to log into an Arvados VM
+
+To see a list of virtual machines that you have access to and determine the name and login information, click on *Settings* menu in the top navigation bar and click on *Virtual machines*. Once on the *Virtual machines* page, The *hostname* columns lists the name of each available VM. The *logins* column will have a value in the form of @["you"]@. Your login name is the text inside the quotes. In this guide the hostname will be *_shell_* and the login will be *_you_*. Replace these with your hostname and login name as appropriate.
+
+
diff --git a/doc/_includes/_ssh_intro.liquid b/doc/_includes/_ssh_intro.liquid
new file mode 100644
index 0000000..64ceb0e
--- /dev/null
+++ b/doc/_includes/_ssh_intro.liquid
@@ -0,0 +1,7 @@
+
+Arvados requires a public SSH key in order to securely log in to an Arvados VM instance, or to access an Arvados Git repository. The three sections below help you get started:
+
+# "Getting your SSH key":#gettingkey
+# "Adding your key to Arvados Workbench":#workbench
+# "Using SSH to log into an Arvados VM instance":#login
+
diff --git a/doc/user/getting_started/ssh-access-unix.html.textile.liquid b/doc/user/getting_started/ssh-access-unix.html.textile.liquid
index 5e9a835..fa7e3c2 100644
--- a/doc/user/getting_started/ssh-access-unix.html.textile.liquid
+++ b/doc/user/getting_started/ssh-access-unix.html.textile.liquid
@@ -6,11 +6,7 @@ title: Accessing an Arvados VM with SSH - Unix Environments
This document is for Unix environments (Linux, OS X, Cygwin). If you are using a Windows environment, please visit the "Accessing an Arvados VM with SSH - Windows Environments":ssh-access-windows.html page.
-Arvados requires a public SSH key in order to securely log in to an Arvados VM instance, or to access an Arvados Git repository. The three sections below help you get started:
-
-# "Getting your SSH key":#gettingkey
-# "Adding your key to Arvados Workbench":#workbench
-# "Using SSH to log into an Arvados VM instance":#login
+{% include 'ssh_intro' %}
h1(#gettingkey). Getting your SSH key
@@ -77,29 +73,7 @@ When everything is set up, @ssh-add -l@ should yield output that looks something
</code></pre>
</notextile>
-You may now proceed to "adding your key to the Arvados Workbench.":#workbench
-
-h1(#workbench). Adding your key to Arvados Workbench
-
-h3. From the Workbench dashboard
-
-If you have no SSH keys registered, there should be a notification asking you to provide your SSH public key. In the Workbench top navigation menu, look for a dropdown menu with your email address in upper right corner. It will have an icon such as <span class="badge badge-alert">1</span> (the number indicates there are new notifications). Click on this icon and a dropdown menu should appear with a message asking you to add your public key. Paste your public key into the text area provided and click on the check button to submit the key. You are now ready to "log into an Arvados VM":#login.
-
-h3. Alternate way to add SSH keys
-
-If you want to add more SSH keys, click on the link with your _email address_ in the upper right corner to access the user settings menu, and click on the menu item *Manage ssh keys* to go to the Authorized keys page.
-
-On the *Authorized keys* page, the click on the button <span class="btn btn-primary disabled">Add a new authorized key</span> in the upper right corner.
-
-The page will reload with a new row of information. Under the *public_key* column heading, click on the cell +New authorized key+. This will open an editing popup as shown in this screenshot:
-
-!{{ site.baseurl }}/images/ssh-adding-public-key.png!
-
-Paste the public key that you copied to the cliboard in the previous section into the popup text box, then click on the check mark to save it. This should refresh the page with the public key that you just added now listed under the *public_key* column. You are now ready to "log into an Arvados VM":#login.
-
-h1(#login). Using SSH to log into an Arvados VM
-
-To see a list of virtual machines that you have access to and determine the name and login information, click on Compute %(rarr)→% Virtual machines. Once on the *Virtual machines* page, The *hostname* columns lists the name of each available VM. The *logins* column will have a value in the form of @["you"]@. Your login name is the text inside the quotes. In this guide the hostname will be _shell_ and the login will be _you_. Replace these with your hostname and login name as appropriate.
+{% include 'ssh_addkey' %}
h3. Connecting to the virtual machine
diff --git a/doc/user/getting_started/ssh-access-windows.html.textile.liquid b/doc/user/getting_started/ssh-access-windows.html.textile.liquid
index 05815aa..7a9ab27 100644
--- a/doc/user/getting_started/ssh-access-windows.html.textile.liquid
+++ b/doc/user/getting_started/ssh-access-windows.html.textile.liquid
@@ -4,13 +4,9 @@ navsection: userguide
title: Accessing an Arvados VM with SSH - Windows Environments
...
-This document is for windows environments. If you are using a Unix environment (Linux, OS X, Cygwin), please visit the "Accessing an Arvados VM with SSH - Unix Environments":ssh-access-unix.html page.
+This document is for Windows environments. If you are using a Unix environment (Linux, OS X, Cygwin), please visit the "Accessing an Arvados VM with SSH - Unix Environments":ssh-access-unix.html page.
-Arvados requires a public SSH key in order to securely log in to an Arvados VM instance, or to access an Arvados Git repository. The three sections below help you get started:
-
-# "Getting your SSH key":#gettingkey
-# "Adding your key to Arvados Workbench":#workbench
-# "Using SSH to log into an Arvados VM instance":#login
+{% include 'ssh_intro' %}
h1(#gettingkey). Getting your SSH key
@@ -52,29 +48,7 @@ Pageant is a PuTTY utility that manages your private keys so is not necessary to
# Pageant will now be running in the system tray. Click the Pageant icon to configure.
# Choose _Add Key_ and add the private key which you created in the previous step.
-You are now ready to proceed to "adding your key to the Arvados Workbench.":#workbench
-
-h1(#workbench). Adding your key to Arvados Workbench
-
-h3. From the Workbench dashboard
-
-If you have no SSH keys registered, there should be a notification asking you to provide your SSH public key. In the Workbench top navigation menu, look for a dropdown menu with your email address in upper right corner. It will have an icon such as <span class="badge badge-alert">1</span> (the number indicates there are new notifications). Click on this icon and a dropdown menu should appear with a message asking you to add your public key. Paste your public key into the text area provided and click on the check button to submit the key. You are now ready to "log into an Arvados VM":#login.
-
-h3. Alternate way to add SSH keys
-
-If you want to add more SSH keys, click on the link with your _email address_ in the upper right corner to access the user settings menu, and click on the menu item *Manage ssh keys* to go to the Authorized keys page.
-
-On the *Authorized keys* page, the click on the button <span class="btn btn-primary disabled">Add a new authorized key</span> in the upper right corner.
-
-The page will reload with a new row of information. Under the *public_key* column heading, click on the cell +New authorized key+. This will open an editing popup as shown in this screenshot:
-
-!{{ site.baseurl }}/images/ssh-adding-public-key.png!
-
-Paste the public key that you copied to the cliboard in the previous section into the popup text box, then click on the check mark to save it. This should refresh the page with the public key that you just added now listed under the *public_key* column. You are now ready to "log into an Arvados VM":#login.
-
-h1(#login). Using SSH to log into an Arvados VM
-
-To see a list of virtual machines that you have access to and determine the name and login information, click on *Settings* menu in the top navigation bar and click on *Virtual machines*. Once on the *Virtual machines* page, The *hostname* columns lists the name of each available VM. The *logins* column will have a value in the form of @["you"]@. Your login name is the text inside the quotes. In this guide the hostname will be *_shell_* and the login will be *_you_*. Replace these with your hostname and login name as appropriate.
+{% include 'ssh_addkey' %}
h3. Initial configuration
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