[ARVADOS] updated: ba64505e002d2d3a00d14ea567e80889534f14bf
git at public.curoverse.com
git at public.curoverse.com
Tue Feb 11 15:57:58 EST 2014
Summary of changes:
.../app/controllers/application_controller.rb | 9 --
.../app/views/users/_notifications.html.erb | 93 --------------------
doc/_config.yml | 2 +-
.../check-environment.html.textile.liquid | 26 ++----
.../getting_started/ssh-access.html.textile.liquid | 12 ++--
doc/user/reference/api-tokens.html.textile.liquid | 56 ++++++++----
.../tutorials/tutorial-keep.html.textile.liquid | 8 ++-
sdk/cli/Gemfile.lock | 24 +++---
sdk/cli/arvados-cli.gemspec | 2 +-
sdk/cli/bin/arv | 2 +-
sdk/python/arvados/collection.py | 9 ++-
sdk/python/arvados/keep.py | 40 ++++++---
sdk/python/bin/arv-get | 11 ++-
services/api/app/models/job.rb | 10 ++-
14 files changed, 125 insertions(+), 179 deletions(-)
delete mode 100644 apps/workbench/app/views/users/_notifications.html.erb
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commit ba64505e002d2d3a00d14ea567e80889534f14bf
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Feb 11 15:59:00 2014 -0500
Updating documentation
diff --git a/doc/user/getting_started/check-environment.html.textile.liquid b/doc/user/getting_started/check-environment.html.textile.liquid
index ac3d90c..559133d 100644
--- a/doc/user/getting_started/check-environment.html.textile.liquid
+++ b/doc/user/getting_started/check-environment.html.textile.liquid
@@ -10,24 +10,10 @@ h1. Checking your environment
First you should "log into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login if you have not already done so.
-Check that you are able to access the Arvados API server using the following command:
-
-notextile. <pre><code>$ <span class="userinput">arv user current</span></code></pre>
-
-If @arv user current@ is able to access the API server, it will print out the unique identifier associated with your account. Here is an example (you will receive a different identifier):
-
-bc. qr1hi-xioed-9z2p3pn12yqdaem
-
-However, if you receive the following message:
-
-bc. ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables
-
-Then follow the instructions for "getting an API token,":{{site.basedoc}}/user/reference/api-tokens.html and return to this document.
-
-The unique identifier represents your identity in the Arvados system and is similar to the concept of a pointer or a foreign key. You may de-reference (get the contents of) any identifier returned by the "arv" command using the @-h@ command line option. For example:
+If @arv user current@ is able to access the API server, it will print out information about your account. Check that you are able to access the Arvados API server using the following command:
<notextile>
-<pre><code>$ <span class="userinput">arv -h user current</span>
+<pre><code>$ <span class="userinput">arv user current</span>
{
"href":"https://qr1hi.arvadosapi.com/arvados/v1/users/qr1hi-xioed-9z2p3pn12yqdaem",
"kind":"arvados#user",
@@ -51,4 +37,10 @@ The unique identifier represents your identity in the Arvados system and is simi
</code></pre>
</notextile>
-You are now ready proceed to the first tutorial: "Storing and retrieving data using Arvados Keep.":{{site.basedoc}}/user/tutorials/tutorial-keep.html
+However, if you receive the following message:
+
+bc. ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables
+
+Then follow the instructions for "getting an API token,":{{site.basedoc}}/user/reference/api-tokens.html and try @arv user current@ again.
+
+Once you are able to access the API server, you are ready proceed to the first tutorial: "Storing and retrieving data using Arvados Keep.":{{site.basedoc}}/user/tutorials/tutorial-keep.html
diff --git a/doc/user/getting_started/ssh-access.html.textile.liquid b/doc/user/getting_started/ssh-access.html.textile.liquid
index 48e6460..3c40315 100644
--- a/doc/user/getting_started/ssh-access.html.textile.liquid
+++ b/doc/user/getting_started/ssh-access.html.textile.liquid
@@ -133,15 +133,15 @@ 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. On the Workbench dashboard (in this guide, this is "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/ ), look for the icon <span class="glyphicon glyphicon-envelope"></span> <span class="badge badge-alert">1</span> in upper right corner. 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.
+If you have no @ssh@ keys registered, there should be a notification asking you to provide your @ssh@ public key. On the Workbench dashboard (in this guide, this is "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/ ), look for the envelope icon <span class="glyphicon glyphicon-envelope"></span> <span class="badge badge-alert">1</span> in upper right corner (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 additional @ssh@ keys, click on the user icon <span class="glyphicon glyphicon-user"></span> in the upper right corner to access the user settings menu, and click on the menu item _Manage ssh keys_ to add an authorized ssh key to your account.
+If you want to add additional @ssh@ keys, click on the user icon <span class="glyphicon glyphicon-user"></span> 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.
-Netx, on _Authorized keys_ page, the click on the button <span class="btn btn-primary disabled">Add a new authorized key</span>
+On _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.
-This will reload the page, and should now show a row of information. Under the *public_key* column heading, click on the cell _none_ . This should open up an editing popup as shown in this screenshot:
+The page will reload with a new row of information. Under the *public_key* column heading, click on the cell +none+ . This will open an editing popup as shown in this screenshot:
!{{ site.baseurl }}/images/ssh-adding-public-key.png!
@@ -149,7 +149,7 @@ Paste the public key from the previous section into the popup text box and click
h1(#login). Using ssh to log into an Arvados VM
-To determine the name and login information of the VM instance that you will connect to, go to the Arvados workbench and click on "Virtual machines" under *Configuration* or use the menu item _Access %(rarr)→% VMs_ to see a list of virtual machines that you have access to. The *hostname* columns lists the name of each available VM. The *logins* column will have a value in the form of @["you"]@. Skip the square brackets and quotes to get your login name. In this guide the hostname will be _shell_ and the login will be _you_. Replace these with your hostname and login as appropriate.
+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"]@. Ignore the square brackets and quotes to get your login name. In this guide the hostname will be _shell_ and the login will be _you_. Replace these with your hostname and login as appropriate.
This section consists of two sets of instructions, depending on whether you will be logging in using a "Unix":#unixvm (Linux, OS X, Cygwin) or "Windows":#windowsvm client.
@@ -177,7 +177,7 @@ The VMs typically have addresses that are not globally routable, so you cannot l
You should now be able to log into the Arvados VM and "check your environment.":check-environment.html
-h3. Configuration (optional)
+h3. Configuration (recommended)
Since the above command line is cumbersome, it can be greatly simplfied by adding the following section your @~/.ssh/config@ file:
diff --git a/doc/user/reference/api-tokens.html.textile.liquid b/doc/user/reference/api-tokens.html.textile.liquid
index 48fea0a..1694c4e 100644
--- a/doc/user/reference/api-tokens.html.textile.liquid
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -8,40 +8,60 @@ title: "Getting an API token"
h1. Reference: Getting an API token
-The Arvados API token is a secret key that enables the @arv@ command line
-client to access Arvados with the proper permissions.
+The Arvados API token is a secret key that enables the @arv@ command line client to access Arvados with the proper permissions.
-Access the Arvados workbench using this link:
-
-"https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/
+Access the Arvados workbench using this link: "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/
(Replace @{{ site.arvados_api_host }}@ with the hostname of your local Arvados instance if necessary.)
-Use the menu to navigate to _Access %(rarr)→% API Tokens._ There should be one or more rows. The column *api_token* contains the actual token string that you will use. Copy the value of *api_token* for the first row onto the clipboard.
-
-Next, open a shell on the system on which you intend to use the Arvados client (refer to "Accessing Arvados over ssh":{{site.basedoc}}/user/getting_started/ssh-access.html ) and enter the following (replace the value of @ARVADOS_API_TOKEN@ with the value you copied from the Workbench):
+First, open a shell on the system on which you intend to use the Arvados client (this may be your local workstation, or an Arvados VM, refer to "Accessing Arvados over ssh":{{site.basedoc}}/user/getting_started/ssh-access.html ) .
-bc. $ export ARVADOS_API_HOST={{ site.arvados_api_host }}
-$ export ARVADOS_API_TOKEN=2jv9kd1o39t0pcfu7aueem7a1zjxhak73w90tzq3gx0es7j1ld
+Click on the user icon <span class="glyphicon glyphicon-user"></span> in the upper right corner to access the user settings menu, and click on the menu item _Manage API token_ to go to the "api client authorizations" page.
-* @ARVADOS_API_HOST@ tells @arv@ which host to connect to
-* @ARVADOS_API_TOKEN@ is the secret key used by the Arvados API server to authenticate access.
+h2. The easy way
-For your convenience, the "API Tokens" Workbench page provides a section at the top of the page that you may copy and paste directly into the shell. It will look something like this:
+For your convenience, the "api client authorizations" page on Workbench provides a "Help" tab that provides a command you may copy and paste directly into the shell. It will look something like this:
bc. ### Pasting the following lines at a shell prompt will allow Arvados SDKs
### to authenticate to your account, youraddress at example.com
read ARVADOS_API_TOKEN <<EOF
-2jv9kd1o39t0pcfu7aueem7a1zjxhak73w90tzq3gx0es7j1ld
+2jv9346o396exampledonotuseexampledonotuseexes7j1ld
EOF
-export ARVADOS_API_TOKEN ARVADOS_API_HOST=qr1hi.arvadosapi.com
+export ARVADOS_API_TOKEN ARVADOS_API_HOST={{ site.arvados_api_host }}
* The @read@ command takes the contents of stdin and puts it into the shell variable named on the command line.
* The @<<EOF@ notation means read each line on stdin and pipe it to the command, terminating on reading the line @EOF at .
* The @export@ command puts a local shell variable into the environment that will be inherited by child processes (e.g. the @arv@ client).
-For your convenience you may add the declarations of @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ to the @~/.bashrc@ file on the system on which you intend to use the Arvados client. If you have already put the variables into the environment with instructions above, you can use these commands to append the environment variables to your @~/.bashrc@:
+h2. Setting the environment manually
+
+Alternately, look for the column *api_token* contains the actual token string that you will use. Copy the value of *api_token* for the first row onto the clipboard.
+
+<notextile>
+<pre><code>$ <span class="userinput">export ARVADOS_API_HOST={{ site.arvados_api_host }}</span>
+$ <span class="userinput">export ARVADOS_API_TOKEN=2jv9346o3966345u7ueuim7a1zaaoueo3w90tzq3gx0es7j1ld</span>
+</code></pre>
+</notextile>
+
+* @ARVADOS_API_HOST@ tells @arv@ which host to connect to
+* @ARVADOS_API_TOKEN@ is the secret key used by the Arvados API server to authenticate access.
+
+h2. settings.conf
+
+Arvados tools will also look for the authentication information in @~/.config/arvados/settings.conf at . If you have already put the variables into the environment with instructions above, you can use these commands to create an Arvados configuration file:
+
+<notextile>
+<pre><code>$ <span class="userinput">echo "ARVADOS_API_HOST=$ARVADOS_API_HOST" > ~/.config/arvados/settings.conf</span>
+$ <span class="userinput">echo "ARVADOS_API_TOKEN=$ARVADOS_API_TOKEN" >> ~/.config/arvados/settings.conf</span>
+</code></pre>
+</notextile>
+
+h2. .bashrc
-bc. $ echo "export ARVADOS_API_HOST=$ARVADOS_API_HOST" >> ~/.bashrc
-$ echo "export ARVADOS_API_TOKEN=$ARVADOS_API_TOKEN" >> ~/.bashrc
+Alternately, you may add the declarations of @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ to the @~/.bashrc@ file on the system on which you intend to use the Arvados client. If you have already put the variables into the environment with instructions above, you can use these commands to append the environment variables to your @~/.bashrc@:
+<notextile>
+<pre><code>$ <span class="userinput">echo "export ARVADOS_API_HOST=$ARVADOS_API_HOST" >> ~/.bashrc</span>
+$ <span class="userinput">echo "export ARVADOS_API_TOKEN=$ARVADOS_API_TOKEN" >> ~/.bashrc</span>
+</code></pre>
+</notextile>
diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index 01ef78a..16c113d 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -23,6 +23,8 @@ h1. Putting Data into Keep
We will start with downloading a freely available VCF file from the "Personal Genome Project (PGP)":http://www.personalgenomes.org subject "hu599905":https://my.personalgenomes.org/profile/hu599905 to a staging directory on the VM, and then add it to Keep.
+In the following tutorials, replace <b><code>you</code></b> with your user id.
+
First, log into the Arvados VM instance and set up the staging area:
notextile. <pre><code>$ <span class="userinput">mkdir /scratch/<b>you</b></span></code></pre>
@@ -39,10 +41,14 @@ $ <span class="userinput">curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse
</code></pre>
</notextile>
-Alternately, if you have your own data, for example @MyData.vcf@, you can use @scp@ or @rsync@ to copy from your local workstation to the shell VM (run this on your local workstation):
+{% include 'notebox_begin' %}
+
+If you have your own data, for example @MyData.vcf@, you can use @scp@ or @rsync@ to copy from your local workstation to the shell VM (run this on your local workstation):
notextile. <pre><code>$ <span class="userinput">scp MyData.vcf <b>you at shell</b>.arvados:/scratch/<b>you</b>/MyData.vcf</span></code></pre>
+{% include 'notebox_end' %}
+
Now use @arv keep put@ to add your VCF data to Keep:
<notextile>
commit fc38c67d9b3b8ae6a1d891e8005c43d6af6edd06
Merge: 8c28550 f7a0c7d
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Feb 11 14:29:14 2014 -0500
Merge remote-tracking branch 'origin/master' into 2061-update-docs
commit 8c285503b45e89a891236221aba26488d2d74832
Merge: 720d44b 18258f6
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Feb 11 14:00:57 2014 -0500
Merge remote-tracking branch 'origin/master' into 2061-update-docs
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