[ARVADOS] updated: beab0d6bf936becea2a92c6778c2008d451db0fc
git at public.curoverse.com
git at public.curoverse.com
Tue Jul 14 16:48:22 EDT 2015
Summary of changes:
doc/_includes/_arv_copy_expectations.liquid | 2 +-
doc/images/api-token-host.png | Bin 0 -> 25207 bytes
doc/user/topics/arv-copy.html.textile.liquid | 31 ++++++++++++++++++++-------
3 files changed, 24 insertions(+), 9 deletions(-)
create mode 100644 doc/images/api-token-host.png
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via 0628f0c1d83fc71d4b0913f4f3fb90e4ad1632f2 (commit)
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commit beab0d6bf936becea2a92c6778c2008d451db0fc
Author: bryan <bcosc at bcosc-VirtualBox.(none)>
Date: Tue Jul 14 16:48:06 2015 -0400
Note #15
diff --git a/doc/user/topics/arv-copy.html.textile.liquid b/doc/user/topics/arv-copy.html.textile.liquid
index 7d7ccc9..bda8026 100644
--- a/doc/user/topics/arv-copy.html.textile.liquid
+++ b/doc/user/topics/arv-copy.html.textile.liquid
@@ -13,11 +13,11 @@ h2. arv-copy
@arv-copy@ allows users to copy collections, pipeline templates, and pipeline instances from one cluster to another. By default, @arv-copy@ will recursively go through a template or instance and copy all dependencies associated with the object.
-For example, let's copy from our <a href="https://cloud.curoverse.com/">beta cloud instance</a> *qr1hi* to *dst_cluster*. The names *qr1hi* and *dst_cluster* are interchangable with any cluster name. You can find the cluster name from the prefix of the uuid of the object you want to copy. For example, in qr1hi-4zz18-tci4vn4fa95w0zx, the cluster name is qr1hi.
+For example, let's copy from our <a href="https://cloud.curoverse.com/">beta cloud instance *qr1hi*</a> to *dst_cluster*. The names *qr1hi* and *dst_cluster* are interchangable with any cluster name. You can find the cluster name from the prefix of the uuid of the object you want to copy. For example, in qr1hi-4zz18-tci4vn4fa95w0zx, the cluster name is qr1hi.
In order for the clusters to be able to communicate with each other, you must create custom configuration files for both clusters. First, go to your *Manage account* page in Workbench and copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ in both of your clusters. Then, create two configuration files, one for each cluster. The names of the files must have the format of *uuid_prefix*.conf. In our example, let's make two files, one for *qr1hi* and one for *dst_cluster*. From your *Manage account* page in *qr1hi* and *dst_cluster*, copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN at .
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/api-token-host.png!
+!{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/api-token-host.png!
Copy your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ into the config files as shown below in the shell account from which you are executing the commands. For example, the default shell you may have access to is shell.qr1hi. You can add these files in ~/.config/arvados/ in the qr1hi shell terminal.
@@ -36,7 +36,7 @@ h3. How to copy a collection
First, select the uuid of the collection you want to copy from the source cluster. The uuid can be found in the collection displace page in the collection summary area (top left box), or from the URL bar (the part after @collections/...@)
-Now copy the collection from *qr1hi* to *dst_cluster*. We will use the uuid @qr1hi-4zz18-tci4vn4fa95w0zx@ as an example. You can find this collection in the lobSTR v.3 project on <a href="https://cloud.curoverse.com/">cloud.curoverse.com</a>.
+Now copy the collection from *qr1hi* to *dst_cluster*. We will use the uuid @qr1hi-4zz18-tci4vn4fa95w0zx@ as an example. You can find this collection in the <a href="https://cloud.curoverse.com/collections/qr1hi-4zz18-tci4vn4fa95w0zx">lobSTR v.3 project on cloud.curoverse.com</a>.
<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster qr1hi-4zz18-tci4vn4fa95w0zx</span>
qr1hi-4zz18-tci4vn4fa95w0zx: 6.1M / 6.1M 100.0%
@@ -74,5 +74,7 @@ If you would like to copy the object without dependencies, you can use the @--no
For example, we can copy the same object using this tag.
+<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial --no-recursive qr1hi-d1hrv-nao0ohw8y7dpf84</span>
-
+</code></pre>
+</notextile>
commit 0628f0c1d83fc71d4b0913f4f3fb90e4ad1632f2
Author: bryan <bcosc at bcosc-VirtualBox.(none)>
Date: Tue Jul 14 16:35:58 2015 -0400
added note #13
diff --git a/doc/_includes/_arv_copy_expectations.liquid b/doc/_includes/_arv_copy_expectations.liquid
index 9f98ecf..6db78e8 100644
--- a/doc/_includes/_arv_copy_expectations.liquid
+++ b/doc/_includes/_arv_copy_expectations.liquid
@@ -1,3 +1,3 @@
{% include 'notebox_begin' %}
-This part of the tutorial assumes that you have a working git repository in the destination cluster. If you do not have a repository created, you can follow the "Adding a new repository":{{site.baseurl}}/user/tutorials/add-new-repository.html page. We will use the 'tutorial' repository created in that page as the example.
+This part of the tutorial assumes that you have a working git repository in the destination cluster. If you do not have a repository created, you can follow the "Adding a new repository":{{site.baseurl}}/user/tutorials/add-new-repository.html page. We will use the *tutorial* repository created in that page as the example.
{% include 'notebox_end' %}
diff --git a/doc/images/api-token-host.png b/doc/images/api-token-host.png
new file mode 100644
index 0000000..cda04d6
Binary files /dev/null and b/doc/images/api-token-host.png differ
diff --git a/doc/user/topics/arv-copy.html.textile.liquid b/doc/user/topics/arv-copy.html.textile.liquid
index 3cf944d..7d7ccc9 100644
--- a/doc/user/topics/arv-copy.html.textile.liquid
+++ b/doc/user/topics/arv-copy.html.textile.liquid
@@ -13,13 +13,13 @@ h2. arv-copy
@arv-copy@ allows users to copy collections, pipeline templates, and pipeline instances from one cluster to another. By default, @arv-copy@ will recursively go through a template or instance and copy all dependencies associated with the object.
-For example, lets copy from our beta cloud instance *qr1hi* to *dst_cluster*. The names *qr1hi* and *dst_cluster* are interchangable with any cluster name. You can find the cluster name from the prefix of the uuid of the object you want to copy.
+For example, let's copy from our <a href="https://cloud.curoverse.com/">beta cloud instance</a> *qr1hi* to *dst_cluster*. The names *qr1hi* and *dst_cluster* are interchangable with any cluster name. You can find the cluster name from the prefix of the uuid of the object you want to copy. For example, in qr1hi-4zz18-tci4vn4fa95w0zx, the cluster name is qr1hi.
In order for the clusters to be able to communicate with each other, you must create custom configuration files for both clusters. First, go to your *Manage account* page in Workbench and copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ in both of your clusters. Then, create two configuration files, one for each cluster. The names of the files must have the format of *uuid_prefix*.conf. In our example, let's make two files, one for *qr1hi* and one for *dst_cluster*. From your *Manage account* page in *qr1hi* and *dst_cluster*, copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN at .
!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/api-token-host.png!
-Copy your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ into the config files as shown below.
+Copy your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ into the config files as shown below in the shell account from which you are executing the commands. For example, the default shell you may have access to is shell.qr1hi. You can add these files in ~/.config/arvados/ in the qr1hi shell terminal.
<notextile>
<pre><code>~$ <span class="userinput">cd ~/.config/arvados</span>
@@ -34,9 +34,9 @@ Now you're ready to copy between *qr1hi* and *dst_cluster*!
h3. How to copy a collection
-First, select the uuid of the collection you want to copy from the source cluster. The uuid can be found inside of a collection in the top left box, or from the URL bar (the part after @collections/...@)
+First, select the uuid of the collection you want to copy from the source cluster. The uuid can be found in the collection displace page in the collection summary area (top left box), or from the URL bar (the part after @collections/...@)
-Now copy the collection from *qr1hi* to *dst_cluster*. We will use the uuid @qr1hi-4zz18-tci4vn4fa95w0zx@ as an example. You can find this collection in the lobSTR v.3 project on *qr1hi*.
+Now copy the collection from *qr1hi* to *dst_cluster*. We will use the uuid @qr1hi-4zz18-tci4vn4fa95w0zx@ as an example. You can find this collection in the lobSTR v.3 project on <a href="https://cloud.curoverse.com/">cloud.curoverse.com</a>.
<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster qr1hi-4zz18-tci4vn4fa95w0zx</span>
qr1hi-4zz18-tci4vn4fa95w0zx: 6.1M / 6.1M 100.0%
@@ -44,7 +44,13 @@ arvados.arv-copy[1234] INFO: Success: created copy with uuid dst_cluster-4zz18-8
</code></pre>
</notextile>
-The output of arv-copy displays the uuid of the collection generated. By default, the output is placed in your home project in the destination cluster. If you want to place your collection inside of a pre-created project, you can specify the project you want it to be in using the tag @--project-uuid@ followed by the project uuid.
+The output of arv-copy displays the uuid of the collection generated in the destination cluster. By default, the output is placed in your home project in the destination cluster. If you want to place your collection inside of a pre-created project, you can specify the project you want it to be in using the tag @--project-uuid@ followed by the project uuid.
+
+For example, this will copy the collection to project dst_cluster-j7d0g-a894213ukjhal12 in the destination cluster.
+
+<notextile> <pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --project-uuid dst_cluster-j7d0g-a894213ukjhal12 qr1hi-4zz18-tci4vn4fa95w0zx</span>
+</code></pre>
+</notextile>
h3. How to copy a pipeline template or pipeline instance
@@ -54,12 +60,19 @@ We will use the uuid @qr1hi-d1hrv-nao0ohw8y7dpf84@ as an example pipeline instan
<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial qr1hi-d1hrv-nao0ohw8y7dpf84</span>
-To git at git.su92l.arvadosapi.com:bcosc.htslib.git
+To git at git.dst_cluster.arvadosapi.com:$USER/tutorial.git
* [new branch] git_git_qr1hi_arvadosapi_com_arvados_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d -> git_git_qr1hi_arvadosapi_com_arvados_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d
arvados.arv-copy[19694] INFO: Success: created copy with uuid dst_cluster-d1hrv-rym2h5ub9m8ofwj
</code></pre>
</notextile>
+New branches in the destination git repo will be created for each branch used in the pipeline template. For example, if your source branch was named ac21f0d45a76294aaca0c0c0fdf06eb72d03368d, your new branch will be named @git_git_qr1hi_arvadosapi_com_reponame_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d at .
+
By default, if you copy a pipeline instance recursively, you will find that the template as well as all the dependencies are in your home project.
-New branches in the destination git repo will be created for each branch used in the pipeline template. For example, if your source branch was named ac21f0d45a76294aaca0c0c0fdf06eb72d03368d, your new branch will be named @git_git_cluster1_arvadosapi_com_reponame_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d at .
+If you would like to copy the object without dependencies, you can use the @--no-recursive@ tag.
+
+For example, we can copy the same object using this tag.
+
+<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial --no-recursive qr1hi-d1hrv-nao0ohw8y7dpf84</span>
+
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