[ARVADOS] updated: 8f589475096eb42dd1eccfbfbfc1fd5bc8f4e8ba
git at public.curoverse.com
git at public.curoverse.com
Tue Jul 14 15:07:53 EDT 2015
Summary of changes:
doc/_includes/_arv_copy_expectations.liquid | 2 +-
doc/user/topics/arv-copy.html.textile.liquid | 45 +++++++++++++++++-----------
2 files changed, 29 insertions(+), 18 deletions(-)
via 8f589475096eb42dd1eccfbfbfc1fd5bc8f4e8ba (commit)
via 7adf48e3633942e40b3943db8a7a31ec23d12a5b (commit)
via d5dbaeb59cb702793b926a63cabbeaa37f96dcfd (commit)
via 603992242f91426818fd56317c6adf4521f9500c (commit)
via 9053b511d514aa3e902259d3070ba439bfae6613 (commit)
from 9d52ea83290cab293229815286579ab6a1584f9e (commit)
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commit 8f589475096eb42dd1eccfbfbfc1fd5bc8f4e8ba
Author: bryan <bcosc at bcosc-VirtualBox.(none)>
Date: Tue Jul 14 15:07:31 2015 -0400
Fixed more syntax errors
diff --git a/doc/user/topics/arv-copy.html.textile.liquid b/doc/user/topics/arv-copy.html.textile.liquid
index 4ee9590..3cf944d 100644
--- a/doc/user/topics/arv-copy.html.textile.liquid
+++ b/doc/user/topics/arv-copy.html.textile.liquid
@@ -15,7 +15,7 @@ h2. arv-copy
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.
-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 .
+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!
@@ -60,6 +60,6 @@ arvados.arv-copy[19694] INFO: Success: created copy with uuid dst_cluster-d1hrv-
</code></pre>
</notextile>
-By default, if you copy a pipeline instance recursively, you will find that the template as well as all the dependcies are in your home project.
+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 .
commit 7adf48e3633942e40b3943db8a7a31ec23d12a5b
Author: bryan <bcosc at bcosc-VirtualBox.(none)>
Date: Tue Jul 14 15:00:54 2015 -0400
Fixed syntax
diff --git a/doc/user/topics/arv-copy.html.textile.liquid b/doc/user/topics/arv-copy.html.textile.liquid
index 88e5c22..4ee9590 100644
--- a/doc/user/topics/arv-copy.html.textile.liquid
+++ b/doc/user/topics/arv-copy.html.textile.liquid
@@ -13,7 +13,7 @@ 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 by the prefix of the uuid of the object you want to copy or the prefix of the @ARVADOS_API_HOST at .
+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.
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 .
@@ -56,10 +56,10 @@ We will use the uuid @qr1hi-d1hrv-nao0ohw8y7dpf84@ as an example pipeline instan
<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial qr1hi-d1hrv-nao0ohw8y7dpf84</span>
To git at git.su92l.arvadosapi.com:bcosc.htslib.git
* [new branch] git_git_qr1hi_arvadosapi_com_arvados_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d -> git_git_qr1hi_arvadosapi_com_arvados_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d
-arvados.arv-copy[19694] INFO: Success: created copy with uuid su92l-d1hrv-rym2h5ub9m8ofwj
+arvados.arv-copy[19694] INFO: Success: created copy with uuid dst_cluster-d1hrv-rym2h5ub9m8ofwj
</code></pre>
</notextile>
-By default, if you copy a pipeline instance recursively, you will find that the template as well as all the dependecies are in your home project.
+By default, if you copy a pipeline instance recursively, you will find that the template as well as all the dependcies are in your home project.
New branches in the destination git repo will be created for each branch used in the pipeline template. For example, if your source branch was named ac21f0d45a76294aaca0c0c0fdf06eb72d03368d, your new branch will be named @git_git_cluster1_arvadosapi_com_reponame_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d at .
commit d5dbaeb59cb702793b926a63cabbeaa37f96dcfd
Author: bryan <bcosc at bcosc-VirtualBox.(none)>
Date: Tue Jul 14 14:19:32 2015 -0400
Fixed more comments
diff --git a/doc/user/topics/arv-copy.html.textile.liquid b/doc/user/topics/arv-copy.html.textile.liquid
index 3b98dc2..88e5c22 100644
--- a/doc/user/topics/arv-copy.html.textile.liquid
+++ b/doc/user/topics/arv-copy.html.textile.liquid
@@ -54,9 +54,12 @@ We will use the uuid @qr1hi-d1hrv-nao0ohw8y7dpf84@ as an example pipeline instan
<notextile>
<pre><code>~$ <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
+ * [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 su92l-d1hrv-rym2h5ub9m8ofwj
</code></pre>
</notextile>
By default, if you copy a pipeline instance recursively, you will find that the template as well as all the dependecies 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 branch_name, your new branch will be named @git_git_cluster1_arvadosapi_com_reponame_git_branch_name at .
+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 .
commit 603992242f91426818fd56317c6adf4521f9500c
Author: bryan <bcosc at bcosc-VirtualBox.(none)>
Date: Tue Jul 14 14:01:19 2015 -0400
Fixed some changes but need to add copy git repos
diff --git a/doc/_includes/_arv_copy_expectations.liquid b/doc/_includes/_arv_copy_expectations.liquid
index c424c56..9f98ecf 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}}/sdk/python/python.html page.
+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/user/topics/arv-copy.html.textile.liquid b/doc/user/topics/arv-copy.html.textile.liquid
index de80afd..3b98dc2 100644
--- a/doc/user/topics/arv-copy.html.textile.liquid
+++ b/doc/user/topics/arv-copy.html.textile.liquid
@@ -53,11 +53,10 @@ h3. How to copy a pipeline template or pipeline instance
We will use the uuid @qr1hi-d1hrv-nao0ohw8y7dpf84@ as an example pipeline instance.
<notextile>
-<pre><code>~$ <span class="userinput">arv-copy --src cluster1 --dst cluster2 --dst-git-repo samplegitrepo/samplename cluster1-p5p6p-abcd123efghi45jkl</span>
+<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial qr1hi-d1hrv-nao0ohw8y7dpf84</span>
</code></pre>
</notextile>
By default, if you copy a pipeline instance recursively, you will find that the template as well as all the dependecies 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 branch_name, your new branch will be named @git_git_cluster1_arvadosapi_com_reponame_git_branch_name at .
commit 9053b511d514aa3e902259d3070ba439bfae6613
Author: bryan <bcosc at bcosc-VirtualBox.(none)>
Date: Tue Jul 14 13:53:49 2015 -0400
added png and need to switch to 6014 to grab the url
diff --git a/doc/_includes/_arv_copy_expectations.liquid b/doc/_includes/_arv_copy_expectations.liquid
index 022a893..c424c56 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 are working from a machine with an SSH key that is allowed to access both clusters (required to copy git repositories). As well as a git repository in the destination cluster. If you do not have a repository created, you can follow the documentation here: (Point to #6014)
+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}}/sdk/python/python.html page.
{% include 'notebox_end' %}
diff --git a/doc/user/topics/arv-copy.html.textile.liquid b/doc/user/topics/arv-copy.html.textile.liquid
index 8987c68..de80afd 100644
--- a/doc/user/topics/arv-copy.html.textile.liquid
+++ b/doc/user/topics/arv-copy.html.textile.liquid
@@ -1,7 +1,7 @@
---
layout: default
navsection: userguide
-title: "Using Arv-copy"
+title: "Using arv-copy"
...
@@ -9,46 +9,55 @@ This tutorial describes how to copy Arvados objects from one cluster to another
{% include 'tutorial_expectations' %}
-h2. Arv-copy
+h2. arv-copy
- at arv-copy@ allows users to copy collections, pipeline templates, and pipeline instances, including all their dependencies from one cluster to another.
+ at 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 *cluster1* to *cluster2*. The names *cluster1* and *cluster2* are interchangable with any cluster name.
+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 by the prefix of the uuid of the object you want to copy or the prefix of the @ARVADOS_API_HOST at .
-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 is very important, they must match the cluster names.
+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.
<notextile>
<pre><code>~$ <span class="userinput">cd ~/.config/arvados</span>
-~$ <span class="userinput">echo "ARVADOS_API_HOST=cluster1.arvadosapi.com" >> cluster1.conf</span>
-~$ <span class="userinput">echo "ARVADOS_API_TOKEN=123456789abcdefghijkl" >> cluster1.conf</span>
-~$ <span class="userinput">echo "ARVADOS_API_HOST=cluster2.arvadosapi.com" >> cluster2.conf</span>
-~$ <span class="userinput">echo "ARVADOS_API_TOKEN=987654321lkjihgfedcba" >> cluster2.conf</span>
+~$ <span class="userinput">echo "ARVADOS_API_HOST=qr1hi.arvadosapi.com" >> qr1hi.conf</span>
+~$ <span class="userinput">echo "ARVADOS_API_TOKEN=123456789abcdefghijkl" >> qr1hi.conf</span>
+~$ <span class="userinput">echo "ARVADOS_API_HOST=dst_cluster.arvadosapi.com" >> dst_cluster.conf</span>
+~$ <span class="userinput">echo "ARVADOS_API_TOKEN=987654321lkjihgfedcba" >> dst_cluster.conf</span>
</code></pre>
</notextile>
+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/...@)
-Now copy the collection from *cluster1* to *cluster2*. We will use the uuid @cluster1-4zz18-1234567890abcde@ as an example.
+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*.
<notextile>
-<pre><code>~$ <span class="userinput">arv-copy --src cluster1 --dst cluster2 cluster1-4zz18-1234567890abcde</span>
-cluster1-4zz18-1234567890abcde: 100M / 100M 100.0%
-arvados.arv-copy[1234] INFO: Success: created copy with uuid cluster2-4zz18-8765943210cdbae
+<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%
+arvados.arv-copy[1234] INFO: Success: created copy with uuid dst_cluster-4zz18-8765943210cdbae
</code></pre>
</notextile>
-The collection will be 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. 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.
h3. How to copy a pipeline template or pipeline instance
{% include 'arv_copy_expectations' %}
-We will use the uuid @cluster1-p5p6p-abcd123efghi45jkl@ as an example pipeline template or instance, and @samplegitrepo/samplename.git@ as an example git repo.
+We will use the uuid @qr1hi-d1hrv-nao0ohw8y7dpf84@ as an example pipeline instance.
<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src cluster1 --dst cluster2 --dst-git-repo samplegitrepo/samplename cluster1-p5p6p-abcd123efghi45jkl</span>
</code></pre>
</notextile>
+By default, if you copy a pipeline instance recursively, you will find that the template as well as all the dependecies 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 branch_name, your new branch will be named @git_git_cluster1_arvadosapi_com_reponame_git_branch_name at .
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