[ARVADOS] updated: 87d84e41215333729a436726ee28068eb430ff38
Git user
git at public.curoverse.com
Thu Dec 1 16:24:20 EST 2016
Summary of changes:
doc/_config.yml | 2 +
doc/_includes/_arvados_cwl_runner.liquid | 62 ++++++++++++++
doc/_includes/_register_cwl_workflow.liquid | 21 +++++
doc/_includes/_what_is_cwl.liquid | 1 +
doc/user/cwl/cwl-runner.html.textile.liquid | 99 ++++------------------
...nning-workflow-command-line.html.textile.liquid | 17 ++++
...tutorial-pipeline-workbench.html.textile.liquid | 2 +-
.../writing-cwl-workflow.html.textile.liquid | 28 ++++++
8 files changed, 148 insertions(+), 84 deletions(-)
create mode 100644 doc/_includes/_arvados_cwl_runner.liquid
create mode 100644 doc/_includes/_register_cwl_workflow.liquid
create mode 100644 doc/_includes/_what_is_cwl.liquid
create mode 100644 doc/user/topics/running-workflow-command-line.html.textile.liquid
create mode 100644 doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
via 87d84e41215333729a436726ee28068eb430ff38 (commit)
from f198e6126e38a30288763e8720f3dee1b4805677 (commit)
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commit 87d84e41215333729a436726ee28068eb430ff38
Author: radhika <radhika at curoverse.com>
Date: Thu Dec 1 16:23:33 2016 -0500
10604: add pages to write and run workflows.
diff --git a/doc/_config.yml b/doc/_config.yml
index a884d38..fdd57c5 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -47,6 +47,7 @@ navbar:
- user/cwl/cwl-runner.html.textile.liquid
- user/cwl/cwl-style.html.textile.liquid
- Working on the command line:
+ - user/topics/running-workflow-command-line.html.textile.liquid
- user/topics/running-pipeline-command-line.html.textile.liquid
- user/topics/arv-run.html.textile.liquid
- Working with git repositories:
@@ -54,6 +55,7 @@ navbar:
- user/tutorials/git-arvados-guide.html.textile.liquid
- Develop an Arvados workflow:
- user/tutorials/intro-crunch.html.textile.liquid
+ - user/tutorials/writing-cwl-workflow.html.textile.liquid
- user/tutorials/running-external-program.html.textile.liquid
- user/topics/crunch-tools-overview.html.textile.liquid
- user/tutorials/tutorial-firstscript.html.textile.liquid
diff --git a/doc/_includes/_arvados_cwl_runner.liquid b/doc/_includes/_arvados_cwl_runner.liquid
new file mode 100644
index 0000000..72c95dd
--- /dev/null
+++ b/doc/_includes/_arvados_cwl_runner.liquid
@@ -0,0 +1,62 @@
+h3. Submit a workflow and wait for results
+
+Use @arvados-cwl-runner@ to submit CWL workflows to Arvados. After submitting the job, it will wait for the workflow to complete and print out the final result to standard output.
+
+*Note:* Once submitted, the workflow runs entirely on Arvados, so even if you interrupt @arvados-cwl-runner@ or log out, the workflow will continue to run.
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner bwa-mem.cwl bwa-mem-input.yml</span>
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
+2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
+2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
+2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
+{
+ "aligned_sam": {
+ "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
+ "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File",
+ "size": 30738986
+ }
+}
+</code></pre>
+</notextile>
+
+h3. Submit a workflow with no waiting
+
+To submit a workflow and exit immediately, use the @--no-wait@ option. This will submit the workflow to Arvados, print out the uuid of the job that was submitted to standard output, and exit.
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --no-wait bwa-mem.cwl bwa-mem-input.yml</span>
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Upload local files: "bwa-mem.cwl"
+2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Uploaded to qr1hi-4zz18-eqnfwrow8aysa9q
+2016-06-30 15:07:52 arvados.cwl-runner[12480] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
+qr1hi-8i9sb-fm2n3b1w0l6bskg
+</code></pre>
+</notextile>
+
+h3. Run a workflow locally
+
+To run a workflow with local control, use @--local at . This means that the host where you run @arvados-cwl-runner@ will be responsible for submitting jobs. With @--local@, if you interrupt @arvados-cwl-runner@ or log out, the workflow will be terminated.
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml</span>
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-07-01 10:05:19 arvados.cwl-runner[16290] INFO: Pipeline instance qr1hi-d1hrv-92wcu6ldtio74r4
+2016-07-01 10:05:28 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Queued
+2016-07-01 10:05:29 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Running
+2016-07-01 10:05:45 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Complete
+2016-07-01 10:05:46 arvados.cwl-runner[16290] INFO: Overall process status is success
+{
+ "aligned_sam": {
+ "size": 30738986,
+ "path": "keep:15f56bad0aaa7364819bf14ca2a27c63+88/HWI-ST1027_129_D0THKACXX.1_1.sam",
+ "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File"
+ }
+}
+</code></pre>
+</notextile>
diff --git a/doc/_includes/_register_cwl_workflow.liquid b/doc/_includes/_register_cwl_workflow.liquid
new file mode 100644
index 0000000..438115b
--- /dev/null
+++ b/doc/_includes/_register_cwl_workflow.liquid
@@ -0,0 +1,21 @@
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --create-workflow bwa-mem.cwl</span>
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Upload local files: "bwa-mem.cwl"
+2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Uploaded to qr1hi-4zz18-7e0hedrmkuyoei3
+2016-07-01 12:21:01 arvados.cwl-runner[15796] INFO: Created template qr1hi-p5p6p-rjleou1dwr167v5
+qr1hi-p5p6p-rjleou1dwr167v5
+</code></pre>
+</notextile>
+
+You can provide a partial input file to set default values for the workflow input parameters:
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --create-workflow bwa-mem.cwl bwa-mem-template.yml</span>
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Upload local files: "bwa-mem.cwl"
+2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Uploaded to qr1hi-4zz18-0f91qkovk4ml18o
+2016-07-01 14:09:50 arvados.cwl-runner[3730] INFO: Created template qr1hi-p5p6p-0deqe6nuuyqns2i
+qr1hi-p5p6p-0deqe6nuuyqns2i
+</code></pre>
+</notextile>
diff --git a/doc/_includes/_what_is_cwl.liquid b/doc/_includes/_what_is_cwl.liquid
new file mode 100644
index 0000000..d7b890d
--- /dev/null
+++ b/doc/_includes/_what_is_cwl.liquid
@@ -0,0 +1 @@
+The "Common Workflow Language (CWL)":http://commonwl.org is a multi-vendor open standard for describing analysis tools and workflows that are portable across a variety of platforms. CWL is the recommended way to develop and run workflows for Arvados. Arvados supports the "CWL v1.0":http://commonwl.org/v1.0 specification.
diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index 3006990..fc0c6b0 100644
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -4,13 +4,17 @@ navsection: userguide
title: Using Common Workflow Language
...
-The "Common Workflow Language (CWL)":http://commonwl.org is a multi-vendor open standard for describing analysis tools and workflows that are portable across a variety of platforms. CWL is the recommended way to develop and run workflows for Arvados. Arvados supports the "CWL v1.0":http://commonwl.org/v1.0 specification.
+{% include 'what_is_cwl' %}
{% include 'tutorial_expectations' %}
-h2. Setting up
+h2. Preparing to work with Arvados cwl runner
-The @arvados-cwl-runner@ client is installed by default on Arvados shell nodes. However, if you do not have @arvados-cwl-runner@, you may install it using @pip@:
+h3. arvados-cwl-runner
+
+The @arvados-cwl-runner@ client is installed by default on Arvados shell nodes.
+
+However, if you do not have @arvados-cwl-runner@, you may install it using @pip@:
<notextile>
<pre><code>~$ <span class="userinput">virtualenv ~/venv</span>
@@ -20,9 +24,11 @@ The @arvados-cwl-runner@ client is installed by default on Arvados shell nodes.
</code></pre>
</notextile>
-h3. Docker
+h3. Check Docker access
-Certain features of @arvados-cwl-runner@ require access to Docker. You can determine if you have access to Docker by running @docker version@:
+Certain features of @arvados-cwl-runner@ require access to Docker.
+
+You can determine if you have access to Docker by running @docker version@:
<notextile>
<pre><code>~$ <span class="userinput">docker version</span>
@@ -44,9 +50,9 @@ Server:
</code></pre>
</notextile>
-If this returns an error, contact the sysadmin of your cluster for assistance. Alternatively, if you have Docker installed on your local workstation, you may follow the instructions above to install @arvados-cwl-runner at .
+If this returns an error, contact the sysadmin of your cluster for assistance.
-h3. Getting the example files
+h3. Get the example files
The tutorial files are located in the documentation section of the Arvados source repository:
@@ -72,60 +78,7 @@ If you do not wish to create an account on "https://cloud.curoverse.com":https:/
h2. Submitting a workflow to an Arvados cluster
-Use @arvados-cwl-runner@ to submit CWL workflows to Arvados. After submitting the job, it will wait for the workflow to complete and print out the final result to standard output. Note that once submitted, the workflow runs entirely on Arvados, so even if you interrupt @arvados-cwl-runner@ or log out, the workflow will continue to run.
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner bwa-mem.cwl bwa-mem-input.yml</span>
-arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
-2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
-2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
-2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
-2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
-2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
-{
- "aligned_sam": {
- "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
- "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
- "class": "File",
- "size": 30738986
- }
-}
-</code></pre>
-</notextile>
-
-To submit a workflow and exit immediately, use the @--no-wait@ option. This will print out the uuid of the job that was submitted to standard output.
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --no-wait bwa-mem.cwl bwa-mem-input.yml</span>
-arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
-2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Upload local files: "bwa-mem.cwl"
-2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Uploaded to qr1hi-4zz18-eqnfwrow8aysa9q
-2016-06-30 15:07:52 arvados.cwl-runner[12480] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-qr1hi-8i9sb-fm2n3b1w0l6bskg
-</code></pre>
-</notextile>
-
-To run a workflow with local control, use @--local at . This means that the host where you run @arvados-cwl-runner@ will be responsible for submitting jobs. With @--local@, if you interrupt @arvados-cwl-runner@ or log out, the workflow will be terminated.
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml</span>
-arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
-2016-07-01 10:05:19 arvados.cwl-runner[16290] INFO: Pipeline instance qr1hi-d1hrv-92wcu6ldtio74r4
-2016-07-01 10:05:28 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Queued
-2016-07-01 10:05:29 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Running
-2016-07-01 10:05:45 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Complete
-2016-07-01 10:05:46 arvados.cwl-runner[16290] INFO: Overall process status is success
-{
- "aligned_sam": {
- "size": 30738986,
- "path": "keep:15f56bad0aaa7364819bf14ca2a27c63+88/HWI-ST1027_129_D0THKACXX.1_1.sam",
- "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
- "class": "File"
- }
-}
-</code></pre>
-</notextile>
+{% include 'arvados_cwl_runner' %}
h2. Work reuse
@@ -145,27 +98,7 @@ h2. Registering a workflow to use in Workbench
Use @--create-workflow@ to register a CWL workflow with Arvados. This enables you to share workflows with other Arvados users, and run them by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button on the Workbench Dashboard.
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --create-workflow bwa-mem.cwl</span>
-arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
-2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Upload local files: "bwa-mem.cwl"
-2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Uploaded to qr1hi-4zz18-7e0hedrmkuyoei3
-2016-07-01 12:21:01 arvados.cwl-runner[15796] INFO: Created template qr1hi-p5p6p-rjleou1dwr167v5
-qr1hi-p5p6p-rjleou1dwr167v5
-</code></pre>
-</notextile>
-
-You can provide a partial input file to set default values for the workflow input parameters:
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --create-workflow bwa-mem.cwl bwa-mem-template.yml</span>
-arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
-2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Upload local files: "bwa-mem.cwl"
-2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Uploaded to qr1hi-4zz18-0f91qkovk4ml18o
-2016-07-01 14:09:50 arvados.cwl-runner[3730] INFO: Created template qr1hi-p5p6p-0deqe6nuuyqns2i
-qr1hi-p5p6p-0deqe6nuuyqns2i
-</code></pre>
-</notextile>
+{% include 'register_cwl_workflow' %}
h2. Making workflows directly executable
@@ -226,7 +159,7 @@ arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107,
h2. Developing workflows
-For an introduction and and detailed documentation about writing CWL, see the "User Guide":http://commonwl.org/v1.0/UserGuide.html and the "Specification":http://commonwl.org/v1.0 .
+For an introduction and and detailed documentation about writing CWL, see the "CWL User Guide":http://commonwl.org/v1.0/UserGuide.html and the "CWL Specification":http://commonwl.org/v1.0 .
To run on Arvados, a workflow should provide a @DockerRequirement@ in the @hints@ section.
diff --git a/doc/user/topics/running-workflow-command-line.html.textile.liquid b/doc/user/topics/running-workflow-command-line.html.textile.liquid
new file mode 100644
index 0000000..f70d3e8
--- /dev/null
+++ b/doc/user/topics/running-workflow-command-line.html.textile.liquid
@@ -0,0 +1,17 @@
+---
+layout: default
+navsection: userguide
+title: "Running an Arvados workflow"
+...
+
+{% include 'what_is_cwl' %}
+
+{% include 'tutorial_expectations' %}
+
+h2. arvados-cwl-runner
+
+The arvados-cwl-runner tool can be used to submit workflows to Arvados cluster using the command prompt.
+
+The following examples assume that you have prepared to run arvados-cwl-runner tool as explained in the "Using Common Workflow Language":{{site.baseurl}}/user/topics/running-workflow-command-line.html.textile.liquid page.
+
+{% include 'arvados_cwl_runner' %}
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index 1565bf5..11746bf 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -20,7 +20,7 @@ h3. Steps
# Select *<i class="fa fa-fw fa-gear"></i> Tutorial bwa mem cwl* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will create a new process in your *Home* project and will open it. You can now supply the inputs for the process. Please note that all required inputs are pupulated with default values and you can change them if you prefer.
# For example, let's see how to change *"reference" parameter* for this workflow. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath the *"reference" parameter* header. This will open a dialog box titled *Choose a dataset for "reference" parameter for cwl-runner in bwa-mem.cwl component*.
# Open the *Home <span class="caret"></span>* menu and select *All Projects*. Search for and select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference*. You will then see a list of files. Select *<i class="fa fa-fw fa-file"></i> 19-fasta.bwt* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
-# Repeat the previous two steps to set the *"read_p1" parameter for cwl-runner script in bwa-mem.cwl component* and *"read_p2" parameter for cwl-runner script in bwa-mem.cwl component* parameters.
+# Repeat the previous two steps to set the *"read_p1" parameter for cwl-runner script in bwa-mem.cwl component* and *"read_p2" parameter for cwl-runner script in bwa-mem.cwl component* parameters.
# Click on the <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> button. The page updates to show you that the process has been submitted to run on the Arvados cluster.
# After the process starts running, you can track the progress by watching log messages from the component(s). This page refreshes automatically. You will see a <span class="label label-success">complete</span> label when the process completes successfully.
# Click on the *Output* link to see the results of the process. This will load a new page listing the output files from this process. You'll see the output SAM file from the alignment tool under the *Files* tab.
diff --git a/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid b/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
new file mode 100644
index 0000000..cd6afcb
--- /dev/null
+++ b/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
@@ -0,0 +1,28 @@
+---
+layout: default
+navsection: userguide
+title: "Writing a CWL workflow"
+...
+
+{% include 'what_is_cwl' %}
+
+{% include 'tutorial_expectations' %}
+
+h2. Registering a CWL workflow
+
+Use @--create-workflow@ to register a CWL workflow with Arvados.
+
+The following examples assume that you have prepared to run arvados-cwl-runner tool as explained in the "Using Common Workflow Language":{{site.baseurl}}/user/topics/running-workflow-command-line.html.textile.liquid page.
+
+{% include 'register_cwl_workflow' %}
+
+h2. Running a CWL workflow
+
+h3. Running the workflow at command prompt
+
+TBD
+
+h3. Running the workflow using Workbench
+
+The workflow can also be executed using Workbench. Go to the Workbench Dashboard and click the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button and select the desired workflow.
+
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