SAGA Tutorial Part 4: Adding File Transfer
In this fourth part of the tutorial, we again build on the previous example and some code that copies our job's output file back to the local machine. This is done using the saga.filesystem API package.
This example assumes that you have SFTP access to the remote resource that you have used in the previous example. Again, this example assumes that you have a working public/private SSH key-pair and that you can sftp into your remote resource using those keys, i.e., your public key is in the ~/.ssh/authorized_hosts file on the remote machine. If you are not sure how this works, you might want to read SSH and GSISSH first.
Copy the code from the previous example 3 to a new file saga_example_remote_staging.py. Add the following code after the last print, right before the except statement:
Note: Make sure that you adjust the paths to reflect your home directory on the remote machine.
outfilesource = 'sftp://localhost/Users/oweidner/mysagajob.stdout'
outfiletarget = 'file://localhost/tmp/'
out = saga.filesystem.File(outfilesource, session=ses)
out.copy(outfiletarget)
print "Staged out %s to %s (size: %s bytes)" % (outfilesource, outfiletarget, out.get_size())Save the file and execute it:
python saga_example_remote_staging.py
The output should look something like this:
Job ID : None
Job State : saga.job.Job.New
...starting job...
Job ID : [ssh://localhost]-[67712]
Job State : saga.job.Job.Running
...waiting for job...
Job State : saga.job.Job.Done
Exitcode : 0
Staged out sftp://localhost/Users/oweidner/mysagajob.stdout to file://localhost/tmp/ (size: 16 bytes)
Your output file should now be in /tmp/mysagajob.stdout and contain the string Hello from SAGA.
In this example we have used SAGA's file handling capabilities. These capabilities are packaged in the bliss.saga.filesystem module (API Doc). Two main classes are defined in this module:
- The filesystem.File class (API Doc) provides a handle to a (remote) file.
- The filesystem.Directory class (API Doc) provides a handle to a (remote) directory.
Together, these two classes can be used to traverse and modify local and remote filesystems. Currently (v. 0.2.4), SAGA supports the SFTP protocol, but other protocol plug-ins are under development.
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