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Answers imbedded under your questions...

1. When I get the public key from the server, what do I do to install it?
I'm presuming you are talking about the private key (often named "id_dsa" or "id_rsa") used for public/private key authentication? The convention is to store this file as /home/<userid>/.ssh/id_dsa (or id_rsa). You could store elsewhere and use the "-i" option on the sftp command to specify the location of the file. Be aware that SSH requires specific permissions on the containing directories and the key file to ensure access is only allowed by the owning user. See here for more information (one long line in your browser):
http://www-01.ibm.com/support/docview.wss?uid=nas117c2d734a7a40463862576440045c22e

2. I will be sending multiple files to the server and would like to
automate the process. What is the best way to do this?
Check out the sftp "-b" batch option to read a set of sftp commands (mkdir, chdir, put...) from a file. Be sure you are current on 5733SC1 PTFs for this - I recall problems with sftp batch processing in some older IBM i releases (corrected via 5733SC1 PTFs)

3. The member name of the files being sent will vary with each
transmission. How can I do this in an automated envrionment?
If you're using the batch option as I described above, your CL program could build the batch script on the fly during each invocation -- just change the filenames in the script as applicable.

4. Does it matter what user profile runs the job?
Shouldn't matter what userid does this. sftp commands are public *USE

5. What OS Level security restrictions are there on using the required
commands?
None/same as 4

6. If the client has a firewall that restricts outbound transmissions to
known ports, what ports need to be opened for SFTP?
Sounds like IBM i is the client side so sftp will chose an arbitrary outbound port on IBM i. On the server side, the default connecting-to inbound port is 22



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