runwithRedirectFrom() call needs error checking and output stream handling

[sheridancbio]

In PdbScriptsPipelineRunCommand.java : runwithRedirectFrom(), a process is created and input is redirected to it, but output streams are ignored and the return code / status code is not checked.

Long standard output or standard error streams can cause the small process buffers to overload .. but in the case of mysql we probably don't expect that. Still, maybe we should redirect output streams to temporary files and then delete them when the mysql commands are complete.

But return codes must be checked to see if the mysql command failed or exited with an error.

[juexinwang]

I can try to deal with that. But I think the better solution is using mysql features directly from spring-boot

[juexinwang]

I have updated this.

[sheridancbio]

This issue is closely related to #13 ... if we properly handle output streams, both of these issues can probably be resolved.

In addition to reporting a detected error during a mysql command, the pdb-annotation-pipeline should stop its processing at the point where the error occurred (unless the error can be recovered from) and tell the user as much as possible about what partial changes were made to the database, so the user can manually correct partial updates if necessary.