swiftwrap.wrapperstaging
-------------------------

.Command line arguments
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|============================
|Argument       | Description      
| -a            | Command line arguments passed to app
| -d            | List of directories to create
| -e            | App to execute
| -err          | Where to write stderr
| -i            | Set stdin
| -if           | Input file(s) 
| -jobdir       | Swift job directory
| -of           | Ouput file(s)     
| -out          | Where to write stdout
| -scratchdir   | Swift scratch directory
| -sk           | Sitedir keep, true/false
| -status       | Provider or files
| -urlprefix    | URL Prefix
| -wt           | Wrapper log always transfer, true/false
|============================

Swift properties related to wrapper staging
-------------------------------------------
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|============================
|Setting	| Description
| use.wrapper.staging | If set to true, enable wrapper staging. Defaults to false.
| wrapper.staging.local.server | Swift passes a URL prefix to swiftwrap.wrapperstaging that determines how to access local files. This setting determines what the prefix is (for example, file://).
|============================

Protocols
---------
Below is a list of protocols supported by _swiftwrap.wrapperstaging and a brief explanation of how they are implemented.

direct://
~~~~~~~~~
The direct protocol allows you to bypass file staging to the swift created
work directory. Instead of making a copy of the file, a symlink will be
created which points to the original location of the file. 
-----
file data <"direct:///home/davidkelly999/staging/absolute/direct/data.txt">;
-----

file://
~~~~~~~
By default, files that use the file:// URI, or files that specify no URI at
all, will act in a way that is similar to the behavior or direct://. A symlink
will be created in the Swift work directory that points to the original
location of the file.
-----
file data <"file:///home/davidkelly999/staging/absolute/file/data.txt">;
file data2 <"/home/davidkelly999/staging/absolute/normal/data.txt">;
-----

gsiftp://
~~~~~~~~~
GSIFTP files will be transferred using the globus-url-copy command.

http://
~~~~~~~
HTTP is implemented in _swiftwrap.wrapperstaging via the wget command.

stage://
~~~~~~~~
If a file begins with stage://, a copy of the file will be made in the work
directory. Files get copied using dd with a 10MB block size.
-----
file data <"stage:///home/davidkelly999/staging/absolute/stage/data.txt">;
-----

Adding new protocols
~~~~~~~~~~~~~~~~~~~~
The file cog/modules/provider-local/resources/cog-provider.properties allows you to set aliases.
Define your new file protocol as an alias to "local". Suppose you would like
to add a new protocol called "megaftp", you could add a line that looks like
this:

-----
alias=megaftp:local
-----

In your swift script, you would reference the file as
megaftp://path/to/file.txt.

NOTE: You will need to recompile after making this change.

Examples of how swiftwrap is called
-----------------------------------

Using absolute pathnames
~~~~~~~~~~~~~~~~~~~~~~~~
In this example, Swift tries to map the file below using an absolute path
-----
file data <"/home/davidkelly999/staging/dd-absolute/data.txt">;
-----
._swiftwrap.wrapperstaging arguments
|====================================
| -if | file://localhost//home/davidkelly999/staging/dd-absolute/data.txt
| -of | catsn.0001.out
| -urlprefix | file:///home/davidkelly999/staging/dd-absolute
| -d | \__root__/home/davidkelly999/staging/dd-absolute\|.
| -a | \__root__/home/davidkelly999/staging/dd-absolute/data.txt
|====================================

Using relative pathnames
~~~~~~~~~~~~~~~~~~~~~~~~
Here is an example using relative pathnames in Swift.
-----
file data <"data.txt">;
-----
._swiftwrap.wrapperstaging arguments
|===================================
| -if | file://localhost/data.txt
| -of | catsn.0001.out
| -urlprefix | file:///home/davidkelly999/staging/dd-relative
| -d | \|.
| -a | data.txt
|===================================