Hmm, it should have picked up all of them. I checked out the repos that contain non-empty COMMANDS files, and our code relies on an invocation service script to assemble the list of commands.  One of these steps could have an error.  What modules/scripts seem to be missing?

-michael


On Tue, May 21, 2013 at 11:46 AM, Land, Miriam L. <landml@ornl.gov> wrote:
--------
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There are other modules with a COMMANDS file.  Were only certain modules picked for this demonstration?

Miriam

From: Michael Sneddon <mwsneddon@lbl.gov<mailto:mwsneddon@lbl.gov>>
Date: Tuesday, May 21, 2013 2:32 PM
To: Miriam Land <landml@ornl.gov<mailto:landml@ornl.gov>>
Cc: Tom Brettin <brettin@mcs.anl.gov<mailto:brettin@mcs.anl.gov>>, Elizabeth Glass <marland@mcs.anl.gov<mailto:marland@mcs.anl.gov>>, Keith Keller <kkeller@lbl.gov<mailto:kkeller@lbl.gov>>, "release-team@kbase.us<mailto:release-team@kbase.us>" <release-team@kbase.us<mailto:release-team@kbase.us>>
Subject: Re: [Release-team] auto generation of command -h output

Yeah, getting everyone to follow the same conventions is going to be a challenge, but at least we have something to work with.  One of the goals of this exercise is to provide Outreach with at least an index of what commands are available in KBase so that we can start checking for accuracy/completeness and post some of this reference information to the website.

-michael


On Tue, May 21, 2013 at 11:20 AM, Land, Miriam L. <landml@ornl.gov<mailto:landml@ornl.gov>> wrote:
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I noticed that there are differences between the modules.  There are some that:

 *   Are empty (phispy)
 *   Are one line and difficult to read (genopheno)
 *   Try to download a file instead of displaying content (sr)
 *   Are much more elaborate and complete than others (http://140.221.85.77/command-docs/pe/coex_cluster.txt vs http://140.221.85.77/command-docs/genome_annotation/a_and_b.txt)

It is going to be difficult for a script to compensate for all the variation.  Otherwise, good place to start.

Miriam

From: Michael Sneddon <mwsneddon@lbl.gov<mailto:mwsneddon@lbl.gov><mailto:mwsneddon@lbl.gov<mailto:mwsneddon@lbl.gov>>>
Date: Tuesday, May 21, 2013 2:06 PM
To: Tom Brettin <brettin@mcs.anl.gov<mailto:brettin@mcs.anl.gov><mailto:brettin@mcs.anl.gov<mailto:brettin@mcs.anl.gov>>>, Elizabeth Glass <marland@mcs.anl.gov<mailto:marland@mcs.anl.gov><mailto:marland@mcs.anl.gov<mailto:marland@mcs.anl.gov>>>
Cc: Keith Keller <kkeller@lbl.gov<mailto:kkeller@lbl.gov><mailto:kkeller@lbl.gov<mailto:kkeller@lbl.gov>>>, "release-team@kbase.us<mailto:release-team@kbase.us><mailto:release-team@kbase.us<mailto:release-team@kbase.us>>" <release-team@kbase.us<mailto:release-team@kbase.us><mailto:release-team@kbase.us<mailto:release-team@kbase.us>>>
Subject: [Release-team] auto generation of command -h output

During this last build meeting, Keith and I put together, using some of Bob's invocation code, a method for capturing the help output of the command-line scripts which service owners have declared using the COMMANDS file.  I put up an example of the output here: http://140.221.85.77/command-docs/

The commands are grouped into folders which are named with the "group-name" declared in the COMMANDS files.  In each of these folders, there is an 'index.txt' file which includes the verbose name of the set of commands on the first line, followed by a list of all the commands that were declared.  For each of these commands, there is a text file in the folder with the actual commands '-h' help output.

If the text file for a command is empty, then for some reason the script with the '-h' option did not run successfully or no help was printed.

Let me know if you have questions.  The format of this output is fairly easy to change.

For those on the release team, this help output generation can be invoked from the invocation service Makefile with the "deploy-command-docs" target.  This output is placed in /kb/deployment/services/invocation/webroot/.  Perhaps we should start including this step by default whenever the invocation service is deployed?

-michael