Arvados

A common convention I would do with run-command version 83a9390a05bbffc2e4ea95dd693af3ab3547fa12 from job qr1hi-8i9sb-fqbtg1lcocoefe0 is:

"command": [
"$(outputname)"
],
"outputname": {
"value": {
"list": "iterator",
"index": "0",
"command": "OUTPUT=$(basename $(basename $(iterator))).sam"
},
"iterator": {
"value": {
"group": "input_dir",
"regex": "(.*)_[0-9]_.*.sam"
}
}

In "command" of output name, I use some sort of command to play with the name of iterator. Iterator is the name of a file from a collection where task.foreach is taking the name of each file. This convention worked perfectly fine.

Now, with run-command version ac21f0d45a76294aaca0c0c0fdf06eb72d03368d, I try the same convention in job qr1hi-8i9sb-i7vykyao0wg0f9a
"command": [
"$(outputname)"
],
"outputname": {
"list": "iterator",
"index": "0",
"command": "$(basename $(basename $(iterator)))"
},
"iterator": {
"group": "input_dir",
"regex": "(.*).fastq.gz"
},

But get the error:

run-command: caught exception
12/5/2014 10:03:50 AM compute29 1 task-print 0 Traceback (most recent call last):
12/5/2014 10:03:50 AM compute29 1 task-print 0 File "/tmp/crunch-src/crunch_scripts/run-command", line 291, in <module>
12/5/2014 10:03:50 AM compute29 1 task-print 0 recursive_foreach(jobp, jobp["task.foreach"])
12/5/2014 10:03:50 AM compute29 1 task-print 0 File "/tmp/crunch-src/crunch_scripts/run-command", line 262, in recursive_foreach
12/5/2014 10:03:50 AM compute29 1 task-print 0 recursive_foreach(params, fvars)
12/5/2014 10:03:50 AM compute29 1 task-print 0 File "/tmp/crunch-src/crunch_scripts/run-command", line 255, in recursive_foreach
12/5/2014 10:03:50 AM compute29 1 task-print 0 items = get_items(params, params[var])
12/5/2014 10:03:50 AM compute29 1 task-print 0 File "/tmp/crunch-src/crunch_scripts/run-command", line 235, in get_items
12/5/2014 10:03:50 AM compute29 1 task-print 0 mode = os.stat(value).st_mode
12/5/2014 10:03:50 AM compute29 1 task-print 0 OSError: [Errno 2] No such file or directory: 'SRR064287_1'

So maybe command is trying to look for iterator in the input collection now?

I've got a workaround by just doing the command within script_parameters, but I just wanted to note this behavior.