Bug #3195
closed
minimum_script_version field in job submission doesn't seem to work
Description
When I try to use minimum_script_version in a component of a pipeline, the job submission fails with the following error. Using new-style 'filters' on job submission does work.
2014-07-05_00:44:33.48783 arv-run-pipeline-instance 25798: create job: ["#<ArgumentError: Invalid operand type 'NilClass' for 'in' ope
rator in filters>"] with attributes {:script=>"run-command", :script_parameters=>{:command=>["bwa", "mem", "-t", "4", "-R", "@RG\\tID:
group_id\\tPL:illumina\\tSM:sample_id", "$(dir $(reference_collection))/$(reference_name)", "$(file $(R1))", "$(file $(R2))"], :refere
nce_collection=>"e26a8b984b361b8eb9de17733e254c20+5819", :reference_name=>"human_g1k_v37.fasta", :R1=>"7eb6160977c6161fee4f365765d3380
1+2370/HWI-ST1027_129_D0THKACXX.1_1.fastq.gz", :R2=>"7eb6160977c6161fee4f365765d33801+2370/HWI-ST1027_129_D0THKACXX.1_2.fastq.gz", :st
dout=>"A.$(reference_name).sam"}, :script_version=>"master", :repository=>"arvados", :nondeterministic=>nil, :output_is_persistent=>fa
lse, :runtime_constraints=>{:docker_image=>"arvados/jobs-java-bwa-samtools"}, :owner_uuid=>"4xphq-j7d0g-ur9v47pkvxu1hds"}
Updated by
Updated by Brett Smith over 10 years ago
Do you have a record of the Job you submitted that triggered this error? The API server has tests for basic cases using the original parameter, and those still pass. At first glance, based only on the exception text, it looks like your search resolved to no commits, and that led to a nonsense filter internally. Definitely the Jobs controller needs to guard against that case. But it'd be helpful to double-check if there's something else going on.
Updated by Brett Smith over 10 years ago
3195-bugfix-job-min-script-ver is up for review to better guard against bogus git refspecs, and render a nicer error when one is provided. That's the most I know to do for now. The parameters in the original bug report don't specify a minimum script version, so it's hard to know what more specifically to test.
Updated by Brett Smith over 10 years ago
- Status changed from New to Resolved
Applied in changeset arvados|commit:f85c6cf14fada8b2ad4b6b7e6e7e9cf9852ce83d.