From a19944a8d07632157c92de2132620ac0ca16232c Mon Sep 17 00:00:00 2001 From: Fabrice Brito Date: Fri, 24 Nov 2023 09:23:16 +0100 Subject: [PATCH] fixes conformance test execution 1.0 --- conformance/results-v1.0.txt | 896 ++++++++++++++++++++--------------- conformance/run-job-1-0.sh | 2 +- 2 files changed, 517 insertions(+), 381 deletions(-) diff --git a/conformance/results-v1.0.txt b/conformance/results-v1.0.txt index a795040..db18038 100644 --- a/conformance/results-v1.0.txt +++ b/conformance/results-v1.0.txt @@ -1,589 +1,725 @@ ---- Running conformance test v1.0 on /usr/local/bin/calrissian --- -calrissian 0.7.0 (cwltool 1.0.20190621234233) -cwltest --tool /usr/local/bin/calrissian --test=conformance_test_v1.0.yaml --verbose --basedir /conformance/common-workflow-language-1.0.2/v1.0 -- --max-ram 8G --max-cores 4 --default-container debian:stretch-slim -Test [1/197] General test of command line generation - -Test [2/197] Test nested prefixes with arrays - -Test [3/197] Test nested command line bindings - -Test [4/197] Test command line with optional input (missing) - -Test [5/197] Test command line with optional input (provided) - -Test [6/197] Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature - -WARNING v1.0/template-tool.cwl:7:9: JSHINT: exports = module.exports = _; -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'exports' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: exports._ = _; -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'exports' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: if (typeof module !== 'undefined' && module.exports) { -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'module' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: exports = module.exports = _; -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'module' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: return setTimeout(function(){ -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: timeout = setTimeout(later, remaining); -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: timeout = setTimeout(later, wait - last); -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: if (!timeout) timeout = setTimeout(later, wait); -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: clearTimeout(timeout); -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'clearTimeout' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: root._ = previousUnderscore; -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'previousUnderscore' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: if (typeof define === 'function' && define.amd) { -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'define' is not defined. -WARNING v1.0/template-tool.cwl:7:9: JSHINT: define('underscore', [], function() { -v1.0/template-tool.cwl:7:9: JSHINT: ^ -v1.0/template-tool.cwl:7:9: JSHINT: W117: 'define' is not defined. -WARNING v1.0/template-tool.cwl:8:9: JSHINT: var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); }; -v1.0/template-tool.cwl:8:9: JSHINT: ^ -v1.0/template-tool.cwl:8:9: JSHINT: W117: '_' is not defined. -Test [7/197] Test command execution in Docker with stdout redirection - -Test [8/197] Test command execution in Docker with shortcut stdout redirection - -Test [9/197] Test command execution in Docker with mediumcut stdout redirection - -Test [10/197] Test command line with stderr redirection - -Test [11/197] Test command line with stderr redirection, brief syntax - -Test [12/197] Test command line with stderr redirection, named brief syntax - -Test [13/197] Test command execution in Docker with stdin and stdout redirection - -Test [14/197] Test default usage of Any in expressions. - -Test [15/197] Test explicitly passing null to Any type inputs with default values. - -Test [16/197] Testing the string 'null' does not trip up an Any with a default value. - -Test [17/197] Test Any without defaults cannot be unspecified. - +Test [1/197] cl_basic_generation: General test of command line generation + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpq9zr0hem --quiet v1.0/v1.0/bwa-mem-tool.cwl v1.0/v1.0/bwa-mem-job.json +Test [2/197] nested_prefixes_arrays: Test nested prefixes with arrays + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpm_awj991 --quiet v1.0/v1.0/binding-test.cwl v1.0/v1.0/bwa-mem-job.json +Test [3/197] nested_cl_bindings: Test nested command line bindings + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp8tyq1orl --quiet v1.0/v1.0/tmap-tool.cwl v1.0/v1.0/tmap-job.json +Test [4/197] cl_optional_inputs_missing: Test command line with optional input (missing) + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpjnwy2z4j --quiet v1.0/v1.0/cat1-testcli.cwl v1.0/v1.0/cat-job.json +Test [5/197] cl_optional_bindings_provided: Test command line with optional input (provided) + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpyr0winnz --quiet v1.0/v1.0/cat1-testcli.cwl v1.0/v1.0/cat-n-job.json +Test [6/197] initworkdir_expreng_requirements: Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpa6a2gza5 --quiet v1.0/v1.0/template-tool.cwl v1.0/v1.0/cat-job.json +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: exports = module.exports = _; +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'exports' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: exports._ = _; +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'exports' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: if (typeof module !== 'undefined' && module.exports) { +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'module' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: exports = module.exports = _; +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'module' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: return setTimeout(function(){ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: timeout = setTimeout(later, remaining); +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: timeout = setTimeout(later, wait - last); +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: if (!timeout) timeout = setTimeout(later, wait); +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: clearTimeout(timeout); +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'clearTimeout' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: root._ = previousUnderscore; +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'previousUnderscore' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: if (typeof define === 'function' && define.amd) { +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'define' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:7:9: JSHINT: define('underscore', [], function() { +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:7:9: JSHINT: W117: 'define' is not defined. +WARNING v1.0/v1.0/template-tool.cwl:8:9: JSHINT: var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); }; +v1.0/v1.0/template-tool.cwl:8:9: JSHINT: ^ +v1.0/v1.0/template-tool.cwl:8:9: JSHINT: W117: '_' is not defined. +Test [7/197] stdout_redirect_docker: Test command execution in Docker with stdout redirection + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpgklvcg5z --quiet v1.0/v1.0/cat3-tool-docker.cwl v1.0/v1.0/cat-job.json +Test [8/197] stdout_redirect_shortcut_docker: Test command execution in Docker with shortcut stdout redirection + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp91t_5dru --quiet v1.0/v1.0/cat3-tool-shortcut.cwl v1.0/v1.0/cat-job.json +Test [9/197] stdout_redirect_mediumcut_docker: Test command execution in Docker with mediumcut stdout redirection + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp0ky1nf8u --quiet v1.0/v1.0/cat3-tool-mediumcut.cwl v1.0/v1.0/cat-job.json +Test [10/197] stderr_redirect: Test command line with stderr redirection + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpnxr0u5xe --quiet v1.0/v1.0/stderr.cwl v1.0/v1.0/empty.json +Test [11/197] stderr_redirect_shortcut: Test command line with stderr redirection, brief syntax + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp8gjeqbfm --quiet v1.0/v1.0/stderr-shortcut.cwl v1.0/v1.0/empty.json +Test [12/197] stderr_redirect_mediumcut: Test command line with stderr redirection, named brief syntax + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpda26p6lq --quiet v1.0/v1.0/stderr-mediumcut.cwl v1.0/v1.0/empty.json +Test [13/197] stdinout_redirect_docker: Test command execution in Docker with stdin and stdout redirection + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5ekn3xc3 --quiet v1.0/v1.0/cat4-tool.cwl v1.0/v1.0/cat-job.json +Test [14/197] expression_any: Test default usage of Any in expressions. + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpzclwqbsm --quiet v1.0/v1.0/null-expression1-tool.cwl v1.0/v1.0/empty.json +Test [15/197] expression_any_null: Test explicitly passing null to Any type inputs with default values. + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmplaxedpt3 --quiet v1.0/v1.0/null-expression1-tool.cwl v1.0/v1.0/null-expression1-job.json +Test [16/197] expression_any_string: Testing the string 'null' does not trip up an Any with a default value. + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprvgzn2yu --quiet v1.0/v1.0/null-expression1-tool.cwl v1.0/v1.0/null-expression2-job.json +Test [17/197] expression_any_nodefaultany: Test Any without defaults cannot be unspecified. + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpg16q9j9v --quiet v1.0/v1.0/null-expression2-tool.cwl v1.0/v1.0/empty.json ERROR Workflow error, try again with --debug for more information: Invalid job input record: -v1.0/null-expression2-tool.cwl:9:3: Missing required input parameter 'i1' -Test [18/197] Test explicitly passing null to Any type without a default value. +v1.0/v1.0/null-expression2-tool.cwl:9:3: Missing required input parameter 'i1' +Test [18/197] expression_any_null_nodefaultany: Test explicitly passing null to Any type without a default value. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpo6hzviui --quiet v1.0/v1.0/null-expression2-tool.cwl v1.0/v1.0/null-expression1-job.json ERROR Workflow error, try again with --debug for more information: Invalid job input record: -v1.0/null-expression2-tool.cwl:9:3: Missing required input parameter 'i1' -Test [19/197] Testing the string 'null' does not trip up an Any without a default value. +v1.0/v1.0/null-expression2-tool.cwl:9:3: Missing required input parameter 'i1' +Test [19/197] expression_any_nullstring_nodefaultany: Testing the string 'null' does not trip up an Any without a default value. -Test [20/197] Testing Any type compatibility in outputSource +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmps5leijla --quiet v1.0/v1.0/null-expression2-tool.cwl v1.0/v1.0/null-expression2-job.json +Test [20/197] any_outputSource_compatibility: Testing Any type compatibility in outputSource -Test [21/197] Test command execution in with stdin and stdout redirection +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1zqbjc2s --quiet v1.0/v1.0/any-type-compat.cwl v1.0/v1.0/any-type-job.json +Test [21/197] stdinout_redirect: Test command execution in with stdin and stdout redirection -Test [22/197] Test ExpressionTool with Javascript engine +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3i9ufpo6 --quiet v1.0/v1.0/cat-tool.cwl v1.0/v1.0/cat-job.json +Test [22/197] expression_parseint: Test ExpressionTool with Javascript engine -Test [23/197] Test outputEval to transform output +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpckfr8nit --quiet v1.0/v1.0/parseInt-tool.cwl v1.0/v1.0/parseInt-job.json +Test [23/197] expression_outputEval: Test outputEval to transform output -Test [24/197] Test two step workflow with imported tools +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpvgi7bz92 --quiet v1.0/v1.0/wc2-tool.cwl v1.0/v1.0/wc-job.json +Test [24/197] wf_wc_parseInt: Test two step workflow with imported tools -Test [25/197] Test two step workflow with inline tools +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmppro8lg_9 --quiet v1.0/v1.0/count-lines1-wf.cwl v1.0/v1.0/wc-job.json +Test [25/197] wf_wc_expressiontool: Test two step workflow with inline tools -Test [26/197] Test single step workflow with Scatter step +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwtiv4peo --quiet v1.0/v1.0/count-lines2-wf.cwl v1.0/v1.0/wc-job.json +Test [26/197] wf_wc_scatter: Test single step workflow with Scatter step -Test [27/197] Test single step workflow with Scatter step and two data links connected to same input, default merge behavior +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4i806dt0 --quiet v1.0/v1.0/count-lines3-wf.cwl v1.0/v1.0/count-lines3-job.json +Test [27/197] wf_wc_scatter_multiple_merge: Test single step workflow with Scatter step and two data links connected to same input, default merge behavior -Test [28/197] Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpj7wu8fwg --quiet v1.0/v1.0/count-lines4-wf.cwl v1.0/v1.0/count-lines4-job.json +Test [28/197] wf_wc_scatter_multiple_nested: Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior -Test [29/197] Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpayp9ebr1 --quiet v1.0/v1.0/count-lines6-wf.cwl v1.0/v1.0/count-lines6-job.json +Test [29/197] wf_wc_scatter_multiple_flattened: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior -Test [30/197] Test that no MultipleInputFeatureRequirement is necessary when workflow step source is a single-item list +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpyrjdmujm --quiet v1.0/v1.0/count-lines7-wf.cwl v1.0/v1.0/count-lines6-job.json +Test [30/197] wf_wc_nomultiple: Test that no MultipleInputFeatureRequirement is necessary when workflow step source is a single-item list -Test [31/197] Test workflow with default value for input parameter (missing) +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpox_gmiyw --quiet v1.0/v1.0/count-lines13-wf.cwl v1.0/v1.0/count-lines6-job.json +Test [31/197] wf_input_default_missing: Test workflow with default value for input parameter (missing) -Test [32/197] Test workflow with default value for input parameter (provided) +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbg8aw4jk --quiet v1.0/v1.0/count-lines5-wf.cwl v1.0/v1.0/empty.json +Test [32/197] wf_input_default_provided: Test workflow with default value for input parameter (provided) -Test [33/197] Test that workflow defaults override tool defaults +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_ddl468t --quiet v1.0/v1.0/count-lines5-wf.cwl v1.0/v1.0/wc-job.json +Test [33/197] wf_default_tool_default: Test that workflow defaults override tool defaults -Test [34/197] Test EnvVarRequirement +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpn_fey0jb --quiet v1.0/v1.0/echo-wf-default.cwl v1.0/v1.0/empty.json +Test [34/197] envvar_req: Test EnvVarRequirement -Test [35/197] Test workflow scatter with single scatter parameter +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1vi_a84f --quiet v1.0/v1.0/env-tool1.cwl v1.0/v1.0/env-job.json +Test [35/197] wf_scatter_single_param: Test workflow scatter with single scatter parameter -Test [36/197] Test workflow scatter with two scatter parameters and nested_crossproduct join method +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpm116x24x --quiet v1.0/v1.0/scatter-wf1.cwl v1.0/v1.0/scatter-job1.json +Test [36/197] wf_scatter_two_nested_crossproduct: Test workflow scatter with two scatter parameters and nested_crossproduct join method -Test [37/197] Test workflow scatter with two scatter parameters and flat_crossproduct join method +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmph4b5rkf4 --quiet v1.0/v1.0/scatter-wf2.cwl v1.0/v1.0/scatter-job2.json +Test [37/197] wf_scatter_two_flat_crossproduct: Test workflow scatter with two scatter parameters and flat_crossproduct join method -Test [38/197] Test workflow scatter with two scatter parameters and dotproduct join method +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprqzfsn8n --quiet v1.0/v1.0/scatter-wf3.cwl#main v1.0/v1.0/scatter-job2.json +Test [38/197] wf_scatter_two_dotproduct: Test workflow scatter with two scatter parameters and dotproduct join method -Test [39/197] Test workflow scatter with single empty list parameter +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpug6kg4vq --quiet v1.0/v1.0/scatter-wf4.cwl#main v1.0/v1.0/scatter-job2.json +Test [39/197] wf_scatter_emptylist: Test workflow scatter with single empty list parameter +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpc94w1mf7 --quiet v1.0/v1.0/scatter-wf1.cwl v1.0/v1.0/scatter-empty-job1.json WARNING [job step step1] Notice: scattering over empty input in 'echo_in'. All outputs will be empty. -Test [40/197] Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty +Test [40/197] wf_scatter_nested_crossproduct_secondempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpm6qemmbt --quiet v1.0/v1.0/scatter-wf2.cwl v1.0/v1.0/scatter-empty-job2.json WARNING [job step step1] Notice: scattering over empty input in 'echo_in2'. All outputs will be empty. -Test [41/197] Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty +Test [41/197] wf_scatter_nested_crossproduct_firstempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpvyuh94tt --quiet v1.0/v1.0/scatter-wf3.cwl#main v1.0/v1.0/scatter-empty-job3.json WARNING [job step step1] Notice: scattering over empty input in 'echo_in1'. All outputs will be empty. -Test [42/197] Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method +Test [42/197] wf_scatter_flat_crossproduct_oneempty: Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbk3otxfo --quiet v1.0/v1.0/scatter-wf3.cwl#main v1.0/v1.0/scatter-empty-job2.json WARNING [job step step1] Notice: scattering over empty input in 'echo_in2'. All outputs will be empty. -Test [43/197] Test workflow scatter with two empty scatter parameters and dotproduct join method +Test [43/197] wf_scatter_dotproduct_twoempty: Test workflow scatter with two empty scatter parameters and dotproduct join method +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpccuztxrg --quiet v1.0/v1.0/scatter-wf4.cwl#main v1.0/v1.0/scatter-empty-job4.json WARNING [job step step1] Notice: scattering over empty input in 'echo_in1', 'echo_in2'. All outputs will be empty. -Test [44/197] Test Any type input parameter +Test [44/197] any_input_param: Test Any type input parameter -Test [45/197] Test nested workflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbtn0ke1d --quiet v1.0/v1.0/echo-tool.cwl v1.0/v1.0/env-job.json +Test [45/197] nested_workflow: Test nested workflow -Test [46/197] Test requirement priority +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpm8gd6hep --quiet v1.0/v1.0/count-lines8-wf.cwl v1.0/v1.0/wc-job.json +Test [46/197] requirement_priority: Test requirement priority -Test [47/197] Test requirements override hints +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphrwrmfsk --quiet v1.0/v1.0/env-wf1.cwl v1.0/v1.0/env-job.json +Test [47/197] requirement_override_hints: Test requirements override hints -Test [48/197] Test requirements on workflow steps +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpp6vr4naq --quiet v1.0/v1.0/env-wf2.cwl v1.0/v1.0/env-job.json +Test [48/197] requirement_workflow_steps: Test requirements on workflow steps -Test [49/197] Test default value on step input parameter +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxhul1pp1 --quiet v1.0/v1.0/env-wf3.cwl v1.0/v1.0/env-job.json +Test [49/197] step_input_default_value: Test default value on step input parameter -Test [50/197] Test use default value on step input parameter with empty source +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdbkpgp1_ --quiet v1.0/v1.0/count-lines9-wf.cwl v1.0/v1.0/empty.json +Test [50/197] step_input_default_value_nosource: Test use default value on step input parameter with empty source +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpons7rqpk --quiet v1.0/v1.0/count-lines11-wf.cwl v1.0/v1.0/empty.json WARNING Workflow checker warning: -v1.0/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible -v1.0/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File" -Test [51/197] Test use default value on step input parameter with null source +v1.0/v1.0/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible +v1.0/v1.0/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File" +Test [51/197] step_input_default_value_nullsource: Test use default value on step input parameter with null source +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpnqrkq68k --quiet v1.0/v1.0/count-lines11-wf.cwl v1.0/v1.0/file1-null.json WARNING Workflow checker warning: -v1.0/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible -v1.0/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File" -Test [52/197] Test default value on step input parameter overridden by provided source +v1.0/v1.0/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible +v1.0/v1.0/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File" +Test [52/197] step_input_default_value_overriden: Test default value on step input parameter overridden by provided source +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp45te19ob --quiet v1.0/v1.0/count-lines11-wf.cwl v1.0/v1.0/cat-job.json WARNING Workflow checker warning: -v1.0/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible -v1.0/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File" -Test [53/197] Test simple workflow - -Test [54/197] Test unknown hints are ignored. - -v1.0/cat5-tool.cwl:12:3: checking item -v1.0/cat5-tool.cwl:12:3: Field `class` contains undefined reference to `http://example.com/BlibberBlubberFakeRequirement` -Test [55/197] Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. - +v1.0/v1.0/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible +v1.0/v1.0/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File" +Test [53/197] wf_simple: Test simple workflow + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp0fymgd_k --quiet v1.0/v1.0/revsort.cwl v1.0/v1.0/revsort-job.json +Test [54/197] hints_unknown_ignored: Test unknown hints are ignored. + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpkptdjt4b --quiet v1.0/v1.0/cat5-tool.cwl v1.0/v1.0/cat-job.json +v1.0/v1.0/cat5-tool.cwl:12:3: Warning: checking item + Warning: Field 'class' contains undefined reference to + 'http://example.com/BlibberBlubberFakeRequirement' +WARNING v1.0/v1.0/cat5-tool.cwl:12:3: Warning: checking item + Warning: Field 'class' contains undefined reference to + 'http://example.com/BlibberBlubberFakeRequirement' +Test [55/197] initial_workdir_secondary_files_expr: Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. + +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp7y7zr2xn --quiet v1.0/v1.0/search.cwl#main v1.0/v1.0/search-job.json WARNING Workflow checker warning: -v1.0/search.cwl:112:9: Parameter 'file' requires secondaryFiles ['${ return - [self.basename+".idx7"]; }'] but -v1.0/search.cwl:107:13: source 'result' does not provide those secondaryFiles. -v1.0/search.cwl:36:7: To resolve, add missing secondaryFiles patterns to definition of - 'result' or -v1.0/search.cwl:61:7: mark missing secondaryFiles in definition of 'file' as optional. -Test [56/197] Test InitialWorkDirRequirement with expression in filename. +v1.0/v1.0/search.cwl:112:9: Parameter 'file' requires secondaryFiles ['${ return + [self.basename+".idx7"]; }'] but +v1.0/v1.0/search.cwl:107:13: source 'result' does not provide those secondaryFiles. +v1.0/v1.0/search.cwl:36:7: To resolve, add missing secondaryFiles patterns to definition of + 'result' or +v1.0/v1.0/search.cwl:61:7: mark missing secondaryFiles in definition of 'file' as optional. +Test [56/197] rename: Test InitialWorkDirRequirement with expression in filename. -Test [57/197] Test if trailing newline is present in file entry in InitialWorkDir +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpz6g2enao --quiet v1.0/v1.0/rename.cwl v1.0/v1.0/rename-job.json +Test [57/197] initial_workdir_trailingnl: Test if trailing newline is present in file entry in InitialWorkDir -Test [58/197] Test inline expressions +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp51tgaepn --quiet v1.0/v1.0/iwdr-entry.cwl v1.0/v1.0/string-job.json +Test [58/197] inline_expressions: Test inline expressions -Test [59/197] Test SchemaDefRequirement definition used in tool parameter +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpsodk9msx --quiet v1.0/v1.0/wc4-tool.cwl v1.0/v1.0/wc-job.json +Test [59/197] schemadef_req_tool_param: Test SchemaDefRequirement definition used in tool parameter -Test [60/197] Test SchemaDefRequirement definition used in workflow parameter +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_2d_vjcu --quiet v1.0/v1.0/schemadef-tool.cwl v1.0/v1.0/schemadef-job.json +Test [60/197] schemadef_req_wf_param: Test SchemaDefRequirement definition used in workflow parameter -Test [61/197] Test parameter evaluation, no support for JS expressions +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpabi4zodt --quiet v1.0/v1.0/schemadef-wf.cwl v1.0/v1.0/schemadef-job.json +Test [61/197] param_evaluation_noexpr: Test parameter evaluation, no support for JS expressions -Test [62/197] Test parameter evaluation, with support for JS expressions +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp895ni_kb --quiet v1.0/v1.0/params.cwl v1.0/v1.0/empty.json +Test [62/197] param_evaluation_expr: Test parameter evaluation, with support for JS expressions -Test [63/197] Test metadata +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpz429c9kh --quiet v1.0/v1.0/params2.cwl v1.0/v1.0/empty.json +Test [63/197] metadata: Test metadata -Test [64/197] Test simple format checking. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprafpdhu_ --quiet v1.0/v1.0/metadata.cwl v1.0/v1.0/cat-job.json +Test [64/197] format_checking: Test simple format checking. -Test [65/197] Test format checking against ontology using subclassOf. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp68bbl_go --quiet v1.0/v1.0/formattest.cwl v1.0/v1.0/formattest-job.json +Test [65/197] format_checking_subclass: Test format checking against ontology using subclassOf. -Test [66/197] Test format checking against ontology using equivalentClass. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5prwafg3 --quiet v1.0/v1.0/formattest2.cwl v1.0/v1.0/formattest2-job.json +Test [66/197] format_checking_equivalentclass: Test format checking against ontology using equivalentClass. -Test [67/197] Test optional output file and optional secondaryFile on output. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbrty_bdz --quiet v1.0/v1.0/formattest3.cwl v1.0/v1.0/formattest2-job.json +Test [67/197] output_secondaryfile_optional: Test optional output file and optional secondaryFile on output. -Test [68/197] Test that valueFrom is ignored when the parameter is null +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpc0crt5gx --quiet v1.0/v1.0/optional-output.cwl v1.0/v1.0/cat-job.json +Test [68/197] valuefrom_ignored_null: Test that valueFrom is ignored when the parameter is null -Test [69/197] Test that second expression in concatenated valueFrom is not ignored +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpje3b_j17 --quiet v1.0/v1.0/vf-concat.cwl v1.0/v1.0/empty.json +Test [69/197] valuefrom_secondexpr_ignored: Test that second expression in concatenated valueFrom is not ignored -Test [70/197] Test valueFrom on workflow step. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp004e7hol --quiet v1.0/v1.0/vf-concat.cwl v1.0/v1.0/cat-job.json +Test [70/197] valuefrom_wf_step: Test valueFrom on workflow step. -Test [71/197] Test valueFrom on workflow step with multiple sources +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwc4olsja --quiet v1.0/v1.0/step-valuefrom-wf.cwl v1.0/v1.0/step-valuefrom-wf.json +Test [71/197] valuefrom_wf_step_multiple: Test valueFrom on workflow step with multiple sources -Test [72/197] Test valueFrom on workflow step referencing other inputs +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp79ihw2qt --quiet v1.0/v1.0/step-valuefrom2-wf.cwl v1.0/v1.0/step-valuefrom-job.json +Test [72/197] valuefrom_wf_step_other: Test valueFrom on workflow step referencing other inputs -WARNING Workflow checker warning: -v1.0/step-valuefrom3-wf.cwl:37:7: 'a' is not an input parameter of ordereddict([('id', - 'file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo'), - ('class', 'CommandLineTool'), ('inputs', [ordereddict([('type', - 'int'), ('inputBinding', ordereddict()), ('id', - 'file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo/c')])]), - ('outputs', [ordereddict([('type', 'string'), ('outputBinding', - ordereddict([('glob', 'step1_out'), ('loadContents', True), - ('outputEval', '$(self[0].contents)')])), ('id', - 'file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo/echo_out')])]), - ('baseCommand', 'echo'), ('stdout', 'step1_out')]), expected c -v1.0/step-valuefrom3-wf.cwl:38:7: 'b' is not an input parameter of ordereddict([('id', - 'file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo'), - ('class', 'CommandLineTool'), ('inputs', [ordereddict([('type', - 'int'), ('inputBinding', ordereddict()), ('id', - 'file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo/c')])]), - ('outputs', [ordereddict([('type', 'string'), ('outputBinding', - ordereddict([('glob', 'step1_out'), ('loadContents', True), - ('outputEval', '$(self[0].contents)')])), ('id', - 'file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo/echo_out')])]), - ('baseCommand', 'echo'), ('stdout', 'step1_out')]), expected c -Test [73/197] Test record type output binding. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpx382676y --quiet v1.0/v1.0/step-valuefrom3-wf.cwl v1.0/v1.0/step-valuefrom-job.json +Test [73/197] record_output_binding: Test record type output binding. -Test [74/197] Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphkh9wyz7 --quiet v1.0/v1.0/record-output.cwl v1.0/v1.0/record-output-job.json +Test [74/197] docker_json_output_path: Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. -Test [75/197] Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxf4j7iko --quiet v1.0/v1.0/test-cwl-out.cwl v1.0/v1.0/empty.json +Test [75/197] docker_json_output_location: Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. -Test [76/197] Test support for returning multiple glob patterns from expression +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwx62i5jy --quiet v1.0/v1.0/test-cwl-out2.cwl v1.0/v1.0/empty.json +Test [76/197] multiple_glob_expr_list: Test support for returning multiple glob patterns from expression -Test [77/197] Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_9ugyyro --quiet v1.0/v1.0/glob-expr-list.cwl v1.0/v1.0/abc.json +Test [77/197] wf_scatter_oneparam_valuefrom: Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) -Test [78/197] Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp6o00jlu2 --quiet v1.0/v1.0/scatter-valuefrom-wf1.cwl v1.0/v1.0/scatter-valuefrom-job1.json +Test [78/197] wf_scatter_twoparam_nested_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input -Test [79/197] Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpp1gzsbg0 --quiet v1.0/v1.0/scatter-valuefrom-wf2.cwl v1.0/v1.0/scatter-valuefrom-job2.json +Test [79/197] wf_scatter_twoparam_flat_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input -Test [80/197] Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp2rv0ka38 --quiet v1.0/v1.0/scatter-valuefrom-wf3.cwl#main v1.0/v1.0/scatter-valuefrom-job2.json +Test [80/197] wf_scatter_twoparam_dotproduct_valuefrom: Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input -Test [81/197] Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcl5n6mqc --quiet v1.0/v1.0/scatter-valuefrom-wf4.cwl#main v1.0/v1.0/scatter-valuefrom-job2.json +Test [81/197] wf_scatter_oneparam_valuefrom_twice_current_el: Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) -Test [82/197] Test valueFrom eval on scattered input parameter +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpiyn5dwm1 --quiet v1.0/v1.0/scatter-valuefrom-wf5.cwl v1.0/v1.0/scatter-valuefrom-job1.json +Test [82/197] wf_scatter_oneparam_valueFrom: Test valueFrom eval on scattered input parameter -Test [83/197] Test workflow two input files with same name. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdq56nziu --quiet v1.0/v1.0/scatter-valuefrom-wf6.cwl v1.0/v1.0/scatter-valuefrom-job3.json +Test [83/197] wf_two_inputfiles_namecollision: Test workflow two input files with same name. -Test [84/197] Test directory input with parameter reference +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpi3108164 --quiet v1.0/v1.0/conflict-wf.cwl#collision v1.0/v1.0/conflict-job.json +Test [84/197] directory_input_param_ref: Test directory input with parameter reference -Test [85/197] Test directory input in Docker +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmptmxwqzsn --quiet v1.0/v1.0/dir.cwl v1.0/v1.0/dir-job.yml +Test [85/197] directory_input_docker: Test directory input in Docker -Test [86/197] Test directory output +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwsvhmdm1 --quiet v1.0/v1.0/dir2.cwl v1.0/v1.0/dir-job.yml +Test [86/197] directory_output: Test directory output -Test [87/197] Test directories in secondaryFiles +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpt_6jyuwb --quiet v1.0/v1.0/dir3.cwl v1.0/v1.0/dir3-job.yml +Test [87/197] directory_secondaryfiles: Test directories in secondaryFiles -Test [88/197] Test dynamic initial work dir +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5ta4nadm --quiet v1.0/v1.0/dir4.cwl v1.0/v1.0/dir4-job.yml +Test [88/197] dynamic_initial_workdir: Test dynamic initial work dir -Test [89/197] Test writable staged files. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpr258kifo --quiet v1.0/v1.0/dir5.cwl v1.0/v1.0/dir-job.yml +Test [89/197] writable_stagedfiles: Test writable staged files. -Test [90/197] Test file literal as input +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwprr306a --quiet v1.0/v1.0/stagefile.cwl v1.0/v1.0/stagefile-job.yml +Test [90/197] input_file_literal: Test file literal as input -Test [91/197] Test expression in InitialWorkDir listing +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp9o9ei96k --quiet v1.0/v1.0/cat3-tool.cwl v1.0/v1.0/file-literal.yml +Test [91/197] initial_workdir_expr: Test expression in InitialWorkDir listing -Test [92/197] Test nameroot/nameext expression in arguments, stdout +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp24coe4ub --quiet v1.0/v1.0/linkfile.cwl v1.0/v1.0/arguments-job.yml +Test [92/197] nameroot_nameext_stdout_expr: Test nameroot/nameext expression in arguments, stdout -Test [93/197] Test directory input with inputBinding +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpq69hcut9 --quiet v1.0/v1.0/nameroot.cwl v1.0/v1.0/wc-job.json +Test [93/197] input_dir_inputbinding: Test directory input with inputBinding -Test [94/197] Test command line generation of array-of-arrays +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp8myfaoes --quiet v1.0/v1.0/dir6.cwl v1.0/v1.0/dir-job.yml +Test [94/197] cl_gen_arrayofarrays: Test command line generation of array-of-arrays -Test [95/197] Test $HOME and $TMPDIR are set correctly +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpvsz6n3jb --quiet v1.0/v1.0/nested-array.cwl v1.0/v1.0/nested-array-job.yml +Test [95/197] env_home_tmpdir: Test $HOME and $TMPDIR are set correctly -Test [96/197] Test $HOME and $TMPDIR are set correctly in Docker +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpl30rtg1y --quiet v1.0/v1.0/envvar.cwl v1.0/v1.0/empty.json +Test [96/197] env_home_tmpdir_docker: Test $HOME and $TMPDIR are set correctly in Docker -Test [97/197] Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpm9kjze5r --quiet v1.0/v1.0/envvar2.cwl v1.0/v1.0/empty.json +Test [97/197] expressionlib_tool_wf_override: Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. -Test [98/197] Test output of InitialWorkDir +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp8_6qegl7 --quiet v1.0/v1.0/js-expr-req-wf.cwl#wf v1.0/v1.0/empty.json +Test [98/197] initial_workdir_output: Test output of InitialWorkDir -Test [99/197] Test embedded subworkflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3k70wkwi --quiet v1.0/v1.0/initialworkdirrequirement-docker-out.cwl v1.0/v1.0/initialworkdirrequirement-docker-out-job.json +Test [99/197] embedded_subworkflow: Test embedded subworkflow -Test [100/197] Test secondaryFiles on array of files. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpt85n698o --quiet v1.0/v1.0/count-lines10-wf.cwl v1.0/v1.0/wc-job.json +Test [100/197] filesarray_secondaryfiles: Test secondaryFiles on array of files. -Test [101/197] Test directory literal output created by ExpressionTool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmppi6wcwcg --quiet v1.0/v1.0/docker-array-secondaryfiles.cwl v1.0/v1.0/docker-array-secondaryfiles-job.json +Test [101/197] exprtool_directory_literal: Test directory literal output created by ExpressionTool -Test [102/197] Test file literal output created by ExpressionTool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp0gqdhprd --quiet v1.0/v1.0/dir7.cwl v1.0/v1.0/dir7.yml +Test [102/197] exprtool_file_literal: Test file literal output created by ExpressionTool -Test [103/197] Test dockerOutputDirectory +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp6fqdhdou --quiet v1.0/v1.0/file-literal-ex.cwl v1.0/v1.0/empty.json +Test [103/197] dockeroutputdir: Test dockerOutputDirectory -ERROR Got workflow error -Traceback (most recent call last): - File "/usr/local/lib/python3.6/site-packages/cwltool/executors.py", line 241, in _runner - job.run(runtime_context, TMPDIR_LOCK) - File "/usr/local/lib/python3.6/site-packages/calrissian/job.py", line 587, in run - self.check_requirements() - File "/usr/local/lib/python3.6/site-packages/calrissian/job.py", line 425, in check_requirements - raise UnsupportedRequirement('Error: feature {}.{} is not supported'.format(feature, field)) -cwltool.errors.UnsupportedRequirement: Error: feature DockerRequirement.dockerOutputDirectory is not supported +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpk3oql0ah --quiet v1.0/v1.0/docker-output-dir.cwl v1.0/v1.0/empty.json +ERROR Found a queued exception, canceling outstanding futures +ERROR Waiting for canceled futures to finish ERROR Workflow or tool uses unsupported feature: Error: feature DockerRequirement.dockerOutputDirectory is not supported -Test [104/197] Test hints with $import +Test [104/197] hints_import: Test hints with $import -Test [105/197] Test warning instead of error when default path is not found +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpuz6thr3_ --quiet v1.0/v1.0/imported-hint.cwl v1.0/v1.0/empty.json +Test [105/197] default_path_notfound_warning: Test warning instead of error when default path is not found -Test [106/197] Test InlineJavascriptRequirement with multiple expressions in the same tool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4qqkwl9d --quiet v1.0/v1.0/default_path.cwl v1.0/v1.0/default_path_job.yml +Test [106/197] inlinejs_req_expressions: Test InlineJavascriptRequirement with multiple expressions in the same tool -Test [107/197] Test if a writable input directory is recursively copied and writable +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbmxcazbu --quiet v1.0/v1.0/inline-js.cwl v1.0/v1.0/empty.json +Test [107/197] input_dir_recurs_copy_writable: Test if a writable input directory is recursively copied and writable -Test [108/197] Test that missing parameters are null (not undefined) in expression +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpgm8_w43i --quiet v1.0/v1.0/recursive-input-directory.cwl v1.0/v1.0/recursive-input-directory.yml +Test [108/197] null_missing_params: Test that missing parameters are null (not undefined) in expression -Test [109/197] Test that provided parameter is not null in expression +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbcezf7wl --quiet v1.0/v1.0/null-defined.cwl v1.0/v1.0/empty.json +Test [109/197] param_notnull_expr: Test that provided parameter is not null in expression -Test [110/197] Test compound workflow document +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpshwxi4wi --quiet v1.0/v1.0/null-defined.cwl v1.0/v1.0/cat-job.json +Test [110/197] wf_compound_doc: Test compound workflow document -Test [111/197] Test that nameroot and nameext are generated from basename at execution time by the runner +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmzzntp7l --quiet v1.0/v1.0/revsort-packed.cwl#main v1.0/v1.0/revsort-job.json +Test [111/197] nameroot_nameext_generated: Test that nameroot and nameext are generated from basename at execution time by the runner -WARNING Workflow checker warning: -v1.0/basename-fields-test.cwl:33:7: 'tool' is not an input parameter of - file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/echo-file-tool.cwl, - expected in -v1.0/basename-fields-test.cwl:26:7: 'tool' is not an input parameter of - file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/echo-file-tool.cwl, - expected in -Test [112/197] Test that file path in $(inputs) for initialworkdir is in $(outdir). +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpvb0u5sq4 --quiet v1.0/v1.0/basename-fields-test.cwl v1.0/v1.0/basename-fields-job.yml +Test [112/197] initialworkpath_output: Test that file path in $(inputs) for initialworkdir is in $(outdir). -Test [113/197] Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpespg1k09 --quiet v1.0/v1.0/initialwork-path.cwl v1.0/v1.0/wc-job.json +Test [113/197] wf_scatter_twopar_oneinput_flattenedmerge: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list -Test [114/197] Test step input with multiple sources with multiple types +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp6i5q3wp_ --quiet v1.0/v1.0/count-lines12-wf.cwl v1.0/v1.0/count-lines6-job.json +Test [114/197] wf_multiplesources_multipletypes: Test step input with multiple sources with multiple types -Test [115/197] Test that shell directives are not interpreted. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpcu19olpe --quiet v1.0/v1.0/sum-wf.cwl v1.0/v1.0/sum-job.json +Test [115/197] shelldir_notinterpreted: Test that shell directives are not interpreted. -Test [116/197] Test that shell directives are quoted. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp0sy9f00q --quiet v1.0/v1.0/shellchar.cwl v1.0/v1.0/empty.json +Test [116/197] shelldir_quoted: Test that shell directives are quoted. -Test [117/197] Test empty writable dir with InitialWorkDirRequirement +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpahpsodks --quiet v1.0/v1.0/shellchar2.cwl v1.0/v1.0/empty.json +Test [117/197] initial_workdir_empty_writable: Test empty writable dir with InitialWorkDirRequirement -Test [118/197] Test empty writable dir with InitialWorkDirRequirement inside Docker +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp85bpj7_s --quiet v1.0/v1.0/writable-dir.cwl v1.0/v1.0/empty.json +Test [118/197] initial_workdir_empty_writable_docker: Test empty writable dir with InitialWorkDirRequirement inside Docker -Test [119/197] Test dynamic resource reqs referencing inputs +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpwzeqwa4f --quiet v1.0/v1.0/writable-dir-docker.cwl v1.0/v1.0/empty.json +Test [119/197] dynamic_resreq_inputs: Test dynamic resource reqs referencing inputs -Test [120/197] Test file literal as input without Docker +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpczsy36hm --quiet v1.0/v1.0/dynresreq.cwl v1.0/v1.0/dynresreq-job.yaml +Test [120/197] fileliteral_input_docker: Test file literal as input without Docker -Test [121/197] Test that OutputBinding.glob is sorted as specified by POSIX +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_6jakjfa --quiet v1.0/v1.0/cat3-nodocker.cwl v1.0/v1.0/file-literal.yml +Test [121/197] outputbinding_glob_sorted: Test that OutputBinding.glob is sorted as specified by POSIX -Test [122/197] Test InitialWorkDirRequirement with a nested directory structure from another step +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4pt0j0u8 --quiet v1.0/v1.0/glob_test.cwl v1.0/v1.0/empty.json +Test [122/197] initialworkdir_nesteddir: Test InitialWorkDirRequirement with a nested directory structure from another step -Test [123/197] Test that boolean flags do not appear on command line if inputBinding is empty and not null +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp69a9mar0 --quiet v1.0/v1.0/iwdr_with_nested_dirs.cwl v1.0/v1.0/empty.json +Test [123/197] booleanflags_cl_noinputbinding: Test that boolean flags do not appear on command line if inputBinding is empty and not null -Test [124/197] Test that expression engine does not fail to evaluate reference to self with unprovided input +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpoa2qw9d4 --quiet v1.0/v1.0/bool-empty-inputbinding.cwl v1.0/v1.0/bool-empty-inputbinding-job.json +Test [124/197] expr_reference_self_noinput: Test that expression engine does not fail to evaluate reference to self with unprovided input -Test [125/197] Test successCodes +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp2zho2_lv --quiet v1.0/v1.0/stage-unprovided-file.cwl v1.0/v1.0/empty.json +Test [125/197] success_codes: Test successCodes -Test [126/197] Test simple workflow with a dynamic resource requirement +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5t7bj7gx --quiet v1.0/v1.0/exit-success.cwl v1.0/v1.0/empty.json +Test [126/197] dynamic_resreq_wf: Test simple workflow with a dynamic resource requirement -Test [127/197] Test that empty array input does not add anything to command line +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp25q3nl4n --quiet v1.0/v1.0/dynresreq-workflow.cwl v1.0/v1.0/dynresreq-job.yaml +Test [127/197] cl_empty_array_input: Test that empty array input does not add anything to command line -Test [128/197] Test that ResourceRequirement on a step level redefines requirement on the workflow level +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpnqrl3810 --quiet v1.0/v1.0/empty-array-input.cwl v1.0/v1.0/empty-array-job.json +Test [128/197] resreq_step_overrides_wf: Test that ResourceRequirement on a step level redefines requirement on the workflow level -Test [129/197] Test valueFrom with constant value overriding provided array inputs +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxvlpvomx --quiet v1.0/v1.0/steplevel-resreq.cwl v1.0/v1.0/empty.json +Test [129/197] valuefrom_constant_overrides_inputs: Test valueFrom with constant value overriding provided array inputs -Test [130/197] Test dynamic resource reqs referencing the size of Files inside a Directory +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp52wmxewa --quiet v1.0/v1.0/valueFrom-constant.cwl v1.0/v1.0/array-of-strings-job.yml +Test [130/197] dynamic_resreq_filesizes: Test dynamic resource reqs referencing the size of Files inside a Directory -Test [131/197] Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp22l1jekz --quiet v1.0/v1.0/dynresreq-dir.cwl v1.0/v1.0/dynresreq-dir-job.yaml +Test [131/197] wf_step_connect_undeclared_param: Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpg0kn6kol --quiet v1.0/v1.0/pass-unconnected.cwl v1.0/v1.0/empty.json WARNING Workflow checker warning: -v1.0/pass-unconnected.cwl:18:7: 'in2' is not an input parameter of - file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/echo-tool.cwl, - expected in -Test [132/197] Test that parameters that don't appear in the `run` process inputs are not present in the input object used to run the tool. +v1.0/v1.0/pass-unconnected.cwl:18:7: 'in2' is not an input parameter of + file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/echo-tool.cwl, + expected in +Test [132/197] wf_step_access_undeclared_param: Test that parameters that don't appear in the `run` process inputs are not present in the input object used to run the tool. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphij2zawh --quiet v1.0/v1.0/fail-unconnected.cwl v1.0/v1.0/empty.json WARNING Workflow checker warning: -v1.0/fail-unconnected.cwl:18:7: 'in2' is not an input parameter of - file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/fail-unspecified-input.cwl, - expected in +v1.0/v1.0/fail-unconnected.cwl:18:7: 'in2' is not an input parameter of + file:///conformance/common-workflow-language-1.0.2/v1.0/v1.0/fail-unspecified-input.cwl, + expected in +Syntax error in parameter reference 'inputs.in2': inputs does not contain key 'in2'.. This could be due to using Javascript code without specifying InlineJavascriptRequirement. +Traceback (most recent call last): + File "/usr/local/lib/python3.10/site-packages/cwl_utils/expression.py", line 315, in do_eval + return interpolate( + File "/usr/local/lib/python3.10/site-packages/cwl_utils/expression.py", line 215, in interpolate + e = evaluator( + File "/usr/local/lib/python3.10/site-packages/cwl_utils/expression.py", line 164, in evaluator + raise JavascriptException( +cwl_utils.errors.JavascriptException: Syntax error in parameter reference 'inputs.in2': inputs does not contain key 'in2'.. This could be due to using Javascript code without specifying InlineJavascriptRequirement. ERROR Exception on step 'step1' -ERROR [step step1] Cannot make job: v1.0/fail-unspecified-input.cwl:16:33: Expression evaluation error: -v1.0/fail-unspecified-input.cwl:16:33: Syntax error in parameter reference 'inputs.in2': inputs does not contain key 'in2'. This could be due to using Javascript code without specifying InlineJavascriptRequirement. +ERROR [step step1] Cannot make job: v1.0/v1.0/fail-unspecified-input.cwl:16:33: Expression evaluation error: +v1.0/v1.0/fail-unspecified-input.cwl:16:33: Syntax error in parameter reference 'inputs.in2': inputs does not contain key 'in2'.. This could be due to using Javascript code without specifying InlineJavascriptRequirement. WARNING Final process status is permanentFail -Test [133/197] Test $HOME and $TMPDIR are set correctly in Docker without using return code - -Test [134/197] Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el) +Test [133/197] env_home_tmpdir_docker: Test $HOME and $TMPDIR are set correctly in Docker without using return code -Test [135/197] SchemaDefRequirement with $import, and packed +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_5fhl2s_ --quiet v1.0/v1.0/envvar3.cwl v1.0/v1.0/empty.json +Test [134/197] wf_scatter_oneparam_valuefrom_inputs: Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el) -Test [136/197] Test specifying secondaryFiles in subdirectories of the job input document. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp181qfkev --quiet v1.0/v1.0/scatter-valuefrom-inputs-wf1.cwl v1.0/v1.0/scatter-valuefrom-job1.json +Test [135/197] packed_import_schema: SchemaDefRequirement with $import, and packed -Test [137/197] Test specifying secondaryFiles in same subdirectory of the job input as the primary input file. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpahz_j0sz --quiet v1.0/v1.0/import_schema-def_packed.cwl#main v1.0/v1.0/import_schema-def_job.yml +Test [136/197] job_input_secondary_subdirs: Test specifying secondaryFiles in subdirectories of the job input document. -Test [138/197] Test simple scatter over an embedded subworkflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpvg7ruuvt --quiet v1.0/v1.0/dir4.cwl v1.0/v1.0/dir4-subdir-1-job.yml +Test [137/197] job_input_subdir_primary_and_secondary_subdirs: Test specifying secondaryFiles in same subdirectory of the job input as the primary input file. -Test [139/197] Test simple multiple input scatter over an embedded subworkflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5swz31xp --quiet v1.0/v1.0/dir4.cwl v1.0/v1.0/dir4-subdir-2-job.yml +Test [138/197] scatter_embedded_subworkflow: Test simple scatter over an embedded subworkflow -Test [140/197] Test twice nested subworkflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpe6gzhep0 --quiet v1.0/v1.0/count-lines18-wf.cwl v1.0/v1.0/count-lines3-job.json +Test [139/197] scatter_multi_input_embedded_subworkflow: Test simple multiple input scatter over an embedded subworkflow -Test [141/197] Test subworkflow of mixed depth with tool first +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpw8e2fkrk --quiet v1.0/v1.0/count-lines14-wf.cwl v1.0/v1.0/count-lines4-job.json +Test [140/197] workflow_embedded_subworkflow_embedded_subsubworkflow: Test twice nested subworkflow -Test [142/197] Test subworkflow of mixed depth with tool after +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpyf02bo9z --quiet v1.0/v1.0/count-lines15-wf.cwl v1.0/v1.0/wc-job.json +Test [141/197] workflow_embedded_subworkflow_with_tool_and_subsubworkflow: Test subworkflow of mixed depth with tool first -Test [143/197] Test record type inputs to and outputs from workflows. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmf21fgnt --quiet v1.0/v1.0/count-lines16-wf.cwl v1.0/v1.0/wc-job.json +Test [142/197] workflow_embedded_subworkflow_with_subsubworkflow_and_tool: Test subworkflow of mixed depth with tool after -Test [144/197] Test integer workflow input and outputs +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpyt8w5tbf --quiet v1.0/v1.0/count-lines17-wf.cwl v1.0/v1.0/wc-job.json +Test [143/197] workflow_records_inputs_and_outputs: Test record type inputs to and outputs from workflows. -Test [145/197] Test optional integer workflow inputs (specified) +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpt1m3spl_ --quiet v1.0/v1.0/record-output-wf.cwl v1.0/v1.0/record-output-job.json +Test [144/197] workflow_integer_input: Test integer workflow input and outputs -Test [146/197] Test optional integer workflow inputs (unspecified) +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp_gjjcf98 --quiet v1.0/v1.0/io-int-wf.cwl v1.0/v1.0/io-int.json +Test [145/197] workflow_integer_input_optional_specified: Test optional integer workflow inputs (specified) -Test [147/197] Test default integer workflow inputs (specified) +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5nqkhblj --quiet v1.0/v1.0/io-int-optional-wf.cwl v1.0/v1.0/io-int.json +Test [146/197] workflow_integer_input_optional_unspecified: Test optional integer workflow inputs (unspecified) -Test [148/197] Test default integer workflow inputs (unspecified) +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpt5s7d5lx --quiet v1.0/v1.0/io-int-optional-wf.cwl v1.0/v1.0/empty.json +Test [147/197] workflow_integer_input_default_specified: Test default integer workflow inputs (specified) -Test [149/197] Test default integer tool and workflow inputs (unspecified) +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprlwxq6cr --quiet v1.0/v1.0/io-int-default-wf.cwl v1.0/v1.0/io-int.json +Test [148/197] workflow_integer_input_default_unspecified: Test default integer workflow inputs (unspecified) -Test [150/197] Test File input with default unspecified to workflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp2v6n19ty --quiet v1.0/v1.0/io-int-default-wf.cwl v1.0/v1.0/empty.json +Test [149/197] workflow_integer_input_default_and_tool_integer_input_default: Test default integer tool and workflow inputs (unspecified) -Test [151/197] Test File input with default specified to workflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1c5xbtg5 --quiet v1.0/v1.0/io-int-default-tool-and-wf.cwl v1.0/v1.0/empty.json +Test [150/197] workflow_file_input_default_unspecified: Test File input with default unspecified to workflow -Test [152/197] Test input union type or File or File array to a tool with one file in array specified. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpn8lrbdjg --quiet v1.0/v1.0/io-file-default-wf.cwl v1.0/v1.0/empty.json +Test [151/197] workflow_file_input_default_specified: Test File input with default specified to workflow -Test [153/197] Test input union type or File or File array to a tool with a few files in array specified. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmps3wz6enq --quiet v1.0/v1.0/io-file-default-wf.cwl v1.0/v1.0/default_path_job.yml +Test [152/197] clt_optional_union_input_file_or_files_with_array_of_one_file_provided: Test input union type or File or File array to a tool with one file in array specified. -Test [154/197] Test input union type or File or File array to a tool with one file specified. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp8c5re6cx --quiet v1.0/v1.0/io-file-or-files.cwl v1.0/v1.0/job-input-array-one-empty-file.json +Test [153/197] clt_optional_union_input_file_or_files_with_many_files_provided: Test input union type or File or File array to a tool with a few files in array specified. -Test [155/197] Test input union type or File or File array to a tool with null specified. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp0aaekzpx --quiet v1.0/v1.0/io-file-or-files.cwl v1.0/v1.0/job-input-array-few-files.json +Test [154/197] clt_optional_union_input_file_or_files_with_single_file_provided: Test input union type or File or File array to a tool with one file specified. -Test [156/197] Test Any parameter with integer input to a tool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpyf9qsy4f --quiet v1.0/v1.0/io-file-or-files.cwl v1.0/v1.0/job-input-one-file.json +Test [155/197] clt_optional_union_input_file_or_files_with_nothing_provided: Test input union type or File or File array to a tool with null specified. -Test [157/197] Test Any parameter with string input to a tool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp7t3itaz9 --quiet v1.0/v1.0/io-file-or-files.cwl v1.0/v1.0/job-input-null.json +Test [156/197] clt_any_input_with_integer_provided: Test Any parameter with integer input to a tool -Test [158/197] Test Any parameter with file input to a tool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmj_hyiw7 --quiet v1.0/v1.0/io-any-1.cwl v1.0/v1.0/io-any-int.json +Test [157/197] clt_any_input_with_string_provided: Test Any parameter with string input to a tool -Test [159/197] Test Any parameter with array input to a tool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmph442ehfn --quiet v1.0/v1.0/io-any-1.cwl v1.0/v1.0/io-any-string.json +Test [158/197] clt_any_input_with_file_provided: Test Any parameter with file input to a tool -Test [160/197] Test Any parameter with record input to a tool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp6a5va07y --quiet v1.0/v1.0/io-any-1.cwl v1.0/v1.0/io-any-file.json +Test [159/197] clt_any_input_with_mixed_array_provided: Test Any parameter with array input to a tool -Test [161/197] Test Any parameter with integer input to a workflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp1t0fqxdv --quiet v1.0/v1.0/io-any-1.cwl v1.0/v1.0/io-any-array.json +Test [160/197] clt_any_input_with_record_provided: Test Any parameter with record input to a tool -Test [162/197] Test Any parameter with string input to a workflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp275pb48s --quiet v1.0/v1.0/io-any-1.cwl v1.0/v1.0/io-any-record.json +Test [161/197] workflow_any_input_with_integer_provided: Test Any parameter with integer input to a workflow -Test [163/197] Test Any parameter with file input to a workflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp9oxxgl5v --quiet v1.0/v1.0/io-any-wf-1.cwl v1.0/v1.0/io-any-int.json +Test [162/197] workflow_any_input_with_string_provided: Test Any parameter with string input to a workflow -Test [164/197] Test Any parameter with array input to a workflow +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpt_fwxahj --quiet v1.0/v1.0/io-any-wf-1.cwl v1.0/v1.0/io-any-string.json +Test [163/197] workflow_any_input_with_file_provided: Test Any parameter with file input to a workflow -Test [165/197] Test Any parameter with record input to a tool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpi31ra379 --quiet v1.0/v1.0/io-any-wf-1.cwl v1.0/v1.0/io-any-file.json +Test [164/197] workflow_any_input_with_mixed_array_provided: Test Any parameter with array input to a workflow -Test [166/197] Test union type input to workflow with default unspecified +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpb6t8d6lm --quiet v1.0/v1.0/io-any-wf-1.cwl v1.0/v1.0/io-any-array.json +Test [165/197] workflow_any_input_with_record_provided: Test Any parameter with record input to a tool -Test [167/197] Test union type input to workflow with default specified as file +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp9xtnq3iv --quiet v1.0/v1.0/io-any-wf-1.cwl v1.0/v1.0/io-any-record.json +Test [166/197] workflow_union_default_input_unspecified: Test union type input to workflow with default unspecified -Test [168/197] Test valueFrom on workflow step from literal (string). +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmposoyw0fk --quiet v1.0/v1.0/io-union-input-default-wf.cwl v1.0/v1.0/empty.json +Test [167/197] workflow_union_default_input_with_file_provided: Test union type input to workflow with default specified as file -Test [169/197] Test valueFrom on workflow step using basename. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpo1b4hg41 --quiet v1.0/v1.0/io-union-input-default-wf.cwl v1.0/v1.0/io-any-file.json +Test [168/197] workflowstep_valuefrom_string: Test valueFrom on workflow step from literal (string). -Test [170/197] Test output arrays in a tool (with ints). +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpu0a1ejqe --quiet v1.0/v1.0/step-valuefrom4-wf.cwl v1.0/v1.0/empty.json +Test [169/197] workflowstep_valuefrom_file_basename: Test valueFrom on workflow step using basename. -Test [171/197] Test output arrays in a workflow (with ints). +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpjq6mcldr --quiet v1.0/v1.0/step-valuefrom5-wf.cwl v1.0/v1.0/wc-job.json +Test [170/197] expression_tool_int_array_output: Test output arrays in a tool (with ints). -Test [172/197] Test output arrays in a workflow (with Files). +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpvweezg7c --quiet v1.0/v1.0/output-arrays-int.cwl v1.0/v1.0/output-arrays-int-job.json +Test [171/197] workflowstep_int_array_input_output: Test output arrays in a workflow (with ints). -Test [173/197] Test Docker ENTRYPOINT usage +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpducrbgg7 --quiet v1.0/v1.0/output-arrays-int-wf.cwl v1.0/v1.0/output-arrays-int-job.json +Test [172/197] workflow_file_array_output: Test output arrays in a workflow (with Files). -ERROR Got workflow error -Traceback (most recent call last): - File "/usr/local/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 777, in collect_output - raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns)) -cwltool.errors.WorkflowException: Did not find output file with glob pattern: '['cow']' - -The above exception was the direct cause of the following exception: +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmprm5g12sv --quiet v1.0/v1.0/output-arrays-file-wf.cwl v1.0/v1.0/output-arrays-file-job.json +Test [173/197] docker_entrypoint: Test Docker ENTRYPOINT usage -Traceback (most recent call last): - File "/usr/local/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 657, in collect_output_ports - compute_checksum=compute_checksum) - File "/usr/local/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 777, in collect_output - raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns)) - File "/usr/local/lib/python3.6/site-packages/schema_salad/sourceline.py", line 252, in __exit__ - raise_from(self.makeError(six.text_type(exc_value)), exc_value) - File "/usr/local/lib/python3.6/site-packages/future/utils/__init__.py", line 400, in raise_from - exec(execstr, myglobals, mylocals) - File "", line 1, in -cwltool.errors.WorkflowException: v1.0/docker-run-cmd.cwl:14:7: Did not find output file with glob pattern: '['cow']' - -The above exception was the direct cause of the following exception: - -Traceback (most recent call last): - File "/usr/local/lib/python3.6/site-packages/cwltool/executors.py", line 241, in _runner - job.run(runtime_context, TMPDIR_LOCK) - File "/usr/local/lib/python3.6/site-packages/calrissian/job.py", line 598, in run - self.finish(completion_result, runtimeContext) - File "/usr/local/lib/python3.6/site-packages/calrissian/job.py", line 395, in finish - outputs = self.collect_outputs(self.outdir, exit_code) - File "/usr/local/lib/python3.6/site-packages/cwltool/command_line_tool.py", line 657, in collect_output_ports - compute_checksum=compute_checksum) - File "/usr/local/lib/python3.6/site-packages/schema_salad/sourceline.py", line 252, in __exit__ - raise_from(self.makeError(six.text_type(exc_value)), exc_value) - File "/usr/local/lib/python3.6/site-packages/future/utils/__init__.py", line 400, in raise_from - exec(execstr, myglobals, mylocals) - File "", line 1, in -cwltool.errors.WorkflowException: Error collecting output for parameter 'cow': -v1.0/docker-run-cmd.cwl:14:7: Did not find output file with glob pattern: '['cow']' +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5_tjnf7c --quiet v1.0/v1.0/docker-run-cmd.cwl v1.0/v1.0/empty.json +ERROR Found a queued exception, canceling outstanding futures +ERROR Waiting for canceled futures to finish ERROR Workflow error, try again with --debug for more information: -Error collecting output for parameter 'cow': -v1.0/docker-run-cmd.cwl:14:7: Did not find output file with glob pattern: '['cow']' -Test 173 failed: /usr/local/bin/calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp43j9fnwf --quiet v1.0/docker-run-cmd.cwl v1.0/empty.json +("Error collecting output for parameter 'cow': v1.0/v1.0/docker-run-cmd.cwl:14:7: Did not find output + file with glob + pattern: ['cow'].", + {}) +Test 173 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp5_tjnf7c --quiet v1.0/v1.0/docker-run-cmd.cwl v1.0/v1.0/empty.json Test Docker ENTRYPOINT usage Returned non-zero +Test [174/197] clt_file_size_property_with_empty_file: Test use of size in expressions for an empty file -Test [174/197] Test use of size in expressions for an empty file +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp88l7odlh --quiet v1.0/v1.0/size-expression-tool.cwl v1.0/v1.0/job-input-array-one-empty-file.json +Test [175/197] clt_file_size_property_with_multi_file: Test use of size in expressions for a few files -Test [175/197] Test use of size in expressions for a few files - -Test [176/197] Test Any without defaults, unspecified, should fail. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxrlz4ays --quiet v1.0/v1.0/size-expression-tool.cwl v1.0/v1.0/job-input-array-few-files.json +Test [176/197] any_without_defaults_unspecified_fails: Test Any without defaults, unspecified, should fail. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp98ea42zh --quiet v1.0/v1.0/echo-tool.cwl v1.0/v1.0/null-expression-echo-job.json ERROR Workflow error, try again with --debug for more information: Invalid job input record: -v1.0/echo-tool.cwl:9:3: Missing required input parameter 'in' -Test [177/197] Test Any without defaults, specified, should fail. +v1.0/v1.0/echo-tool.cwl:9:3: Missing required input parameter 'in' +Test [177/197] any_without_defaults_specified_fails: Test Any without defaults, specified, should fail. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpg2lmecyt --quiet v1.0/v1.0/echo-tool.cwl v1.0/v1.0/null-expression1-job.json ERROR Workflow error, try again with --debug for more information: Invalid job input record: -v1.0/echo-tool.cwl:9:3: Missing required input parameter 'in' -Test [178/197] Test default value on step input parameter, no ExpressionTool +v1.0/v1.0/echo-tool.cwl:9:3: Missing required input parameter 'in' +Test [178/197] step_input_default_value_noexp: Test default value on step input parameter, no ExpressionTool -Test [179/197] Test default value on step input parameter overridden by provided source, no ExpressionTool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpdz1gys9l --quiet v1.0/v1.0/count-lines9-wf-noET.cwl v1.0/v1.0/empty.json +Test [179/197] step_input_default_value_overriden_noexp: Test default value on step input parameter overridden by provided source, no ExpressionTool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpyd5byai7 --quiet v1.0/v1.0/count-lines11-wf-noET.cwl v1.0/v1.0/cat-job.json WARNING Workflow checker warning: -v1.0/count-lines11-wf-noET.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible -v1.0/count-lines11-wf-noET.cwl:17:7: with sink 'file1' of type "File" -Test [180/197] Test nested workflow, without ExpressionTool +v1.0/v1.0/count-lines11-wf-noET.cwl:6:3: Source 'file1' of type ["null", "File"] may be + incompatible +v1.0/v1.0/count-lines11-wf-noET.cwl:17:7: with sink 'file1' of type "File" +Test [180/197] nested_workflow_noexp: Test nested workflow, without ExpressionTool -Test [181/197] Test step input with multiple sources with multiple types, without ExpressionTool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmfwpzmp3 --quiet v1.0/v1.0/count-lines8-wf-noET.cwl v1.0/v1.0/wc-job.json +Test [181/197] wf_multiplesources_multipletypes_noexp: Test step input with multiple sources with multiple types, without ExpressionTool -Test [182/197] Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpz1ztsvlp --quiet v1.0/v1.0/sum-wf-noET.cwl v1.0/v1.0/sum-job.json +Test [182/197] dynamic_resreq_wf_optional_file_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpbm1ddtcj --quiet v1.0/v1.0/dynresreq-workflow-tooldefault.cwl v1.0/v1.0/empty.json WARNING Workflow checker warning: -v1.0/dynresreq-workflow-tooldefault.cwl:6:3: Source 'special_file' of type ["null", "File"] may be - incompatible -v1.0/dynresreq-workflow-tooldefault.cwl:15:7: with sink 'special_file' of type "File" -Test [183/197] Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input. +v1.0/v1.0/dynresreq-workflow-tooldefault.cwl:6:3: Source 'special_file' of type ["null", "File"] + may be incompatible +v1.0/v1.0/dynresreq-workflow-tooldefault.cwl:15:7: with sink 'special_file' of type "File" +Test [183/197] dynamic_resreq_wf_optional_file_step_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input. +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpg7aao98a --quiet v1.0/v1.0/dynresreq-workflow-stepdefault.cwl v1.0/v1.0/empty.json WARNING Workflow checker warning: -v1.0/dynresreq-workflow-stepdefault.cwl:6:3: Source 'special_file' of type ["null", "File"] may be - incompatible -v1.0/dynresreq-workflow-stepdefault.cwl:15:7: with sink 'special_file' of type "File" -Test [184/197] Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input. +v1.0/v1.0/dynresreq-workflow-stepdefault.cwl:6:3: Source 'special_file' of type ["null", "File"] + may be incompatible +v1.0/v1.0/dynresreq-workflow-stepdefault.cwl:15:7: with sink 'special_file' of type "File" +Test [184/197] dynamic_resreq_wf_optional_file_wf_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input. -Test [185/197] Test default value on step input parameter overridden by provided source. With passthrough first step +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpxu_99_9j --quiet v1.0/v1.0/dynresreq-workflow-inputdefault.cwl v1.0/v1.0/empty.json +Test [185/197] step_input_default_value_overriden_2nd_step: Test default value on step input parameter overridden by provided source. With passthrough first step +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpia_tkuvp --quiet v1.0/v1.0/count-lines11-extra-step-wf.cwl v1.0/v1.0/cat-job.json WARNING Workflow checker warning: -v1.0/count-lines11-extra-step-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be - incompatible -v1.0/count-lines11-extra-step-wf.cwl:17:7: with sink 'file1' of type "File" -Test [186/197] Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool +v1.0/v1.0/count-lines11-extra-step-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be + incompatible +v1.0/v1.0/count-lines11-extra-step-wf.cwl:17:7: with sink 'file1' of type "File" +Test [186/197] step_input_default_value_overriden_2nd_step_noexp: Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpps6_k8ik --quiet v1.0/v1.0/count-lines11-extra-step-wf-noET.cwl v1.0/v1.0/cat-job.json WARNING Workflow checker warning: -v1.0/count-lines11-extra-step-wf-noET.cwl:6:3: Source 'file1' of type ["null", "File"] may be - incompatible -v1.0/count-lines11-extra-step-wf-noET.cwl:17:7: with sink 'file1' of type "File" -Test [187/197] Test default value on step input parameter overridden by provided source. With null producing first step +v1.0/v1.0/count-lines11-extra-step-wf-noET.cwl:6:3: Source 'file1' of type ["null", "File"] may be + incompatible +v1.0/v1.0/count-lines11-extra-step-wf-noET.cwl:17:7: with sink 'file1' of type "File" +Test [187/197] step_input_default_value_overriden_2nd_step_null: Test default value on step input parameter overridden by provided source. With null producing first step -Test [188/197] Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmppjh8h88f --quiet v1.0/v1.0/count-lines11-null-step-wf.cwl v1.0/v1.0/empty.json +Test [188/197] step_input_default_value_overriden_2nd_step_null_noexp: Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool -Test [189/197] Pipe to stdin from user provided local File via a Directory literal +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpmbgto6v4 --quiet v1.0/v1.0/count-lines11-null-step-wf-noET.cwl v1.0/v1.0/empty.json +Test [189/197] stdin_from_directory_literal_with_local_file: Pipe to stdin from user provided local File via a Directory literal -Test [190/197] Pipe to stdin from literal File via a Directory literal +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpaexckmfv --quiet v1.0/v1.0/cat-from-dir.cwl v1.0/v1.0/cat-from-dir-job.yaml +Test [190/197] stdin_from_directory_literal_with_literal_file: Pipe to stdin from literal File via a Directory literal -Test [191/197] Test non-stdin reference to literal File via a Directory literal +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp3r9r1ip_ --quiet v1.0/v1.0/cat-from-dir.cwl v1.0/v1.0/cat-from-dir-with-literal-file.yaml +Test [191/197] directory_literal_with_literal_file_nostdin: Test non-stdin reference to literal File via a Directory literal -Test [192/197] Test CommandLineTool without inputs +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpllcjsujd --quiet v1.0/v1.0/cat3-from-dir.cwl v1.0/v1.0/cat-from-dir-with-literal-file.yaml +Test [192/197] no_inputs_commandlinetool: Test CommandLineTool without inputs -Test [193/197] Test CommandLineTool without outputs +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpssgx_ef7 --quiet v1.0/v1.0/no-inputs-tool.cwl +Test [193/197] no_outputs_commandlinetool: Test CommandLineTool without outputs -Test [194/197] Test Workflow without inputs +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpti1qzzz1 --quiet v1.0/v1.0/no-outputs-tool.cwl v1.0/v1.0/cat-job.json +Test [194/197] no_inputs_workflow: Test Workflow without inputs -Test [195/197] Test Workflow without outputs +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp6nk9dk9l --quiet v1.0/v1.0/no-inputs-wf.cwl +Test [195/197] no_outputs_workflow: Test Workflow without outputs -Test [196/197] Test an anonymous enum inside an array inside a record +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmpveqzwkq0 --quiet v1.0/v1.0/no-outputs-wf.cwl v1.0/v1.0/cat-job.json +Test [196/197] anonymous_enum_in_array: Test an anonymous enum inside an array inside a record -Test [197/197] Test an anonymous enum inside an array inside a record, SchemaDefRequirement +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmphhh_11d4 --quiet v1.0/v1.0/anon_enum_inside_array.cwl v1.0/v1.0/anon_enum_inside_array.yml +Test [197/197] schema-def_anonymous_enum_in_array: Test an anonymous enum inside an array inside a record, SchemaDefRequirement +Running: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmplw21evl7 --quiet v1.0/v1.0/anon_enum_inside_array_inside_schemadef.cwl v1.0/v1.0/anon_enum_inside_array_inside_schemadef.yml 195 tests passed, 1 failures, 1 unsupported features - -1 tool tests failed diff --git a/conformance/run-job-1-0.sh b/conformance/run-job-1-0.sh index d343298..6b22d78 100755 --- a/conformance/run-job-1-0.sh +++ b/conformance/run-job-1-0.sh @@ -6,5 +6,5 @@ NAMESPACE_NAME="calrissian-conformance" kubectl create --namespace="$NAMESPACE_NAME" -f ConformanceTestsJob-1.0.yaml kubectl wait --namespace="$NAMESPACE_NAME" --for=condition=Ready --selector=job-name=conformance-tests-1-0 pods -kubectl logs --namespace="$NAMESPACE_NAME" -f jobs/conformance-tests-1-0 | egrep -v 'The `label`' > results-v1.1.txt +kubectl logs --namespace="$NAMESPACE_NAME" -f jobs/conformance-tests-1-0 | egrep -v 'The `label`' > results-v1.0.txt kubectl cp $NAMESPACE_NAME/inspect-volumes:/output/badges-1.0.2/ badges/1.0.2