@@ -466,7 +466,10 @@ def app
466466 file_name = "test_file_name"
467467 content = "This is a test file, with content 1."
468468 request = {
469- file_name => content
469+ files : [ {
470+ filename : file_name ,
471+ content : content
472+ } ]
470473 }
471474 post ( "/api/v2/#{ PROJECT } #{ workspace . id } , request )
472475 expect ( last_response . status ) . to eq ( 200 )
@@ -499,7 +502,12 @@ def app
499502 it 'requests a file from the workspace' do
500503 # Write a file to the workspace
501504 workspace_id = Vulcan ::Workspace . all [ 0 ] . id
502- request = { "test_file_name" : "This is a test file, with content 1" }
505+ request = {
506+ files : [ {
507+ filename : "test_file_name" ,
508+ content : "This is a test file, with content 1"
509+ } ]
510+ }
503511 post ( "/api/v2/#{ PROJECT } #{ workspace_id } , request )
504512 expect ( last_response . status ) . to eq ( 200 )
505513
@@ -558,6 +566,27 @@ def app
558566 expect ( last_response . status ) . to eq ( 200 )
559567 end
560568
569+ it 'alerts if snakemake is still running' do
570+ auth_header ( :editor )
571+ workspace = Vulcan ::Workspace . all [ 0 ]
572+ write_files_to_workspace ( workspace . id )
573+ request = {
574+ params : {
575+ count_bytes : true ,
576+ count_chars : false ,
577+ add : 2 ,
578+ add_and_multiply_by : 4
579+ }
580+ }
581+ post ( "/api/v2/#{ PROJECT } #{ workspace . id } , request )
582+ config_id = json_body [ :config_id ]
583+ post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ config_id } )
584+ post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ config_id } )
585+ expect ( last_response . status ) . to eq ( 429 )
586+ expect ( json_body [ :error ] ) . to eq ( "workflow is still running..." )
587+ end
588+
589+
561590 it 'can run the first step of a workflow' do
562591 auth_header ( :editor )
563592 workspace = Vulcan ::Workspace . all [ 0 ]
@@ -572,6 +601,7 @@ def app
572601 }
573602 }
574603 post ( "/api/v2/#{ PROJECT } #{ workspace . id } , request )
604+ expect ( last_response . status ) . to eq ( 200 )
575605 post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ json_body [ :config_id ] } )
576606 run_id = json_body [ :run_id ]
577607 expect ( last_response . status ) . to eq ( 200 )
@@ -609,7 +639,7 @@ def app
609639 expect ( json_body [ :run_id ] ) . to_not be_nil
610640 run_id = json_body [ :run_id ]
611641 # Make sure jobs are finished
612- check_jobs_status ( [ "count" , "arithmetic" , "checker" ] ) do
642+ check_jobs_status ( [ "count" , "arithmetic" , "checker" ] , 5 ) do
613643 get ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ run_id } )
614644 end
615645 # Outputs are created
@@ -624,7 +654,6 @@ def app
624654 expect ( remote_manager . file_exists? ( obj . log_path ) ) . to be_truthy
625655 end
626656
627-
628657 it 'can run one step and then another' do
629658 auth_header ( :editor )
630659 workspace = Vulcan ::Workspace . all [ 0 ]
@@ -638,6 +667,7 @@ def app
638667 }
639668
640669 post ( "/api/v2/#{ PROJECT } #{ workspace . id } , request )
670+ expect ( last_response . status ) . to eq ( 200 )
641671 post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ json_body [ :config_id ] } )
642672 expect ( last_response . status ) . to eq ( 200 )
643673 run_id = json_body [ :run_id ]
@@ -659,7 +689,7 @@ def app
659689 expect ( last_response . status ) . to eq ( 200 )
660690 config_id = json_body [ :config_id ]
661691 # Sometimes snakemake still needs a minute to shut-down even though slurm reports the job as complete
662- run_workflow_with_retry do
692+ run_workflow_with_retry ( 5 ) do
663693 post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ config_id } )
664694 end
665695 expect ( last_response . status ) . to eq ( 200 )
@@ -700,18 +730,27 @@ def app
700730 }
701731 }
702732 post ( "/api/v2/#{ PROJECT } #{ workspace . id } , request )
703- post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ json_body [ :config_id ] } )
733+ config_id = json_body [ :config_id ]
734+ post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ config_id } )
704735 run_id = json_body [ :run_id ]
705736 check_jobs_status ( [ "count" , "arithmetic" , "checker" ] ) do
706737 get ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ run_id } )
707738 end
708739 expect ( last_response . status ) . to eq ( 200 )
709740
710- # Next step involves writing files to the workspace
711- request = { "test_file_name" : "This is a test file, with content 1" }
741+ # Next step involves UI steps - so we just simulate this by writing files to the workspace
742+ request = {
743+ files : [ {
744+ filename : "ui_job_one.txt" ,
745+ content : "This is a test file, with content 1"
746+ } , {
747+ filename : "ui_job_two.txt" ,
748+ content : "This is a test file, with content 2"
749+ } ]
750+ }
712751 post ( "/api/v2/#{ PROJECT } #{ workspace . id } , request )
713752
714- # Run the last job, send the same params as before
753+ # Run the last job, send the same params as before (this is what the UI does)
715754 request = {
716755 params : {
717756 count_bytes : true ,
@@ -720,8 +759,9 @@ def app
720759 add_and_multiply_by : 4
721760 }
722761 }
762+
763+ # The config has not changed - just the files
723764 post ( "/api/v2/#{ PROJECT } #{ workspace . id } , request )
724- config_id = json_body [ :config_id ]
725765 run_workflow_with_retry do
726766 post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ config_id } )
727767 end
@@ -751,26 +791,6 @@ def app
751791
752792 end
753793
754- it 'alerts if snakemake is still running' do
755- auth_header ( :editor )
756- workspace = Vulcan ::Workspace . all [ 0 ]
757- write_files_to_workspace ( workspace . id )
758- request = {
759- params : {
760- count_bytes : true ,
761- count_chars : false ,
762- add : 2 ,
763- add_and_multiply_by : 4
764- }
765- }
766- post ( "/api/v2/#{ PROJECT } #{ workspace . id } , request )
767- config_id = json_body [ :config_id ]
768- post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ config_id } )
769- post ( "/api/v2/#{ PROJECT } #{ workspace . id } #{ config_id } )
770- expect ( last_response . status ) . to eq ( 429 )
771- expect ( json_body [ :error ] ) . to eq ( "workflow is still running..." )
772- end
773-
774794 end
775795
776796 context 'status checking' , long_running : true do
@@ -790,14 +810,14 @@ def app
790810
791811 end
792812
793- it 'invokes the first step of a workflow' do
813+ it 'checks the status of the first step of a workflow' do
794814 auth_header ( :editor )
795815 workspace = Vulcan ::Workspace . all [ 0 ]
796816 write_files_to_workspace ( workspace . id )
797817 request = {
798818 params : {
799- count_bytes : true ,
800- count_chars : false
819+ count_bytes : false ,
820+ count_chars : true
801821 }
802822 }
803823 # TODO: add a meta key that can switch profiles
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