Merge pull request galaxyproject#4176 from galaxyproject/violetear-elver

Fix TRS import for workflows with capital letters

_plugins/gtn.rb

@@ -308,7 +308,7 @@ def convert_workflow_path_to_trs(str)
       return 'GTN_TRS_ERROR_NIL' if str.nil?
 
       m = str.match(%r{topics/(?<topic>.*)/tutorials/(?<tutorial>.*)/workflows/(?<workflow>.*)\.ga})
-      return "/api/ga4gh/trs/v2/tools/#{m[:topic]}-#{m[:tutorial]}/versions/#{m[:workflow]}" if m
+      return "/api/ga4gh/trs/v2/tools/#{m[:topic]}-#{m[:tutorial]}/versions/#{m[:workflow].downcase}" if m
 
       'GTN_TRS_ERROR'
     end

bin/workflow-test.rb

@@ -1,29 +1,74 @@
 #!/usr/bin/env ruby
 # frozen_string_literal: true
 
+require 'open3'
 require 'json'
 
 GALAXIES = {
-  eu: { url: 'https://usegalaxy.eu', key: ENV.fetch('GALAXY_EU_KEY', nil) },
+  eu: { url: 'https://usegalaxy.eu', key: ENV.fetch('GALAXY_EU_KEY', "NONE") },
 }
 
 def test_workflow(workflow_file, galaxy_id)
+  directory = File.dirname(workflow_file)
   workflow_base = File.basename(workflow_file, '.ga')
-  workflow_output_json = File.join(File.dirname(workflow_file), "#{workflow_base}.#{galaxy_id}.json")
+  workflow_output_json = File.join(directory, "#{workflow_base}.#{galaxy_id}.json")
   galaxy_url = GALAXIES[galaxy_id][:url]
   galaxy_user_key = GALAXIES[galaxy_id][:key]
-  cmd = %(
-    planemo --verbose test
-      --galaxy_url #{galaxy_url}
-      --galaxy_user_key #{galaxy_user_key}
-      --no_shed_install
-      --engine external_galaxy
-      --polling_backoff 1
-      --test_output_json #{workflow_output_json}
-      #{workflow_file}
-  ).split.map(&:strip).join(' ').strip
-  puts cmd
-  `#{cmd}`
+  cmd = [
+    'planemo', '--verbose', 'test', '--galaxy_url', galaxy_url,
+    '--galaxy_user_key', galaxy_user_key, '--no_shed_install', '--engine',
+    'external_galaxy', '--polling_backoff', '1', '--test_output_json',
+    workflow_output_json, workflow_file
+  ]
+  p cmd.join(' ')
+
+  Open3.popen3(*cmd) do |stdin, stdout, stderr, wait_thr|
+    File.open("#{directory}/#{workflow_base}.#{galaxy_id}.log", 'w') do |f|
+      f.write(stdout.read)
+    end
+    File.open("#{directory}/#{workflow_base}.#{galaxy_id}.err", 'w') do |f|
+      f.write(stderr.read)
+    end
+    exit_status = wait_thr.value # Process::Status object returned
+    puts "#{workflow_file} => #{exit_status} (#{stderr})"
+  end
 end
 
-test_workflow(ARGV[0], :eu)
+workflows = %w(
+  ./topics/assembly/tutorials/debruijn-graph-assembly/workflows/debruijn-graph.ga
+  ./topics/assembly/tutorials/general-introduction/workflows/assembly-general-introduction.ga
+  ./topics/assembly/tutorials/unicycler-assembly/workflows/unicycler.ga
+  ./topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.ga
+  ./topics/computational-chemistry/tutorials/md-simulation-gromacs/workflows/main_workflow.ga
+  ./topics/ecology/tutorials/obisindicators/workflows/Obis-indicators.ga
+  ./topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.ga
+  ./topics/fair/tutorials/ro-crate-submitting-life-monitor/sort-and-change-case-workflow/sort-and-change-case.ga
+  ./topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga
+  ./topics/genome-annotation/tutorials/repeatmasker/workflows/RepeatMasker.ga
+  ./topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga
+  ./topics/introduction/tutorials/galaxy-intro-101-everyone/workflows/main_workflow.ga
+  ./topics/introduction/tutorials/galaxy-intro-peaks2genes/workflows/Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.ga
+  ./topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.ga
+  ./topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.ga
+  ./topics/metagenomics/tutorials/beer-data-analysis/workflows/main_workflow.ga
+  ./topics/metagenomics/tutorials/general-tutorial/workflows/amplicon.ga
+  ./topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/Nanopore_Datasets_Pathogen_Tracking_among_all_samples.ga
+  ./topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-Count-Matrix-Filtering.ga
+  ./topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-FASTQ-to-Count-Matrix.ga
+  ./topics/single-cell/tutorials/scrna-case_alevin/workflows/Generating-a-single-cell-matrix-using-Alevin-1.9.ga
+  ./topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga
+  ./topics/statistics/tutorials/machinelearning/workflows/machine_learning.ga
+  ./topics/transcriptomics/tutorials/rna-interactome/workflows/rna-rna-interactome-data-analysis-chira.ga
+  ./topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/workflows/rna-seq-viz-with-heatmap2.ga
+  ./topics/transcriptomics/tutorials/small_ncrna_clustering/workflows/blockclust_clustering.ga
+  ./topics/variant-analysis/tutorials/non-dip/workflows/Calling_variants_in_non-diploid_systems.ga
+)
+
+threads = []
+
+workflows.each do |workflow|
+  threads << Thread.new do
+    test_workflow(workflow, :eu)
+  end
+end
+threads.map(&:join)