[ARVADOS] updated: c4e7c6d5a1a9604c1c1e53a5aa749eb1e45f92a1
git at public.curoverse.com
git at public.curoverse.com
Wed Dec 31 18:10:09 EST 2014
Summary of changes:
.../app/controllers/virtual_machines_controller.rb | 3 -
.../helpers/api_client_authorizations_helper.rb | 2 -
.../app/helpers/authorized_keys_helper.rb | 2 -
apps/workbench/app/helpers/groups_helper.rb | 2 -
apps/workbench/app/helpers/humans_helper.rb | 2 -
apps/workbench/app/helpers/job_tasks_helper.rb | 2 -
apps/workbench/app/helpers/keep_disks_helper.rb | 2 -
apps/workbench/app/helpers/links_helper.rb | 2 -
apps/workbench/app/helpers/logs_helper.rb | 2 -
apps/workbench/app/helpers/nodes_helper.rb | 2 -
apps/workbench/app/helpers/projects_helper.rb | 2 -
apps/workbench/app/helpers/repositories_helper.rb | 2 -
apps/workbench/app/helpers/sessions_helper.rb | 2 -
apps/workbench/app/helpers/specimens_helper.rb | 2 -
apps/workbench/app/helpers/traits_helper.rb | 2 -
.../app/helpers/user_agreements_helper.rb | 2 -
apps/workbench/app/helpers/users_helper.rb | 2 -
apps/workbench/app/helpers/vcf_pipeline_helper.rb | 234 ---------------------
.../app/helpers/virtual_machines_helper.rb | 2 -
.../app/views/authorized_keys/_show_help.html.erb | 10 -
.../test/unit/api_client_authorization_test.rb | 7 -
apps/workbench/test/unit/authorized_key_test.rb | 7 -
apps/workbench/test/unit/human_test.rb | 7 -
apps/workbench/test/unit/job_task_test.rb | 7 -
apps/workbench/test/unit/keep_disk_test.rb | 4 -
apps/workbench/test/unit/log_test.rb | 7 -
apps/workbench/test/unit/node_test.rb | 7 -
apps/workbench/test/unit/pipeline_template_test.rb | 7 -
apps/workbench/test/unit/repository_test.rb | 7 -
apps/workbench/test/unit/specimen_test.rb | 7 -
apps/workbench/test/unit/trait_test.rb | 7 -
apps/workbench/test/unit/user_agreement_test.rb | 7 -
apps/workbench/test/unit/virtual_machine_test.rb | 7 -
33 files changed, 369 deletions(-)
delete mode 100644 apps/workbench/app/helpers/api_client_authorizations_helper.rb
delete mode 100644 apps/workbench/app/helpers/authorized_keys_helper.rb
delete mode 100644 apps/workbench/app/helpers/groups_helper.rb
delete mode 100644 apps/workbench/app/helpers/humans_helper.rb
delete mode 100644 apps/workbench/app/helpers/job_tasks_helper.rb
delete mode 100644 apps/workbench/app/helpers/keep_disks_helper.rb
delete mode 100644 apps/workbench/app/helpers/links_helper.rb
delete mode 100644 apps/workbench/app/helpers/logs_helper.rb
delete mode 100644 apps/workbench/app/helpers/nodes_helper.rb
delete mode 100644 apps/workbench/app/helpers/projects_helper.rb
delete mode 100644 apps/workbench/app/helpers/repositories_helper.rb
delete mode 100644 apps/workbench/app/helpers/sessions_helper.rb
delete mode 100644 apps/workbench/app/helpers/specimens_helper.rb
delete mode 100644 apps/workbench/app/helpers/traits_helper.rb
delete mode 100644 apps/workbench/app/helpers/user_agreements_helper.rb
delete mode 100644 apps/workbench/app/helpers/users_helper.rb
delete mode 100644 apps/workbench/app/helpers/vcf_pipeline_helper.rb
delete mode 100644 apps/workbench/app/helpers/virtual_machines_helper.rb
delete mode 100644 apps/workbench/app/views/authorized_keys/_show_help.html.erb
delete mode 100644 apps/workbench/test/unit/api_client_authorization_test.rb
delete mode 100644 apps/workbench/test/unit/authorized_key_test.rb
delete mode 100644 apps/workbench/test/unit/human_test.rb
delete mode 100644 apps/workbench/test/unit/job_task_test.rb
delete mode 100644 apps/workbench/test/unit/keep_disk_test.rb
delete mode 100644 apps/workbench/test/unit/log_test.rb
delete mode 100644 apps/workbench/test/unit/node_test.rb
delete mode 100644 apps/workbench/test/unit/pipeline_template_test.rb
delete mode 100644 apps/workbench/test/unit/repository_test.rb
delete mode 100644 apps/workbench/test/unit/specimen_test.rb
delete mode 100644 apps/workbench/test/unit/trait_test.rb
delete mode 100644 apps/workbench/test/unit/user_agreement_test.rb
delete mode 100644 apps/workbench/test/unit/virtual_machine_test.rb
via c4e7c6d5a1a9604c1c1e53a5aa749eb1e45f92a1 (commit)
from 49b58cc43218106f1633c389598894d59447a26b (commit)
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commit c4e7c6d5a1a9604c1c1e53a5aa749eb1e45f92a1
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Dec 31 16:33:57 2014 -0500
Remove cruft. No issue #
diff --git a/apps/workbench/app/controllers/virtual_machines_controller.rb b/apps/workbench/app/controllers/virtual_machines_controller.rb
index c3512e2..a62ba81 100644
--- a/apps/workbench/app/controllers/virtual_machines_controller.rb
+++ b/apps/workbench/app/controllers/virtual_machines_controller.rb
@@ -1,7 +1,4 @@
class VirtualMachinesController < ApplicationController
- def index_pane_list
- %w(recent help)
- end
def index
@objects ||= model_class.all
@vm_logins = {}
diff --git a/apps/workbench/app/helpers/api_client_authorizations_helper.rb b/apps/workbench/app/helpers/api_client_authorizations_helper.rb
deleted file mode 100644
index 98ddddc..0000000
--- a/apps/workbench/app/helpers/api_client_authorizations_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module ApiClientAuthorizationsHelper
-end
diff --git a/apps/workbench/app/helpers/authorized_keys_helper.rb b/apps/workbench/app/helpers/authorized_keys_helper.rb
deleted file mode 100644
index 9a486f2..0000000
--- a/apps/workbench/app/helpers/authorized_keys_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module AuthorizedKeysHelper
-end
diff --git a/apps/workbench/app/helpers/groups_helper.rb b/apps/workbench/app/helpers/groups_helper.rb
deleted file mode 100644
index c091b2f..0000000
--- a/apps/workbench/app/helpers/groups_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module GroupsHelper
-end
diff --git a/apps/workbench/app/helpers/humans_helper.rb b/apps/workbench/app/helpers/humans_helper.rb
deleted file mode 100644
index ca84af0..0000000
--- a/apps/workbench/app/helpers/humans_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module HumansHelper
-end
diff --git a/apps/workbench/app/helpers/job_tasks_helper.rb b/apps/workbench/app/helpers/job_tasks_helper.rb
deleted file mode 100644
index b08a1ae..0000000
--- a/apps/workbench/app/helpers/job_tasks_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module JobTasksHelper
-end
diff --git a/apps/workbench/app/helpers/keep_disks_helper.rb b/apps/workbench/app/helpers/keep_disks_helper.rb
deleted file mode 100644
index 9cf6b4a..0000000
--- a/apps/workbench/app/helpers/keep_disks_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module KeepDisksHelper
-end
diff --git a/apps/workbench/app/helpers/links_helper.rb b/apps/workbench/app/helpers/links_helper.rb
deleted file mode 100644
index f6bc988..0000000
--- a/apps/workbench/app/helpers/links_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module LinksHelper
-end
diff --git a/apps/workbench/app/helpers/logs_helper.rb b/apps/workbench/app/helpers/logs_helper.rb
deleted file mode 100644
index 99736f0..0000000
--- a/apps/workbench/app/helpers/logs_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module LogsHelper
-end
diff --git a/apps/workbench/app/helpers/nodes_helper.rb b/apps/workbench/app/helpers/nodes_helper.rb
deleted file mode 100644
index 673b561..0000000
--- a/apps/workbench/app/helpers/nodes_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module NodesHelper
-end
diff --git a/apps/workbench/app/helpers/projects_helper.rb b/apps/workbench/app/helpers/projects_helper.rb
deleted file mode 100644
index db5c5ce..0000000
--- a/apps/workbench/app/helpers/projects_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module ProjectsHelper
-end
diff --git a/apps/workbench/app/helpers/repositories_helper.rb b/apps/workbench/app/helpers/repositories_helper.rb
deleted file mode 100644
index 2860b5a..0000000
--- a/apps/workbench/app/helpers/repositories_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module RepositoriesHelper
-end
diff --git a/apps/workbench/app/helpers/sessions_helper.rb b/apps/workbench/app/helpers/sessions_helper.rb
deleted file mode 100644
index 309f8b2..0000000
--- a/apps/workbench/app/helpers/sessions_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module SessionsHelper
-end
diff --git a/apps/workbench/app/helpers/specimens_helper.rb b/apps/workbench/app/helpers/specimens_helper.rb
deleted file mode 100644
index 8c30d97..0000000
--- a/apps/workbench/app/helpers/specimens_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module SpecimensHelper
-end
diff --git a/apps/workbench/app/helpers/traits_helper.rb b/apps/workbench/app/helpers/traits_helper.rb
deleted file mode 100644
index a4260eb..0000000
--- a/apps/workbench/app/helpers/traits_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module TraitsHelper
-end
diff --git a/apps/workbench/app/helpers/user_agreements_helper.rb b/apps/workbench/app/helpers/user_agreements_helper.rb
deleted file mode 100644
index ab8d3d3..0000000
--- a/apps/workbench/app/helpers/user_agreements_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module UserAgreementsHelper
-end
diff --git a/apps/workbench/app/helpers/users_helper.rb b/apps/workbench/app/helpers/users_helper.rb
deleted file mode 100644
index 2310a24..0000000
--- a/apps/workbench/app/helpers/users_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module UsersHelper
-end
diff --git a/apps/workbench/app/helpers/vcf_pipeline_helper.rb b/apps/workbench/app/helpers/vcf_pipeline_helper.rb
deleted file mode 100644
index 9a3d6e7..0000000
--- a/apps/workbench/app/helpers/vcf_pipeline_helper.rb
+++ /dev/null
@@ -1,234 +0,0 @@
-module VcfPipelineHelper
- require 'csv'
-
- def reset_vcf_pipeline_instance(pi, input_manifest)
- params = {
- 'PICARD_ZIP' => '7a4073e29bfa87154b7102e75668c454+83+K at van',
- 'GATK_BUNDLE' => '0a37aaf212464efa2a77ff9ba51c0148+10524+K at van',
- 'GATK_TAR_BZ2' => '482ebab0408e173370c499f0b7c00878+93+K at van',
- 'BWA' => '73be5598809c66f260fedd253c8608bd+67+K at van',
- 'SAM' => '55d2115faa608eb95dab4f875b7511b1+72+K at van',
- 'REGION_PADDING' => '10',
- 'REGIONS' => 'e52c086f41c2f089d88ec2bbd45355d3+87+K at van/SeqCap_EZ_Exome_v2.hg19.bed',
- 'STAND_CALL_CONF' => '4.0',
- 'STAND_EMIT_CONF' => '4.0',
- "bwa/INPUT" => input_manifest
- }
- pi.components = PipelineTemplate.find(pi.pipeline_uuid).components
- pi.update_job_parameters(params)
- pi.active = true
- pi.success = nil
- end
-
- def vcf_pipeline_summary(pi)
- stats = {}
- collection_link = Link.
- where(head_uuid: pi.uuid,
- link_class: 'client-defined',
- name: 'vcffarm-pipeline-invocation').
- last
- if collection_link
- stats[:collection_uuid] = collection_link.tail_uuid
- else
- pi.components[:steps].each do |step|
- if step[:name] == 'bwa'
- step[:params].each do |param|
- if param[:name] == 'INPUT'
- stats[:collection_uuid] = param[:data_locator] || param[:value]
- break
- end
- end
- end
- end
- end
- if stats[:collection_uuid]
- Link.where(tail_uuid: stats[:collection_uuid],
- head_kind: Group)[0..0].each do |c2p|
- stats[:project_uuid] = c2p.head_uuid
- group = Group.find stats[:project_uuid]
- stats[:project_name] = group.name rescue nil
- end
- Link.where(tail_uuid: stats[:collection_uuid],
- head_kind: Specimen)[0..0].each do |c2s|
- stats[:specimen_uuid] = c2s.head_uuid
- specimen = Specimen.find stats[:specimen_uuid]
- stats[:specimen_id] = specimen.properties[:specimen_id] rescue nil
- end
- end
- stats[:runtime] = {}
- stats[:alignment_for_step] = {}
- stats[:alignment] = {}
- stats[:coverage] = []
- pi.components[:steps].each do |step|
- if step[:warehousejob]
- if step[:name] == 'bwa' and step[:warehousejob][:starttime]
- stats[:runtime][:started_at] = step[:warehousejob][:starttime]
- end
- if step[:warehousejob][:finishtime]
- stats[:runtime][:finished_at] =
- [ step[:warehousejob][:finishtime],
- stats[:runtime][:finished_at] ].compact.max
- end
- end
- if step[:name] == 'picard-casm' and
- step[:complete] and
- step[:output_data_locator]
- tsv = IO.
- popen("whget -r #{step[:output_data_locator]}/ -").
- readlines.
- collect { |x| x.strip.split "\t" }
- casm = {}
- head = []
- tsv.each do |data|
- if data.size < 4 or data[0].match /^\#/
- next
- elsif data[0] == 'CATEGORY' or data[1].match /[^\d\.]/
- head = data
- elsif data[0] == 'PAIR'
- head.each_with_index do |name, index|
- x = data[index]
- if x and x.match /^\d+$/
- x = x.to_i
- elsif x and x.match /^\d+\.\d+$/
- x = x.to_f
- end
- name = name.downcase.to_sym
- casm[name] ||= []
- casm[name] << x
- end
- end
- end
- stats[:picard_alignment_summary] = casm
- end
- if step[:name] == 'gatk-stats' and
- step[:complete] and
- step[:output_data_locator]
- csv = IO.
- popen("whget #{step[:output_data_locator]}/mincoverage_nlocus.csv").
- readlines.
- collect { |x| x.strip.split ',' }
- csv.each do |depth, nlocus, percent|
- stats[:coverage][depth.to_i] = nlocus.to_i
- end
- end
- if step[:name] == 'gatk-realign' and
- step[:complete] and
- step[:output_data_locator]
- logs = IO.
- popen("whget #{step[:warehousejob][:metakey]}").
- readlines.
- collect(&:strip)
- logs.each do |logline|
- if (re = logline.match /\s(\d+) stderr INFO .* (\d+) reads were filtered out.*of (\d+) total/)
- stats[:alignment_for_step][re[1]] ||= {}
- stats[:alignment_for_step][re[1]][:filtered_reads] = re[2].to_i
- stats[:alignment_for_step][re[1]][:total_reads] = re[3].to_i
- elsif (re = logline.match /(\d+) reads.* failing BadMate/)
- stats[:alignment][:bad_mate_reads] = re[1].to_i
- elsif (re = logline.match /(\d+) reads.* failing MappingQualityZero/)
- stats[:alignment][:mapq0_reads] = re[1].to_i
- end
- end
- end
- if step[:name] == 'gatk-merge-call' and
- step[:complete] and
- step[:output_data_locator]
- stats[:vcf_file_name] = "#{stats[:project_name]}-#{stats[:specimen_id]}-#{step[:output_data_locator][0..31]}.vcf"
- logs = IO.
- popen("whget #{step[:warehousejob][:metakey]}").
- readlines.
- collect(&:strip)
- logs.each do |logline|
- if (re = logline.match /(\d+) reads were filtered out.*of (\d+) total/)
- stats[:alignment][:filtered_reads] = re[1].to_i
- stats[:alignment][:total_realigned_reads] = re[2].to_i
- elsif (re = logline.match /(\d+) reads.* failing BadMate/)
- stats[:alignment][:bad_mate_reads] = re[1].to_i
- elsif (re = logline.match /(\d+) reads.* failing UnmappedRead/)
- stats[:alignment][:unmapped_reads] = re[1].to_i
- end
- end
-
- stats[:chromosome_calls] = {}
- tsv = IO.
- popen("whget #{step[:output_data_locator]}/merged.vcf | egrep -v '^#' | cut -f1 | uniq -c").
- readlines.
- collect { |x| x.strip.split }
- tsv.each do |n_variants, sequence_name|
- stats[:chromosome_calls][sequence_name] = n_variants.to_i
- end
-
- stats[:inferred_sex] = false
- calls = stats[:chromosome_calls]
- if calls['X'] and calls['X'] > 200
- if !calls['Y']
- stats[:inferred_sex] = 'female'
- elsif calls['Y'] * 60 < calls['X']
- # if Y < X/60 they are presumed to be misalignments
- stats[:inferred_sex] = 'female'
- elsif calls['Y'] * 25 > calls['X']
- # if Y > X/25 we presume a Y chromosome was present
- stats[:inferred_sex] = 'male'
- end
- end
- end
- end
- stats[:alignment][:total_reads] = 0
- stats[:alignment][:filtered_reads] ||= 0
- stats[:alignment][:bad_mate_reads] ||= 0
- stats[:alignment][:mapq0_reads] ||= 0
- stats[:alignment_for_step].values.each do |a4s|
- stats[:alignment][:total_reads] += (a4s[:total_reads] || 0)
- stats[:alignment][:filtered_reads] += (a4s[:filtered_reads] || 0)
- stats[:alignment][:bad_mate_reads] += (a4s[:bad_mate_reads] || 0)
- stats[:alignment][:mapq0_reads] += (a4s[:mapq0_reads] || 0)
- end
-
- if stats[:collection_uuid]
- csv = CSV.parse IO.
- popen("whget #{stats[:collection_uuid]}/SampleSheet.csv -").
- read
- if !csv.empty?
- pivoted = []
- csv[0].each_with_index do |head, col|
- pivoted << csv.collect { |row| row[col] }
- end
- stats[:source_data_csv_columns] = pivoted
- end
- end
-
- picardas = stats[:picard_alignment_summary]
- stats[:summary_csv_columns] =
- [['PROJECT', stats[:project_name]],
- ['SPECIMEN', stats[:specimen_id]],
- ['VCF_FILE_NAME', stats[:vcf_file_name]],
- ['INFERRED_SEX', stats[:inferred_sex]],
- ['SOURCE_DATA', stats[:collection_uuid]],
- ['PIPELINE_UUID', pi.pipeline_uuid],
- ['PIPELINE_RUN_UUID', pi.uuid],
- ['PIPELINE_RUN_START', (stats[:runtime][:started_at] rescue nil)],
- ['PIPELINE_RUN_FINISH', (stats[:runtime][:finished_at] rescue nil)],
- ['N_READS_RAW',
- (n_raw = picardas[:total_reads].inject(0,:+) rescue nil)],
- ['N_READS_MAPPED',
- (n_mapped = picardas[:reads_aligned_in_pairs].inject(0,:+) rescue nil)],
- ['PERCENT_READS_MAPPED',
- (100.0 * n_mapped / n_raw rescue nil)],
- ['N_READS_ON_TARGET',
- (n_on_target = stats[:alignment][:total_reads] - stats[:alignment][:filtered_reads] rescue nil)],
- ['PERCENT_READS_ON_TARGET',
- (100.0 * n_on_target / n_raw rescue nil)],
- ['PERCENT_TARGET_COVERAGE_1X',
- (100.0 * stats[:coverage][1] / stats[:coverage][0] rescue nil)],
- ['PERCENT_TARGET_COVERAGE_10X',
- (100.0 * stats[:coverage][10] / stats[:coverage][0] rescue nil)],
- ['PERCENT_TARGET_COVERAGE_20X',
- (100.0 * stats[:coverage][20] / stats[:coverage][0] rescue nil)],
- ['PERCENT_TARGET_COVERAGE_50X',
- (100.0 * stats[:coverage][50] / stats[:coverage][0] rescue nil)],
- ['PERCENT_TARGET_COVERAGE_100X',
- (100.0 * stats[:coverage][100] / stats[:coverage][0] rescue nil)]]
-
- stats
- end
-end
diff --git a/apps/workbench/app/helpers/virtual_machines_helper.rb b/apps/workbench/app/helpers/virtual_machines_helper.rb
deleted file mode 100644
index cbb398d..0000000
--- a/apps/workbench/app/helpers/virtual_machines_helper.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-module VirtualMachinesHelper
-end
diff --git a/apps/workbench/app/views/authorized_keys/_show_help.html.erb b/apps/workbench/app/views/authorized_keys/_show_help.html.erb
deleted file mode 100644
index 42fff3c..0000000
--- a/apps/workbench/app/views/authorized_keys/_show_help.html.erb
+++ /dev/null
@@ -1,10 +0,0 @@
-<p>
- More information about how to log in to VMs:
-</p>
-<ul>
- <li>
- <%= link_to raw('Arvados Docs → User Guide → SSH access'),
- "#{Rails.configuration.arvados_docsite}/user/getting_started/ssh-access-unix.html",
- target: "_blank"%>.
- </li>
-</ul>
diff --git a/apps/workbench/test/unit/api_client_authorization_test.rb b/apps/workbench/test/unit/api_client_authorization_test.rb
deleted file mode 100644
index b5b07d1..0000000
--- a/apps/workbench/test/unit/api_client_authorization_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class ApiClientAuthorizationTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/authorized_key_test.rb b/apps/workbench/test/unit/authorized_key_test.rb
deleted file mode 100644
index b8d9b67..0000000
--- a/apps/workbench/test/unit/authorized_key_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class AuthorizedKeyTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/human_test.rb b/apps/workbench/test/unit/human_test.rb
deleted file mode 100644
index 2863cbf..0000000
--- a/apps/workbench/test/unit/human_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class HumanTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/job_task_test.rb b/apps/workbench/test/unit/job_task_test.rb
deleted file mode 100644
index 3c7c1e7..0000000
--- a/apps/workbench/test/unit/job_task_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class JobTaskTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/keep_disk_test.rb b/apps/workbench/test/unit/keep_disk_test.rb
deleted file mode 100644
index 42ab63b..0000000
--- a/apps/workbench/test/unit/keep_disk_test.rb
+++ /dev/null
@@ -1,4 +0,0 @@
-require 'test_helper'
-
-class KeepDiskTest < ActiveSupport::TestCase
-end
diff --git a/apps/workbench/test/unit/log_test.rb b/apps/workbench/test/unit/log_test.rb
deleted file mode 100644
index f2afee2..0000000
--- a/apps/workbench/test/unit/log_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class LogTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/node_test.rb b/apps/workbench/test/unit/node_test.rb
deleted file mode 100644
index ccc3765..0000000
--- a/apps/workbench/test/unit/node_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class NodeTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/pipeline_template_test.rb b/apps/workbench/test/unit/pipeline_template_test.rb
deleted file mode 100644
index a28a2c9..0000000
--- a/apps/workbench/test/unit/pipeline_template_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class PipelineTemplateTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/repository_test.rb b/apps/workbench/test/unit/repository_test.rb
deleted file mode 100644
index 327170c..0000000
--- a/apps/workbench/test/unit/repository_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class RepositoryTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/specimen_test.rb b/apps/workbench/test/unit/specimen_test.rb
deleted file mode 100644
index a9abc8c..0000000
--- a/apps/workbench/test/unit/specimen_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class SpecimenTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/trait_test.rb b/apps/workbench/test/unit/trait_test.rb
deleted file mode 100644
index 45df2ed..0000000
--- a/apps/workbench/test/unit/trait_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class TraitTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/user_agreement_test.rb b/apps/workbench/test/unit/user_agreement_test.rb
deleted file mode 100644
index 7c0ac65..0000000
--- a/apps/workbench/test/unit/user_agreement_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class UserAgreementTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
diff --git a/apps/workbench/test/unit/virtual_machine_test.rb b/apps/workbench/test/unit/virtual_machine_test.rb
deleted file mode 100644
index 69258b5..0000000
--- a/apps/workbench/test/unit/virtual_machine_test.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-require 'test_helper'
-
-class VirtualMachineTest < ActiveSupport::TestCase
- # test "the truth" do
- # assert true
- # end
-end
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