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require_relative "toxbank-setup.rb"
require File.join(File.expand_path(File.dirname(__FILE__)),".." ,".." ,"toxbank-investigation", "util.rb")
begin
puts "Service URI is: #{$investigation[:uri]}"
rescue
puts "Configuration Error: $investigation[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
exit
end
class TBInvestigationWorkflow < MiniTest::Test
i_suck_and_my_tests_are_order_dependent!
# Permission Matrix for owner, user1 (with GET permission (e.G.: group-permission) and user2 (no permission)
# Sum = isSummarySearchable=true
# noSum = isSummarySearchable=false
# Pub = isPublished = true
# noPub = isPublished = false
# noPub noSum noPub noSum
# noSum Pub Pub+Sum noSum Pub Pub+Sum
# owner user1 user1 user1 user2 user2 user2
# GET y n y y n n n
# POST,PUT,DEL y n n n n n n
# /metadata y n y y n n y
# /protocol y n y y n n y
# Download y n y y n n n
# Search ? n n y n n y
# define different users
@@owner = $pi[:subjectid]
@@user1 = $secondpi[:subjectid]
@@user2 = $guestid
def setup
OpenTox::RestClientWrapper.subjectid = @@owner #set owner as the logged in user
end
## Owner keeps all private
# create a new investigation by uploading a zip file,
# Summary is not searchable, not published. { access=custom(owner only) in the GUI }
def test_01_post_investigation
@@uri = ""
file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", "BII-I-1b-tb2.zip"
response = OpenTox::RestClientWrapper.post $investigation[:uri], {:file => File.open(file)}, { :subjectid => @@owner }
task_uri = response.chomp
task = OpenTox::Task.new task_uri
task.wait
uri = task.resultURI
assert_equal "Completed", task.hasStatus, "Task should be completed but is: #{task.hasStatus}. Task URI is #{task_uri} ."
@@uri = URI(uri)
end
# check if @@uri is not in search-index
def test_02_investigation_not_in_searchindex
response = OpenTox::RestClientWrapper.get "#{$search_service[:uri]}/search/index/investigation?resourceUri=#{CGI.escape(@@uri.to_s)}",{},{:subjectid => @@owner}
assert_equal 200, response.code
refute_match /#{@@uri}/, response.to_s
end
# check for flag "isPublished" is false,
# @note default behaviour on new investigations
def test_03_check_published_false
data = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@owner}
@g = RDF::Graph.new
RDF::Reader.for(:rdfxml).new(data.to_s){|r| r.each{|s| @g << s}}
@g.query(:predicate => RDF::TB.isPublished){|r| assert_match /false/, r[2].to_s}
end
# check for flag "isSummarySearchable" is false,
# @note default behaviour on new investigations
def test_03b_check_searchable_false
data = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@owner}
@g = RDF::Graph.new
RDF::Reader.for(:rdfxml).new(data.to_s){|r| r.each{|s| @g << s}}
@g.query(:predicate => RDF::TB.isSummarySearchable){|r| assert_match /false/, r[2].to_s}
end
# check all permissions for owner
def test_04a_all_permission
["GET","POST","PUT","DELETE"].each do |permission|
response = OpenTox::Authorization.authorize "#{@@uri}", permission, @@owner
assert_equal true, response
end
end
# get metadata for owner
def test_04b_get_metadata_pi
response = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@owner}
assert_equal 200, response.code
end
# get related protocol uris for owner
def test_04c_get_protocol_pi
response = OpenTox::RestClientWrapper.get "#{@@uri}/protocol", {}, {:accept => "application/rdf+xml", :subjectid => @@owner}
assert_equal 200, response.code
end
def test_04d_get_download_owner
response = OpenTox::RestClientWrapper.get "#{@@uri}", {}, {:accept => "application/zip", :subjectid => @@owner}
assert_equal 200, response.code
end
## now check permissions for user1
## expect nothing allowed
##################################
# no get permission for user1
def test_05a_no_get_permission
response = OpenTox::Authorization.authorize "#{@@uri}", "GET", @@user1
assert_equal false, response
end
# do not get metadata for user1
def test_05b_get_metadata
assert_raises OpenTox::UnauthorizedError do
response = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@user1}
end
end
# do not get protocol for user1
def test_05c_get_protocol
assert_raises OpenTox::UnauthorizedError do
response = OpenTox::RestClientWrapper.get "#{@@uri}/protocol", {}, {:accept => "application/rdf+xml", :subjectid => @@user1}
end
end
# do not get download for user1
def test_05d_get_download
assert_raises OpenTox::UnauthorizedError do
response = OpenTox::RestClientWrapper.get "#{@@uri}", {}, {:accept => "application/zip", :subjectid => @@user1}
end
end
# no post/put/delete permission for user1
def test_05e_no_cud_permission
["POST", "PUT", "DELETE"].each do |permission|
response = OpenTox::Authorization.authorize "#{@@uri}", permission, @@user1
assert_equal false, response
end
end
## now check permissions for user2
## expect nothing allowed
##################################
# do not get for user2
def test_06a_get_permission
response = OpenTox::Authorization.authorize "#{@@uri}", "GET", @@user2
assert_equal false, response
end
# do not get metadata for user2
def test_06b_get_metadata
assert_raises OpenTox::UnauthorizedError do
response = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@user2}
end
end
# do not get protocol for user2
def test_06c_get_protocol
assert_raises OpenTox::UnauthorizedError do
response = OpenTox::RestClientWrapper.get "#{@@uri}/protocol", {}, {:accept => "application/rdf+xml", :subjectid => @@user2}
end
end
# do not get download for user2
def test_06d_get_download
assert_raises OpenTox::UnauthorizedError do
response = OpenTox::RestClientWrapper.get "#{@@uri}", {}, {:accept => "application/zip", :subjectid => @@user2}
end
end
# no post/put/delete permission for user2
def test_06e_no_cud_permission
["POST", "PUT", "DELETE"].each do |permission|
response = OpenTox::Authorization.authorize "#{@@uri}", permission, @@user2
assert_equal false, response
end
end
# give the investigation a tb-group membership access by policy
###############################################################
def test_08_put_group_access
@@toxbank_uri = `curl -Lk -X GET -H "Accept:text/uri-list" -H "subjectid:#{@@owner}" #{$user_service[:uri]}/project?search=ToxBank`.chomp.sub("\n","")
response = OpenTox::RestClientWrapper.put @@uri.to_s, { :allowReadByGroup => "#{@@toxbank_uri}"},{ :subjectid => @@owner }
task_uri = response.chomp
task = OpenTox::Task.new task_uri
task.wait
uri = task.resultURI
assert_equal uri, @@uri.to_s
end
# get permission for user1
def test_08a_get_permission
response = OpenTox::Authorization.authorize "#{@@uri}", "GET", @@user1
assert_equal true, response
end
# repeat with permissions for toxbank group
def test_08b_repeat_05bcd
test_05b_get_metadata
test_05c_get_protocol
test_05d_get_download
test_05e_no_cud_permission
test_02_investigation_not_in_searchindex
end
## make publish
###############
def test_09_put_published
response = OpenTox::RestClientWrapper.put @@uri.to_s, { :published => "true"},{ :subjectid => @@owner }
task_uri = response.chomp
task = OpenTox::Task.new task_uri
task.wait
uri = task.resultURI
assert_equal uri, @@uri.to_s
end
## check changes for user1
##########################
# allowed
def test_09a_get_user1
response = OpenTox::RestClientWrapper.get "#{@@uri}", {}, {:accept => "text/uri-list", :subjectid => @@user1}
assert_equal 200, response.code
end
# denied
def test_09b_put_user1
assert_raises OpenTox::UnauthorizedError do
response = OpenTox::RestClientWrapper.put "#{@@uri}", {}, {:published => "true", :subjectid => @@user1}
end
end
# denied
def test_09c_post_user1
assert_raises OpenTox::UnauthorizedError do
response = OpenTox::RestClientWrapper.post "#{@@uri}", {}, {:published => "true", :subjectid => @@user1}
end
end
# denied
def test_09d_delete_user1
assert_raises OpenTox::UnauthorizedError do
response = OpenTox::RestClientWrapper.delete "#{@@uri}", {}, {:subjectid => @@user1}
end
end
# allowed
# get metadata for user1
def test_09e_get_metadata_user1
response = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@user1}
assert_equal 200, response.code
end
# allowed
# get related protocol uris for user1
def test_09f_get_protocol_user1
response = OpenTox::RestClientWrapper.get "#{@@uri}/protocol", {}, {:accept => "application/rdf+xml", :subjectid => @@user1}
assert_equal 200, response.code
end
# allowed
def test_09g_get_download_user1
response = OpenTox::RestClientWrapper.get "#{@@uri}", {}, {:accept => "application/zip", :subjectid => @@user1}
assert_equal 200, response.code
end
def test_09h_not_indexed
test_02_investigation_not_in_searchindex
end
## make searchable
##################
def test_10_put_searchable
response = OpenTox::RestClientWrapper.put @@uri.to_s, { :summarySearchable => "true"},{ :subjectid => @@owner }
task_uri = response.chomp
task = OpenTox::Task.new task_uri
task.wait
uri = task.resultURI
assert_equal uri, @@uri.to_s
end
def test_11a_repeat_user1_tests
test_09a_get_user1
test_09b_put_user1
test_09c_post_user1
test_09d_delete_user1
test_09e_get_metadata_user1
test_09f_get_protocol_user1
test_09g_get_download_user1
end
def test_11b_is_indexed
response = OpenTox::RestClientWrapper.get "#{$search_service[:uri]}/search/index/investigation?resourceUri=#{CGI.escape(@@uri.to_s)}",{},{:subjectid => @@owner}
assert_equal 200, response.code
assert_match /#{@@uri}/, response.to_s
end
def test_12_remove_group_access
response = OpenTox::RestClientWrapper.put @@uri.to_s, { :allowReadByGroup => ""},{ :subjectid => @@owner }
task_uri = response.chomp
task = OpenTox::Task.new task_uri
task.wait
uri = task.resultURI
assert_equal uri, @@uri.to_s
end
# searchable + published without GET policy
def test_13a_repeat_05bcd
test_05a_no_get_permission
test_05d_get_download
test_05e_no_cud_permission
test_11b_is_indexed
end
# get metadata for user1
def test_13c_get_metadata_user1
response = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@user1 }
assert_equal 200, response.code
end
# get related protocol uris for user1
def test_13d_get_protocol_user1
response = OpenTox::RestClientWrapper.get "#{@@uri}/protocol", {}, {:accept => "application/rdf+xml", :subjectid => @@user1 }
assert_equal 200, response.code
end
def test_20_update_modified_time
response = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@owner }
g = RDF::Graph.new
RDF::Reader.for(:rdfxml).new(response.to_s){|r| r.each{|s| g << s}}
g.query(:predicate => RDF::DC.modified){|r| @modified_time1 = r[2].to_s}
t_start = Time.parse(@modified_time1).to_i
response = OpenTox::RestClientWrapper.put @@uri.to_s, { :allowReadByGroup => "#{@@toxbank_uri}"},{ :subjectid => @@owner }
sleep 2
response = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@owner }
g = RDF::Graph.new
RDF::Reader.for(:rdfxml).new(response.to_s){|r| r.each{|s| g << s}}
g.query(:predicate => RDF::DC.modified){|r| @modified_time2 = r[2].to_s}
t_end = Time.parse(@modified_time2).to_i
assert t_end > t_start, "modified time is not updated"
end
# delete investigation/{id}
# @note expect code 200
def test_99_a_delete_investigation
result = OpenTox::RestClientWrapper.delete @@uri.to_s, {}, {:subjectid => @@owner}
assert_equal 200, result.code
#assert result.match(/^Investigation [a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12} deleted$/)
assert !OpenTox::Authorization.uri_has_policy(@@uri.to_s)
end
## check for user1 and user2 with only isSum=true is set
## expect no get { GUI option 'make searchable' during first upload }
########################################################
def test_99_b_post_investigation
@@uri = ""
file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", "BII-I-1b-tb2.zip"
response = OpenTox::RestClientWrapper.post $investigation[:uri], {:file => File.open(file), :summarySearchable => "true"}, { :subjectid => @@owner }
task_uri = response.chomp
task = OpenTox::Task.new task_uri
task.wait
uri = task.resultURI
assert_equal "Completed", task.hasStatus, "Task should be completed but is: #{task.hasStatus}. Task URI is #{task_uri} ."
@@uri = URI(uri)
end
# check for flag "isSummarySearchable" is true,
def test_99_c_check_searchable_true
data = OpenTox::RestClientWrapper.get "#{@@uri}/metadata", {}, {:accept => "application/rdf+xml", :subjectid => @@owner}
@g = RDF::Graph.new
RDF::Reader.for(:rdfxml).new(data.to_s){|r| r.each{|s| @g << s}}
@g.query(:predicate => RDF::TB.isSummarySearchable){|r| assert_match /true/, r[2].to_s}
end
## expect no get for user1 and user2
####################################
def test_99_d_repeat_tests
# user1
test_05a_no_get_permission
test_05b_get_metadata
test_05c_get_protocol
test_05d_get_download
test_05e_no_cud_permission
#user2
test_06a_get_permission
test_06b_get_metadata
test_06c_get_protocol
test_06d_get_download
test_06e_no_cud_permission
end
# delete investigation/{id}
# @note expect code 200
def test_99_x_delete_investigation
result = OpenTox::RestClientWrapper.delete @@uri.to_s, {}, {:subjectid => @@owner}
assert_equal 200, result.code
assert !OpenTox::Authorization.uri_has_policy(@@uri.to_s)
end
end
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