openseek-api 0.17.4 → 0.18

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: d4505a02456e1b9eae6997fa15a68a8ea7177da8d0ef36a52b132ca259edbd0f
-  data.tar.gz: 0a5c4c6bea8e8837aab53212246af5567ba7bf98575b6927c59d13fe6705e379
+  metadata.gz: 21865600a0ceaaff363c08e4e0e660a55411aa73b949a35d62b735124f91f2aa
+  data.tar.gz: 02c0d8727073ed1c3316940082aaa1b06e6e23fb024668a4caa53912a1e8e536
 SHA512:
-  metadata.gz: 60f7f2978d93105ba37e1c1ac455084ba209400587907e5396807e69d2b6dbb242501d98febd3248bbec86bcc37e9a98d13f391be1eb841d261b5902889165dd
-  data.tar.gz: 54eccd8957541cb323fa9c48b34e79f9ed539ea973b74aeaa8541c3c5b62ac83a2987479085caadca5af391714cdbfa5bb4efe1c07bde98f9aaa075d5639163b
+  metadata.gz: b2846dcdfa758be102e69803bb2f2bc9cb22ea42e74fe8f7414045d2f1a3587edb21aca746406b748ec15f00e328c98905ef0c0bb4eda36524234c4adbfe993d
+  data.tar.gz: 206c44dd96d672a6e2e24805cb2ffa02125ae0130654c2dc69e4f61ac6b0d9598301be9994cce04e4e95c8836463b8fc40898f0b3c3f581d5e41a6b4de104b25

data/lib/fairdom/openbis_api/application_server_query.rb

@@ -3,13 +3,13 @@ module Fairdom
     class ApplicationServerQuery < OpenbisQuery
       attr_reader :as_endpoint
 
-      def initialize(as_endpoint, token)
-        super(token)
+      def initialize(as_endpoint, token, is_test = false)
+        super(token, is_test)
         @as_endpoint = as_endpoint
       end
 
       def root_command_options
-        " -endpoints '{%as%:%#{as_endpoint}%\,%sessionToken%:%#{token}%}'"
+        " -endpoints '{%as%:%#{as_endpoint}%\,%sessionToken%:%#{token}%,%is_test%:%#{is_test}%}'"
       end
     end
   end

data/lib/fairdom/openbis_api/authentication.rb

@@ -3,10 +3,11 @@ module Fairdom
     class Authentication < OpenbisQuery
       attr_reader :as_endpoint, :username, :password
 
-      def initialize(username, password, as_endpoint)
+      def initialize(username, password, as_endpoint, is_test = false)
         @username = username
         @password = password
         @as_endpoint = as_endpoint
+        @is_test = is_test
       end
 
       def login
@@ -18,7 +19,7 @@ module Fairdom
       end
 
       def root_command_options
-        " -account '{%username%:%#{username}%\,%password%:%#{password}%}' -endpoints '{%as%:%#{as_endpoint}%}'"
+        " -account '{%username%:%#{username}%\,%password%:%#{password}%}' -endpoints '{%as%:%#{as_endpoint}%,%is_test%:%#{is_test}%}'"
       end
     end
   end

data/lib/fairdom/openbis_api/data_store_query.rb

@@ -5,13 +5,13 @@ module Fairdom
     class DataStoreQuery < OpenbisQuery
       attr_reader :dss_endpoint
 
-      def initialize(dss_endpoint, token)
-        super(token)
+      def initialize(dss_endpoint, token, is_test = false)
+        super(token, is_test)
         @dss_endpoint = dss_endpoint
       end
 
       def root_command_options
-        " -endpoints '{%dss%:%#{dss_endpoint}%\,%sessionToken%:%#{token}%}'"
+        " -endpoints '{%dss%:%#{dss_endpoint}%\,%sessionToken%:%#{token}%,%is_test%:%#{is_test}%}'"
       end
     end
   end

data/lib/fairdom/openbis_api/openbis_query.rb

@@ -3,10 +3,11 @@ require 'fairdom/openbis_api/java_execution'
 module Fairdom
   module OpenbisApi
     class OpenbisQuery
-      attr_reader :token
+      attr_reader :token, :is_test
 
-      def initialize(token)
+      def initialize(token, is_test = false)
         @token = token
+        @is_test = is_test
       end
 
       def query(options)

data/lib/fairdom/openbis_api/versions.rb

@@ -1,6 +1,6 @@
 module Fairdom
   module OpenbisApi
-    VERSION = '0.17.4'.freeze
-    JAR_VERSION = '0.18'.freeze
+    VERSION = '0.18'.freeze
+    JAR_VERSION = '0.19'.freeze
   end
 end

data/test/application_query_test.rb

@@ -9,13 +9,10 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
   include Fairdom::OpenbisApi
 
   def setup
-    @as_endpoint = 'https://openbis-api.fair-dom.org/openbis/openbis'
     @as_endpoint = 'https://127.0.0.1:8443/openbis/openbis'
-    username = 'apiuser'
-    password = 'apiuser'
     username = 'seek'
     password = 'seek'
-    @token = Authentication.new(username, password, @as_endpoint).login['token']
+    @token = Authentication.new(username, password, @as_endpoint, true).login['token']
 
     @options = { entityType: 'Experiment', queryType: 'PROPERTY', property: 'NAME', propertyValue: 'Low light diurnal' }
   end
@@ -24,11 +21,11 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
     @as_endpoint = 'https://127.0.0.1:8443/openbis/openbis'
     username = 'seek'
     password = 'seek'
-    @token = Authentication.new(username, password, @as_endpoint).login['token']
+    @token = Authentication.new(username, password, @as_endpoint, true).login['token']
   end
 
   def test_query_property
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
     experiments = result['experiments']
     refute experiments.empty?
@@ -36,7 +33,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
   def test_query_for_spaces
     @options = { entityType: 'Space', queryType: 'ATTRIBUTE', attribute: 'PermID', attributeValue: '' }
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
     spaces = result['spaces']
     refute spaces.empty?
@@ -62,14 +59,14 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
   end
 
   def test_query_property_no_result
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     @options[:propertyValue] = 'Some_value'
     result = instance.query(@options)
     assert result.empty?
   end
 
   def test_unrecognized_type
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     invalid_type = 'SomeType'
     @options[:entityType] = 'Some_value'
     assert_raise OpenbisQueryException do
@@ -78,21 +75,21 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
   end
 
   def test_empty_property
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     @options[:property] = ''
     result = instance.query(@options)
     assert result.empty?
   end
 
   def test_any_property
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     @options[:property] = 'any_property'
     result = instance.query(@options)
     assert result.empty?
   end
 
   def test_query_perm_id_attribute
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     @options[:queryType] = 'ATTRIBUTE'
     @options[:attribute] = 'permId'
     @options[:attributeValue] = '20180418141729157-47'
@@ -102,7 +99,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
   end
 
   def test_query_multiple_perm_id_attribute_values
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     @options[:queryType] = 'ATTRIBUTE'
     @options[:attribute] = 'permId'
     @options[:attributeValue] = '20180424181519696-54,20180418141729157-47'
@@ -112,7 +109,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
   end
 
   def test_query_all_permid
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     @options[:queryType] = 'ATTRIBUTE'
     @options[:attribute] = 'PermID'
     @options[:attributeValue] = ''
@@ -122,7 +119,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
   def test_query_for_dataset_gives_rich_metadata
     @options = { entityType: 'DataSet', queryType: 'ATTRIBUTE', attribute: 'PermID', attributeValue: '20180424182903704-59' }
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     #puts result
@@ -145,7 +142,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
     puts 'no such test data'
     return
     @options = { entityType: 'DataSet', queryType: 'ATTRIBUTE', attribute: 'PermID', attributeValue: '20180418150033700-51' }
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     puts result
@@ -171,7 +168,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'DataSet', queryType: 'ALL' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -184,7 +181,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'Sample', queryType: 'ALL' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -197,7 +194,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'Space', queryType: 'ALL' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -210,7 +207,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
     local_setup
     @options = { entityType: 'Experiment', queryType: 'ALL' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     puts result.to_json
@@ -223,7 +220,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
       local_setup
       @options = { entityType: 'ExperimentType', queryType: 'ALL' }
 
-      instance = ApplicationServerQuery.new(@as_endpoint, @token)
+      instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
       result = instance.query(@options)
 
       puts result.to_json
@@ -236,7 +233,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'SampleType', queryType: 'ALL' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -249,7 +246,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'DataSetType', queryType: 'ALL' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -265,7 +262,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'Sample', queryType: 'TYPE', typeCode: 'EXPERIMENTAL_STEP' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -279,7 +276,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'DataSet', queryType: 'TYPE', typeCode: 'RAW_DATA' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -307,7 +304,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
     local_setup
     @options = { entityType: 'ExperimentType', queryType: "ATTRIBUTE", :attribute=>"CODE", :attributeValue=>"DEFAULT_EXPERIMENT" }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     puts result.to_json
@@ -323,7 +320,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
     @options = { entityType: 'Experiment', queryType: 'ATTRIBUTE',
               attribute: 'PermID', attributeValue: '20180424181519696-54'}
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     puts result.to_json
@@ -340,7 +337,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'Experiment', queryType: 'TYPE', typeCode: 'DEFAULT_EXPERIMENT' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     puts result.to_json
@@ -350,7 +347,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'Experiment', queryType: 'TYPE', typeCodes: 'DEFAULT_EXPERIMENT,MATERIALS' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -365,7 +362,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'SampleType', queryType: 'SEMANTIC', predicateAccessionId: 'is_a', descriptorAccessionId: 'assay' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -380,7 +377,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'SampleType', queryType: 'ATTRIBUTE', attribute: 'CODE', attributeValue: 'EXPERIMENTAL_STEP' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -389,7 +386,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'SampleType', queryType: 'ATTRIBUTE', attribute: 'CODE', attributeValue: 'UNKNOWN' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -398,7 +395,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
     @options = { entityType: 'SampleType', queryType: 'ATTRIBUTE', attribute: 'CODE', attributeValue: 'EXPERIMENTAL_STEP,UNKNOWN' }
 
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
     result = instance.query(@options)
 
     # puts result
@@ -409,7 +406,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
   def test_checking_sample_with_parent_and_children
     local_setup
-    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    instance = ApplicationServerQuery.new(@as_endpoint, @token, true)
 
     @options[:entityType] = 'Sample'
     @options[:queryType] = 'ATTRIBUTE'

data/test/authentication_test.rb

@@ -15,14 +15,14 @@ class AuthenticationTest < Test::Unit::TestCase
   end
 
   def test_successful_authentication
-    au = Authentication.new(@username, @password, @as_endpoint)
+    au = Authentication.new(@username, @password, @as_endpoint, true)
     session_token = au.login
     assert_not_nil session_token['token']
   end
 
   def test_failed_authentication
     invalid_password = 'blabla'
-    au = Authentication.new(@username, invalid_password, @as_endpoint)
+    au = Authentication.new(@username, invalid_password, @as_endpoint, true)
     assert_raise OpenbisQueryException do
       au.login
     end

data/test/data_store_download_test.rb

@@ -13,14 +13,14 @@ class DataStoreDownloadTest < Test::Unit::TestCase
     @as_endpoint = 'https://openbis-api.fair-dom.org/openbis/openbis'
     username = 'apiuser'
     password = 'apiuser'
-    @token = Authentication.new(username, password, @as_endpoint).login['token']
+    @token = Authentication.new(username, password, @as_endpoint, true).login['token']
 
     @dest_folder = File.dirname(__FILE__) + '/tmp/'
     FileUtils.mkdir_p @dest_folder unless File.exist?(@dest_folder)
   end
 
   def test_download_file
-    instance = DataStoreDownload.new(@dss_endpoint, @token)
+    instance = DataStoreDownload.new(@dss_endpoint, @token, true)
     dest = @dest_folder + 'utf8.txt'
     options = { downloadType: 'file', permID: '20160210130359377-22', source: 'original/utf8.txt', dest: dest }
     FileUtils.remove_file(dest) if File.exist?(dest)
@@ -29,7 +29,7 @@ class DataStoreDownloadTest < Test::Unit::TestCase
   end
 
   def test_download_file_with_space_in_name
-    instance = DataStoreDownload.new(@dss_endpoint, @token)
+    instance = DataStoreDownload.new(@dss_endpoint, @token, true)
     dest = @dest_folder + 'Genes List Nature Paper Test.docx'
     options = { downloadType: 'file', permID: '20160322172551664-35', source: 'original/Genes List Nature Paper Test.docx', dest: dest }
     FileUtils.remove_file(dest) if File.exist?(dest)
@@ -38,7 +38,7 @@ class DataStoreDownloadTest < Test::Unit::TestCase
   end
 
   def test_download_folder
-    instance = DataStoreDownload.new(@dss_endpoint, @token)
+    instance = DataStoreDownload.new(@dss_endpoint, @token, true)
     source = 'original/DEFAULT'
     dest = @dest_folder
     options = { downloadType: 'folder', permID: '20160215111736723-31', source: source, dest: dest }
@@ -50,7 +50,7 @@ class DataStoreDownloadTest < Test::Unit::TestCase
   end
 
   def test_download_dataset_files
-    instance = DataStoreDownload.new(@dss_endpoint, @token)
+    instance = DataStoreDownload.new(@dss_endpoint, @token, true)
     source = 'original'
     dest = @dest_folder
     options = { downloadType: 'dataset', permID: '20151217153943290-5', source: source, dest: dest }

data/test/data_store_query_test.rb

@@ -13,19 +13,19 @@ class DataStoreQueryTest < Test::Unit::TestCase
     @as_endpoint = 'https://openbis-api.fair-dom.org/openbis/openbis'
     username = 'apiuser'
     password = 'apiuser'
-    @token = Authentication.new(username, password, @as_endpoint).login['token']
+    @token = Authentication.new(username, password, @as_endpoint, true).login['token']
 
     @options = { entityType: 'DataSetFile', queryType: 'PROPERTY', property: 'SEEK_DATAFILE_ID', propertyValue: 'DataFile_1' }
   end
 
   def test_query
-    instance = DataStoreQuery.new(@dss_endpoint, @token)
+    instance = DataStoreQuery.new(@dss_endpoint, @token, true)
     result = instance.query(@options)
     assert !result['datasetfiles'].empty?
   end
 
   def test_query_permid_attribute
-    instance = DataStoreQuery.new(@dss_endpoint, @token)
+    instance = DataStoreQuery.new(@dss_endpoint, @token, true)
     @options[:queryType] = 'ATTRIBUTE'
     @options[:attribute] = 'DataSetPermID'
     @options[:attributeValue] = '20151217153943290-5'
@@ -35,7 +35,7 @@ class DataStoreQueryTest < Test::Unit::TestCase
   end
 
   def test_query_multiple_permid_attribute_values
-    instance = DataStoreQuery.new(@dss_endpoint, @token)
+    instance = DataStoreQuery.new(@dss_endpoint, @token, true)
     @options[:queryType] = 'ATTRIBUTE'
     @options[:attribute] = 'DataSetPermID'
     @options[:attributeValue] = '20151217153943290-5,20160210130359377-22'
@@ -44,7 +44,7 @@ class DataStoreQueryTest < Test::Unit::TestCase
   end
 
   def test_query_all_permid
-    instance = DataStoreQuery.new(@dss_endpoint, @token)
+    instance = DataStoreQuery.new(@dss_endpoint, @token, true)
     @options[:queryType] = 'ATTRIBUTE'
     @options[:attribute] = 'DataSetPermID'
     @options[:attributeValue] = ''
@@ -53,7 +53,7 @@ class DataStoreQueryTest < Test::Unit::TestCase
   end
 
   def test_query_no_result
-    instance = DataStoreQuery.new(@dss_endpoint, @token)
+    instance = DataStoreQuery.new(@dss_endpoint, @token, true)
     @options[:propertyValue] = 'Some_value'
     result = instance.query(@options)
     assert result.empty?

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: openseek-api
 version: !ruby/object:Gem::Version
-  version: 0.17.4
+  version: '0.18'
 platform: ruby
 authors:
 - Stuart Owen
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-28 00:00:00.000000000 Z
+date: 2022-02-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: terrapin
@@ -119,7 +119,7 @@ files:
 - jars/lib/jackson-databind-2.9.2.jar
 - jars/lib/json-simple-1.1.1.jar
 - jars/lib/openBIS-API-V3-batteries-included-20.10.1-r1615554298.jar
-- jars/openseek-api-0.18.jar
+- jars/openseek-api-0.19.jar
 - lib/fairdom/openbis_api/application_server_query.rb
 - lib/fairdom/openbis_api/authentication.rb
 - lib/fairdom/openbis_api/data_store_download.rb