openseek-api 0.11.1 → 0.17.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 47fef9b0bb2f18aaf48ea82848138030f8682dae
-  data.tar.gz: bd03b076759ff1af113ef8406ceb8cf9d8eaddaf
+  metadata.gz: 2b7f35b7cf469adc2213897aa6c7773442f7f1fd
+  data.tar.gz: 66131aa714fe2b3b75df7996fe1d3d587b1438b2
 SHA512:
-  metadata.gz: 8f2c7092c5a27d3618a6efcf987c36ebb4cde9f94dbcd813fcfa44f172349650319e14d29c78007bd61083aef54591030de3cceac954453300dada1eaf59f92e
-  data.tar.gz: eff1438b2718996b7dde34d6c223d82f5355a5cfdc2b370e94eb09dfd794704b332aa4f8790284f235fb496402cb9746ab827243087647c7eb7f0f0801e84248
+  metadata.gz: 9d29d059d8c169583e4f6bcf4a12391d0c0ccc1319a9df54a130e7a066d8a1d7e8425db9722c42d9a1c4d9200a7cb8b3d8e83a48c4e8d3b1962f6def12529b5f
+  data.tar.gz: 2467f43d78a874b3e7277e77444cf485b0444c5a4654fa428241d716a2a59a4e37c647ba6cb004ef932ecca18ecb5febde004c8d9ab915d94d32f61c20a4855a

data/.ruby-version

@@ -1 +1 @@
-ruby-2.2.8
+ruby-2.2.7

data/Gemfile.lock

@@ -1,8 +1,8 @@
 PATH
   remote: .
   specs:
-    openseek-api (0.11.1)
-      terrapin (~> 0.6)
+    openseek-api (0.17.1)
+      terrapin
 
 GEM
   remote: https://rubygems.org/
@@ -107,4 +107,4 @@ DEPENDENCIES
   test-unit
 
 BUNDLED WITH
-   1.16.1
+   1.15.4

data/lib/fairdom/openbis_api/versions.rb

@@ -1,6 +1,6 @@
 module Fairdom
   module OpenbisApi
-    VERSION = '0.11.1'.freeze
-    JAR_VERSION = '0.11'.freeze
+    VERSION = '0.17.1'.freeze
+    JAR_VERSION = '0.17'.freeze
   end
 end

data/openseek-api-gem.gemspec

@@ -5,7 +5,7 @@ require 'fairdom/openbis_api/versions'
 Gem::Specification.new do |spec|
   spec.name        = 'openseek-api'
   spec.version     = Fairdom::OpenbisApi::VERSION
-  spec.authors     = ['Stuart Owen', 'Quyen Nguyen']
+  spec.authors     = ['Stuart Owen', 'Quyen Nguyen', 'Tomasz Zielinski']
   spec.email       = ['thucquyendn@gmail.com']
   spec.homepage    = 'https://github.com/fairdom/openseek-api-gem'
   spec.summary     = 'ruby gem to talk to openbis-api java libaries, for use within SEEK4Science'
@@ -17,7 +17,7 @@ Gem::Specification.new do |spec|
   spec.require_paths = ['lib']
 
   # runtime dependencies
-  spec.add_dependency('terrapin', ['~> 0.6'])
+  spec.add_dependency('terrapin', ['>= 0'])
 
   # development dependencies
   spec.add_development_dependency('coveralls', ['>= 0'])

data/test/application_query_test.rb

@@ -10,11 +10,21 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
 
   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']
 
-    @options = { entityType: 'Experiment', queryType: 'PROPERTY', property: 'SEEK_STUDY_ID', propertyValue: 'Study_1' }
+    @options = { entityType: 'Experiment', queryType: 'PROPERTY', property: 'NAME', propertyValue: 'Low light diurnal' }
+  end
+
+  def local_setup
+    @as_endpoint = 'https://127.0.0.1:8443/openbis/openbis'
+    username = 'seek'
+    password = 'seek'
+    @token = Authentication.new(username, password, @as_endpoint).login['token']
   end
 
   def test_query_property
@@ -30,24 +40,25 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
     result = instance.query(@options)
     spaces = result['spaces']
     refute spaces.empty?
-    assert_equal 2, spaces.count
-    space = spaces[0]
-    assert_equal 'API-SPACE', space['code']
-    assert_equal 'use for testing openbis api integration', space['description'].strip
+    assert_equal 7, spaces.count
+     space = spaces[0]
+    # assert_equal 'API-SPACE', space['code']
+    # assert_equal 'use for testing openbis api integration', space['description'].strip
     experiments = space['experiments']
-    assert_equal 1, experiments.size
-    assert_equal ['20151216143716562-2'], experiments
+    assert_equal 0, experiments.size
+    # assert_equal ['20151216143716562-2'], experiments
 
     projects = space['projects']
-    assert_equal ['20151216135152196-1'], projects
+    assert_equal 0, projects.size
+    # assert_equal ['20151216135152196-1'], projects
 
     datasets = space['datasets']
-    assert_equal 8, datasets.size
-    assert_includes datasets, '20160210130359377-22'
+    assert_equal 0, datasets.size
+    #assert_includes datasets, '20160210130359377-22'
 
-    space = spaces[1]
-    assert_equal 'DEFAULT', space['code']
-    assert_nil space['description']
+    # space = spaces[1]
+    #assert_equal 'DEFAULT', space['code']
+    # assert_nil space['description']
   end
 
   def test_query_property_no_result
@@ -84,7 +95,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
     instance = ApplicationServerQuery.new(@as_endpoint, @token)
     @options[:queryType] = 'ATTRIBUTE'
     @options[:attribute] = 'permId'
-    @options[:attributeValue] = '20151216143716562-2'
+    @options[:attributeValue] = '20180418141729157-47'
     result = instance.query(@options)
     experiments = result['experiments']
     refute experiments.empty?
@@ -94,7 +105,7 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
     instance = ApplicationServerQuery.new(@as_endpoint, @token)
     @options[:queryType] = 'ATTRIBUTE'
     @options[:attribute] = 'permId'
-    @options[:attributeValue] = '20151216112932823-1,20151216143716562-2'
+    @options[:attributeValue] = '20180424181519696-54,20180418141729157-47'
     result = instance.query(@options)
     experiments = result['experiments']
     refute experiments.empty?
@@ -108,4 +119,305 @@ class ApplicationServerQueryTest < Test::Unit::TestCase
     result = instance.query(@options)
     refute result['experiments'].empty?
   end
+
+  def test_query_for_dataset_gives_rich_metadata
+    @options = { entityType: 'DataSet', queryType: 'ATTRIBUTE', attribute: 'PermID', attributeValue: '20180424182903704-59' }
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    #puts result
+
+
+    datasets = result['datasets']
+    assert_equal 1, datasets.size
+
+    dataset = datasets[0]
+    assert_equal '20180424182903704-59', dataset['permId']
+    # assert_equal 'apiuser', dataset['registerator']
+
+    params = dataset['properties']
+    assert_not_nil params
+    assert_equal 'TOMEK test set', params['NAME']
+
+  end
+
+  def test_query_for_dataset_can_retrive_sampleonly_dataset
+    puts 'no such test data'
+    return
+    @options = { entityType: 'DataSet', queryType: 'ATTRIBUTE', attribute: 'PermID', attributeValue: '20180418150033700-51' }
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    puts result
+
+
+    datasets = result['datasets']
+    assert_equal 1, datasets.size
+
+    dataset = datasets[0]
+    assert_equal '20180418150033700-51', dataset['permId']
+    assert_equal 'seek', dataset['registerator']
+
+    assert_nil dataset['experiment']
+    assert_equal '20171002172111346-37', dataset['sample']
+    params = dataset['properties']
+    assert_not_nil params
+    assert_equal 'DS One', params['NAME']
+
+  end
+
+
+  def test_all_datasets_query
+
+    @options = { entityType: 'DataSet', queryType: 'ALL' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+
+    datasets = result['datasets']
+    assert_equal 6, datasets.size
+  end
+
+  def test_all_samples_query
+
+    @options = { entityType: 'Sample', queryType: 'ALL' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+
+    samples = result['samples']
+    assert_equal 16, samples.size
+  end
+
+  def test_all_spaces_query
+
+    @options = { entityType: 'Space', queryType: 'ALL' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+
+    spaces = result['spaces']
+    assert_equal 7, spaces.size
+  end
+
+  def test_all_experiments_query
+    local_setup
+    @options = { entityType: 'Experiment', queryType: 'ALL' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    puts result.to_json
+
+    experiments = result['experiments']
+    assert_equal 24, experiments.size
+  end
+
+  def test_all_experimentstypes_query
+      local_setup
+      @options = { entityType: 'ExperimentType', queryType: 'ALL' }
+
+      instance = ApplicationServerQuery.new(@as_endpoint, @token)
+      result = instance.query(@options)
+
+      puts result.to_json
+
+      types = result['experimenttypes']
+      assert_equal 6, types.size
+  end
+
+  def test_all_sampletypes_query
+
+    @options = { entityType: 'SampleType', queryType: 'ALL' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+
+    types = result['sampletypes']
+    assert_equal 25, types.size
+  end
+
+  def test_all_datasetstypes_query
+
+    @options = { entityType: 'DataSetType', queryType: 'ALL' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+
+    types = result['datasettypes']
+    assert_equal 6, types.size
+  end
+
+
+
+
+  def test_samples_with_type_query
+
+    @options = { entityType: 'Sample', queryType: 'TYPE', typeCode: 'EXPERIMENTAL_STEP' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+
+    samples = result['samples']
+    assert_equal 8, samples.size
+
+  end
+
+  def test_datasets_with_type_query
+
+    @options = { entityType: 'DataSet', queryType: 'TYPE', typeCode: 'RAW_DATA' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+
+    sets = result['datasets']
+    assert_equal 4, sets.size
+
+  end
+
+
+
+  def test_local_setup
+    @token = nil
+
+    local_setup
+    assert_not_nil @token
+  end
+
+
+
+
+
+  def test_experimentstypes_with_code_query
+
+    local_setup
+    @options = { entityType: 'ExperimentType', queryType: "ATTRIBUTE", :attribute=>"CODE", :attributeValue=>"DEFAULT_EXPERIMENT" }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    puts result.to_json
+
+    types = result['experimenttypes']
+    assert_equal 1, types.size
+  end
+
+
+  def test_experiments_by_permi_id_query
+    local_setup
+
+    @options = { entityType: 'Experiment', queryType: 'ATTRIBUTE',
+              attribute: 'PermID', attributeValue: '20180424181519696-54'}
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    puts result.to_json
+
+    exps = result['experiments']
+    assert_equal 1, exps.size
+
+
+  end
+
+
+  def test_experiments_with_type_query
+    local_setup
+
+    @options = { entityType: 'Experiment', queryType: 'TYPE', typeCode: 'DEFAULT_EXPERIMENT' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    puts result.to_json
+
+    exps = result['experiments']
+    assert_equal 3, exps.size
+
+    @options = { entityType: 'Experiment', queryType: 'TYPE', typeCodes: 'DEFAULT_EXPERIMENT,MATERIALS' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+
+    exps = result['experiments']
+    assert_equal 15, exps.size
+
+  end
+
+  def test_type_by_semantic
+    local_setup
+
+    @options = { entityType: 'SampleType', queryType: 'SEMANTIC', predicateAccessionId: 'is_a', descriptorAccessionId: 'assay' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+
+    sampleTypes = result['sampletypes']
+    assert_equal 2, sampleTypes.size
+
+  end
+
+  def test_type_by_codes
+    local_setup
+
+    @options = { entityType: 'SampleType', queryType: 'ATTRIBUTE', attribute: 'CODE', attributeValue: 'EXPERIMENTAL_STEP' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+    sampleTypes = result['sampletypes']
+    assert_equal 1, sampleTypes.size
+
+    @options = { entityType: 'SampleType', queryType: 'ATTRIBUTE', attribute: 'CODE', attributeValue: 'UNKNOWN' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+    sampleTypes = result['sampletypes']
+    assert_equal 1, sampleTypes.size
+
+    @options = { entityType: 'SampleType', queryType: 'ATTRIBUTE', attribute: 'CODE', attributeValue: 'EXPERIMENTAL_STEP,UNKNOWN' }
+
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+    result = instance.query(@options)
+
+    # puts result
+    sampleTypes = result['sampletypes']
+    assert_equal 2, sampleTypes.size
+
+  end
+
+  def test_checking_sample_with_parent_and_children
+    local_setup
+    instance = ApplicationServerQuery.new(@as_endpoint, @token)
+
+    @options[:entityType] = 'Sample'
+    @options[:queryType] = 'ATTRIBUTE'
+    @options[:attribute] = 'PermID'
+    @options[:attributeValue] = '20180418145851124-48'
+    result = instance.query(@options)
+
+    assert_equal 1,result['samples'].size
+    puts result['samples'][0]
+  end
 end

data/test/data_store_query_test.rb

@@ -30,6 +30,7 @@ class DataStoreQueryTest < Test::Unit::TestCase
     @options[:attribute] = 'DataSetPermID'
     @options[:attributeValue] = '20151217153943290-5'
     result = instance.query(@options)
+    #puts result
     assert !result['datasetfiles'].empty?
   end
 

metadata

@@ -1,30 +1,31 @@
 --- !ruby/object:Gem::Specification
 name: openseek-api
 version: !ruby/object:Gem::Version
-  version: 0.11.1
+  version: 0.17.1
 platform: ruby
 authors:
 - Stuart Owen
 - Quyen Nguyen
+- Tomasz Zielinski
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-04-23 00:00:00.000000000 Z
+date: 2018-06-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: terrapin
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
@@ -113,49 +114,13 @@ files:
 - LICENSE
 - README.md
 - Rakefile
-- jars/lib/aopalliance.jar
-- jars/lib/aspectjweaver.jar
-- jars/lib/cglib-nodep.jar
-- jars/lib/cisd-args4j.jar
-- jars/lib/commons-codec.jar
-- jars/lib/commons-io.jar
-- jars/lib/commons-lang.jar
-- jars/lib/commons-logging.jar
-- jars/lib/dom4j-1.6.1.jar
-- jars/lib/dss_upload_gui.jar
-- jars/lib/geronimo-stax-api_1.0_spec-1.0.jar
-- jars/lib/guava-11.0.2.jar
-- jars/lib/httpclient.jar
-- jars/lib/httpcore.jar
-- jars/lib/ij.jar
-- jars/lib/image-viewer.jar
-- jars/lib/jackson-annotations-2.8.5.jar
-- jars/lib/jackson-core-2.8.5.jar
-- jars/lib/jackson-databind-2.8.5.jar
-- jars/lib/javassist-3.16.1-GA.jar
-- jars/lib/jline.jar
-- jars/lib/json-simple-1.1.jar
-- jars/lib/jsr305-1.3.9.jar
-- jars/lib/jython.jar
-- jars/lib/log4j.jar
-- jars/lib/openbis_api-16.05.2-r37019.jar
-- jars/lib/poi-ooxml-schemas.jar
-- jars/lib/poi-ooxml.jar
-- jars/lib/poi.jar
-- jars/lib/reflections-0.9.9-RC1.jar
-- jars/lib/sis-base.jar
-- jars/lib/spring-aop.jar
-- jars/lib/spring-beans.jar
-- jars/lib/spring-context.jar
-- jars/lib/spring-core.jar
-- jars/lib/spring-expression.jar
-- jars/lib/spring-web.jar
-- jars/lib/spring-webmvc.jar
-- jars/lib/stax-api.jar
-- jars/lib/stream-supporting-httpinvoker.jar
-- jars/lib/xml-apis-1.0.b2.jar
-- jars/lib/xmlbeans-2.3.0.jar
-- jars/openseek-api-0.11.jar
+- grep
+- jars/lib/jackson-annotations-2.9.2.jar
+- jars/lib/jackson-core-2.9.2.jar
+- jars/lib/jackson-databind-2.9.2.jar
+- jars/lib/json-simple-1.1.1.jar
+- jars/lib/openBIS-API-V3-batteries-included-16.05.7-r1522065804.jar
+- jars/openseek-api-0.17.jar
 - lib/fairdom/openbis_api/application_server_query.rb
 - lib/fairdom/openbis_api/authentication.rb
 - lib/fairdom/openbis_api/data_store_download.rb
@@ -189,7 +154,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.13
+rubygems_version: 2.6.11
 signing_key: 
 specification_version: 4
 summary: ruby gem to talk to openbis-api java libaries, for use within SEEK4Science