intermine 1.04.00 → 1.05.00

checksums.yaml

@@ -1,7 +1,7 @@
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+SHA1:
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+  data.tar.gz: 54bb79ac11337ea032fac6d80d048eeee2bc3f9b
+SHA512:
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+  data.tar.gz: be4e1a916016776010c7bbd7610db539b0e00fdf8bfc548b80ee9c1a52284a40c92eefc3e8ce461920324f4725aff9211b68a945a8c3da3b00be4a814a544429

data/Gemfile.lock

@@ -0,0 +1,19 @@
+PATH
+  remote: .
+  specs:
+    intermine (1.05.00)
+      json
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    json (2.0.2)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  intermine!
+
+BUNDLED WITH
+   1.13.1

data/README.rdoc

@@ -75,5 +75,5 @@ Support is available on our development mailing list: dev@intermine.org
 
 == License
 
-This code is Open Source under the LGPL. Source code for all InterMine code
-can be checked out from svn://subversion.flymine.org/flymine
+This code is Open Source under the LGPL. Source code for this gem
+can be checked out from https://github.com/intermine/intermine-ws-ruby

data/lib/intermine/lists.rb

@@ -93,6 +93,11 @@ module InterMine::Lists
             details.each {|k,v| instance_variable_set('@' + k, v)}
             @unmatched_identifiers = []
             @tags ||= []
+            @uri = URI.parse(@manager.service.root)
+            @http = Net::HTTP.new(@uri.host, @uri.port)
+            if @uri.scheme == 'https'
+                @http.use_ssl = true
+            end
         end
 
         # True if the list has no elements.
@@ -219,7 +224,9 @@ module InterMine::Lists
             return if (@name == new_name)
             uri = URI.parse(@manager.service.root + Service::LIST_RENAME_PATH)
             params = @manager.service.params.merge("oldname" => @name, "newname" => new_name)
-            res = Net::HTTP.post_form(uri, params)
+            res = @http.start() do |http|
+                Net::HTTP.post_form(uri, params)
+            end
             @manager.process_list_creation_response(res)
             @name = new_name
         end
@@ -334,7 +341,9 @@ module InterMine::Lists
             s = @manager.service
             params = s.params.merge(ENRICHMENT_DEFAULTS).merge(opts).merge(:widget => widget, :list => @name)
             uri = URI.parse(s.root + Service::LIST_ENRICHMENT_PATH)
-            res = Net::HTTP.post_form(uri, params)
+            res = @http.start() do |http|
+                Net::HTTP.post_form(uri, params)
+            end
             return case res
             when Net::HTTPSuccess
                 JSON.parse(res.body)["results"].map {|row| SymbolAcceptingHash[row] }
@@ -392,7 +401,9 @@ module InterMine::Lists
             q = (list.is_a?(List)) ? list.list_query : list
             params = q.params.merge(@manager.service.params).merge("listName" => @name)
             uri = URI.parse(q.list_append_uri)
-            res = Net::HTTP.post_form(uri, params)
+            res = @http.start() do |http|
+                Net::HTTP.post_form(uri, params)
+            end
             handle_response(res)
         end
 
@@ -420,7 +431,7 @@ module InterMine::Lists
             req.content_type = "text/plain"
             req.content_length = f.size
 
-            res = Net::HTTP.start(uri.host, uri.port) do |http|
+            res = @http.start() do |http|
                 http.request(req)
             end
             handle_response(res)
@@ -482,6 +493,11 @@ module InterMine::Lists
             @service = service
             @lists = {}
             @temporary_lists = []
+            @uri = URI.parse(@service.root)
+            @http = Net::HTTP.new(@uri.host, @uri.port)
+            if @uri.scheme == 'https'
+                @http.use_ssl = true
+            end
             do_at_exit(self)
         end
 
@@ -585,7 +601,7 @@ module InterMine::Lists
                 uri = URI.parse(@service.root + Service::LISTS_PATH)
                 params = {"name" => name}
                 req = Net::HTTP::Delete.new(uri.path + "?" + params_to_query_string(params))
-                res = Net::HTTP.start(uri.host, uri.port) do |http|
+                res = @http.start do |http|
                     http.request(req)
                 end
                 check_response_for_error(res)
@@ -630,7 +646,9 @@ module InterMine::Lists
             uri = URI.parse(@service.root + Service::LIST_SUBTRACTION_PATH)
             params = @service.params.merge("name" => name, "description" => description, "references" => ref_names.join(';'),
                                            "subtract" => del_names.join(';'), "tags" => tags.join(';'))
-            res = Net::HTTP.post_form(uri, params)
+            res = @http.start() do |http|
+                Net::HTTP.post_form(uri, params)
+            end
             return process_list_creation_response(res)
         end
 
@@ -654,7 +672,9 @@ module InterMine::Lists
         def add_tags(list, *tags)
             uri = URI.parse(@service.root + Service::LIST_TAG_PATH)
             params = @service.params.merge("name" => list.name, "tags" => tags.join(";"))
-            res = Net::HTTP.post_form(uri, params)
+            res = @http.start() do |http|
+                Net::HTTP.post_form(uri, params)
+            end
             check_response_for_error(res)
             return JSON.parse(res.body)["tags"]
         end
@@ -671,7 +691,7 @@ module InterMine::Lists
             )
             req_path = uri.path + "?" + params_to_query_string(params)
             req = Net::HTTP::Delete.new(req_path)
-            res = Net::HTTP.start(uri.host, uri.port) do |http|
+            res = @http.start() do |http|
                 http.request(req)
             end
             check_response_for_error(res)
@@ -685,9 +705,9 @@ module InterMine::Lists
                 "name" => list.name
             )
             req_path = uri.path + "?" + params_to_query_string(params)
-            res = Net::HTTP.start(uri.host, uri.port) {|http|
-                  http.get(req_path)
-            }
+            res = @http.start() do |http|
+                http.get(req_path)
+            end
             check_response_for_error(res)
             return JSON.parse(res.body)["tags"]
         end
@@ -747,7 +767,9 @@ module InterMine::Lists
                 "name" => name, "lists" => list_names.join(";"), 
                 "description" => description, "tags" => tags.join(';')
             )
-            res = Net::HTTP::post_form(uri, params)
+            res = @http.start() do |http|
+                Net::HTTP::post_form(uri, params)
+            end
             return process_list_creation_response(res)
         end
 
@@ -776,7 +798,9 @@ module InterMine::Lists
             }
             service_params = @service.params
             params = query.params.merge(list_params).merge(service_params)
-            return Net::HTTP.post_form(URI.parse(uri), params)
+            @http.start() do |http|
+                return Net::HTTP.post_form(URI.parse(uri), params)
+            end
         end
 
         # Routine for creating a List in a webservice from a list of Ids.
@@ -805,7 +829,7 @@ module InterMine::Lists
             req.content_type = "text/plain"
             req.content_length = f.size
 
-            res = Net::HTTP.start(uri.host, uri.port) do |http|
+            res = @http.start() do |http|
                 http.request(req)
             end
             f.close

data/lib/intermine/model.rb

@@ -518,35 +518,12 @@ module Metadata
 
                 klass = Module.new
                 fd_names = @fields.values.map { |x| x.name }
-                fds = @fields.values
                 attr_names = @fields.values.select { |x| x.is_a?(AttributeDescriptor)}.map {|x| x.name}
                 klass.class_eval do
                     include *supers
                     attr_reader *attr_names
                 end
 
-                klass.class_eval do
-
-                    define_method(:to_h) do
-                        ret = Hash.new
-                        fds.each do |fd|
-                            if fd.is_a?(AttributeDescriptor)
-                                ret.store(fd.name, send(fd.name))
-                            elsif fd.is_a?(CollectionDescriptor)
-                                ret.store(fd.name, send(fd.name).map {|v| v.to_h})
-                            else
-                                ret.store(fd.name, send(fd.name).to_h)
-                            end
-                        end
-                        ret.store("id", objectId)
-                        return ret
-                    end
-
-                    define_method(:to_json) do |*a|
-                        to_h.to_json(*a)
-                    end
-                end
-
                 @fields.values.each do |fd|
                     if fd.is_a?(CollectionDescriptor)
                         klass.class_eval do

data/lib/intermine/results.rb

@@ -233,12 +233,18 @@ module InterMine::Results
             @query = query
             @start = start
             @size = size
+            @http = Net::HTTP.new(@uri.host, @uri.port)
+            if @uri.scheme == 'https'
+                @http.use_ssl = true
+            end
         end
 
         # Run a request to get the size of the result set.
         def get_size
             query = params("jsoncount")
-            res = Net::HTTP.post_form(@uri, query)
+            res = @http.start() do |http|
+                Net::HTTP.post_form(@uri, query)
+            end
             case res
             when Net::HTTPSuccess
                 return check_result_set(res.body)["count"]
@@ -331,7 +337,7 @@ module InterMine::Results
         def each_line(data)
             req = Net::HTTP::Post.new(@uri.path)
             req.set_form_data(data)
-            Net::HTTP.new(@uri.host, @uri.port).start {|http|
+            @http.start {|http|
                 http.request(req) {|resp|
                     holdover = ""
                     resp.read_body {|chunk|

data/lib/intermine/service.rb

@@ -165,6 +165,9 @@ module InterMine
             @root_path = root_uri.path
 
             @http = Net::HTTP.new(root_uri.host, root_uri.port)
+            if root_uri.scheme == 'https'
+                @http.use_ssl = true
+            end
 
             v_path = @root + VERSION_PATH
             begin

data/lib/intermine/version.rb

@@ -3,7 +3,7 @@ module Intermine
     # Webservice Client Version number
     #
     # Changes:
-    #   1.04.00 - Added to_h and to_json methods for result objects
+    #   1.05.00 - Add support for HTTPS
     #   1.03.00 - Add support for indexed sequence service
     #   1.02.00 - Allow the lazy fetching to be optional
     #   1.01.01 - Improved lazy reference fetching
@@ -22,5 +22,5 @@ module Intermine
     #   0.98.09 - Major changes to results - now with thorough-going Enumerable support
     #   0.98.08 - Added column summary support
     #
-    VERSION = "1.04.00"
+    VERSION = "1.05.00"
 end

data/test/test_model.rb

@@ -1,6 +1,5 @@
 require File.dirname(__FILE__) + "/test_helper.rb"
 require "intermine/model"
-require "json"
 
 require "test/unit"
 
@@ -221,58 +220,6 @@ class TestModel < Test::Unit::TestCase
 
     end
 
-    def test_to_h
-
-        manager = @model.make_new("Manager", {
-            "name" => "David Brent",
-            "seniority" => 42,
-            "age" => 39,
-            "fullTime" => true,
-            "department" => {
-                "name" => "Sales",
-                "employees" => [
-                    { "name" => "Tom" },
-                    { "name" => "Dick" },
-                    { "name" => "Harry" }
-                ]
-            }
-        })
-
-        manager_h = manager.to_h
-
-        assert_equal(manager_h["name"], "David Brent")
-        assert_equal(manager_h["age"], 39)
-        assert_equal(manager_h["department"]["name"], "Sales")
-        assert_equal(manager_h["department"]["employees"][1]["name"], "Dick")
-        assert_equal(manager_h["department"]["employees"].size, 3)
-    end
-
-    def test_to_json
-
-        manager = @model.make_new("Manager", {
-            "name" => "David Brent",
-            "seniority" => 42,
-            "age" => 39,
-            "fullTime" => true,
-            "department" => {
-                "name" => "Sales",
-                "employees" => [
-                    { "name" => "Tom" },
-                    { "name" => "Dick" },
-                    { "name" => "Harry" }
-                ]
-            }
-        })
-
-        manager_h = JSON[manager.to_h.to_json]
-
-        assert_equal(manager_h["name"], "David Brent")
-        assert_equal(manager_h["age"], 39)
-        assert_equal(manager_h["department"]["name"], "Sales")
-        assert_equal(manager_h["department"]["employees"][1]["name"], "Dick")
-        assert_equal(manager_h["department"]["employees"].size, 3)
-    end
-
     def test_inheritance
 
         manager = @model.make_new("Manager", { "name" => "David Brent" })

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: intermine
 version: !ruby/object:Gem::Version
-  version: 1.04.00
+  version: 1.05.00
 platform: ruby
 authors:
 - Alex Kalderimis
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-08 00:00:00.000000000 Z
+date: 2017-05-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json
@@ -54,14 +54,21 @@ description: "= Webservice Client Library for InterMine Data-Warehouses\n\nThis
   details, see the accompanying documentation and the unit tests\nfor interface examples.
   Further documentation is available at www.intermine.org.\n\n== Support\n\nSupport
   is available on our development mailing list: dev@intermine.org\n\n== License\n\nThis
-  code is Open Source under the LGPL. Source code for all InterMine code\ncan be checked
-  out from svn://subversion.flymine.org/flymine\n"
+  code is Open Source under the LGPL. Source code for this gem\ncan be checked out
+  from https://github.com/intermine/intermine-ws-ruby\n"
 email:
 - dev@intermine.org
 executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- Gemfile
+- Gemfile.lock
+- LICENCE
+- MANIFEST
+- README.rdoc
+- Rakefile
+- contact_header.rdoc
 - lib/intermine/lists.rb
 - lib/intermine/model.rb
 - lib/intermine/query.rb
@@ -87,12 +94,6 @@ files:
 - test/test_service.rb
 - test/test_sugar.rb
 - test/unit_tests.rb
-- MANIFEST
-- LICENCE
-- Rakefile
-- README.rdoc
-- Gemfile
-- contact_header.rdoc
 homepage: http://www.intermine.org
 licenses:
 - LGPL
@@ -118,7 +119,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: intermine
-rubygems_version: 2.0.0.preview3.1
+rubygems_version: 2.5.2
 signing_key: 
 specification_version: 4
 summary: Webservice Client Library for InterMine Data-Warehouses