intermine 1.02.00 → 1.03.00

data/lib/intermine/query.rb

@@ -543,6 +543,10 @@ module InterMine::PathQuery
             end
         end
 
+        def sequences(range)
+            return Results::SeqReader.new(@service.root, clone, range)
+        end
+
         # Return all result record objects returned by running this query.
         def all
             return self.results

data/lib/intermine/results.rb

@@ -390,6 +390,32 @@ module InterMine::Results
 
     end
 
+    class JsonReader < ResultsReader
+
+        include Enumerable
+
+        def each
+            processor = lambda { |line|
+                x = line.chomp.chomp(",")
+                x.empty? ? nil : JSON.parse(x)
+            }
+            read_result_set(params("json"), processor) { |x| yield x }
+        end
+    end
+
+    class SeqReader < JsonReader
+
+        def initialize(base, query, range = {})
+            super(base + Service::SEQUENCE_PATH, query, 0, nil)
+            @range = range
+        end
+
+        def params(format = "json")
+            @query.params.merge(@range)
+        end
+
+    end
+
     class SummaryReader < ResultsReader
 
         include Enumerable

data/lib/intermine/service.rb

@@ -95,6 +95,7 @@ module InterMine
         MODEL_PATH = "/model/json"
         TEMPLATES_PATH = "/templates"
         QUERY_RESULTS_PATH = "/query/results"
+        SEQUENCE_PATH = "/sequence"
         QUERY_TO_LIST_PATH = "/query/tolist/json"
         QUERY_APPEND_PATH = "/query/append/tolist/json"
         TEMPLATE_RESULTS_PATH = "/template/results"

data/lib/intermine/version.rb

@@ -3,6 +3,7 @@ module Intermine
     # Webservice Client Version number
     #
     # Changes:
+    #   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
     #   1.01.00 - Test compatibility with 1.8.7, 1.9.2, 2.0.0-rc1
@@ -20,5 +21,5 @@ module Intermine
     #   0.98.09 - Major changes to results - now with thorough-going Enumerable support
     #   0.98.08 - Added column summary support
     #
-    VERSION = "1.02.00"
+    VERSION = "1.03.00"
 end

data/test/live_results.rb

@@ -136,6 +136,15 @@ class LiveResultsTest < Test::Unit::TestCase
         trideps = @q.summaries("department.name", *@summary_args).select {|s| s["count"] == @dep_size}
         assert_equal(@exp_trideps, trideps.length)
     end
+
+    def testSubSequences
+       q = @service.query("Employee").select(:name).where(:name => "D*")
+       c = q.count
+       seqs = q.sequences(:start => 1, :end => 5).map {|s| s["seq"]}
+       assert_equal(c, seqs.size)
+       assert(seqs.all? {|s| s.size == 4})
+    end
+
 end
 
 class LiveTemplateResultsTest < LiveResultsTest 

metadata

@@ -1,130 +1,185 @@
---- !ruby/object:Gem::Specification
+--- !ruby/object:Gem::Specification 
 name: intermine
-version: !ruby/object:Gem::Version
-  version: 1.02.00
+version: !ruby/object:Gem::Version 
   prerelease: 
+  version: 1.03.00
 platform: ruby
-authors:
-- Alex Kalderimis
+authors: 
+  - Alex Kalderimis
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-27 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: json
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-description: ! "= Webservice Client Library for InterMine Data-Warehouses\n\nThis
-  library provides an interface to the InterMine webservices\nAPI. It makes construction
-  and execution of queries more \nstraightforward, safe and convenient, and allows
-  for results\nto be used directly in Ruby code. As well as traditional row based\naccess,
-  the library provides an object-orientated record result\nformat (similar to ActiveRecords),
-  and allows for fast, memory \nefficient iteration of result sets.\n\n== Example\n\nGet
-  all protein domains associated with a set of genes and print their names:\n\n    require
-  \"intermine/service\"\n\n    Service.new(\"www.flymine.org/query\").\n        new_query(\"Pathway\")\n
-  \       select(:name).\n        where(\"genes.symbol\" => [\"zen\", \"hox\", \"h\",
-  \"bib\"]).\n        each_row { |row| puts row[:name]}\n\n== Who is this for?\n\nInterMine
-  data warehouses are typically constructed to hold\nBiological data, and as this
-  library facilitates programmatic\naccess to these data, this install is primarily
-  aimed at \nbioinformaticians. In particular, users of the following services\nmay
-  find it especially useful:\n * FlyMine (http://www.flymine.org/query)\n * YeastMine
-  (http://yeastmine.yeastgenome.org/yeastmine)\n * RatMine (http://ratmine.mcw.edu/ratmine)\n
-  * modMine (http://intermine.modencode.org/release-23)\n * metabolicMine (http://www.metabolicmine.org/beta)\n\n==
-  How to use this library:\n\nWe have tried to construct an interface to this library
-  that\ndoes not require you to learn an entirely new set of concepts. \nAs such,
-  as well as the underlying methods that are common\nto all libraries, there is an
-  additional set of aliases and sugar\nmethods that emulate the DSL style of SQL:\n\n===
-  SQL style\n\n  service = Service.new(\"www.flymine.org/query\")\n  service.model.\n
-  \    table(\"Gene\").\n     select(\"*\", \"pathways.*\").\n     where(:symbol =>
-  \"zen\").\n     order_by(:symbol).\n     outerjoin(:pathways).\n     each_row do
-  |r|\n       puts r\n     end\n\n=== Common InterMine interface\n\n  service = Service.new(\"www.flymine.org/query\")\n
-  \ query = service.new_query(\"Gene\")\n  query.add_views(\"*\", \"pathways.*\")\n
-  \ query.add_constraint(\"symbol\", \"=\", \"zen\")\n  query.add_sort_order(:symbol)\n
-  \ query.add_join(:pathways)\n  query.each_row do |r|\n    puts r\n  end\n\nFor more
-  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"
-email:
-- dev@intermine.org
+
+date: 2013-07-04 00:00:00 Z
+dependencies: 
+  - !ruby/object:Gem::Dependency 
+    name: json
+    version_requirements: &id001 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ">="
+          - !ruby/object:Gem::Version 
+            version: "0"
+    requirement: *id001
+    prerelease: false
+    type: :runtime
+description: |
+  = Webservice Client Library for InterMine Data-Warehouses
+  
+  This library provides an interface to the InterMine webservices
+  API. It makes construction and execution of queries more 
+  straightforward, safe and convenient, and allows for results
+  to be used directly in Ruby code. As well as traditional row based
+  access, the library provides an object-orientated record result
+  format (similar to ActiveRecords), and allows for fast, memory 
+  efficient iteration of result sets.
+  
+  == Example
+  
+  Get all protein domains associated with a set of genes and print their names:
+  
+      require "intermine/service"
+  
+      Service.new("www.flymine.org/query").
+          new_query("Pathway")
+          select(:name).
+          where("genes.symbol" => ["zen", "hox", "h", "bib"]).
+          each_row { |row| puts row[:name]}
+  
+  == Who is this for?
+  
+  InterMine data warehouses are typically constructed to hold
+  Biological data, and as this library facilitates programmatic
+  access to these data, this install is primarily aimed at 
+  bioinformaticians. In particular, users of the following services
+  may find it especially useful:
+   * FlyMine (http://www.flymine.org/query)
+   * YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
+   * RatMine (http://ratmine.mcw.edu/ratmine)
+   * modMine (http://intermine.modencode.org/release-23)
+   * metabolicMine (http://www.metabolicmine.org/beta)
+  
+  == How to use this library:
+  
+  We have tried to construct an interface to this library that
+  does not require you to learn an entirely new set of concepts. 
+  As such, as well as the underlying methods that are common
+  to all libraries, there is an additional set of aliases and sugar
+  methods that emulate the DSL style of SQL:
+  
+  === SQL style
+  
+    service = Service.new("www.flymine.org/query")
+    service.model.
+       table("Gene").
+       select("*", "pathways.*").
+       where(:symbol => "zen").
+       order_by(:symbol).
+       outerjoin(:pathways).
+       each_row do |r|
+         puts r
+       end
+  
+  === Common InterMine interface
+  
+    service = Service.new("www.flymine.org/query")
+    query = service.new_query("Gene")
+    query.add_views("*", "pathways.*")
+    query.add_constraint("symbol", "=", "zen")
+    query.add_sort_order(:symbol)
+    query.add_join(:pathways)
+    query.each_row do |r|
+      puts r
+    end
+  
+  For more details, see the accompanying documentation and the unit tests
+  for interface examples. Further documentation is available at www.intermine.org.
+  
+  == Support
+  
+  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
+
+email: 
+  - dev@intermine.org
 executables: []
+
 extensions: []
+
 extra_rdoc_files: []
-files:
-- lib/intermine/lists.rb
-- lib/intermine/model.rb
-- lib/intermine/query.rb
-- lib/intermine/results.rb
-- lib/intermine/service.rb
-- lib/intermine/version.rb
-- test/data/lists.json
-- test/data/model.json
-- test/data/resultobjs.json
-- test/data/resultrow.json
-- test/data/resultset.json
-- test/data/testmodel_model.xml
-- test/live_results.rb
-- test/live_summary_test.rb
-- test/live_test.rb
-- test/test.rb
-- test/test_helper.rb
-- test/test_lists.rb
-- test/test_model.rb
-- test/test_query.rb
-- test/test_result_row.rb
-- test/test_results.rb
-- test/test_service.rb
-- test/test_sugar.rb
-- test/unit_tests.rb
-- LICENCE
-- Gemfile
-- MANIFEST
-- README.rdoc
-- Rakefile
-- contact_header.rdoc
+
+files: 
+  - lib/intermine/lists.rb
+  - lib/intermine/model.rb
+  - lib/intermine/query.rb
+  - lib/intermine/results.rb
+  - lib/intermine/service.rb
+  - lib/intermine/version.rb
+  - test/data/lists.json
+  - test/data/model.json
+  - test/data/resultobjs.json
+  - test/data/resultrow.json
+  - test/data/resultset.json
+  - test/data/testmodel_model.xml
+  - test/live_results.rb
+  - test/live_summary_test.rb
+  - test/live_test.rb
+  - test/test.rb
+  - test/test_helper.rb
+  - test/test_lists.rb
+  - test/test_model.rb
+  - test/test_query.rb
+  - test/test_result_row.rb
+  - test/test_results.rb
+  - 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
+licenses: 
+  - LGPL
 post_install_message: 
-rdoc_options:
-- --title
-- InterMine Webservice Client
-- --main
-- README.rdoc
-- --line-numbers
-require_paths:
-- lib
-required_ruby_version: !ruby/object:Gem::Requirement
+rdoc_options: 
+  - --title
+  - InterMine Webservice Client
+  - --main
+  - README.rdoc
+  - --line-numbers
+require_paths: 
+  - lib
+required_ruby_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
-required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 2
+        segments: 
+          - 0
+        version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
+  requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 2
+        segments: 
+          - 0
+        version: "0"
 requirements: []
+
 rubyforge_project: intermine
-rubygems_version: 1.8.23
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: Webservice Client Library for InterMine Data-Warehouses
-test_files:
-- test/unit_tests.rb
+test_files: 
+  - test/unit_tests.rb