intermine 0.98.06 → 0.98.08

data/Rakefile

@@ -52,10 +52,17 @@ end
 
 Rake::TestTask.new(:live_tests) do |t|
     t.libs << "test"
-    t.test_files = FileList['test/live_test.rb']
+    t.test_files = FileList['test/live_test.rb'] << FileList['test/live_summary_test.rb']
     t.verbose = true
 end
 
+Rake::TestTask.new(:live_summary) do |t|
+    t.libs << "test"
+    t.test_files = FileList['test/live_summary_test.rb']
+    t.verbose = true
+end
+
+
 Rake::RDocTask.new do |t|
     t.title = 'InterMine Webservice Client Documentation'
     t.rdoc_files.include 'README.rdoc'

data/lib/intermine/model.rb

@@ -27,6 +27,10 @@ module Metadata
     #
     class Model
 
+        FLOAT_TYPES = ["Float", "Double", "float", "double"]
+        INT_TYPES = ["Integer", "int",  "long", "Long", "short", "Short"]
+        BOOL_TYPES = ["Boolean", "boolean"]
+        NUMERIC_TYPES = FLOAT_TYPES | INT_TYPES
 
         # The name of the model
         attr_reader :name
@@ -497,9 +501,9 @@ module Metadata
         #
         def to_module
             if @module.nil?
-                nums = ["Float", "Double", "float", "double"]
-                ints = ["Integer", "int"]
-                bools = ["Boolean", "boolean"]
+                nums = Model::FLOAT_TYPES
+                ints = Model::INT_TYPES
+                bools = Model::BOOL_TYPES
 
                 supers = @extends.map { |x| @model.get_cd(x).to_module }
 

data/lib/intermine/query.rb

@@ -276,6 +276,12 @@ module InterMine::PathQuery
         # URLs for internal consumption.
         attr_reader :list_upload_uri, :list_append_uri
 
+        # The number of rows to return - defaults to nil (all rows)
+        attr_accessor :size
+
+        # The index of the first row to return - defaults to 0 (first row)
+        attr_accessor :start
+
         # Construct a new query object. You should not use this directly.
         # Instead use the factory methods in Service. 
         #
@@ -290,6 +296,8 @@ module InterMine::PathQuery
             if root
                 @root = InterMine::Metadata::Path.new(root, model).rootClass
             end
+            @size = nil
+            @start = 0
             @constraints = []
             @joins = []
             @views = []
@@ -377,6 +385,38 @@ module InterMine::PathQuery
             return Results::ResultsReader.new(@url, self, start, size)
         end
 
+        # Set the maximum number of rows this query will return. 
+        #
+        # This method can be used to set a default maximum size for 
+        # a query. Set to nil for all rows. The value given here 
+        # will be overridden by any value supplied by #each_row
+        # or #each_result, unless that value is nil, in which 
+        # case this value will be used. If unset, the query will return all results.
+        #
+        # Returns self for method chaining.
+        #
+        # See also #size= and #offset
+        #
+        def limit(size)
+            @size = size
+            return self
+        end
+
+        # Set the index of the first row of results this query will return. 
+        #
+        # This method can be used to set a value for the query offset. 
+        # The value given here will be overridden by any value supplied by #each_row
+        # or #each_result. If unset, results will start from the first row.
+        #
+        # Returns self for method chaining.
+        #
+        # See also #start= and #limit
+        #
+        def offset(start) 
+            @start = start
+            return self
+        end
+
         # Iterate over the results of this query one row at a time.
         #
         # Rows support both array-like index based access as well as 
@@ -390,7 +430,9 @@ module InterMine::PathQuery
         #     puts r.to_h # Materialize the row an a Hash
         #   end
         #
-        def each_row(start=0, size=nil)
+        def each_row(start=nil, size=nil)
+            start = start.nil? ? @start : start
+            size  = size.nil? ? @size : size
             results_reader(start, size).each_row {|row|
                 yield row
             }
@@ -405,7 +447,9 @@ module InterMine::PathQuery
         #     end
         #   end
         #
-        def each_result(start=0, size=nil)
+        def each_result(start=nil, size=nil)
+            start = start.nil? ? @start : start
+            size  = size.nil? ? @size : size
             results_reader(start, size).each_result {|row|
                 yield row
             }
@@ -430,7 +474,9 @@ module InterMine::PathQuery
         #   rows.last["symbol"]
         #   => "eve"
         #
-        def rows(start=0, size=nil)
+        def rows(start=nil, size=nil)
+            start = start.nil? ? @start : start
+            size  = size.nil? ? @size : size
             res = []
             results_reader(start, size).each_row {|row|
                 res << row
@@ -445,7 +491,9 @@ module InterMine::PathQuery
         #  genes.last.symbol
         #  => "eve"
         #
-        def results(start=0, size=nil)
+        def results(start=nil, size=nil)
+            start = start.nil? ? @start : start
+            size  = size.nil? ? @size : size
             res = []
             results_reader(start, size).each_result {|row|
                 res << row
@@ -453,6 +501,43 @@ module InterMine::PathQuery
             res
         end
 
+        def summary_items(summary_path, start=0, size=nil)
+            q = self.clone
+            q.add_views(summary_path)
+            rr = q.results_reader(start, size)
+            if block_given?
+                rr.each_summary(summary_path) {|summary|
+                    yield summary
+                }
+            else
+                ret  = []
+                rr.each_summary(summary_path) {|summary|
+                    ret << summary
+                }
+                return ret
+            end
+        end
+
+        def summarise(summary_path, start=0, size=nil)
+            path = make_path(add_prefix(summary_path))
+            q = self.clone
+            q.add_views(summary_path)
+            rr = q.results_reader(start, size)
+            if InterMine::Metadata::Model::NUMERIC_TYPES.include? path.end_type
+                h = {}
+                rr.each_summary(summary_path) { |summary|
+                    h = Hash[summary.map {|k, v| [k, v.to_f]}]
+                }
+                return h
+            else
+                h = {}
+                rr.each_summary(summary_path) {|summary|
+                    h[summary["item"]] = summary["count"]
+                }
+                return h
+            end
+        end
+
         # Return all result record objects returned by running this query.
         def all
             return self.results
@@ -525,12 +610,14 @@ module InterMine::PathQuery
                 y = add_prefix(x)
                 if y.end_with?("*")
                     prefix = y.chomp(".*")
-                    path = InterMine::Metadata::Path.new(prefix, @model, subclasses)
-                    attrs = path.end_cd.attributes.map {|x| prefix + "." + x.name}
+                    path = make_path(prefix)
+                    attrs = path.end_cd.attributes.map {|x| 
+                        prefix + "." + x.name
+                    }
                     add_views(attrs)
                 else
-                    path = InterMine::Metadata::Path.new(y, @model, subclasses)
-                    path = InterMine::Metadata::Path.new(y.to_s + ".id", @model, subclasses) unless path.is_attribute?
+                    path = make_path(y)
+                    path = make_path(y.to_s + ".id") unless path.is_attribute?
                     if @root.nil?
                         @root = path.rootClass
                     end
@@ -540,6 +627,10 @@ module InterMine::PathQuery
             return self
         end
 
+        def make_path(path)
+            return InterMine::Metadata::Path.new(path, @model, subclasses)
+        end
+
         alias add_to_select add_views
 
         # Replace any currently existing views with the given view list. 

data/lib/intermine/results.rb

@@ -251,20 +251,10 @@ module InterMine::Results
 
         # Iterate over the result set one ResultsRow at a time
         def each_row
-            container = ''
-            each_line(params("jsonrows")) do |line|
-                if line.start_with?("[")
-                    begin
-                        row = ResultsRow.new(line.chomp("," + $/), @query.views)
-                    rescue => e
-                        raise ServiceError, "Error parsing #{line}: #{e.message}"
-                    end
-                    yield row
-                else
-                    container << line
-                end
-            end
-            check_result_set(container)
+            processor = lambda {|x| ResultsRow.new(x.chomp("," + $/), @query.views) }
+            read_result_set(params("jsonrows"), processor) {|x|
+                yield x
+            }
         end
 
         # Iterate over the resultset, one object at a time, where the
@@ -284,21 +274,40 @@ module InterMine::Results
         #
         def each_result
             model = @query.model
+            processor = lambda {|x| model.make_new(JSON.parse(x.chomp("," + $/)))}
+            read_result_set(params("jsonobjects"), processor) {|x|
+                yield x
+            }
+        end
+
+        def each_summary(summary_path)
+            extra = {"summaryPath" => @query.add_prefix(summary_path)}
+            p = params("jsonrows").merge(extra)
+            processor = lambda {|x| JSON.parse(x.chomp("," + $/)) }
+            read_result_set(p, processor) {|x|
+                yield x
+            }
+        end
+
+        def read_result_set(parameters, processor)
             container = ''
-            each_line(params("jsonobjects")) do |line|            
-                line.chomp!("," + $/)
-                if line.start_with?("{") and line.end_with?("}")
+            in_results = false
+            each_line(parameters) do |line|
+                if line.start_with?("]")
+                    in_results = false
+                end
+                if in_results
                     begin
-                        data = JSON.parse(line)
-                        result = model.make_new(data)
-                    rescue JSON::ParserError => e
-                        raise ServiceError, "Error parsing #{line}: #{e.message}"
+                        row = processor.call(line)
                     rescue => e
-                        raise ServiceError, "Could not instantiate this result object: #{e.message}"
+                        raise ServiceError, "Error parsing #{line}: #{e.message}"
                     end
-                    yield result
+                    yield row
                 else
                     container << line
+                    if line.chomp($/).end_with?("[")
+                        in_results = true
+                    end
                 end
             end
             check_result_set(container)

data/lib/intermine/version.rb

@@ -1,3 +1,3 @@
 module Intermine
-  VERSION = "0.98.06"
+  VERSION = "0.98.08"
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: intermine
 version: !ruby/object:Gem::Version 
-  hash: 411
+  hash: 391
   prerelease: false
   segments: 
   - 0
   - 98
-  - 6
-  version: 0.98.06
+  - 8
+  version: 0.98.08
 platform: ruby
 authors: 
 - Alex Kalderimis
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-08-03 00:00:00 +01:00
+date: 2011-10-26 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency