cmap 0.4.0 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 73a72a40cc5dded9d995413e09c76024968b7482
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+  data.tar.gz: e51eb88311d3af6e68564dd1e99c01fe941fb80b
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+  data.tar.gz: a697dcc4d94b53ee96ee893c266316c3cf6f695e8fd173f7e02066584fed26519b6e53024897eb4a4edfee19d1893744f14fddffcc68108089bbe03025584c9c

data/cmap.gemspec

@@ -25,5 +25,5 @@ Gem::Specification.new do |spec|
 
   spec.add_dependency "pg", "0.18.3"
   spec.add_dependency "pry"
-  spec.add_dependency "directed_graph", '0.3.0'
+  spec.add_dependency "directed_graph", "0.6.0"
 end

data/lib/cmap.rb

@@ -6,7 +6,7 @@ require 'pry'
 
 require 'directed_graph'
 
-require_relative "./cmap/graph_sanitizer.rb"
+require_relative "./cmap/sanitize_graph.rb"
 require_relative "./cmap/subquery_expander.rb"
 require_relative "./cmap/edges_to_queries.rb"
 require_relative "./cmap/propositions_to_graph.rb"

data/lib/cmap/edges_to_queries.rb

@@ -19,11 +19,11 @@ module Cmap; class EdgesToQueries
   private
 
   def unique_edges
-    edges.uniq {|e| [e.destination_vertex, e.value]}
+    edges.uniq {|e| [e.destination_vertex.data[:sanitized_name], e.data[:sanitized_value]]}
   end
 
   def add_columns_queries
-    unique_edges.map {|e| "alter table #{schema_name}.#{table_name} add column #{e.destination_vertex} int2;"}
+    unique_edges.map {|e| "alter table #{schema_name}.#{table_name} add column #{e.destination_vertex.data[:sanitized_name]} int2;"}
   end
 
   def grouped_edges
@@ -35,7 +35,7 @@ module Cmap; class EdgesToQueries
   end
 
   def updates
-    u = (grouped_edges[false] || []).map {|e| "#{e.destination_vertex}=(#{e.value})::int"}.join(", ")
+    u = (grouped_edges[false] || []).map {|e| "#{e.destination_vertex.data[:sanitized_name]}=(#{e.data[:sanitized_value]})::int"}.join(", ")
     return [] if u.empty?
     ["update #{schema_name}.#{table_name} set #{u};"]
   end

data/lib/cmap/propositions_to_graph.rb

@@ -4,22 +4,35 @@ module Cmap; class PropositionsToGraph
 
   def initialize(propositions_path)
     @propositions_path = propositions_path
+    @vertices = []
   end
 
   def graph
-    DirectedGraph::Graph.new(edges)
+    SanitizeGraph.new(DirectedGraph::Graph.new(edges)).sanitize
   end
 
   private
 
   def edges
     @edges ||= propositions.inject([]) do |memo, e|
-      origin_vertex, value, destination_vertex = e
-      memo << DirectedGraph::Edge.new(origin_vertex: origin_vertex, destination_vertex: destination_vertex, value: value)
+      origin_vertex_name, value, destination_vertex_name = e
+      origin_vertex = find_vertex_or_create(origin_vertex_name)
+      destination_vertex = find_vertex_or_create(destination_vertex_name)
+      data = { :value => value }
+      memo << DirectedGraph::Edge.new(origin_vertex: origin_vertex, destination_vertex: destination_vertex, data: data)
       memo
     end
   end
 
+  def find_vertex_or_create(vertex_name)
+    vertex = @vertices.find {|v| v.name == vertex_name}
+    return vertex if vertex
+    data = { :name => vertex_name }
+    v = DirectedGraph::Vertex.new(name: vertex_name, data: data)
+    @vertices << v
+    v
+  end
+
   def propositions
     csv_path = File.expand_path(propositions_path, File.dirname(__FILE__))
     CSV.read(csv_path, { :col_sep => "\t", :quote_char => '"' })

data/lib/cmap/propositions_to_sql.rb

@@ -21,12 +21,8 @@ module Cmap; class PropositionsToSql
     propositions_to_graph.graph
   end
 
-  def sanitized_graph
-    GraphSanitizer.new(raw_graph).sanitized_graph
-  end
-
   def graph_to_sql
-    GraphToSql.new(table_name, schema_name, sanitized_graph, subquery_gsubs)
+    GraphToSql.new(table_name, schema_name, raw_graph, subquery_gsubs)
   end
 
 end; end

data/lib/cmap/sanitize_graph.rb

@@ -0,0 +1,42 @@
+module Cmap; class SanitizeGraph
+
+	def initialize(graph)
+		@graph = graph
+	end
+
+	def sanitize
+		sanitize_vertices
+		sanitize_edges
+		@graph
+	end
+
+	private
+
+	def sanitize_vertices
+		@graph.vertices.each { |v| v.data[:sanitized_name] = sanitize_string(v.data[:name]) }
+	end
+
+	def ordered_vertices
+		# HACK: this sorting makes the assumption vertices lower in the graph have longer ids
+		@ordered_vertices ||= @graph.vertices.sort do |a, b|
+			b.name.length <=> a.name.length
+		end
+	end
+
+	def sanitize_edges
+    @graph.edges.each { |edge| sanitize_edge(edge) }
+  end
+
+  def sanitize_edge(edge)
+    ordered_vertices.each do |v|
+    	edge.data[:sanitized_value] = edge.data[:value].gsub(v.data[:name], v.data[:sanitized_name])
+    end
+  end
+
+  private
+
+  def sanitize_string(string)
+    string.gsub(/[^0-9a-zA-Z]+/, '_').downcase
+  end
+
+end; end

data/lib/cmap/subquery_expander.rb

@@ -9,12 +9,17 @@ module Cmap; class SubqueryExpander
   end
 
   def update_query?(edge)
-    edge.value != query(edge)
+    edge.data[:sanitized_value] != query(edge)
   end
 
   def query(edge)
-    r = edge.value
-    replacements = [["+table_name+", table_name], ["+schema_name+", schema_name], ["+destination_vertex+", edge.destination_vertex], ["+origin_vertex+", edge.origin_vertex]]
+    r = edge.data[:sanitized_value]
+    replacements = [
+      ["+table_name+", table_name],
+      ["+schema_name+", schema_name],
+      ["+destination_vertex+", edge.destination_vertex.data[:sanitized_name]],
+      ["+origin_vertex+", edge.origin_vertex.data[:sanitized_name]]
+    ]
     (subquery_gsubs + replacements).each {|gsub| r = r.gsub(*gsub)}
     r
   end

data/lib/cmap/version.rb

@@ -1,3 +1,3 @@
 module Cmap
-  VERSION = "0.4.0"
+  VERSION = "0.5.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cmap
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.5.0
 platform: ruby
 authors:
 - MrPowers
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-01-04 00:00:00.000000000 Z
+date: 2016-01-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -86,14 +86,14 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.3.0
+        version: 0.6.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.3.0
+        version: 0.6.0
 description: Converts cmap exports that follow strict conventions into postgreSQL
   for data analysis
 email:
@@ -116,10 +116,10 @@ files:
 - example/cmap_to_sql.rb
 - lib/cmap.rb
 - lib/cmap/edges_to_queries.rb
-- lib/cmap/graph_sanitizer.rb
 - lib/cmap/graph_to_sql.rb
 - lib/cmap/propositions_to_graph.rb
 - lib/cmap/propositions_to_sql.rb
+- lib/cmap/sanitize_graph.rb
 - lib/cmap/sql_runner.rb
 - lib/cmap/subquery_expander.rb
 - lib/cmap/version.rb

data/lib/cmap/graph_sanitizer.rb

@@ -1,44 +0,0 @@
-module Cmap; class GraphSanitizer
-
-  attr_reader :graph
-
-  def initialize(graph)
-    @graph = graph
-    @sanitized_vertex_lookup = {}
-  end
-
-  def sanitized_graph
-    DirectedGraph::Graph.new(sanitized_edges)
-  end
-
-  def edges_with_sanitized_vertices
-    graph.edges.map do |edge|
-      origin_vertex = sanitize_string(edge.origin_vertex)
-      destination_vertex = sanitize_string(edge.destination_vertex)
-
-      @sanitized_vertex_lookup[edge.origin_vertex] = origin_vertex
-      @sanitized_vertex_lookup[edge.destination_vertex] = destination_vertex
-
-      {origin_vertex: origin_vertex, destination_vertex: destination_vertex, value: edge.value}
-    end
-  end
-
-  def sanitize_edge_value(edge_args)
-    @sanitized_vertex_lookup.keys.sort.reverse.each do |original_vertex_name|
-      edge_args[:value].gsub!(original_vertex_name, @sanitized_vertex_lookup[original_vertex_name])
-    end
-    edge_args
-  end
-
-  def sanitized_edges
-    edges_with_sanitized_vertices.map do |edge_args|
-      DirectedGraph::Edge.new(sanitize_edge_value(edge_args))
-    end
-  end
-
-  def sanitize_string(string)
-    string.gsub(/[^0-9a-zA-Z]+/, '_').downcase
-  end
-
-end; end
-