conceptql 0.0.1 → 0.0.3

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data/CHANGELOG.md

@@ -1,6 +1,44 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
+## 0.0.3 - 2014-08-12
+
+### Added
+- FakeGrapher class to make it easier to generate diagrams with experimental nodes
+- fake_graph command has returned to the `conceptql` program
+- GraphNodifier now supports:
+    - condition_type as condition_occurrence
+    - drg as procedure_occurrence
+    - vsac as misc
+
+### Deprecated
+- Nothing.
+
+### Removed
+- Nothing.
+
+### Fixed
+- Tree now runs #deep_symbolize_keys on incoming statements
+
+
+## 0.0.2 - 2014-07-11
+
+### Added
+- Nothing.
+
+### Deprecated
+- Nothing.
+
+### Removed
+- Several commands from `conceptql` program
+    - fake_graph
+    - show_db_graph
+    - show_and_tell_db
+
+### Fixed
+- Nothing.
+
+
 ## 0.0.1 - 2014-07-11
 
 ### Added

data/README.md

@@ -101,6 +101,8 @@ You might want to just take an existing statement from the statements in [test_c
 4. Push to the branch (`git push origin my-new-feature`)
 5. Create new Pull Request
 
+Or, use the [conceptql-dev-box](https://github.com/outcomesinsights/conceptql-dev-box) to get yourself setup and hack on ConceptQL that way.
+
 ## Thanks
 - [Outcomes Insights, Inc.](http://outins.com)
     - Many thanks for allowing me to release a portion of my work as Open Source Software!

data/doc/spec.md

@@ -1205,4 +1205,14 @@ Filter node is the opposite of Except.  It only includes L if R matches.
 ### AS option for Except
 Just like Filter has an :as option, add one to Except node.  This would simplify some of the algorithms I've developed.
 
+
+### How to Handle fact_relationship Table from CDMv5
+Each relationship type could be a binary node box read as L <relationship> R. E.g. L 'parent of' R would take a L stream and only pass on parents of rows in R stream.
+
+We could implement a single node that takes a relationship as an argument (on top of the L and R arguments) or we could create a node class for each relationship.  I think it would be better to have a single relationship node class and take the relationship as the argument.
+
+The next question is: how do we actually join the two streams?  I suppose we could translate each "type" into a "domain" and then join where l.domain = domain_concept_id_1 and l.entity_id = fact_id_1 and R.domain = domain_concept_id_2 and R.entity_id = fact_id_2 where the relationship chosen = relationship_concept_id.
+
+Yup, that should work.  Phew!
+
 [^AIA]: J. Allen. Maintaining knowledge about temporal intervals. Communications of the ACM (1983) vol. 26 (11) pp. 832-843

data/lib/conceptql/cli.rb

@@ -34,7 +34,7 @@ module ConceptQL
       aliases: :s,
       desc: 'schema for database (PostgreSQL only)'
 
-    desc 'run_statement statement_file', 'Evals the statement from the statement file and executes it agains the DB specified by DB_URL'
+    desc 'run_statement statement_file', 'Reads the ConceptQL statement from the statement file and executes it against the DB'
     def run_statement(statement_file)
       q = ConceptQL::Query.new(db(options), criteria_from_file(statement_file))
       puts q.query.sql
@@ -42,29 +42,25 @@ module ConceptQL
       pp q.execute
     end
 
-    desc 'fake_graph file', 'Evals the file and shows the contents as a ConceptQL graph'
-    def fake_graph(file)
-      require_relative 'graph'
-      require_relative 'tree'
-      require_relative 'graph_nodifier'
-      ConceptQL::Graph.new(criteria_from_file(file),
-         dangler: true,
-         tree: ConceptQL::Tree.new(nodifier: ConceptQL::GraphNodifier.new)
-      ).graph_it('/tmp/graph')
-      system('open /tmp/graph.pdf')
-    end
-
-    desc 'show_graph file', 'Evals the file and shows the contents as a ConceptQL graph'
+    desc 'show_graph statement_file', 'Reads the ConceptQL statement from the file and shows the contents as a ConceptQL graph'
     def show_graph(file)
       graph_it(criteria_from_file(file))
     end
 
-    desc 'show_and_tell_file file', 'Evals the file and shows the contents as a ConceptQL graph, then executes the statement against our test database'
+    desc 'show_and_tell_file statement_file', 'Reads the ConceptQL statement from the file and shows the contents as a ConceptQL graph, then executes the statement against the DB'
     option :full
-    def show_and_tell_file(file)
+    def show_and_tell(file)
       show_and_tell(criteria_from_file(file), options)
     end
 
+    desc 'fake_graph file', 'Reads the ConceptQL statement from the file and shows the contents as a ConceptQL graph'
+    def fake_graph(file)
+      require_relative 'fake_grapher'
+      ConceptQL::FakeGrapher.new.graph_it(criteria_from_file(file), '/tmp/graph')
+      system('open /tmp/graph.pdf')
+    end
+
+    private
     desc 'show_and_tell_db conceptql_id', 'Fetches the ConceptQL from a DB and shows the contents as a ConceptQL graph, then executes the statement against our test database'
     option :full
     def show_and_tell_db(conceptql_id)
@@ -79,7 +75,6 @@ module ConceptQL
       graph_it(result[:statement].to_hash, db, result[:label])
     end
 
-    private
     def fetch_conceptql(conceptql_id)
       my_db = db(options)
       my_db.extension(:pg_array, :pg_json)

data/lib/conceptql/fake_grapher.rb

@@ -0,0 +1,20 @@
+require_relative 'graph'
+require_relative 'tree'
+require_relative 'graph_nodifier'
+
+module ConceptQL
+  class FakeGrapher
+    attr :options
+
+    def initialize(options = {})
+      @options = {
+        dangler: true,
+        tree: ConceptQL::Tree.new(nodifier: ConceptQL::GraphNodifier.new)
+      }.merge(options)
+    end
+
+    def graph_it(statement, output_file)
+      ConceptQL::Graph.new(statement, options).graph_it(output_file)
+    end
+  end
+end

data/lib/conceptql/graph_nodifier.rb

@@ -11,10 +11,12 @@ module ConceptQL
         condition: :condition_occurrence,
         primary_diagnosis: :condition_occurrence,
         icd9: :condition_occurrence,
+        condition_type: :condition_occurrence,
 
         # Procedures
         procedure: :procedure_occurrence,
         cpt: :procedure_occurrence,
+        drg: :procedure_occurrence,
         hcpcs: :procedure_occurrence,
         icd9_procedure: :procedure_occurrence,
         procedure_cost: :procedure_cost,
@@ -45,7 +47,8 @@ module ConceptQL
         date_range: :date,
 
         # Miscelaneous nodes
-        concept: :misc
+        concept: :misc,
+        vsac: :misc
       }
 
       attr :values, :name
@@ -78,10 +81,14 @@ module ConceptQL
     class BinaryOperatorNode < DotNode
       def display_name
         output = name
-        output += "\n#{options.map{|k,v| "#{k}: #{v}"}.join("\n")}" unless options.nil? || options.empty?
+        output += "\n#{displayable_options.map{|k,v| "#{k}: #{v}"}.join("\n")}"
         output
       end
 
+      def displayable_options
+        options.select{ |k,v| ![:left, :right].include?(k) } || {}
+      end
+
       def left
         options[:left]
       end
@@ -116,7 +123,9 @@ module ConceptQL
     BINARY_OPERATOR_TYPES = %w(before after meets met_by started_by starts contains during overlaps overlapped_by finished_by finishes coincides except person_filter less_than less_than_or_equal equal not_equal greater_than greater_than_or_equal filter).map { |temp| [temp, "not_#{temp}"] }.flatten.map(&:to_sym)
 
     def create(type, values)
-      return BinaryOperatorNode.new(type, values) if BINARY_OPERATOR_TYPES.include?(type)
+      if BINARY_OPERATOR_TYPES.include?(type)
+        return BinaryOperatorNode.new(type, values)
+      end
       DotNode.new(type, values)
     end
   end

data/lib/conceptql/tree.rb

@@ -10,7 +10,7 @@ module ConceptQL
     end
 
     def root(query)
-      @root ||= traverse(query.statement.symbolize_keys)
+      @root ||= traverse(query.statement.deep_symbolize_keys)
     end
 
     private

data/lib/conceptql/version.rb

@@ -1,3 +1,3 @@
 module ConceptQL
-  VERSION = "0.0.1"
+  VERSION = "0.0.3"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: conceptql
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.3
 platform: ruby
 authors:
 - Ryan Duryea
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-11 00:00:00.000000000 Z
+date: 2014-08-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -161,6 +161,7 @@ files:
 - lib/conceptql/behaviors/dottable.rb
 - lib/conceptql/cli.rb
 - lib/conceptql/date_adjuster.rb
+- lib/conceptql/fake_grapher.rb
 - lib/conceptql/graph.rb
 - lib/conceptql/graph_nodifier.rb
 - lib/conceptql/logger.rb