conceptql 0.2.0 → 0.4.0

data/.gitignore

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-*.gem
-*.rbc
-.*.sw*
-.*.un~
-.bundle
-.config
-.yardoc
-.idea
-Gemfile.lock
-InstalledFiles
-_yardoc
-coverage
-demos
-images/
-jsons/
-lib/bundler/man
-pkg
-rdoc
-spec/reports
-test/tmp
-test/version_tmp
-tmp
-yamls/

data/Gemfile

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-source 'https://rubygems.org'
-
-# Specify your gem's dependencies in conceptql.gemspec
-gemspec

data/Guardfile

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-# A sample Guardfile
-# More info at https://github.com/guard/guard#readme
-
-
-# Note: The cmd option is now required due to the increasing number of ways
-#       rspec may be run, below are examples of the most common uses.
-#  * bundler: 'bundle exec rspec'
-#  * bundler binstubs: 'bin/rspec'
-#  * spring: 'bin/rspec' (This will use spring if running and you have
-#                          installed the spring binstubs per the docs)
-#  * zeus: 'zeus rspec' (requires the server to be started separately)
-#  * 'just' rspec: 'rspec'
-
-guard :rspec, cmd: "bundle exec rspec" do
-  require "guard/rspec/dsl"
-  dsl = Guard::RSpec::Dsl.new(self)
-
-  # Feel free to open issues for suggestions and improvements
-
-  # RSpec files
-  rspec = dsl.rspec
-  watch(rspec.spec_helper) { rspec.spec_dir }
-  watch(rspec.spec_support) { rspec.spec_dir }
-  watch(rspec.spec_files)
-
-  # Ruby files
-  ruby = dsl.ruby
-  dsl.watch_spec_files_for(ruby.lib_files)
-
-  # Rails files
-  rails = dsl.rails(view_extensions: %w(erb haml slim))
-  dsl.watch_spec_files_for(rails.app_files)
-  dsl.watch_spec_files_for(rails.views)
-
-  watch(rails.controllers) do |m|
-    [
-      rspec.spec.("routing/#{m[1]}_routing"),
-      rspec.spec.("controllers/#{m[1]}_controller"),
-      rspec.spec.("acceptance/#{m[1]}")
-    ]
-  end
-
-  # Rails config changes
-  watch(rails.spec_helper)     { rspec.spec_dir }
-  watch(rails.routes)          { "#{rspec.spec_dir}/routing" }
-  watch(rails.app_controller)  { "#{rspec.spec_dir}/controllers" }
-
-  # Capybara features specs
-  watch(rails.view_dirs)     { |m| rspec.spec.("features/#{m[1]}") }
-
-  # Turnip features and steps
-  watch(%r{^spec/acceptance/(.+)\.feature$})
-  watch(%r{^spec/acceptance/steps/(.+)_steps\.rb$}) do |m|
-    Dir[File.join("**/#{m[1]}.feature")][0] || "spec/acceptance"
-  end
-end

data/LICENSE.txt

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-Copyright (c) 2014 Outcomes Insights, Inc.
-
-MIT License
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/Rakefile

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-require "bundler/gem_tasks"

data/conceptql.gemspec

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-# coding: utf-8
-lib = File.expand_path('../lib', __FILE__)
-$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
-require 'conceptql/version'
-
-Gem::Specification.new do |spec|
-  spec.name          = 'conceptql'
-  spec.version       = ConceptQL::VERSION
-  spec.authors       = ['Ryan Duryea']
-  spec.email         = ['aguynamedryan@gmail.com']
-  spec.summary       = %q{Generate OMOP CDMv4-compatible queries from a ConceptQL file}
-  spec.description   = %q{ConceptQL is a query language for specifying queries to be run OMOP CDMv4 structured data}
-  spec.homepage      = 'https://github.com/outcomesinsights/conceptql'
-  spec.license       = 'MIT'
-
-  spec.files         = `git ls-files`.split($/)
-  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
-  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
-  spec.require_paths = ['lib']
-
-  spec.add_dependency 'facets', '~> 3.0'
-  spec.add_dependency 'sequelizer', '~> 0.0'
-  spec.add_dependency 'thor', '~> 0.19'
-  spec.add_dependency 'pg', '~> 0.17'
-  spec.add_dependency 'ruby-graphviz', '~> 1.2'
-  spec.add_dependency 'csv2xlsx', '~> 0'
-  spec.add_development_dependency 'bundler', '~> 1.5'
-  spec.add_development_dependency 'rake', '~> 10.3'
-  spec.add_development_dependency 'rspec', '~> 3.2'
-  spec.add_development_dependency 'guard-rspec', '~> 4.5'
-  spec.add_development_dependency 'byebug', '~> 4.0'
-end

data/doc/implementation_notes.md

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-# ConceptQL Implementation Notes
-And here is where I record information about some of the decisions I made.
-
-## Define/Recall
-- Sequel's create table statement runs out-of-band with rest of ConceptQL statemnt
-    - Gets executed immediately
-    - This is going to be very slow for large datasets :-(
-- I had to retool Tree and Query and Graph to expect an array of concepts in a ConceptQL statement
-    - I'm not sure I like this
-    - A ConceptQL statement perhaps should be only a single statement at the end
-- Defines need to occur before they are used
-    - Most languages have a "forward definition" ability
-        - I have no use cases for when we might need those?
-        - Perhaps a definition that uses a definition that doesn't exist?
-        - Is that recursive?
-    - Is that something we want/need in ConceptQL?
-
-
-## Values
-- I had considered comparing a result set with a between operator, but this implies that the R stream needs a range somehow
-    - I don't think supporting a range is a good idea right now
-
-
-## Bad Ideas
-Here is where I intend to record bad ideas that appear to be blind allies
-
-### Removing person-only rows from a stream after ANDing
-- Theoretically, any result set that passes up through an AND node carries all the valid person IDs with it, so it is redundant to carry results that are just person-only.  It would make sense to eliminate them.
-- NO BAD IDEA
-    - We have to check to see if the stream is exclusively person-only.  In that case, it is unsafe to eliniate those results because we'd end up removing all results from the stream
-        - We could implement this check, but let's do that later when we want to optimize things
-             - Also, what happens if we cast to visit later and we've removed all person-only results?  This could cause odd behavior
-
-### Treating Patient Streams as "Eternal" when they encounter a temporal node
-I had created a rather sophisticated system of how to handle a patient stream entering a temporal node.
-
-The basic premise is that patient information (gender, race, etc) is "timeless" or "eternal" and so if a patient stream is the R stream in a temporal node and the L stream is, say, a stream of MIs, what is the result?  I proposed that the MI would be filtered down to only those patients that appear in the R stream.
-
-Likewise, if the MI stream is the R stream and the person stream is the L stream, what's the result?  Same thing.  Only patients common to both streams are passed through the L stream.  But patients DO have a date associated with them: their date of birth.  And, by passing a patient stream through a time_shift node of say, +50yr, we can use that patient stream in the R stream of a temporal node to filter the L stream by the patient being 50 years old.