snomed_model 0.1.0

checksums.yaml

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data/.rspec

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+--format documentation
+--color
+--require spec_helper

data/.rubocop.yml

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+AllCops:
+  TargetRubyVersion: 2.6
+
+Style/StringLiterals:
+  Enabled: true
+  EnforcedStyle: double_quotes
+
+Style/StringLiteralsInInterpolation:
+  Enabled: true
+  EnforcedStyle: double_quotes
+
+Layout/LineLength:
+  Max: 120

data/CHANGELOG.md

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+## [Unreleased]
+
+## [0.1.0] - 2024-01-03
+
+- Initial release

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,84 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at siva.g@westagilelabs.com. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior,  harassment of an individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

data/Gemfile

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+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+# Specify your gem's dependencies in snomed_model.gemspec
+gemspec
+
+gem "rake", "~> 13.0"
+
+gem "rspec", "~> 3.0"
+
+gem "rubocop", "~> 1.21"
+
+gem 'pry'

data/Gemfile.lock

@@ -0,0 +1,173 @@
+PATH
+  remote: .
+  specs:
+    snomed_model (0.1.0)
+      activerecord (~> 7.1, >= 7.1.2)
+      dag (~> 0.0.9)
+      pg (~> 1.5, >= 1.5.4)
+      pg_ltree
+      standalone_migrations (~> 7.1, >= 7.1.3)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    actionpack (7.1.2)
+      actionview (= 7.1.2)
+      activesupport (= 7.1.2)
+      nokogiri (>= 1.8.5)
+      racc
+      rack (>= 2.2.4)
+      rack-session (>= 1.0.1)
+      rack-test (>= 0.6.3)
+      rails-dom-testing (~> 2.2)
+      rails-html-sanitizer (~> 1.6)
+    actionview (7.1.2)
+      activesupport (= 7.1.2)
+      builder (~> 3.1)
+      erubi (~> 1.11)
+      rails-dom-testing (~> 2.2)
+      rails-html-sanitizer (~> 1.6)
+    activemodel (7.1.2)
+      activesupport (= 7.1.2)
+    activerecord (7.1.2)
+      activemodel (= 7.1.2)
+      activesupport (= 7.1.2)
+      timeout (>= 0.4.0)
+    activesupport (7.1.2)
+      base64
+      bigdecimal
+      concurrent-ruby (~> 1.0, >= 1.0.2)
+      connection_pool (>= 2.2.5)
+      drb
+      i18n (>= 1.6, < 2)
+      minitest (>= 5.1)
+      mutex_m
+      tzinfo (~> 2.0)
+    ast (2.4.2)
+    base64 (0.2.0)
+    bigdecimal (3.1.5)
+    builder (3.2.4)
+    coderay (1.1.3)
+    concurrent-ruby (1.2.2)
+    connection_pool (2.4.1)
+    crass (1.0.6)
+    dag (0.0.9)
+    diff-lcs (1.5.0)
+    drb (2.2.0)
+      ruby2_keywords
+    erubi (1.12.0)
+    i18n (1.14.1)
+      concurrent-ruby (~> 1.0)
+    io-console (0.7.1)
+    irb (1.11.0)
+      rdoc
+      reline (>= 0.3.8)
+    json (2.7.1)
+    language_server-protocol (3.17.0.3)
+    loofah (2.22.0)
+      crass (~> 1.0.2)
+      nokogiri (>= 1.12.0)
+    method_source (1.0.0)
+    minitest (5.20.0)
+    mutex_m (0.2.0)
+    nokogiri (1.16.0-x86_64-darwin)
+      racc (~> 1.4)
+    parallel (1.24.0)
+    parser (3.2.2.4)
+      ast (~> 2.4.1)
+      racc
+    pg (1.5.4)
+    pg_ltree (1.2.1)
+      activerecord (>= 5.2, < 8.0)
+      pg (>= 0.19, < 2)
+    pry (0.14.2)
+      coderay (~> 1.1)
+      method_source (~> 1.0)
+    psych (5.1.2)
+      stringio
+    racc (1.7.3)
+    rack (3.0.8)
+    rack-session (2.0.0)
+      rack (>= 3.0.0)
+    rack-test (2.1.0)
+      rack (>= 1.3)
+    rackup (2.1.0)
+      rack (>= 3)
+      webrick (~> 1.8)
+    rails-dom-testing (2.2.0)
+      activesupport (>= 5.0.0)
+      minitest
+      nokogiri (>= 1.6)
+    rails-html-sanitizer (1.6.0)
+      loofah (~> 2.21)
+      nokogiri (~> 1.14)
+    railties (7.1.2)
+      actionpack (= 7.1.2)
+      activesupport (= 7.1.2)
+      irb
+      rackup (>= 1.0.0)
+      rake (>= 12.2)
+      thor (~> 1.0, >= 1.2.2)
+      zeitwerk (~> 2.6)
+    rainbow (3.1.1)
+    rake (13.1.0)
+    rdoc (6.6.2)
+      psych (>= 4.0.0)
+    regexp_parser (2.8.3)
+    reline (0.4.1)
+      io-console (~> 0.5)
+    rexml (3.2.6)
+    rspec (3.12.0)
+      rspec-core (~> 3.12.0)
+      rspec-expectations (~> 3.12.0)
+      rspec-mocks (~> 3.12.0)
+    rspec-core (3.12.2)
+      rspec-support (~> 3.12.0)
+    rspec-expectations (3.12.3)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.12.0)
+    rspec-mocks (3.12.6)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.12.0)
+    rspec-support (3.12.1)
+    rubocop (1.59.0)
+      json (~> 2.3)
+      language_server-protocol (>= 3.17.0)
+      parallel (~> 1.10)
+      parser (>= 3.2.2.4)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.8, < 3.0)
+      rexml (>= 3.2.5, < 4.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 2.4.0, < 3.0)
+    rubocop-ast (1.30.0)
+      parser (>= 3.2.1.0)
+    ruby-progressbar (1.13.0)
+    ruby2_keywords (0.0.5)
+    standalone_migrations (7.1.3)
+      activerecord (>= 6.0.0, < 7.2)
+      nokogiri (~> 1.14)
+      railties (>= 6.0.0, < 7.2)
+      rake (>= 10.0)
+    stringio (3.1.0)
+    thor (1.3.0)
+    timeout (0.4.1)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
+    unicode-display_width (2.5.0)
+    webrick (1.8.1)
+    zeitwerk (2.6.12)
+
+PLATFORMS
+  x86_64-darwin-19
+
+DEPENDENCIES
+  pry
+  rake (~> 13.0)
+  rspec (~> 3.0)
+  rubocop (~> 1.21)
+  snomed_model!
+
+BUNDLED WITH
+   2.3.15

data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2024 siva-wal
+
+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/README.md

@@ -0,0 +1,37 @@
+# SnomedModel
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/snomed_model`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Install the gem and add to the application's Gemfile by executing:
+
+    $ bundle add snomed_model
+
+If bundler is not being used to manage dependencies, install the gem by executing:
+
+    $ gem install snomed_model
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and the created tag, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/snomed_model. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [code of conduct](https://github.com/[USERNAME]/snomed_model/blob/master/CODE_OF_CONDUCT.md).
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+
+## Code of Conduct
+
+Everyone interacting in the SnomedModel project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/snomed_model/blob/master/CODE_OF_CONDUCT.md).

data/Rakefile

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+require "standalone_migrations"
+require File.expand_path("./lib/snomed_model.rb")
+
+load File.expand_path("./lib/tasks/snomed.rake")
+
+StandaloneMigrations::Tasks.load_tasks
+
+RSpec::Core::RakeTask.new(:spec)
+
+require "rubocop/rake_task"
+
+RuboCop::RakeTask.new
+
+task default: %i[spec rubocop]

data/build_concept_full_relationship.rb

@@ -0,0 +1,103 @@
+require 'dag'
+require 'csv'
+require 'pry'
+
+snomed_rel_file_path = "/Users/sivagollapalli/work/snomed-database-loader/PostgreSQL/tmp_extracted/sct2_StatedRelationship_Full_INT_20210131.txt"
+
+hash = Hash.new
+
+File.open(snomed_rel_file_path, 'r') do |f|
+  f.each_line do |line|
+    row = line.split("\t")
+
+    source = row[4].to_s
+    destination = row[5].to_s
+    relation = row[7].to_s
+
+    if hash[source].nil?
+      hash[source] = []
+    end
+
+    hash[source] << destination if relation == '116680003'
+  end
+end
+
+def build_or_find_vertex(dag, code)
+  vertex = dag.vertices.select { |c| c[:payload][:code] == code }.first
+
+  return vertex if vertex
+
+  dag.add_vertex(payload: {code: code})
+end
+
+def get_path(code, hash)
+  dag = DAG.new
+
+  queue = Queue.new 
+  queue.push(code)
+
+  loop do 
+    source = queue.pop
+    break if hash[source].nil?
+    destination = hash[source].uniq
+
+    source_vertex = build_or_find_vertex(dag, source)
+
+    if destination.size > 1
+      destination.each do |des|
+        desti_vertex =  build_or_find_vertex(dag, des)
+
+        dag.add_edge from: source_vertex, to: desti_vertex  
+
+        queue.push(des)
+
+        break if des == '138875005'
+      end
+    else
+      destination = destination.first
+
+      destination_vertex = build_or_find_vertex(dag, destination) # dag.add_vertex(payload: {code: destination})
+
+      dag.add_edge from: source_vertex, to: destination_vertex  
+      queue.push(destination)
+
+      break if destination == '138875005'
+    end
+  end
+
+  dag
+end
+
+dag = get_path('155597006', hash)
+
+vertex = build_or_find_vertex(dag, '155597006')
+
+def find_all_paths(dag, start, path=[])
+  path += [start]
+
+  paths = [path]
+
+  start.successors.each do |ver|
+    newpaths = find_all_paths(dag, ver, path)
+
+    newpaths.each do |newpath|
+      paths += [newpath]
+    end
+  end
+
+  paths 
+end
+
+paths = [] 
+
+find_all_paths(dag, vertex).each do |path|
+  next if path.size == 1
+
+  vertex_str = path.map do |v| 
+    v[:payload][:code]
+  end.join('.')
+
+  paths << "INSERT INTO test VALUES ('#{vertex_str}');"
+end
+
+pp paths

data/db/config.yml

@@ -0,0 +1,17 @@
+default: &default
+  adapter: postgresql
+  pool: 5
+  timeout: 5000
+  host: <%= ENV['SNOMED_DB_HOST'] %>
+  username: <%= ENV['SNOMED_DB_USERNAME'] %>
+  database: 'snomedct'
+  password: <%= ENV['SNOMED_DB_PWD'] %>
+
+development:
+  <<: *default
+
+production:
+  <<: *default
+
+test: &test
+  <<: *default

data/db/migrate/20240106111800_add_concept_table.rb

@@ -0,0 +1,10 @@
+class AddConceptTable < ActiveRecord::Migration[7.1]
+  def change
+    create_table :concepts do |t|
+      t.string :effectivetime, null: false
+      t.string :active, null: false
+      t.string :moduleid, null: false
+      t.string :definitionstatusid, null: false
+    end
+  end
+end

data/db/migrate/20240106124817_add_index_to_concepts.rb

@@ -0,0 +1,5 @@
+class AddIndexToConcepts < ActiveRecord::Migration[7.1]
+  def change
+    add_index :concepts, [:id, :effectivetime], unique: true
+  end
+end

data/db/migrate/20240106153438_add_description_table.rb

@@ -0,0 +1,16 @@
+class AddDescriptionTable < ActiveRecord::Migration[7.1]
+  def change
+    create_table :descriptions do |t|
+      t.string :effectivetime, null: false
+      t.string :active, null: false
+      t.string :moduleid, null: false
+      t.string :conceptid, null: false
+      t.string :languagecode, null: false
+      t.string :typeid, null: false
+      t.text :term, null: false
+      t.string :casesignificanceid, null: false
+    end
+
+    add_index :descriptions, [:id, :effectivetime], unique: true
+  end
+end

data/db/migrate/20240106161110_add_relationship_table.rb

@@ -0,0 +1,17 @@
+class AddRelationshipTable < ActiveRecord::Migration[7.1]
+  def change
+    create_table :relationships do |t|
+      t.string :effectivetime, null: false
+      t.string :active, null: false
+      t.string :moduleid, null: false
+      t.string :sourceid, null: false
+      t.string :destinationid, null: false
+      t.string :relationshipgroup, null: false
+      t.string :typeid, null: false
+      t.text :characteristictypeid, null: false
+      t.string :modifierid, null: false
+    end
+
+    add_index :relationships, [:id, :effectivetime], unique: true
+  end
+end

data/db/migrate/20240109131657_enable_ltree_extension.rb

@@ -0,0 +1,5 @@
+class EnableLtreeExtension < ActiveRecord::Migration[7.1]
+  def change
+    enable_extension "ltree"
+  end
+end

data/db/migrate/20240109131738_add_hirerachy_table.rb

@@ -0,0 +1,7 @@
+class AddHirerachyTable < ActiveRecord::Migration[7.1]
+  def change
+    create_table :hirerachies do |t|
+      t.ltree :path
+    end
+  end
+end

data/db/schema.rb

@@ -0,0 +1,55 @@
+# This file is auto-generated from the current state of the database. Instead
+# of editing this file, please use the migrations feature of Active Record to
+# incrementally modify your database, and then regenerate this schema definition.
+#
+# This file is the source Rails uses to define your schema when running `bin/rails
+# db:schema:load`. When creating a new database, `bin/rails db:schema:load` tends to
+# be faster and is potentially less error prone than running all of your
+# migrations from scratch. Old migrations may fail to apply correctly if those
+# migrations use external dependencies or application code.
+#
+# It's strongly recommended that you check this file into your version control system.
+
+ActiveRecord::Schema[7.1].define(version: 2024_01_09_131738) do
+  # These are extensions that must be enabled in order to support this database
+  enable_extension "ltree"
+  enable_extension "plpgsql"
+
+  create_table "concepts", force: :cascade do |t|
+    t.string "effectivetime", null: false
+    t.string "active", null: false
+    t.string "moduleid", null: false
+    t.string "definitionstatusid", null: false
+    t.index ["id", "effectivetime"], name: "index_concepts_on_id_and_effectivetime", unique: true
+  end
+
+  create_table "descriptions", force: :cascade do |t|
+    t.string "effectivetime", null: false
+    t.string "active", null: false
+    t.string "moduleid", null: false
+    t.string "conceptid", null: false
+    t.string "languagecode", null: false
+    t.string "typeid", null: false
+    t.text "term", null: false
+    t.string "casesignificanceid", null: false
+    t.index ["id", "effectivetime"], name: "index_descriptions_on_id_and_effectivetime", unique: true
+  end
+
+  create_table "hirerachies", force: :cascade do |t|
+    t.ltree "path"
+  end
+
+  create_table "relationships", force: :cascade do |t|
+    t.string "effectivetime", null: false
+    t.string "active", null: false
+    t.string "moduleid", null: false
+    t.string "sourceid", null: false
+    t.string "destinationid", null: false
+    t.string "relationshipgroup", null: false
+    t.string "typeid", null: false
+    t.text "characteristictypeid", null: false
+    t.string "modifierid", null: false
+    t.index ["id", "effectivetime"], name: "index_relationships_on_id_and_effectivetime", unique: true
+  end
+
+end

data/lib/snomed_model/concept.rb

@@ -0,0 +1,159 @@
+module SnomedModel
+  class Concept < ActiveRecord::Base
+    attr_accessor :paths
+
+    ROOT_CONCEPT = "138875005".freeze
+    DISEASE_CONCEPT = "64572001".freeze
+    CLINICAL_FINDING = "404684003".freeze
+
+    has_many :descriptions, -> { active }, foreign_key: :conceptid
+    has_many :synonyms, -> { active.synonyms }, foreign_key: :conceptid, class_name: "Description"
+
+    scope :active, -> { where(active: "1") }
+    scope :leaf_concepts, lambda {
+      concepts = SnomedModel::Relationship
+                  .select("destinationid::bigint")
+                  .active
+                  .where(typeid: SnomedModel::Relationship::IS_A_RELATION)
+                  .group(:destinationid)
+                  
+      SnomedModel::Concept.active.where.not(id: concepts)
+    }
+
+    def direct_descendant
+      Description
+        .active
+        .where(conceptid: Relationship.active.direct_descendant(id).pluck(:sourceid))
+    end
+
+    def direct_ancestors
+      Description
+        .active
+        .where(conceptid: Relationship.active.direct_ancestors(id).pluck(:destinationid))
+    end
+
+    def detail
+      Description.active.detail(id)
+    end
+
+    def build_or_find_vertex(dag, code)
+      vertex = dag.vertices.detect { |c| c[:code] == code }
+      return vertex if vertex
+
+      dag.add_vertex(code: code)
+    end
+
+    def ancestor_relationships
+      Relationship.active.direct_ancestors(id)
+    end
+
+    def decedant_relationships
+      Relationship.active.direct_descendant(id)
+    end
+    
+    def build_ancestor_dag
+      code = id
+      dag = DAG.new
+      queue = Queue.new
+      queue.push(code)
+
+      loop do
+        source = queue.pop
+        destinations = Concept.find(source).ancestor_relationships.distinct(:destinationid).pluck(:destinationid)
+        break unless destinations.any?
+
+        source_vertex = build_or_find_vertex(dag, source)
+        destinations.each do |dest|
+          add_edge(dag, source_vertex, dest)
+          queue.push(dest)
+          break if dest == ROOT_CONCEPT
+        end
+      end
+      dag
+    end
+
+    def build_descendant_dag(dag)
+      code = id
+      queue = Queue.new
+      queue.push(code)
+      leaf_nodes = []
+
+      loop do
+        puts "queue length #{queue.length}"
+        break if queue.empty?
+
+        destination = queue.pop
+        puts "current code is #{destination}"
+        sources = Concept.find(destination).decedant_relationships.distinct(:sourceid).pluck(:sourceid)
+        if sources.empty?
+          leaf_nodes << destination
+        end
+
+        sources.each do |source|
+          source_vertex = build_or_find_vertex(dag, source)
+          add_edge(dag, source_vertex, destination)
+          queue.push(source)
+        end
+      end
+      [dag, leaf_nodes]
+    end
+
+    def add_edge(dag, source_vertex, destination)
+      dest_vertex = build_or_find_vertex(dag, destination)
+      dag.add_edge from: source_vertex, to: dest_vertex
+    end
+
+    def find_all_paths(dag, start, path = [])
+      path += [start]
+      if start[:code] == ROOT_CONCEPT
+        @paths = (paths.presence || []) + [path]
+        path = []
+      end
+      start.successors.each do |ver|
+        find_all_paths(dag, ver, path)
+      end
+
+      paths
+    end
+
+    def build_paths
+      dag = build_ancestor_dag
+
+      start = build_or_find_vertex(dag, id)
+
+      paths = find_all_paths(dag, start).map do |path|
+        path_str = path.map do |v|
+          v[:code]
+        end.reverse.join(".")
+
+        { path: path_str }
+      end
+
+      Hirerachy.insert_all(paths)
+    end
+
+    def fetch_concepts(paths)
+      concepts = paths.each_with_object([]) do |path, array|
+        array << path.subpath.split(".")
+      end.flatten.uniq
+
+      Concept.active.includes(:descriptions).where(id: (concepts - [id.to_s]))
+    end
+
+    def descendant
+      fetch_concepts(Hirerachy.descendant(id))
+    end
+
+    def ancestors
+      fetch_concepts(Hirerachy.ancestors(id))
+    end
+
+    def disease?
+      ancestors.exists?(id: DISEASE_CONCEPT)
+    end
+
+    def clinical_finding?
+      ancestors.exists?(id: CLINICAL_FINDING)
+    end
+  end
+end

data/lib/snomed_model/description.rb

@@ -0,0 +1,15 @@
+module SnomedModel
+  class Description < ActiveRecord::Base
+    FSN = "900000000000003001".freeze
+    SYNONYM = "900000000000013009".freeze
+    PREFERRED = "900000000000548007".freeze
+
+    belongs_to :concept, foreign_key: "conceptid"
+
+    scope :active, -> { where(active: "1") }
+    scope :detail, ->(id) { where(conceptid: id) }
+    scope :fsns, -> { where(typeid: FSN) }
+    scope :synonyms, -> { where(typeid: SYNONYM) }
+    scope :preferred, -> { where(typeid: PREFERRED) }
+  end
+end

data/lib/snomed_model/hirerachy.rb

@@ -0,0 +1,13 @@
+module SnomedModel
+  class Hirerachy < ActiveRecord::Base
+    ltree :path
+
+    scope :concept_paths, ->(conceptid) { where("path ~ ?", "*.#{conceptid}.*") }
+    scope :descendant, lambda { |conceptid|
+      select("subpath(path, index(path, '#{conceptid}'), nlevel(path)) as subpath").concept_paths(conceptid)
+    }
+    scope :ancestors, lambda { |conceptid|
+      select("subpath(path, 0, index(path, '#{conceptid}')) as subpath").concept_paths(conceptid)
+    }
+  end
+end

data/lib/snomed_model/relationship.rb

@@ -0,0 +1,13 @@
+module SnomedModel
+  class Relationship < ActiveRecord::Base
+    IS_A_RELATION = "116680003".freeze
+
+    scope :active, -> { where(active: "1") }
+    scope :direct_descendant, lambda { |conceptid|
+      where(typeid: IS_A_RELATION, destinationid: conceptid)
+    }
+    scope :direct_ancestors, lambda { |conceptid|
+      where(typeid: IS_A_RELATION, sourceid: conceptid)
+    }
+  end
+end

data/lib/snomed_model/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module SnomedModel
+  VERSION = "0.1.0"
+end

data/lib/snomed_model.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+require "active_record"
+require "yaml"
+require "erb"
+require "dag"
+require "pg_ltree"
+
+require_relative "snomed_model/version"
+require_relative "snomed_model/concept"
+require_relative "snomed_model/description"
+require_relative "snomed_model/relationship"
+require_relative "snomed_model/hirerachy"
+
+module SnomedModel
+  class Error < StandardError; end
+  # Your code goes here...
+end
+
+file = File.expand_path("./db/config.yml")
+config = YAML.load_file(file, aliases: true)
+env = config[ENV["SNOMED_ENV"] || "development"]
+
+ActiveRecord::Base.establish_connection(
+  adapter:  env["adapter"],
+  database: ERB.new(env["database"]).result,
+  username: ERB.new(env["username"]).result,
+  password: ERB.new(env["password"]).result,
+  host:     ERB.new(env["host"]).result
+)

data/lib/tasks/snomed.rake

@@ -0,0 +1,98 @@
+namespace :snomed do 
+  task :load_concepts, [:arg] do |_, args|
+    file = args[:arg]
+    records = []
+
+    File.open(file, "r") do |f|
+      f.each_line do |line|
+        row = line.split("\t")
+        
+        next if row[0] == "id"
+        
+        records << {
+          id: row[0],
+          effectivetime: row[1],
+          active: row[2],
+          moduleid: row[3],
+          definitionstatusid: row[4].to_i
+        }
+      end
+    end
+    SnomedModel::Concept.insert_all(records)
+  end
+
+  task :load_descriptions, [:arg] do |_, args|
+    file = args[:arg]
+    records = []
+
+    File.open(file, "r") do |f|
+      f.each_line do |line|
+        row = line.split("\t")
+        
+        next if row[0] == "id"
+        
+        records << {
+          id: row[0],
+          effectivetime: row[1],
+          active: row[2],
+          moduleid: row[3],
+          conceptid: row[4],
+          languagecode: row[5],
+          typeid: row[6],
+          term: row[7],
+          casesignificanceid: row[8].to_i
+        }
+      end
+    end
+    records.each_slice(10000) do |batch|
+      p "Inserting batch....."
+      SnomedModel::Description.insert_all(batch)
+    end
+  end
+
+  task :load_relationships, [:arg] do |_, args|
+    file = args[:arg]
+    records = []
+
+    File.open(file, "r") do |f|
+      f.each_line do |line|
+        row = line.split("\t")
+        
+        next if row[0] == "id"
+        
+        records << {
+          id: row[0],
+          effectivetime: row[1],
+          active: row[2],
+          moduleid: row[3],
+          sourceid: row[4],
+          destinationid: row[5],
+          relationshipgroup: row[6],
+          typeid: row[7],
+          characteristictypeid: row[8],
+          modifierid: row[9].to_i,
+        }
+      end
+    end
+    records.each_slice(10000) do |batch|
+      p "Inserting batch....."
+      SnomedModel::Relationship.insert_all(batch)
+    end
+  end
+
+  task :build_paths_for_sample_data do
+    Concept.leaf_concepts.order('random()').limit(100).map do |concept|
+      puts "Building path for #{concept.id}....."
+      concept.build_paths
+    end
+  end
+
+  task :build_paths do
+    Concept.leaf_concepts.find_in_batches do |group|
+      group.map do |concept|
+        puts "Building path for #{concept.id}....."
+        concept.build_paths
+      end
+    end
+  end
+end

data/sig/snomed_model.rbs

@@ -0,0 +1,4 @@
+module SnomedModel
+  VERSION: String
+  # See the writing guide of rbs: https://github.com/ruby/rbs#guides
+end

metadata

@@ -0,0 +1,157 @@
+--- !ruby/object:Gem::Specification
+name: snomed_model
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Siva Gollapalli
+autorequire:
+bindir: exe
+cert_chain: []
+date: 2024-04-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: activerecord
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '7.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 7.1.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '7.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 7.1.2
+- !ruby/object:Gem::Dependency
+  name: standalone_migrations
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '7.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 7.1.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '7.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 7.1.3
+- !ruby/object:Gem::Dependency
+  name: pg
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.5.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.5.4
+- !ruby/object:Gem::Dependency
+  name: dag
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.0.9
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.0.9
+- !ruby/object:Gem::Dependency
+  name: pg_ltree
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description:
+email:
+- sivagollapalli88@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".rspec"
+- ".rubocop.yml"
+- CHANGELOG.md
+- CODE_OF_CONDUCT.md
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- build_concept_full_relationship.rb
+- db/config.yml
+- db/migrate/20240106111800_add_concept_table.rb
+- db/migrate/20240106124817_add_index_to_concepts.rb
+- db/migrate/20240106153438_add_description_table.rb
+- db/migrate/20240106161110_add_relationship_table.rb
+- db/migrate/20240109131657_enable_ltree_extension.rb
+- db/migrate/20240109131738_add_hirerachy_table.rb
+- db/schema.rb
+- lib/snomed_model.rb
+- lib/snomed_model/concept.rb
+- lib/snomed_model/description.rb
+- lib/snomed_model/hirerachy.rb
+- lib/snomed_model/relationship.rb
+- lib/snomed_model/version.rb
+- lib/tasks/snomed.rake
+- sig/snomed_model.rbs
+homepage:
+licenses:
+- MIT
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.6.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.2.3
+signing_key:
+specification_version: 4
+summary: Provides ORM layer to query SNOMED
+test_files: []