salad 0.0.1

data/lib/salad/generate_gem_help.rb

@@ -0,0 +1,242 @@
+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+# Generates gem_help.rb by extracting documentation from gem source files
+# Usage: ruby generate_gem_help.rb > lib/salad/gem_help.rb
+
+require 'json'
+
+def get_gem_description(gem_name)
+  descriptions = {
+    bananomia: "Wrapper for Bionomia API - access specimen and collection records",
+    bell_pepper: "Wrapper for BELS API - georeference locality descriptions via the Biodiversity Enhanced Location Services",
+    bok_choy: "Wrapper for BHLnames API - access Biodiversity Heritage Library names data",
+    checkerberry: "Wrapper for GNverifier API - verify and search scientific names across curated databases",
+    colrapi: "Wrapper for Catalogue of Life (ChecklistBank) API - access global taxonomic checklists and name data",
+    crawlyflower: "Wrapper for WoRMS API - access World Register of Marine Species data",
+    hookkaido: "Wrapper for OWL Ontology API - access ontology data",
+    nasturtium: "Wrapper for iNaturalist API - access species observations and biodiversity data",
+    plazucchini: "Wrapper for Plazi TreatmentBank API - access taxonomic treatments and species data",
+    syconium: "Wrapper for OpenAlex API - access research publications and academic data",
+    wikimelon: "Wrapper for Wikidata API - access linked open knowledge data"
+  }
+  descriptions[gem_name] || "API wrapper for biodiversity data"
+end
+
+def get_gem_api_url(gem_name)
+  urls = {
+    bananomia: "https://bionomia.net",
+    bell_pepper: "https://bels.geo-vocab.org/",
+    bok_choy: "https://www.biodiversitylibrary.org/api",
+    checkerberry: "https://verifier.globalnames.org",
+    colrapi: "https://www.checklistbank.org/api",
+    crawlyflower: "https://www.marinespecies.org/rest/",
+    hookkaido: "https://www.ontobee.org",
+    nasturtium: "https://api.inaturalist.org/v1",
+    plazucchini: "https://api.plazi.org",
+    syconium: "https://api.openalex.org",
+    wikimelon: "https://www.wikidata.org/w/api.php"
+  }
+  urls[gem_name] || ""
+end
+
+class YardDocExtractor
+  def initialize(lib_filepath, test_dir = nil)
+    @lib_filepath = lib_filepath
+    @test_dir = test_dir
+    @content = File.read(lib_filepath) if File.exist?(lib_filepath)
+    @test_content = load_test_files(test_dir)
+  end
+
+  def extract_all_methods
+    return {} unless @content
+
+    methods = {}
+    lines = @content.split("\n")
+    i = 0
+
+    while i < lines.size
+      line = lines[i]
+
+      # Find method definition
+      if line.match?(/^\s*def\s+self\.(\w+)/)
+        method_name = line.match(/def\s+self\.(\w+)/)[1]
+
+        # Look backwards for docstring
+        docstring_lines = []
+        j = i - 1
+        while j >= 0 && lines[j].match?(/^\s*#/)
+          docstring_lines.unshift(lines[j])
+          j -= 1
+        end
+
+        docstring_text = docstring_lines.join("\n")
+        data = parse_docstring(docstring_text)
+
+        # Extract examples from test files
+        data[:examples] = extract_examples_for_method(method_name)
+
+        methods[method_name.to_sym] = data
+      end
+
+      i += 1
+    end
+
+    methods
+  end
+
+  def load_test_files(test_dir)
+    return "" unless test_dir && File.directory?(test_dir)
+
+    test_content = ""
+    Dir.glob("#{test_dir}/**/*_test.rb").each do |file|
+      test_content += File.read(file) + "\n"
+    end
+    test_content
+  end
+
+  private
+
+  def extract_examples_for_method(method_name)
+    return [] unless @test_content && @test_content.length > 0
+
+    examples = []
+
+    # Look for method calls in test files
+    # Patterns: ModuleName.method_name(...) or Gem.method_name(...)
+    @test_content.scan(/([A-Z][a-z]*\.)?#{Regexp.escape(method_name)}\([^)]*\)/) do |match|
+      example = $&
+      examples << example unless examples.include?(example) || example.length > 100
+    end
+
+    examples[0...3]  # Return up to 3 examples
+  end
+
+  def parse_docstring(docstring_text)
+    lines = docstring_text.split("\n")
+    clean_lines = lines.map { |line| line.sub(/^\s*#\s?/, '').rstrip }
+
+    # Extract summary
+    summary_idx = clean_lines.index { |l| !l.empty? && !l.start_with?('@') }
+    summary = summary_idx ? clean_lines[summary_idx] : ""
+
+    # Extract @param lines
+    params = {}
+    current_param = nil
+
+    clean_lines.each do |line|
+      if line.start_with?('@param ')
+        params[current_param[:name]] = current_param[:desc] if current_param
+
+        if line =~ /@param\s+(\w+)\s+\[([^\]]+)\]\s*(.*?)$/
+          param_name = $1.to_sym
+          param_desc = $3.strip
+          current_param = { name: param_name, desc: param_desc }
+        elsif line =~ /@param\s+(\w+)\s+(.*)$/
+          param_name = $1.to_sym
+          param_desc = $2.strip
+          current_param = { name: param_name, desc: param_desc }
+        end
+      elsif line.start_with?('@') && current_param
+        params[current_param[:name]] = current_param[:desc]
+        current_param = nil
+      elsif current_param && !line.empty?
+        current_param[:desc] += " #{line}"
+      end
+    end
+
+    params[current_param[:name]] = current_param[:desc] if current_param
+
+    { summary: summary, params: params }
+  end
+end
+
+# Configuration for all gems with their test paths (from source repos).
+# Lib paths are resolved from installed gem specs. Test paths are looked up
+# under SFG_SRC_DIR (defaults to ~/src/github.com/speciesfilegroup).
+require 'rubygems'
+
+SFG_GEMS = %i[
+  bananomia bell_pepper bok_choy checkerberry colrapi crawlyflower
+  hookkaido nasturtium plazucchini syconium wikimelon
+].freeze
+
+SFG_SRC_DIR = ENV.fetch('SFG_SRC_DIR', File.expand_path('~/src/github.com/speciesfilegroup'))
+
+def gem_lib_path(name)
+  Gem::Specification.find_by_name(name.to_s).full_gem_path + "/lib/#{name}.rb"
+rescue Gem::MissingSpecError
+  nil
+end
+
+GEMS_CONFIG = SFG_GEMS.each_with_object({}) do |name, h|
+  h[name] = {
+    lib: gem_lib_path(name),
+    test: File.join(SFG_SRC_DIR, name.to_s, 'test')
+  }
+end.freeze
+
+# Extract documentation from all gems
+gem_docs = {}
+GEMS_CONFIG.each do |gem_name, paths|
+  extractor = YardDocExtractor.new(paths[:lib], paths[:test])
+  gem_docs[gem_name] = extractor.extract_all_methods
+end
+
+# Generate Ruby code
+ruby_code = "# frozen_string_literal: true\n\n"
+ruby_code += "module Salad\n"
+ruby_code += "  GEM_HELP = {\n"
+
+gem_docs.each do |gem_name, methods|
+  ruby_code += "    #{gem_name.inspect} => {\n"
+  ruby_code += "      description: \"#{get_gem_description(gem_name)}\",\n"
+  ruby_code += "      api: \"#{get_gem_api_url(gem_name)}\",\n"
+  ruby_code += "      endpoints: {\n"
+
+  methods.each do |method_name, data|
+    ruby_code += "        #{method_name.inspect} => {\n"
+    ruby_code += "          description: #{data[:summary].inspect},\n"
+
+    # Add params
+    if data[:params].any?
+      ruby_code += "          params: {\n"
+      data[:params].each do |param_name, param_desc|
+        clean_desc = param_desc.gsub(/\n/, ' ').strip
+        ruby_code += "            #{param_name.inspect} => #{clean_desc.inspect},\n"
+      end
+      ruby_code += "          },\n"
+    else
+      ruby_code += "          params: {},\n"
+    end
+
+    # Add examples
+    examples = data[:examples] || []
+    if examples.any?
+      ruby_code += "          examples: [\n"
+      examples.each do |example|
+        ruby_code += "            #{example.inspect},\n"
+      end
+      ruby_code += "          ],\n"
+    else
+      ruby_code += "          examples: [],\n"
+    end
+
+    ruby_code += "        },\n"
+  end
+
+  ruby_code += "      },\n"
+  ruby_code += "    },\n"
+end
+
+ruby_code += "  }.freeze\n"
+ruby_code += "end\n"
+
+puts ruby_code
+
+# Print summary stats
+STDERR.puts "\n=== GENERATION SUMMARY ===\n\n"
+gem_docs.each do |gem_name, methods|
+  STDERR.puts "#{gem_name.to_s.ljust(15)}: #{methods.size} endpoints"
+end
+STDERR.puts "\nTotal endpoints: #{gem_docs.values.map(&:size).sum}"

data/lib/salad/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module Salad
+  VERSION = '0.0.1'
+end

data/lib/salad.rb

@@ -0,0 +1,126 @@
+# frozen_string_literal: true
+
+require 'salad/version'
+require 'salad/catalogue_of_life'
+
+module Salad
+  GEMS = %w[
+    bananomia
+    bell_pepper
+    bok_choy
+    checkerberry
+    colrapi
+    crawlyflower
+    hookkaido
+    nasturtium
+    plazucchini
+    syconium
+    wikimelon
+  ].freeze
+
+  SERVICES = {
+    bels:               'bell_pepper',
+    bhlnames:           'bok_choy',
+    bionomia:           'bananomia',
+    catalogue_of_life:  'colrapi',
+    checklistbank:      'colrapi',
+    clb:                'colrapi',
+    col:                'colrapi',
+    gnverifier:         'checkerberry',
+    inaturalist:        'nasturtium',
+    owl:                'hookkaido',
+    openalex:           'syconium',
+    plazi:              'plazucchini',
+    wikidata:           'wikimelon',
+    worms:              'crawlyflower'
+  }.freeze
+
+  class << self
+    def gem_module(gem_name)
+      name = gem_name.split('_').map(&:capitalize).join
+      Object.const_get(name)
+    rescue NameError
+      raise NameError, "Cannot find top-level module for gem #{gem_name.inspect} (expected #{name})"
+    end
+
+    def services
+      SERVICES
+    end
+
+    # Top-level constants Salad will offer for case-insensitive tab-completion
+    # in the REPL.
+    def completable_names
+      @completable_names ||= (['Salad'] + GEMS.map { |g| gem_module(g).to_s }).freeze
+    end
+
+    # Regex matching any non-empty prefix of length >= 3 of any completable name.
+    # Built by enumerating prefixes and joining with `|`. Each prefix is escaped
+    # so weird characters in a name can't change the regex's meaning. The 3-char
+    # minimum keeps short ambiguous input (`s`, `c`) falling through to Pry's
+    # default completion.
+    COMPLETABLE_PREFIX_MIN = 3
+
+    def completable_prefix_regex
+      @completable_prefix_regex ||= build_prefix_regex(completable_names)
+    end
+
+    # Names offered as completions after `help `. Uses CamelCase module names
+    # for the bundled gems (so `help nast<TAB>` -> `help Nasturtium`) plus the
+    # lowercase service aliases (so `help inat<TAB>` -> `help inaturalist`).
+    # `Salad` itself is the literal services-listing topic.
+    def help_completable_names
+      @help_completable_names ||= (completable_names + SERVICES.keys.map(&:to_s)).uniq.freeze
+    end
+
+    # Reverse lookup: 'Nasturtium' -> 'nasturtium', 'BellPepper' -> 'bell_pepper'.
+    # Returns nil for unknown module names.
+    def gem_for_module(module_name)
+      @gem_for_module ||= GEMS.each_with_object({}) do |g, h|
+        h[gem_module(g).to_s] = g
+      end.freeze
+      @gem_for_module[module_name]
+    end
+
+    def help_completable_prefix_regex
+      @help_completable_prefix_regex ||= build_prefix_regex(help_completable_names, prefix: 'help\\s+')
+    end
+
+    def build_prefix_regex(names, prefix: '')
+      prefixes = names.flat_map { |n| (COMPLETABLE_PREFIX_MIN..n.length).map { |i| n[0...i] } }
+      Regexp.new("\\A#{prefix}(?:#{prefixes.map { |p| Regexp.escape(p) }.join('|')})\\z", Regexp::IGNORECASE)
+    end
+
+    def help
+      puts 'Salad services — access by service name or gem name:'
+      service_width = SERVICES.keys.map { |s| s.to_s.length }.max
+      gem_width = SERVICES.values.map(&:length).max
+      SERVICES.sort.each do |service, gem_name|
+        mod = begin
+          gem_module(gem_name).to_s
+        rescue NameError
+          '(not loaded)'
+        end
+        printf "  Salad.%-#{service_width}s  Salad.%-#{gem_width}s  ->  %s\n", service, gem_name, mod
+      end
+      nil
+    end
+  end
+
+  COL_SCOPED_SERVICES = %i[catalogue_of_life col].freeze
+
+  SERVICES.each do |service, gem_name|
+    if COL_SCOPED_SERVICES.include?(service)
+      define_singleton_method(service) do
+        @catalogue_of_life ||= CatalogueOfLife.new
+      end
+    else
+      define_singleton_method(service) { gem_module(gem_name) }
+    end
+  end
+
+  GEMS.each do |gem_name|
+    define_singleton_method(gem_name) { gem_module(gem_name) }
+  end
+end
+
+Salad::GEMS.each { |g| require g }

metadata

@@ -0,0 +1,297 @@
+--- !ruby/object:Gem::Specification
+name: salad
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Geoff Ower
+bindir: exe
+cert_chain: []
+date: 1980-01-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.15'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.15'
+- !ruby/object:Gem::Dependency
+  name: bond
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.5'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.5'
+- !ruby/object:Gem::Dependency
+  name: rb-readline
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.5'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.5'
+- !ruby/object:Gem::Dependency
+  name: bananomia
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: bell_pepper
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: bok_choy
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+- !ruby/object:Gem::Dependency
+  name: checkerberry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+- !ruby/object:Gem::Dependency
+  name: colrapi
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: crawlyflower
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+- !ruby/object:Gem::Dependency
+  name: hookkaido
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: nasturtium
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: plazucchini
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+- !ruby/object:Gem::Dependency
+  name: syconium
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+- !ruby/object:Gem::Dependency
+  name: wikimelon
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.6'
+description: salad bundles the SpeciesFileGroup Ruby API wrappers (bananomia, bell_pepper,
+  bok_choy, checkerberry, colrapi, crawlyflower, hookkaido, nasturtium, plazucchini,
+  syconium, wikimelon) and ships a `salad` executable that launches a Pry console
+  with all of them pre-loaded and available under both their service names (Salad.inaturalist)
+  and their gem names (Salad.nasturtium).
+email:
+- gdower@illinois.edu
+executables:
+- salad
+extensions: []
+extra_rdoc_files: []
+files:
+- CHANGELOG.md
+- LICENSE.txt
+- README.md
+- exe/salad
+- lib/salad.rb
+- lib/salad/bond_completer.rb
+- lib/salad/catalogue_of_life.rb
+- lib/salad/console.rb
+- lib/salad/gem_help.rb
+- lib/salad/generate_gem_help.rb
+- lib/salad/version.rb
+homepage: https://github.com/SpeciesFileGroup/salad
+licenses:
+- MIT
+metadata:
+  homepage_uri: https://github.com/SpeciesFileGroup/salad
+  source_code_uri: https://github.com/SpeciesFileGroup/salad
+  changelog_uri: https://github.com/SpeciesFileGroup/salad/releases/tag/v0.0.1
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.7.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.6.9
+specification_version: 4
+summary: Unified Pry console for SpeciesFileGroup biodiversity API wrappers.
+test_files: []