specify_cli 0.0.5

data/lib/specify/configuration/host_config.rb

@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+module Specify
+  module Configuration
+    # HostConfigs are configurations that map file directories to host names.
+    class HostConfig < Config
+      # Retutrns a new HostConfig for +file+ (a YAML file).
+      def initialize(file = nil)
+        super(file)
+        @saved = true
+      end
+
+      # Returns +true+ if +directory+ is mapped to a host name.
+      def directory?(directory)
+        params.key? directory
+      end
+
+      # Maps +directory+ to +host+.
+      def map_directory(directory, host)
+        raise "Directory '#{directory}' already mapped" if params[directory]
+        params[directory] = host
+        touch
+      end
+
+      # Returns a Hash with the parameters for the current directory mappings
+      # from the configuration YAML file.
+      def params
+        super.fetch :dir_names
+      end
+
+      # Returns the host name that is mapped to +directory+
+      def resolve_host(directory)
+        params.fetch directory
+      end
+    end
+  end
+end

data/lib/specify/database.rb

@@ -0,0 +1,140 @@
+# frozen_string_literal: true
+
+module Specify
+  # Databases represent _Specify_ database.
+  class Database
+    # The Sequel::Database instance for the current connection.
+    attr_accessor :connection
+
+    # The name of the _Specify_ database.
+    attr_reader :database
+
+    # The name of the MySQL/MariaDB host for the _Specify_ database.
+    attr_reader :host
+
+    # The port for the MySQL/MariaDB server for the _Specify_ database.
+    attr_reader :port
+
+    # An Array of Specify::Session instances currently registered (and open).
+    attr_reader :sessions
+
+    # The MySQL/MariaDB user for the database. This is typically the _Specify_
+    # <em>master user</em>.
+    attr_reader :user
+
+    # Creates a new Database from +config_file+ file (a _YAML_ file).
+    #
+    # +config_file+ should have the structure:
+    #     ---
+    #     :hosts:
+    #       <hostname>:
+    #         :port: <port_number>
+    #         :databases:
+    #           <database_name>:
+    #             :db_user:
+    #               :name: <mysql_username>
+    #               :password: <password>
+    #             :sp_user: <specify_username>
+    #
+    # Items prefices with +:+ will be deserialized as symbols. Leave
+    # +:password:+ blank to be prompted.
+    #
+    # +host+: the name of the MySQL/MariaDB host for the database.
+    # +database+: the name of the MySQL/MariaDB database.
+    def self.load_config(host, database, config_file = nil)
+      config = Configuration::DBConfig.new(host, database, config_file)
+      new(database, config.connection)
+    end
+
+    # Returns a new Database for the +database+ (the name of the database) on
+    # +host+.
+    #
+    # +port+: the port for the MySQL/MariaDB server for the database.
+    #
+    # +user+: the MySQL/MariaDB user (typically the _Specify_
+    # <em>master user</em>).
+    #
+    # +password+: the password for the MySQL/MariaDB user.
+    def initialize(database,
+                   host: 'localhost',
+                   port: 3306,
+                   user: 'root',
+                   password: nil)
+      @database = database
+      @host = host
+      @port = port
+      @user = user
+      @password = password || prompt
+      @connection = nil
+      @sessions = []
+      ObjectSpace.define_finalizer(self, method(:close))
+      yield(self) if block_given?
+    end
+
+    # Adds a new Session to the sessions pool.
+    def <<(session)
+      session.open
+      session.add_observer self
+      sessions << session
+    end
+
+    # Closes all sessions.
+    def close
+      return if sessions.empty?
+      sessions.each do |session|
+        session.close
+        session.delete_observer self
+      end
+      # TODO: should close database connection
+    end
+
+    # Establishes a connection and creates the object if it does not already
+    # exist. Loads all Specify::Model classes.
+    #
+    # Returns the Sequel::Database object for the database.
+    def connect
+      return connection if connection
+      @connection = Sequel.connect adapter: :mysql2,
+                                   user: @user,
+                                   password: @password,
+                                   host: @host,
+                                   port: @port,
+                                   database: @database
+      require_relative 'models'
+      connection
+    end
+
+    # Creates a string representation of +self+.
+    def inspect
+      "#{self} database: #{@database}, host: #{@host}, port: #{@port}"\
+      ", user: #{@user}, connected: #{connection ? true : false}"
+    end
+
+    # Createas a new Session for +user+ (String, an existing
+    # Specify::Model::User#name) in +collection+ (String, an existing
+    # Specify::Model::Collection#name) and adds it to the #sessions pool.
+    #
+    # Returns the new Session.
+    def start_session(user, collection)
+      connect
+      session = Session.new user, collection
+      self << session
+      session
+    end
+
+    # Deletes a +session+ (a Session) from the sessions pool when +session+
+    # has been closed.
+    def update(session)
+      sessions.delete session
+    end
+
+    private
+
+    def prompt
+      print 'password: '
+      password = STDIN.noecho(&:gets).chomp
+      puts
+      password
+    end
+  end
+end

data/lib/specify/models.rb

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+Sequel.extension :inflector
+
+Sequel.inflections do |inflect|
+  inflect.irregular 'taxon', 'taxa'
+end
+
+String.inflections do |inflect|
+  inflect.irregular 'taxon', 'taxa'
+end
+
+require_relative 'models/tree_queryable'
+require_relative 'models/createable'
+require_relative 'models/updateable'
+require_relative 'models/accession'
+require_relative 'models/agent'
+require_relative 'models/app_resource_data'
+require_relative 'models/app_resource_dir'
+require_relative 'models/auto_numbering_scheme'
+require_relative 'models/collecting_event'
+require_relative 'models/collection'
+require_relative 'models/collection_object'
+require_relative 'models/determination'
+require_relative 'models/discipline'
+require_relative 'models/division'
+require_relative 'models/geography'
+require_relative 'models/institution'
+require_relative 'models/locality'
+require_relative 'models/preparation'
+require_relative 'models/preparation_type'
+require_relative 'models/record_set'
+require_relative 'models/record_set_item'
+require_relative 'models/taxonomy'
+require_relative 'models/user'
+require_relative 'models/view_set_object'
+
+module Specify
+  # Model contains Sequel::Model classes for the _Specify_ schema.
+  module Model
+    AMBIGUOUS_MATCH_ERROR = 'Ambiguous results during search'
+  end
+end

data/lib/specify/models/accession.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # Accessions are _interactions_ that represent the formal transferral of
+    # ownership of one or more #collection_objects (instances of
+    # Specify::Model::CollectionObjects).
+    #
+    # An Accession belongs to a #division (an instance of
+    # Specify::Model::Division).
+    class Accession < Sequel::Model(:accession)
+      include Createable
+      include Updateable
+
+      many_to_one :division,
+                  key: :DivisionID
+      many_to_one :created_by,
+                  class: 'Specify::Model::Agent',
+                  key: :CreatedByAgentID
+      many_to_one :modified_by,
+                  class: 'Specify::Model::Agent',
+                  key: :ModifiedByAgentID
+      one_to_many :collection_objects,
+                  key: :AccessionID
+
+      # Returns a String with the accession number (a number under which all
+      # information relating to an accession is filed).
+      def number
+        self[:AccessionNumber]
+      end
+    end
+  end
+end

data/lib/specify/models/agent.rb

@@ -0,0 +1,138 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # Agents represent entities (people or organizations).
+    #
+    # An Agent represents a Specify::Model::User in a Specify::Model::Division;
+    # that agent will be associated with every record creation and modification
+    # carried out by the user in the database.
+    class Agent < Sequel::Model(:agent)
+      include Updateable
+
+      many_to_one :user,
+                  key: :SpecifyUserID
+      many_to_one :division,
+                  key: :DivisionID
+
+      one_to_many :created_accessions,
+                  class: 'Specify::Model::Accession',
+                  key: :CreatedByAgentID
+      one_to_many :modified_accessions,
+                  class: 'Specify::Model::Accession',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_app_resource_data,
+                  class: 'Specify::Model::AppResourceData',
+                  key: :CreatedByAgentID
+      one_to_many :modified_app_resource_data,
+                  class: 'Specify::Model::AppResourceData',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_app_resource_dirs,
+                  class: 'Specify::Model::AppResourceDir',
+                  key: :CreatedByAgentID
+      one_to_many :modified_app_resource_dirs,
+                  class: 'Specify::Model::AppResourceDir',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_autonumbering_schemes,
+                  class: 'Specify::Model::AutonumberinScheme',
+                  key: :CreatedByAgentID
+      one_to_many :modified_autonumbering_schemes,
+                  class: 'Specify::Model::AutonumberinScheme',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_collecting_events,
+                  class: 'Specify::Model::CollectingEvent',
+                  key: :CreatedByAgentID
+      one_to_many :modified_collecting_events,
+                  class: 'Specify::Model::CollectingEvent',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_colection_objects,
+                  class: 'Specify::Model::CollectionObject',
+                  key: :CreatedByAgentID
+      one_to_many :modified_colection_objects,
+                  class: 'Specify::Model::CollectionObject',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_determinations,
+                  class: 'Specify::Model::Determination',
+                  key: :CreatedByAgentID
+      one_to_many :modified_determinations,
+                  class: 'Specify::Model::Determination',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_localities,
+                  class: 'Specify::Model::Locality',
+                  key: :CreatedByAgentID
+      one_to_many :modified_localities,
+                  class: 'Specify::Model::Locality',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_preparations,
+                  class: 'Specify::Model::Preparation',
+                  key: :CreatedByAgentID
+      one_to_many :modified_preparations,
+                  class: 'Specify::Model::Preparation',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_preparation_types,
+                  class: 'Specify::Model::PreparationType',
+                  key: :CreatedByAgentID
+      one_to_many :modified_preparation_types,
+                  class: 'Specify::Model::PreparationType',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_record_sets,
+                  class: 'Specify::Model::RecordSet',
+                  key: :CreatedByAgentID
+      one_to_many :modified_record_sets,
+                  class: 'Specify::Model::RecordSet',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_record_set_items,
+                  class: 'Specify::Model::RecordSetItem',
+                  key: :CreatedByAgentID
+      one_to_many :modified_record_set_items,
+                  class: 'Specify::Model::RecordSetItem',
+                  key: :ModifiedByAgentID
+
+      one_to_many :created_view_set_objects,
+                  class: 'Specify::Model::ViewSetObject',
+                  key: :CreatedByAgentID
+      one_to_many :modified_view_set_objects,
+                  class: 'Specify::Model::ViewSetObject',
+                  key: :ModifiedByAgentID
+
+      # Returns a String that is the first name of a person.
+      def first_name
+        self[:FirstName]
+      end
+
+      # Returns a String of attributes concatanated according to the
+      # +formatter+.
+      def full_name(formatter = nil)
+        formatter ||= "#{last_name}, #{first_name} #{middle_name}"
+        formatter.strip
+      end
+
+      # Returns a String that is the last name of a person or the name of an
+      # organization.
+      def last_name
+        self[:LastName]
+      end
+
+      # Returns a String that is the middle name of a person.
+      def middle_name
+        self[:MiddleInitial]
+      end
+
+      # Creates a string representation of +self+.
+      def to_s
+        full_name
+      end
+    end
+  end
+end

data/lib/specify/models/app_resource_data.rb

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # AppResourceData hold data the _Specify_ application uses (usually in the
+    # form of _XML_ files that are stored as blobs).
+    #
+    # An AppResourceData belongs to a #viewsetobj (an instance of
+    # Specify::Model::ViewSetObject) or AppResource (not implemented).
+    class AppResourceData < Sequel::Model(:spappresourcedata)
+      include Createable
+      include Updateable
+
+      many_to_one :viewsetobj,
+                  class: 'Specify::Model::ViewSetObject',
+                  key: :SpViewSetObjID
+      many_to_one :created_by,
+                  class: 'Specify::Model::Agent',
+                  key: :CreatedByAgentID
+      many_to_one :modified_by,
+                  class: 'Specify::Model::Agent',
+                  key: :ModifiedByAgentID
+
+      # Stores the contents of +data_file+ (typically an _.xml_ file) as a
+      # blob in the database.
+      def import(data_file)
+        self.data = Sequel.blob(File.read(data_file))
+        save
+      end
+    end
+  end
+end

data/lib/specify/models/app_resource_dir.rb

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # AppResourceDirs associate instances of Specify::Model::ViewSetObject
+    # or AppResource (not implemented) with other Specify::Model classes,
+    # such as Specify::Model::Collection, Specify::Model::Discipline, or
+    # Specify::Model::User, as well as the abstract/custom Specify::UserType,
+    # and are used to locate a relevant ViewSetObject or AppResource for a
+    # given instance of one of these classes.
+    #
+    # Resources (ViewSetObjects or AppResurces) are usually _XML_ files used
+    # by the _Specify_ application. The files are stored in the AppResourceDirs
+    # associated #view_set_object's or AppResource (not implemented)
+    # Specify::Model::AppResourceData.
+    class AppResourceDir < Sequel::Model(:spappresourcedir)
+      include Createable
+      include Updateable
+
+      many_to_one :discipline,
+                  key: :DisciplineID
+      many_to_one :collection,
+                  key: :CollectionID
+      many_to_one :user,
+                  key: :SpecifyUserID
+      one_to_one :view_set_object,
+                 class: 'Specify::Model::ViewSetObject',
+                 key: :SpAppResourceDirID
+      many_to_one :created_by,
+                  class: 'Specify::Model::Agent',
+                  key: :CreatedByAgentID
+      many_to_one :modified_by,
+                  class: 'Specify::Model::Agent',
+                  key: :ModifiedByAgentID
+
+      # Returns a String that is the discipline type (same as
+      # Specify::Model::Discipline#name) +self+ belongs to.
+      def discipline_type
+        self[:DisciplineType]
+      end
+    end
+  end
+end