specify_cli 0.0.5

data/lib/specify/models/division.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # Divisions are the next highest level of scope within a Specify::Database.
+    #
+    # A Division belongs to the single instance of Specify::Model::Institution
+    # within a Specify::Database.
+    #
+    # A Division has one or more instances of Specify::Model::Discipline.
+    #
+    # Specify::Model::Agent instances are scoped to the Division level.
+    class Division < Sequel::Model(:division)
+      include Updateable
+
+      many_to_one :institution,
+                  key: :InstitutionID
+      many_to_many :auto_numbering_schemes,
+                   left_key: :DivisionID,
+                   right_key: :AutoNumberingSchemeID,
+                   join_table: :autonumsch_div
+      one_to_many :accessions,
+                  key: :DivisionID
+    end
+  end
+end

data/lib/specify/models/geography.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+require_relative 'geography/administrative_division'
+require_relative 'geography/geographic_name'
+require_relative 'geography/geography'

data/lib/specify/models/geography/administrative_division.rb

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # AdministrativeDivision is the _rank_ class for the
+    # Specify::Model::Geography _tree_. An AdministrativeDivision holds
+    # information about a formal political subdivison in a <em>geographic
+    # tree</em>.
+    #
+    # A AdministrativeDivision has a _parent_ (another instance of
+    # AdministrativeDivision) unless it is the root rank of the _tree_ and can
+    # have one _child_ (another instance of AdministrativeDivision).
+    class AdministrativeDivision < Sequel::Model(:geographytreedefitem)
+      include Updateable
+
+      many_to_one :geography,
+                  key: :GeographyTreeDefID
+      one_to_many :geographic_names,
+                  key: :GeographyTreeDefItemID
+      one_to_one :child,
+                 class: self,
+                 key: :ParentItemID
+      many_to_one :parent, class: self,
+                  key: :ParentItemID
+
+      # Returns a String with the name of the formal political subdivision.
+      def name
+        self.Name
+      end
+    end
+  end
+end

data/lib/specify/models/geography/geographic_name.rb

@@ -0,0 +1,66 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # GeographicName is the _item_ class for the Specify::Model::Geography
+    # _tree_. A GeographicName holds information about the items to be
+    # classified, i.e. concepts of geographic names. Each GeographicName belongs
+    # to a Specify::Model::AdministrativeDivision, that represents the formal
+    # political subdivision in a geography.
+    #
+    # A GeographicName has a _parent_ (another instance of GeographicName)
+    # unless it is the root geographic name of the _tree_ and can have
+    # _children_ (other instances of GeographicName).
+    class GeographicName < Sequel::Model(:geography)
+      include Updateable
+
+      many_to_one :geography,
+                  key: :GeographyTreeDefID
+      many_to_one :rank,
+                  class: 'Specify::Model::AdministrativeDivision',
+                  key: :GeographyTreeDefItemID
+      many_to_one :parent,
+                  class: self,
+                  key: :ParentID
+      many_to_one :accepted_name,
+                  class: self,
+                  key: :AcceptedID
+      one_to_many :children,
+                  class: self,
+                  key: :ParentID
+      one_to_many :synonyms,
+                  class: self,
+                  key: :AcceptedID
+      one_to_many :localities,
+                  key: :GeographyID
+
+      # Assigns new instances that are created from a
+      # Specify::Model::AdministrativeDivision to the administrative division's
+      # Specify::Model::Geography. Sets _Version_, timestamp for
+      # creation, and a GUID for the record.
+      def before_create
+        self.geography = rank&.geography ||
+                         parent.rank&.geography
+        self[:Version] = 0
+        self[:TimestampCreated] = Time.now
+        self[:GUID] = SecureRandom.uuid
+        super
+      end
+
+      # Returns +true+ if +self+ has _children_.
+      def children?
+        !children.empty?
+      end
+
+      # Creates a string representation of +self+.
+      def inspect
+        "id: #{self.GeographyID}; Full Name: '#{self.FullName}'"
+      end
+
+      # Returns a String with the geographic name.
+      def name
+        self[:Name]
+      end
+    end
+  end
+end

data/lib/specify/models/geography/geography.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # Geography is the _tree_ class for the <em>geographic tree</em>.
+    # Geographies hold all Specify::Model::AdministrativeDivision and
+    # Specify::Model::GeographicName instances belonging to a geography used by
+    # a Specify::Model::Discipline.
+    class Geography < Sequel::Model(:geographytreedef)
+      include TreeQueryable
+      include Updateable
+
+      one_to_many :disciplines,
+                  key: :GeographyTreeDefID
+      one_to_many :ranks,
+                  class: 'Specify::Model::AdministrativeDivision',
+                  key: :GeographyTreeDefID
+      one_to_many :names,
+                  class: 'Specify::Model::GeographicName',
+                  key: :GeographyTreeDefID
+    end
+  end
+end

data/lib/specify/models/institution.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # Institution is the highest level of scope within a Specify::Database.
+    #
+    # A Specify::Database has a single instance of Institution. The Institution
+    # has one or more instances of Specify::Model::Division.
+    class Institution < Sequel::Model(:institution)
+      include Updateable
+    end
+  end
+end

data/lib/specify/models/locality.rb

@@ -0,0 +1,50 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # Localities are places where something has been collected.
+    #
+    # A Locality can belong to a Specify::Model::GeographicName, and is
+    # required to join a Specify::Model::CollectingEvent to a
+    # Specify::Model::GeographicName.
+    class Locality < Sequel::Model(:locality)
+      include Createable
+      include Updateable
+
+      many_to_one :discipline,
+                  key: :DisciplineID
+      many_to_one :geographic_name,
+                  key: :GeographyID
+      many_to_one :created_by,
+                  class: 'Specify::Model::Agent',
+                  key: :CreatedByAgentID
+      many_to_one :modified_by,
+                  class: 'Specify::Model::Agent',
+                  key: :ModifiedByAgentID
+
+      # Sequel hook that assigns a GUID and sets the #coordinate_notation
+      # to +3+.
+      def before_create
+        self[:GUID] = SecureRandom.uuid
+        self[:SrcLatLongUnit] = 3
+        super
+      end
+
+      # Creates a string representation of +self+.
+      def inspect
+        geo = geographic_name ? "(#{geographic_name.FullName})" : ''
+        "id: #{self.LocalityID.to_s}, #{self.LocalityName} #{geo}"
+      end
+
+      # Returns an Integer in the range 0-3 that designates the format in which
+      # latidtudes and longitudes are stored:
+      # [0] Decimal degrees
+      # [1] Degrees, minutes, and decimal seconds
+      # [2] Degrees and decimal minutes
+      # [3] None
+      def coordinate_notation
+        self[:SrcLatLongUnit]
+      end
+    end
+  end
+end

data/lib/specify/models/preparation.rb

@@ -0,0 +1,53 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # Preparations are the physical (or virtual) represenatations of a
+    # Specify::Model::CollectionObject in a Speciy::Model::Collection.
+    #
+    # Collection objects represent the organisms or artifacts collected, the
+    # preparations are items derived from that organism or artifacts which are
+    # the actual units in a collections physical storage. In an ornithological
+    # collection, for example, the collection object will be the bird collected,
+    # preparations will be the skin, the skeleton, or any other physcial (or
+    # virtual derivatives).
+    #
+    # A preparation belongs to a Specify::Model::PreparationType, that
+    # provides a controlled vocabulary for available types of preparations (e.g.
+    # skin, skeletons, EtOH).
+    #
+    # A preparation has a #count, that is the number of items in a preparation.
+    # If, for example, the preparation is a jar of shrimps in ethanol, the
+    # preparation_type could be `EtOH`, and if there are 10 shrimps in the jar,
+    # the #count would be +10+.
+    class Preparation < Sequel::Model(:preparation)
+      include Createable
+      include Updateable
+
+      many_to_one :collection_object,
+                  key: :CollectionObjectID
+      many_to_one :collection,
+                  class: 'Specify::Model::Collection',
+                  key: :CollectionMemberID
+      many_to_one :preparation_type,
+                  key: :PrepTypeID
+      many_to_one :created_by,
+                  class: 'Specify::Model::Agent',
+                  key: :CreatedByAgentID
+      many_to_one :modified_by,
+                  class: 'Specify::Model::Agent',
+                  key: :ModifiedByAgentID
+
+      # Sequel hook that assigns a GUID.
+      def before_create
+        self[:GUID] = SecureRandom.uuid
+        super
+      end
+
+      # Returns the number of items in a preparation.
+      def count
+        self.CountAmt
+      end
+    end
+  end
+end

data/lib/specify/models/preparation_type.rb

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # PreparationTypes, are categopries of Specify::Model::Preparation.
+    # A PreparationType providess a controlled vocabulary for available types of
+    # preparations, where the element in the controlled vocabulary is the #name.
+    class PreparationType < Sequel::Model(:preptype)
+      include Createable
+      include Updateable
+
+      many_to_one :collection,
+                  key: :CollectionID
+      one_to_many :preparations,
+                  key: :PrepTypeID
+      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 with the name of +self+ (a short name that is an
+      # element of a controlled vocabulary).
+      def name
+        self[:Name]
+      end
+    end
+  end
+end

data/lib/specify/models/record_set.rb

@@ -0,0 +1,55 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # RecordSets are groups of records of certain classes in the Specify::Model,
+    # for example Specify::Model::CollectionObject (currently the only supported
+    # class for record sets).
+    #
+    # A RecordSet ontains Specify::Model::RecordSetItem instances. The items are
+    # ordered in the RecordSet, and the order is determined bu the
+    # Specify::Model::RecordSetItem#order_number.
+    class RecordSet < Sequel::Model(:recordset)
+      include Createable
+      include Updateable
+
+      many_to_one :user,
+                  key: :SpecifyUserID
+      many_to_one :collection,
+                  class: 'Specify::Model::Collection',
+                  key: :CollectionMemberID
+      one_to_many :record_set_items,
+                  key: :RecordSetID
+      many_to_many :collection_objects,
+                   left_key: :RecordSetID,
+                   right_key: :RecordId,
+                   join_table: :recordsetitem
+      many_to_one :created_by,
+                  class: 'Specify::Model::Agent',
+                  key: :CreatedByAgentID
+      many_to_one :modified_by,
+                  class: 'Specify::Model::Agent',
+                  key: :ModifiedByAgentID
+
+      # Sequel hook that sets the _TableID_ that determines the kind of record
+      # set (currently, only record sets of Specify::Model::CollectionObject
+      # instances are supported - _TableID_ = +1+). Also sets the _Type_.
+      def before_create
+        self[:TableID] = 1
+        self[:Type] = 0 # FIXME: guess
+        super
+      end
+
+      # Returns the highest order number of items in +self+.
+      def highest_order_number
+        record_set_items_dataset.max(:OrderNumber)
+      end
+
+      # Returns the order number for the next item added to +self+
+      def next_order_number
+        return 0 unless highest_order_number
+        highest_order_number + 1
+      end
+    end
+  end
+end

data/lib/specify/models/record_set_item.rb

@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # RecordSetItems are orderd items in a Specify::Model::RecordSet.
+    #
+    # A RecordSetItem represents instances of Specify::Model classes that are
+    # contained in a Specify::Model::RecordSet. The only class currently
+    # supported is Specify::Model::CollectionObject.
+    class RecordSetItem < Sequel::Model(:recordsetitem)
+      many_to_one :record_set,
+                  key: :RecordSetID
+      many_to_one :collection_object,
+                  key: :RecordId
+
+      # Sequel hook that sets #order_number for newly created records.
+      def before_create
+        self[:OrderNumber] = record_set.next_order_number
+        super
+      end
+
+      # Returns the index (an Integer) that marks the position of +self+ in a
+      # Specify::Model::RecordSet.
+      def order_number
+        self[:OrderNumber]
+      end
+    end
+  end
+end

data/lib/specify/models/taxonomy.rb

@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+
+require_relative 'taxonomy/common_name'
+require_relative 'taxonomy/rank'
+require_relative 'taxonomy/taxon'
+require_relative 'taxonomy/taxonomy'

data/lib/specify/models/taxonomy/common_name.rb

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # CommonNames are vernacular names for a Specify::Model::Taxon.
+    class CommonName < Sequel::Model(:commonnametx)
+      include Createable
+      include Updateable
+
+      many_to_one :taxon,
+                  key: :TaxonID
+    end
+  end
+end

data/lib/specify/models/taxonomy/rank.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Specify
+  module Model
+    # Rank is the _rank_ class for the Specify::Model::Taxonomy _tree_. A
+    # Rank holds information about a formal Linnean classification rank in
+    # a <em>taxonomic tree</em>.
+    #
+    # A Rank has a _parent_ (another instance of Rank) unless it is the root
+    # rank of the _tree_ and can have one _child_ (another instance of Rank).
+    class Rank < Sequel::Model(:taxontreedefitem)
+      include Updateable
+
+      many_to_one :taxonomy,
+                  key: :TaxonTreeDefID
+      one_to_many :taxa,
+                  key: :TaxonTreeDefItemID
+      one_to_one :child,
+                 class: self,
+                 key: :ParentItemID
+      many_to_one :parent, class: self,
+                  key: :ParentItemID
+
+      # Returns a String with the name of the formal Linnean classification
+      # rank.
+      def name
+        self[:Name]
+      end
+    end
+  end
+end