Arrow tables with deeply nested lists and structs can make Arrow.jl spend too much tim

<a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/us

second this. We see extremely high latency when doing CI: <a href="https://github.com/

There are some epic types getting compiled here. <p dir

Deeply nested structs cause long compilation times,about apache/arrow-julia

Comments (9)

KristofferC commented on June 24, 2024 1

There are some epic types getting compiled here. For example, here is the show method:

precompile(Tuple{typeof(Base.show), Base.IOContext{Base.GenericIOBuffer{Array{UInt8, 1}}}, Base.Multimedia.MIME{Symbol("text/plain")}, Tables.Schema{(:resourceType, :id, :meta, :implicitRules, :language, :text, :contained, :extension, :modifierExtension, :identifier, :basedOn, :partOf, :status, :category, :code, :subject, :focus, :encounter, :effectiveDateTime, :effectivePeriod, :effectiveTiming, :effectiveInstant, :issued, :performer, :valueQuantity, :valueCodeableConcept, :valueString, :valueBoolean, :valueInteger, :valueRange, :valueRatio, :valueSampledData, :valueTime, :valueDateTime, :valuePeriod, :dataAbsentReason, :interpretation, :note, :bodySite, :method, :specimen, :device, :referenceRange, :hasMember, :derivedFrom, :component, :yy__patient_id, :yy_system, :yy_sub_resource), Tuple{Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :versionId, :lastUpdated, :source, :profile, :security, :tag), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}}}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :status, :div), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}}}}, Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Union{Base.Missing, Base.SubArray{Union{Base.Missing, NamedTuple{(:id, :extension, :use, :type, :system, :value, :period, :assigner), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :coding, :text), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}, Union{Base.Missing, String}}}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :start, :end), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}}}}, Union{Base.Missing, NamedTuple{(:id, :extension, :reference, :type, :identifier, :display), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :use, :type, :system, :value, :period, :assigner), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :coding, :text), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}, Union{Base.Missing, String}}}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :start, :end), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}}}}, Union{Base.Missing, String}}}}, Union{Base.Missing, String}}}}}}}, 1, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :use, :type, :system, :value, :period, :assigner), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :coding, :text), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}, Union{Base.Missing, String}}}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :start, :end), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}}}}, Union{Base.Missing, NamedTuple{(:id, :extension, :reference, :type, :identifier, :display), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :use, :type, :system, :value, :period, :assigner), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :coding, :text), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}, Union{Base.Missing, String}}}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :start, :end), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}}}}, Union{Base.Missing, String}}}}, Union{Base.Missing, String}}}}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :coding, :text), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}, Union{Base.Missing, String}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.BoolVector{Union{Base.Missing, Bool}}}, (:id, :extension, :system, :version, :code, :display, :userSelected)}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.BoolVector{Union{Base.Missing, Bool}}}, (:id, :extension, :system, :version, :code, :display, :userSelected)}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, (:id, :extension, :coding, :text)}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :start, :end), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.Primitive{Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Array{Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}, 1}}, Arrow.Primitive{Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Array{Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}, 1}}}, (:id, :extension, :start, :end)}, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :reference, :type, :identifier, :display), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :use, :type, :system, :value, :period, :assigner), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :coding, :text), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}, Union{Base.Missing, String}}}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :start, :end), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}}}}, Union{Base.Missing, String}}}}, Union{Base.Missing, String}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :use, :type, :system, :value, :period, :assigner), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :coding, :text), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}, Union{Base.Missing, String}}}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :start, :end), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}}}}, Union{Base.Missing, String}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :coding, :text), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Array{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1}}, Union{Base.Missing, String}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, 1, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.BoolVector{Union{Base.Missing, Bool}}}, (:id, :extension, :system, :version, :code, :display, :userSelected)}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :system, :version, :code, :display, :userSelected), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, Bool}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.BoolVector{Union{Base.Missing, Bool}}}, (:id, :extension, :system, :version, :code, :display, :userSelected)}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, (:id, :extension, :coding, :text)}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :start, :end), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.Primitive{Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Array{Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}, 1}}, Arrow.Primitive{Union{Base.Missing, Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}}, Array{Arrow.Timestamp{Arrow.Flatbuf.TimeUnit.T(0x0002), Symbol("Etc/UTC")}, 1}}}, (:id, :extension, :start, :end)}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, (:id, :extension, :use, :type, :system, :value, :period, :assigner)}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, (:id, :extension, :reference, :type, :identifier, :display)}}, (:id, :extension, :use, :type, :system, :value, :period, :assigner)}, Tuple{Base.UnitRange{Int64}}, true}}, Union{Base.Missing, Base.SubArray{Union{Base.Missing, NamedTuple{(:id, :extension, :reference, :type, :identifier, :display), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :use, :type, :system, :value, :period, :assigner), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, String}, Union{Base.Missing, NamedTuple{(:id, :extension, :coding, :text), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, 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Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.BoolVector{Union{Base.Missing, Bool}}}, (:id, :extension, :system, :version, :code, :display, :userSelected)}}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, (:id, :extension, :coding, :text)}}, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :low, :high), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, NamedTuple{(:id, :extension, :value, :comparator, :unit, :system, :code), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Float32}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}}}}, Union{Base.Missing, NamedTuple{(:id, :extension, :value, :comparator, :unit, :system, :code), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, 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Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.Primitive{Union{Base.Missing, Float32}, Array{Float32, 1}}, Vararg{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, 4}}, (:id, :extension, :value, :comparator, :unit, :system, :code)}, Arrow.Struct{Union{Base.Missing, NamedTuple{(:id, :extension, :value, :comparator, :unit, :system, :code), Tuple{Union{Base.Missing, String}, Union{Base.Missing, Array{Union{Base.Missing, String}, 1}}, Union{Base.Missing, Float32}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}}}}, Tuple{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Arrow.List{Union{Base.Missing, Base.SubArray{Union{Base.Missing, String}, 1, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, Tuple{Base.UnitRange{Int64}}, true}}, Int32, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, Arrow.Primitive{Union{Base.Missing, Float32}, Array{Float32, 1}}, Vararg{Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}, 4}}, (:id, :extension, :value, :comparator, :unit, :system, :code)}}, (:id, :extension, :low, :high)}, Arrow.List{Union{Base.Missing, String}, Int32, Array{UInt8, 1}}}, (:id, :extension, :modifierExtension, :low, :high, :type, :appliesTo, :age, :text)}}}, (:id, :extension, :modifierExtension, :code, :valueQuantity, :valueCodeableConcept, :valueString, :valueBoolean, :valueInteger, :valueRange, :valueRatio, :valueSampledData, :valueTime, :valueDateTime, :valuePeriod, :dataAbsentReason, :interpretation, :referenceRange)}, Tuple{Base.UnitRange{Int64}}, true}}, Union{Base.Missing, String}, Union{Base.Missing, String}, Union{Base.Missing, String}}}})

That line is 234870 characters.

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xitology commented on June 24, 2024 1

@Moelf, you made a point that IO with Arrow requires materializing exact field types, otherwise it would be slow. This is not so. Rust is capable of reading and writing Arrow data of arbitrary form, and can do it fast despite being a statically compiled language. People write SQL engines over Arrow in Rust, and they certainly don't know the type of each table and each column in advance. They can do it because in a column-oriented layout any data is ultimately stored as a collection of arrays of primitive types. By reducing any operation on composite data to operations on the underlying primitive arrays, they can process data effectively even if they don't know the exact layout of the composite fields during compilation.

DataFrames API does it exactly right by making the step of materializing the row type explicit. The user can request it and pay the compilation cost if they want to process a DataFrame as a vector of tuples, but that's their choice. In fact, Arrow.jl works exactly the same, but only with top-level Table objects, and not with fields of composite types. Which is a problem, as my bug report demonstrates.

What I would propose... support two variants of each composite array type: transparent and opaque. The transparent is the current one while the opaque would hide the type of its content. The current definitions almost work, if we represent, say, an opaque Struct array as Arrow.Struct{Any, Any, Any}. We will only need to add a field to store column names (and allow data to be a vector). The API could provide a way to switch between transparent and opaque forms, but I'd argue the opaque form should be the default: this way you could read and process any Arrow data compilation-free.

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Moelf commented on June 24, 2024

second this. We see extremely high latency when doing CI: https://github.com/JuliaHEP/UnROOT.jl/actions/runs/8317241942/job/22757761446#step:6:548

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xitology commented on June 24, 2024

There are some epic types getting compiled here.

Perhaps, composite arrow arrays should not carry the types of the underlying data arrays in their own type signature?

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Moelf commented on June 24, 2024

they kind of have to -- the type tree has to exist somewhere, in Julia, it's natural to let the type tree exists using Julia's typing functionality. But we could have precompiled more in Arrow (for common compositions of primitive types and containers)

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xitology commented on June 24, 2024

they kind of have to -- the type tree has to exist somewhere, in Julia, it's natural to let the type tree exists using Julia's typing functionality. But we could have precompiled more in Arrow

You don't have to create an exact Julia type for composite fields. After all, you do not create a Julia type for the table as a whole.

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Moelf commented on June 24, 2024

right, alternative to using Julia's typing system, is to use values, conceptually it's like instead of NamedTuple, just use Dict for the type tree. But then, reading bytes from disk or network I/O will be much slower because Julia won't know what bytes will turn into.

In that case people may start to complain why Arrow is so slow or type unstable, idk, we need to try to see the tradeoffs

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xitology commented on June 24, 2024

right, alternative to using Julia's typing system, is to use values, conceptually it's like instead of NamedTuple, just use Dict for the type tree. But then, reading bytes from disk or network I/O will be much slower because Julia won't know what bytes will turn into.

That's just not true for a column-oriented data format like Arrow. The whole point of column layout is to make processing fast without knowing the exact data layout during compilation. Otherwise, statically compiled languages like C or Rust wouldn't be able to process Arrow data fast.

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Moelf commented on June 24, 2024

It's similar to why naive for row in eachrow(df::DataFrame) is slow, but if you use DataFramesMeta.jl or convert to a TypedTable from TypedTables.jl the row iteration would be faster again.

In C or Rust, you need to know the column type at compile time, you CAN'T just do:

auto df = openarrow(path)
auto col = df.mycol1
auto val = col[1]

but you can do the moral equivalent of this in Julia. Fundamentally, the type information (schema) of the Arrow table lives as "values" (bytes) on-disk, you have to somehow process that info and at run-time generate a type tree -- using Julia's typing system or using Dict is implementation detail.

For Rust and C, it's still doing this type of thing, but in more staged-fashion ¹ and probably more efficient, wheres in Arrow.jl I think it really leans heavily on Julia's typing system and compose everything using Julia type composition -- which may not have been smart from the result.

for example, get the types first from metadata, and build the types in explicitly separate stages ↩

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