NewickSpec.hs

{-# LANGUAGE OverloadedStrings #-}

-- |
-- Module      :  ELynx.Export.Tree.NewickSpec
-- Copyright   :  (c) Dominik Schrempf 2020
-- License     :  GPL-3.0-or-later
--
-- Maintainer  :  dominik.schrempf@gmail.com
-- Stability   :  unstable
-- Portability :  portable
--
-- Creation date: Wed Feb 13 11:01:53 2019.
module ELynx.Export.Tree.NewickSpec
  ( spec,
  )
where

import Data.Bifunctor
import qualified Data.ByteString.Char8 as BS
import qualified Data.ByteString.Lazy.Char8 as BL
import ELynx.Data.Tree
import ELynx.Data.Tree.Arbitrary ()
import ELynx.Export.Tree.Newick
import ELynx.Import.Tree.Newick
import ELynx.Tools
import Test.Hspec
import Test.QuickCheck hiding (label)

samplePhyloByteStringTree :: Tree Phylo BS.ByteString
samplePhyloByteStringTree = parseByteStringWith (newick Standard) sampleNewickByteString1

sampleNewickByteString1 :: BL.ByteString
sampleNewickByteString1 = "(Aeropyrum0:0.5478645225,(((((((((Arabidopsi:0.0701001024,Oryza_sati:0.0765988261):0.0309636193,Gymnosperm:0.0520325624):0.0338982245,Physcomitr:0.0768008916):0.0895714685,(Chlamydomo:0.1136227755,Dunaliella:0.1406347323):0.1117340620):0.0818876186,Rhodophyta:0.3405656487):0.0363527066,((((((Babesia_bo:0.1646969208,Theileria0:0.1519889486):0.1908081096,Plasmodium:0.3250696762):0.0637865908,(Toxoplasma:0.1153570425,Eimeria000:0.1671916078):0.0980136930):0.0518956330,Cryptospor:0.3175062809):0.1607708388,Ciliophora:0.5687502950):0.0624078848,(Phytophtho:0.2016424948,((Thalassios:0.1202730781,Phaeodacty:0.1290341329):0.1772775509,Phaeophyce:0.1989260715):0.0312359673):0.1154768302):0.0311952864):0.0149160316,(((((((((Candida_al:0.1027755272,Saccharomy:0.1190206560):0.1333487870,Neurospora:0.1977309079):0.0522926266,Schizosacc:0.2019603227):0.0567441011,(Cryptococc:0.1948614959,Ustilago_m:0.1564451295):0.0775729694):0.0323959951,Glomus_int:0.1573670796):0.0194701292,Chytridiom:0.2228415254):0.0384370601,Encephalit:1.4622174644):0.0416231688,(((Drosophila:0.2160627753,(Mammalians:0.1080484094,Tunicates0:0.1739253014):0.0289624371):0.0346633757,Hydrozoa00:0.2058137032):0.0480963050,Monosiga_b:0.3020637584):0.0654894239):0.0380915725,(Dictyostel:0.3453588998,Mastigamoe:0.3844779231):0.0478795653):0.0129578395):1.7592083381,((Archaeoglo:0.5402784445,Methanococ:0.4088567459):0.0993669265,Pyrococcus:0.4058713829):0.1734405968):0.2193511807,Pyrobaculu:0.7507718047):0.1646616482,Sulfolobus:0.5404967897);"

prop_invariant :: Tree Phylo Int -> Bool
prop_invariant t =
  parseByteStringWith (newick Standard) (toNewick t)
    ==
    -- We have to convert Int to ByteString, but we cannot use
    -- arbitrary instances with ByteStrings because many
    -- characters are disallowed and break the Newick string.
    second (BL.toStrict . getName) t

spec :: Spec
spec = describe "parseByteStringWith newick $ toNewickPhyloByteString" $ do
  it "should be an invariant for a sample tree" $ do
    let bs = toNewick samplePhyloByteStringTree
    parseByteStringWith
      (newick Standard)
      bs
      `shouldBe` samplePhyloByteStringTree
  it "should be an invariant for a sample tree" $ property prop_invariant