Types.hs

{-# LANGUAGE TemplateHaskell #-}
module Tests.Types
    ( tgroup_Types
    ) where

import Test.Tasty.TH
import Test.Tasty.HUnit
import qualified Data.Text as T

import Tests.Utils
import Types
import Language
import BuiltinFunctions (builtinModule)
import NGLess.NGLEnvironment (NGLVersion(..))

tgroup_Types = $(testGroupGenerator)


mods = [builtinModule (NGLVersion 1 3)]

isOkTypes :: Script -> IO ()
isOkTypes script = case checktypes mods script of
    (Right _) -> return ()
    (Left err) -> assertFailure ("Type error on good code (error was '"++show err++"'")

isOkTypesText scriptText = case parsetest scriptText >>= checktypes mods of
    (Right _) -> return ()
    (Left err) -> assertFailure ("Type error on good code (error was '"++show err++"') for script: '"++T.unpack scriptText++"'")

isErrorText scriptText = isError $ parsetest scriptText>>= checktypes mods


case_bad_type_fastq = isError $ checktypes mods (Script Nothing [(0,FunctionCall (FuncName "fastq") (ConstInt 3) [] Nothing)])
case_good_type_fastq = isOkTypes (Script Nothing [(0,FunctionCall (FuncName "fastq") (ConstStr "fastq.fq") [] Nothing)])

case_type_complete = isOkTypesText
    "ngless '0.0'\n\
    \reads = fastq('input1.fq')\n\
    \reads = unique(reads,max_copies=2)\n\
    \preprocess(reads) using |read|:\n\
    \    read = read[5:]\n\
    \    read = substrim(read, min_quality=24)\n\
    \    if len(read) < 30:\n\
    \        discard\n"

case_indent_empty_line = isOkTypesText
    "ngless '0.0'\n\
    \reads = fastq('input1.fq')\n\
    \preprocess(reads) using |read|:\n\
    \    read = read[5:]\n\
    \    \n\
    \    if len(read) < 24:\n\
    \        discard\n"


case_invalid_func_fastq = isError $ checktypes mods $
    Script Nothing [(0,FunctionCall (FuncName "fastq") (ConstStr "fastq.fq") [(Variable "fname", ConstInt 10)] Nothing)]

-- unique

case_valid_funique_mc = isOkTypesText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \unique(x, max_copies=10)\n"

case_invalid_funique_mc = isErrorText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \unique(x, max_copies='test')\n"


-- substrim

case_valid_fsubstrim_mq = isOkTypesText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \preprocess(x) using |read|:\n\
    \    read = read[5:]\n\
    \    read = substrim(read, min_quality=2)\n"

case_invalid_fsubstrim_mq = isErrorText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \preprocess(x) using |read|:\n\
    \    read = read[5:]\n\
    \    read = substrim(read, min_quality='2')\n"

case_invalid_fmap_ref = isErrorText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \map(x, reference=10)\n"


case_valid_fmap_ref = isOkTypesText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \map(x, reference='xpto')\n"

-- count
case_valid_fannot_gff = isOkTypesText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \y = map(x, reference='xpto')\n\
    \count(y, gff_file='xpto')"

case_invalid_fannot_gff = isErrorText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \y = map(x, reference='xpto')\n\
    \count(y, gff_file={xpto})"

case_valid_fannot_mode = isOkTypesText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \y = map(x, reference='xpto')\n\
    \count(y, mode={union})"

case_invalid_fannot_mode = isErrorText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \y = map(x, reference='xpto')\n\
    \count(y, mode='union')"

case_valid_fannot_features = isOkTypesText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \y = map(x, reference='xpto')\n\
    \count(y, features=['gene'])"

case_invalid_fannot_features = isErrorText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \y = map(x, reference='xpto')\n\
    \count(y, features={gene})"

case_valid_fcount_min = isOkTypesText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \y = map(x, reference='xpto')\n\
    \z = count(y, features=['gene'], min=10)"


-- write


case_valid_fwrite_format = isOkTypesText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \y = map(x, reference='xpto')\n\
    \z = count(y, features=['gene'])\n\
    \write(z, format={tsv})"

case_invalid_fwrite_format = isErrorText
    "ngless '0.0'\n\
    \x = fastq('fq')\n\
    \y = map(x, reference='xpto')\n\
    \z = count(y, features=[{gene}])\n\
    \write(count(z), format='tsv')"

case_mixed_addition = isErrorText
    "ngless '0.0'\n\
    \nglessIsNotJS = 1 + '2'\n"