removed a lot of unused (?) ToJSON and FromJSON instances

src/Poseidon/ColumnTypes.hs

@@ -8,9 +8,6 @@ import           Poseidon.ColumnTypesUtils
 
 import           Country                    (Country, alphaTwoUpper,
                                              decodeAlphaTwo)
-import           Data.Aeson                 (FromJSON, ToJSON, Value (..),
-                                             defaultOptions, genericToEncoding,
-                                             parseJSON, toEncoding, toJSON)
 import qualified Data.Csv                   as Csv
 import qualified Data.Text                  as T
 import qualified Data.Text.Read             as T
@@ -43,8 +40,6 @@ instance Ord GeneticSex where
     compare _ _                                      = EQ
 instance Csv.ToField GeneticSex where   toField x  = Csv.toField $ show x
 instance Csv.FromField GeneticSex where parseField = parseTypeCSV "Genetic_Sex"
-instance ToJSON GeneticSex where        toJSON x   = String $ T.pack $ show x
-instance FromJSON GeneticSex where      parseJSON  = parseTypeJSON "JannoSex"
 
 -- | A datatype for the Group_Name .janno column
 newtype GroupName = GroupName T.Text deriving (Eq, Ord)
@@ -92,8 +87,6 @@ instance Show JannoRelationDegree where
     show OtherDegree  = "other"
 instance Csv.ToField JannoRelationDegree where   toField x = Csv.toField $ show x
 instance Csv.FromField JannoRelationDegree where parseField = parseTypeCSV "Relation_Degree"
-instance ToJSON JannoRelationDegree where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoRelationDegree
 
 -- | A datatype for the Relation_Type .janno column
 newtype JannoRelationType = JannoRelationType T.Text deriving (Eq)
@@ -124,8 +117,6 @@ instance Makeable JannoCountryISO where
         Just c  -> return $ JannoCountryISO c
 instance Csv.ToField JannoCountryISO where   toField x = Csv.toField $ show x
 instance Csv.FromField JannoCountryISO where parseField = parseTypeCSV "Country_ISO"
-instance ToJSON JannoCountryISO where        toJSON x  = String $ T.pack $ show x
-instance FromJSON JannoCountryISO where      parseJSON = parseTypeJSON "Country_ISO"
 
 -- | A datatype for the Location .janno column
 newtype JannoLocation = JannoLocation T.Text deriving (Eq)
@@ -150,8 +141,6 @@ instance Makeable JannoLatitude where
 instance Show JannoLatitude where          show (JannoLatitude x) = show x
 instance Csv.ToField JannoLatitude where   toField (JannoLatitude x) = Csv.toField x
 instance Csv.FromField JannoLatitude where parseField = parseTypeCSV "Latitude"
-instance ToJSON JannoLatitude where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoLatitude
 
 -- | A datatype for the Longitude .janno column
 newtype JannoLongitude = JannoLongitude Double deriving (Eq, Ord, Generic)
@@ -168,8 +157,6 @@ instance Makeable JannoLongitude where
 instance Show JannoLongitude where          show (JannoLongitude x) = show x
 instance Csv.ToField JannoLongitude where   toField (JannoLongitude x) = Csv.toField x
 instance Csv.FromField JannoLongitude where parseField = parseTypeCSV "Longitude"
-instance ToJSON JannoLongitude where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoLongitude
 
 -- | A datatype for the Date_Type .janno column
 data JannoDateType =
@@ -191,8 +178,6 @@ instance Show JannoDateType where
     show Modern     = "modern"
 instance Csv.ToField JannoDateType where   toField x = Csv.toField $ show x
 instance Csv.FromField JannoDateType where parseField = parseTypeCSV "Date_Type"
-instance ToJSON JannoDateType where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoDateType
 
 -- | A datatype for the Date_C14_Labnr .janno column
 newtype JannoDateC14Labnr = JannoDateC14Labnr T.Text deriving (Eq)
@@ -210,8 +195,6 @@ instance Makeable JannoDateC14UncalBP where
 instance Show JannoDateC14UncalBP where          show (JannoDateC14UncalBP x) = show x
 instance Csv.ToField JannoDateC14UncalBP where   toField (JannoDateC14UncalBP x) = Csv.toField x
 instance Csv.FromField JannoDateC14UncalBP where parseField = parseTypeCSV "Date_C14_Uncal_BP"
-instance ToJSON JannoDateC14UncalBP where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoDateC14UncalBP
 
 -- | A datatype for the Date_C14_Uncal_BP_Err .janno column
 newtype JannoDateC14UncalBPErr = JannoDateC14UncalBPErr Int deriving (Eq, Ord, Generic)
@@ -225,8 +208,6 @@ instance Makeable JannoDateC14UncalBPErr where
 instance Show JannoDateC14UncalBPErr where          show (JannoDateC14UncalBPErr x) = show x
 instance Csv.ToField JannoDateC14UncalBPErr where   toField (JannoDateC14UncalBPErr x) = Csv.toField x
 instance Csv.FromField JannoDateC14UncalBPErr where parseField = parseTypeCSV "Date_C14_Uncal_BP_Err"
-instance ToJSON JannoDateC14UncalBPErr where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoDateC14UncalBPErr
 
 -- | A datatype for the Date_BC_AD_Start .janno column
 newtype JannoDateBCADStart = JannoDateBCADStart Int deriving (Eq, Ord, Generic)
@@ -245,8 +226,6 @@ instance Makeable JannoDateBCADStart where
 instance Show JannoDateBCADStart where          show (JannoDateBCADStart x) = show x
 instance Csv.ToField JannoDateBCADStart where   toField (JannoDateBCADStart x) = Csv.toField x
 instance Csv.FromField JannoDateBCADStart where parseField = parseTypeCSV "Date_BC_AD_Start"
-instance ToJSON JannoDateBCADStart where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoDateBCADStart
 
 -- | A datatype for the Date_BC_AD_Median .janno column
 newtype JannoDateBCADMedian = JannoDateBCADMedian Int deriving (Eq, Ord, Generic)
@@ -265,8 +244,6 @@ instance Makeable JannoDateBCADMedian where
 instance Show JannoDateBCADMedian where          show (JannoDateBCADMedian x) = show x
 instance Csv.ToField JannoDateBCADMedian where   toField (JannoDateBCADMedian x) = Csv.toField x
 instance Csv.FromField JannoDateBCADMedian where parseField = parseTypeCSV "Date_BC_AD_Median"
-instance ToJSON JannoDateBCADMedian where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoDateBCADMedian
 
 -- | A datatype for the Date_BC_AD_Stop .janno column
 newtype JannoDateBCADStop = JannoDateBCADStop Int deriving (Eq, Ord, Generic)
@@ -285,8 +262,6 @@ instance Makeable JannoDateBCADStop where
 instance Show JannoDateBCADStop where          show (JannoDateBCADStop x) = show x
 instance Csv.ToField JannoDateBCADStop where   toField (JannoDateBCADStop x) = Csv.toField x
 instance Csv.FromField JannoDateBCADStop where parseField = parseTypeCSV "Date_BC_AD_Stop"
-instance ToJSON JannoDateBCADStop where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoDateBCADStop
 
 -- | A datatype for the Date_Note .janno column
 newtype JannoDateNote = JannoDateNote T.Text deriving (Eq, Ord)
@@ -319,8 +294,6 @@ instance Makeable JannoNrLibraries where
 instance Show JannoNrLibraries where          show (JannoNrLibraries x) = show x
 instance Csv.ToField JannoNrLibraries where   toField (JannoNrLibraries x) = Csv.toField x
 instance Csv.FromField JannoNrLibraries where parseField = parseTypeCSV "Nr_Libraries"
-instance ToJSON JannoNrLibraries where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoNrLibraries
 
 -- | A datatype for the Library_Names .janno column
 newtype JannoLibraryName = JannoLibraryName T.Text deriving (Eq)
@@ -361,8 +334,6 @@ instance Show JannoCaptureType where
     show ReferenceGenome    = "ReferenceGenome"
 instance Csv.ToField JannoCaptureType where   toField x = Csv.toField $ show x
 instance Csv.FromField JannoCaptureType where parseField = parseTypeCSV "Capture_Type"
-instance ToJSON JannoCaptureType where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoCaptureType
 
 -- | A datatype for the UDG .janno column
 data JannoUDG =
@@ -387,8 +358,6 @@ instance Show JannoUDG where
     show Mixed = "mixed"
 instance Csv.ToField JannoUDG where   toField x = Csv.toField $ show x
 instance Csv.FromField JannoUDG where parseField = parseTypeCSV "UDG"
-instance ToJSON JannoUDG where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoUDG
 
 -- | A datatype for the Library_Built .janno column
 data JannoLibraryBuilt =
@@ -413,8 +382,6 @@ instance Show JannoLibraryBuilt where
     show Other     = "other"
 instance Csv.ToField JannoLibraryBuilt where   toField x = Csv.toField $ show x
 instance Csv.FromField JannoLibraryBuilt where parseField = parseTypeCSV "Library_Built"
-instance ToJSON JannoLibraryBuilt where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoLibraryBuilt
 
 -- | A datatype for the Genotype_Ploidy .janno column
 data JannoGenotypePloidy =
@@ -433,8 +400,6 @@ instance Show JannoGenotypePloidy where
     show Haploid = "haploid"
 instance Csv.ToField JannoGenotypePloidy where   toField x = Csv.toField $ show x
 instance Csv.FromField JannoGenotypePloidy where parseField = parseTypeCSV "Genotype_Ploidy"
-instance ToJSON JannoGenotypePloidy where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoGenotypePloidy
 
 -- | A datatype for the Genotype_Ploidy .janno column
 newtype JannoDataPreparationPipelineURL = JannoDataPreparationPipelineURL T.Text deriving (Eq, Ord, Generic)
@@ -446,8 +411,6 @@ instance Makeable JannoDataPreparationPipelineURL where
 instance Show JannoDataPreparationPipelineURL where          show (JannoDataPreparationPipelineURL x) = T.unpack x
 instance Csv.ToField JannoDataPreparationPipelineURL where   toField (JannoDataPreparationPipelineURL x) = Csv.toField x
 instance Csv.FromField JannoDataPreparationPipelineURL where parseField = parseTypeCSV "Data_Preparation_Pipeline_URL"
-instance ToJSON JannoDataPreparationPipelineURL where        toJSON (JannoDataPreparationPipelineURL x) = String x
-instance FromJSON JannoDataPreparationPipelineURL
 
 -- | A datatype for the Endogenous .janno column
 newtype JannoEndogenous = JannoEndogenous Double deriving (Eq, Ord, Generic)
@@ -464,8 +427,6 @@ instance Makeable JannoEndogenous where
 instance Show JannoEndogenous where          show (JannoEndogenous x) = show x
 instance Csv.ToField JannoEndogenous where   toField (JannoEndogenous x) = Csv.toField x
 instance Csv.FromField JannoEndogenous where parseField = parseTypeCSV "Endogenous"
-instance ToJSON JannoEndogenous where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoEndogenous
 
 -- | A datatype for the Nr_SNPs .janno column
 newtype JannoNrSNPs = JannoNrSNPs Int deriving (Eq, Ord, Generic)
@@ -482,8 +443,6 @@ instance Makeable JannoNrSNPs where
 instance Show JannoNrSNPs where          show (JannoNrSNPs x) = show x
 instance Csv.ToField JannoNrSNPs where   toField (JannoNrSNPs x) = Csv.toField x
 instance Csv.FromField JannoNrSNPs where parseField = parseTypeCSV "Nr_SNPs"
-instance ToJSON JannoNrSNPs where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoNrSNPs
 
 -- | A datatype for the Coverage_on_Target_SNPs .janno column
 newtype JannoCoverageOnTargets = JannoCoverageOnTargets Double deriving (Eq, Ord, Generic)
@@ -497,8 +456,6 @@ instance Makeable JannoCoverageOnTargets where
 instance Show JannoCoverageOnTargets where          show (JannoCoverageOnTargets x) = show x
 instance Csv.ToField JannoCoverageOnTargets where   toField (JannoCoverageOnTargets x) = Csv.toField x
 instance Csv.FromField JannoCoverageOnTargets where parseField = parseTypeCSV "Coverage_on_Target_SNPs"
-instance ToJSON JannoCoverageOnTargets where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoCoverageOnTargets
 
 -- | A datatype for the Damage .janno column
 newtype JannoDamage = JannoDamage Double deriving (Eq, Ord, Generic)
@@ -515,8 +472,6 @@ instance Makeable JannoDamage where
 instance Show JannoDamage where          show (JannoDamage x) = show x
 instance Csv.ToField JannoDamage where   toField (JannoDamage x) = Csv.toField x
 instance Csv.FromField JannoDamage where parseField = parseTypeCSV "Damage"
-instance ToJSON JannoDamage where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoDamage
 
 -- | A datatype for the Contamination .janno column
 newtype JannoContamination = JannoContamination T.Text deriving (Eq)
@@ -567,8 +522,6 @@ instance Show JannoGeneticSourceAccessionID where
     show (OtherID x)         = T.unpack x
 instance Csv.ToField JannoGeneticSourceAccessionID where   toField x  = Csv.toField $ show x
 instance Csv.FromField JannoGeneticSourceAccessionID where parseField = parseTypeCSV "Genetic_Source_Accession_IDs"
-instance ToJSON JannoGeneticSourceAccessionID where        toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoGeneticSourceAccessionID
 
 -- | A datatype for the Primary_Contact .janno column
 newtype JannoPrimaryContact = JannoPrimaryContact T.Text deriving (Eq)

src/Poseidon/ColumnTypesUtils.hs

@@ -3,9 +3,6 @@
 
 module Poseidon.ColumnTypesUtils where
 
-import           Data.Aeson          (FromJSON, ToJSON, Value (..), parseJSON,
-                                      toJSON, withText)
-import           Data.Aeson.Types    (Parser)
 import           Data.ByteString     as S
 import qualified Data.Csv            as Csv
 import qualified Data.Text           as T
@@ -25,9 +22,6 @@ parseTypeCSV colname x = case T.decodeUtf8' x of
         Left e  -> fail $ show e ++ " in column " ++ colname
         Right t -> make t
 
-parseTypeJSON :: forall a. (Makeable a, Typeable a) => String -> Value -> Parser a
-parseTypeJSON colname = withText colname make
-
 -- template haskell function to generate repetitive instances
 makeInstances :: Name -> String -> DecsQ
 makeInstances name col = do
@@ -38,6 +32,4 @@ makeInstances name col = do
       instance Show $(conT name) where          show $(conP conName [varP x]) = T.unpack $(varE x)
       instance Csv.ToField $(conT name) where   toField $(conP conName [varP x]) = Csv.toField $(varE x)
       instance Csv.FromField $(conT name) where parseField = parseTypeCSV col
-      instance ToJSON $(conT name) where        toJSON $(conP conName [varP x]) = String $(varE x)
-      instance FromJSON $(conT name) where      parseJSON = parseTypeJSON col
       |]

src/Poseidon/Janno.hs

@@ -54,13 +54,6 @@ import           Control.Monad                        (unless, when)
 import qualified Control.Monad.Except                 as E
 import           Control.Monad.IO.Class               (liftIO)
 import qualified Control.Monad.Writer                 as W
-import           Data.Aeson                           (FromJSON, Options (..),
-                                                       ToJSON, Value (..),
-                                                       defaultOptions,
-                                                       genericToEncoding,
-                                                       parseJSON, toEncoding,
-                                                       toJSON)
-import           Data.Aeson.Types                     (emptyObject)
 import           Data.Bifunctor                       (second)
 import qualified Data.ByteString.Char8                as Bchs
 import qualified Data.ByteString.Lazy.Char8           as Bch
@@ -73,7 +66,6 @@ import           Data.List                            (elemIndex, foldl',
                                                        (\\))
 import           Data.Maybe                           (fromJust)
 import qualified Data.Text                            as T
-import qualified Data.Text.Encoding                   as T
 import qualified Data.Vector                          as V
 import           Generics.SOP.TH                      (deriveGeneric)
 import           GHC.Generics                         (Generic)
@@ -97,37 +89,13 @@ instance (Csv.ToField a, Show a) => Csv.ToField (ListColumn a) where
     toField x = Bchs.intercalate ";" $ map Csv.toField $ getListColumn x
 instance (Csv.FromField a) => Csv.FromField (ListColumn a) where
     parseField x = fmap ListColumn . mapM Csv.parseField $ Bchs.splitWith (==';') x
-instance (ToJSON a) => ToJSON (ListColumn a) where
-    toEncoding (ListColumn x) = toEncoding x
-instance (FromJSON a) => FromJSON (ListColumn a) where
-    parseJSON x
-        | isAesonString x = ListColumn . singleton <$> parseJSON x
-        | otherwise = ListColumn <$> parseJSON x
-        where
-            isAesonString (String _) = True
-            isAesonString _          = False
-            singleton a = [a]
 
 -- | A datatype to collect additional, unpecified .janno file columns (a hashmap in cassava/Data.Csv)
 newtype CsvNamedRecord = CsvNamedRecord Csv.NamedRecord deriving (Show, Eq, Generic)
 
 getCsvNR :: CsvNamedRecord -> Csv.NamedRecord
 getCsvNR (CsvNamedRecord x) = x
 
--- Aeson does not encode ByteStrings, so that's why we have to go through Text
-instance ToJSON CsvNamedRecord where
-    toJSON (CsvNamedRecord x) =
-        let listOfBSTuples = HM.toList x
-            listOfTextTuples = map (\(a,b) -> (T.decodeUtf8 a, T.decodeUtf8 b)) listOfBSTuples
-        in toJSON listOfTextTuples
-instance FromJSON CsvNamedRecord where
-    parseJSON x
-        | x == emptyObject = pure $ CsvNamedRecord $ HM.fromList []
-        | otherwise = do
-            listOfTextTuples <- parseJSON x -- :: [(T.Text, T.Text)]
-            let listOfBSTuples = map (\(a,b) -> (T.encodeUtf8 a, T.encodeUtf8 b)) listOfTextTuples
-            pure $ CsvNamedRecord $ HM.fromList listOfBSTuples
-
 -- | A  data type to represent a janno file
 newtype JannoRows = JannoRows [JannoRow]
     deriving (Show, Eq, Generic)
@@ -151,10 +119,6 @@ instance Monoid JannoRows where
     mempty = JannoRows []
     mconcat = foldl' mappend mempty
 
-instance ToJSON JannoRows where
-    toEncoding = genericToEncoding defaultOptions
-instance FromJSON JannoRows
-
 -- | A data type to represent a sample/janno file row
 -- See https://github.com/poseidon-framework/poseidon2-schema/blob/master/janno_columns.tsv
 -- for more details
@@ -248,11 +212,6 @@ jannoHeaderString = map Bchs.unpack jannoHeader
 jannoRefHashMap :: HM.HashMap Bchs.ByteString ()
 jannoRefHashMap = HM.fromList $ map (\x -> (x, ())) jannoHeader
 
-instance ToJSON JannoRow where
-    toEncoding = genericToEncoding (defaultOptions {omitNothingFields = True})
-
-instance FromJSON JannoRow
-
 instance Csv.FromNamedRecord JannoRow where
     parseNamedRecord m = JannoRow
         <$> filterLookup         m "Poseidon_ID"