convert-annotation 0.5.0.0 → 0.5.0.1

raw patch · 3 files changed

+18/−15 lines, 3 filesdep +reqdep −wreq

Dependencies added: req

Dependencies removed: wreq

Files

• app/Main.hs +3/−3
• convert-annotation.cabal +2/−2
• src/HUGOConvert.hs +13/−10

@@ -108,7 +108,7 @@ col :: Options -> [T.Text] -> Int col opts =     fromMaybe (error "Column not found.") . elemIndex (unHelpful $ column opts)-    + -- | Convert the entire file at once, no streaming. strictConvert :: Options               -> Maybe (RMart s)@@ -121,7 +121,7 @@      let newH  = maybe h (\x -> h <> [x]) $ newCol         xs    = fmap (!! c) body-        +     newXS <- convertMultiple opts rMart rData $ xs      let addToRow newX row =@@ -174,7 +174,7 @@         toRGeneAnn (fromJust rMart) (RType queryType)     whichAnn (MSigDBRData _)   =         error "MSigDBRData annotation not yet supported."-        + -- | The conversion process for all in memory. convertMultiple :: Options                 -> Maybe (RMart s)

@@ -1,5 +1,5 @@ name:                convert-annotation-version:             0.5.0.0+version:             0.5.0.1 synopsis:            Convert the annotation of a gene to another in a delimited file using a variety of different databases. description:         Please see README.org homepage:            http://github.com/GregorySchwartz/convert-annotation#readme@@ -29,7 +29,7 @@                      , aeson                      , lens                      , lens-aeson-                     , wreq+                     , req                      , HTTP                      , safe                      , inline-r

@@ -13,36 +13,39 @@  -- Standard import Data.Monoid+import Control.Exception (throwIO)  -- Cabal import qualified Data.Text as T import Data.Aeson import Data.Aeson.Lens import Control.Lens-import Network.Wreq+import Network.HTTP.Req import Safe  -- Local import Types +instance MonadHttp IO where+    handleHttpException = throwIO+ -- | Get the HUGO annotation. toHUGOAnn :: HUGOType -> UnknownAnn -> IO (Maybe Ann) toHUGOAnn _ (UnknownAnn "") = return Nothing toHUGOAnn (HUGOType queryType) (UnknownAnn query) = do-    let opts = set (header "Accept") ["application/json"] defaults+    let opts = header "Accept" "application/json" -    r <- getWith opts-       $ "http://rest.genenames.org/search/"-      <> T.unpack queryType-      <> "/"-      <> T.unpack query+    r <- req GET+            (http "rest.genenames.org" /: "search" /: queryType /: query)+            NoReqBody+            jsonResponse+            opts -    let getSymbols = responseBody-                   . key "response"+    let getSymbols = key "response"                    . key "docs"                    . _Array                    . traverse                    . key "symbol"                    . _String -    return . fmap Ann . headMay . toListOf getSymbols $ r+    return . fmap Ann . headMay . toListOf getSymbols $ (responseBody r :: Value)