[upload] fix csv upload job response

Now the job doesn't return 'succeeded' fields when it actually fails.

bin/gargantext-adaptative-phylo/Main.hs

@@ -16,11 +16,24 @@ Adaptative Phylo binaries
 
 module Main where
 
+import Control.Concurrent.Async (mapConcurrently)
+import Crypto.Hash.SHA256 (hash)
 import Data.Aeson
+import Data.Either (Either(..))
 import Data.List  (concat, nub, isSuffixOf)
 import Data.String (String)
+import GHC.IO (FilePath) 
+import qualified Prelude as Prelude
+import System.Environment
+import System.Directory (listDirectory,doesFileExist)
 import Data.Text  (Text, unwords, unpack, replace, pack)
-import Crypto.Hash.SHA256 (hash)
+import Data.Time.Calendar (fromGregorian, diffGregorianDurationClip, cdMonths, diffDays, showGregorian)
+
+import qualified Data.ByteString.Char8 as C8
+import qualified Data.ByteString.Lazy as Lazy
+import qualified Data.Vector as Vector
+import qualified Gargantext.Core.Text.Corpus.Parsers.CSV as Csv
+import qualified Data.Text as T
 
 import Gargantext.Prelude
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
@@ -36,20 +49,6 @@ import Gargantext.Core.Viz.Phylo.PhyloTools  (printIOMsg, printIOComment, setCon
 import Gargantext.Core.Viz.Phylo.PhyloExport (toPhyloExport, dotToFile)
 -- import Gargantext.API.Ngrams.Prelude (toTermList)
 
-import GHC.IO (FilePath) 
-import Prelude (Either(Left, Right),toInteger)
-import System.Environment
-import System.Directory (listDirectory,doesFileExist)
-import Control.Concurrent.Async (mapConcurrently)
-
-import Data.Time.Calendar (fromGregorian, diffGregorianDurationClip, cdMonths, diffDays, showGregorian)
-
-import qualified Data.ByteString.Char8 as C8
-import qualified Data.ByteString.Lazy as Lazy
-import qualified Data.Vector as Vector
-import qualified Gargantext.Core.Text.Corpus.Parsers.CSV as Csv
-import qualified Data.Text as T
-
 -- import Debug.Trace (trace)
 
 data PhyloStage = PhyloWithCliques | PhyloWithLinks deriving (Show)
@@ -84,13 +83,13 @@ toDays y m d = fromIntegral
 toPhyloDate :: Int -> Int -> Int -> TimeUnit -> Date
 toPhyloDate y m d tu = case tu of 
   Year  _ _ _ -> y
-  Month _ _ _ -> toMonths (toInteger y) m d
-  Week  _ _ _ -> div (toDays (toInteger y) m d) 7
-  Day   _ _ _ -> toDays (toInteger y) m d
+  Month _ _ _ -> toMonths (Prelude.toInteger y) m d
+  Week  _ _ _ -> div (toDays (Prelude.toInteger y) m d) 7
+  Day   _ _ _ -> toDays (Prelude.toInteger y) m d
 
 
 toPhyloDate' :: Int -> Int -> Int -> Text
-toPhyloDate' y m d = pack $ showGregorian $ fromGregorian (toInteger y) m d
+toPhyloDate' y m d = pack $ showGregorian $ fromGregorian (Prelude.toInteger y) m d
 
 
 --------------
@@ -113,9 +112,14 @@ termsInText pats txt = nub $ concat $ map (map unwords) $ extractTermsWithList p
 
 
 -- | To transform a Wos file (or [file]) into a list of Docs
-wosToDocs :: Int -> Patterns -> TimeUnit -> FilePath -> IO ([Document])
+wosToDocs :: Int -> Patterns -> TimeUnit -> FilePath -> IO [Document]
 wosToDocs limit patterns time path = do 
   files <- getFilesFromPath path
+  let parseFile' file = do
+        eParsed <- parseFile WOS (path <> file)
+        case eParsed of
+          Right ps -> pure ps
+          Left e   -> panic $ "Error: " <> (pack e)
   take limit
     <$> map (\d -> let title = fromJust $ _hd_title d
                        abstr = if (isJust $ _hd_abstract d)
@@ -134,22 +138,27 @@ wosToDocs limit patterns time path = do
     <$> mapConcurrently (\file -> 
           filter (\d -> (isJust $ _hd_publication_year d)
                      && (isJust $ _hd_title d))
-                <$> parseFile WOS (path <> file) ) files
+             <$> parseFile' file) files
 
 
 -- To transform a Csv file into a list of Document
-csvToDocs :: CorpusParser -> Patterns -> TimeUnit -> FilePath -> IO ([Document])
+csvToDocs :: CorpusParser -> Patterns -> TimeUnit -> FilePath -> IO [Document]
 csvToDocs parser patterns time path = 
   case parser of
     Wos  _     -> undefined
-    Csv  limit -> Vector.toList
-      <$> Vector.take limit
-      <$> Vector.map (\row -> Document (toPhyloDate  (csv_publication_year row) (csv_publication_month row) (csv_publication_day row) time)
+    Csv  limit -> do
+      eR <- Csv.readFile path
+      case eR of
+        Right r ->
+          pure $ Vector.toList
+            $ Vector.take limit
+            $ Vector.map (\row -> Document (toPhyloDate  (csv_publication_year row) (csv_publication_month row) (csv_publication_day row) time)
                                            (toPhyloDate' (csv_publication_year row) (csv_publication_month row) (csv_publication_day row))
                                            (termsInText patterns $ (csv_title row) <> " " <> (csv_abstract row))
                                            Nothing
                                            []
-                     ) <$> snd <$> Csv.readFile path
+                         ) $ snd r
+        Left e -> panic $ "Error: " <> (pack e)
     Csv' limit -> Vector.toList
       <$> Vector.take limit
       <$> Vector.map (\row -> Document (toPhyloDate  (csv'_publication_year row) (csv'_publication_month row) (csv'_publication_day row) time)

bin/gargantext-cli/CleanCsvCorpus.hs

@@ -15,6 +15,7 @@ compress the contexts around the main terms of the query.
 module CleanCsvCorpus  where
 
 --import GHC.IO (FilePath)
+import Data.Either (Either(..))
 import Data.SearchEngine as S
 import qualified Data.Set as S
 import Data.Text (pack)
@@ -39,8 +40,9 @@ main = do
   --let q = ["water", "scarcity", "morocco", "shortage","flood"]
   let q = ["gratuit", "gratuité", "culture", "culturel"]
 
-  (h,csvDocs) <- CSV.readFile rPath
-
+  eDocs <- CSV.readFile rPath
+  case eDocs of
+    Right (h, csvDocs) -> do
       putStrLn $ "Number of documents before:" <> show (V.length csvDocs)
       putStrLn $ "Mean size of docs:" <> show ( CSV.docsSize csvDocs)
 
@@ -53,3 +55,4 @@ main = do
       putStrLn $ "Mean size of docs:" <> show (CSV.docsSize docs')
 
       CSV.writeFile wPath (h, docs')
+    Left e -> panic $ "Error: " <> (pack e)

bin/gargantext-cli/Main.hs

@@ -17,30 +17,24 @@ Main specifications to index a corpus with a term list
 
 module Main where
 
-import Data.ByteString.Lazy (writeFile)
-
-import Data.Text (pack)
-import qualified Data.Text as DT
-
-import Data.Tuple.Extra (both)
-import qualified Data.Vector as DV
-
+import Control.Concurrent.Async as CCA (mapConcurrently)
+import Control.Concurrent (getNumCapabilities, myThreadId, threadCapability)
 import Control.Monad (zipWithM)
 import Control.Monad.IO.Class
-
-import Data.Map (Map)
-import qualified Data.Map    as DM
-
-import GHC.Generics
 import Data.Aeson
-
-import Data.Text (Text)
+import Data.ByteString.Lazy (writeFile)
+import Data.Either (Either(..))
 import Data.List (cycle, concat, unwords)
 import Data.List.Split (chunksOf)
+import Data.Map (Map)
+import qualified Data.Map    as DM
+import Data.Text (pack, Text)
+import qualified Data.Text as DT
+import Data.Tuple.Extra (both)
+import qualified Data.Vector as DV
+import GHC.Generics
 import System.IO (hPutStr, hFlush, stderr)
 import System.Environment
-import Control.Concurrent.Async as CCA (mapConcurrently)
-import Control.Concurrent (getNumCapabilities, myThreadId, threadCapability)
 
 import Gargantext.Prelude
 import Gargantext.Core
@@ -92,11 +86,13 @@ main = do
   [corpusFile, termListFile, outputFile] <- getArgs
 
   --corpus :: IO (DM.IntMap [[Text]])
-  corpus <- DM.fromListWith (<>)
+  eCorpusFile <- readFile corpusFile
+  case eCorpusFile of
+    Right cf -> do
+      let corpus = DM.fromListWith (<>)
                    . DV.toList
                    . DV.map (\n -> (csv_publication_year n, [(csv_title n) <> " " <> (csv_abstract n)]))
-                             . snd
-                           <$> readFile corpusFile
+                   . snd $ cf
 
       -- termListMap :: [Text]
       termList <- csvMapTermList termListFile
@@ -108,6 +104,7 @@ main = do
       -- r <- mapConcurrentlyChunked (filterTermsAndCooc patterns) (DM.toList corpus)
       r <-  mapConcurrently (filterTermsAndCooc patterns) (DM.toList corpus)
       writeFile outputFile $ encode (CoocByYears r)
+    Left e -> panic $ "Error: " <> (pack e)
 
 
 

bin/gargantext-phylo/Main.hs

@@ -24,6 +24,16 @@ import Data.Maybe
 import Data.Text (Text, unwords)
 import GHC.Generics
 import GHC.IO (FilePath)
+import System.Directory (doesFileExist)
+import System.Environment
+import qualified Data.ByteString.Lazy as L
+import qualified Data.List   as DL
+import qualified Data.Map    as DM
+import qualified Data.Text   as DT
+import qualified Data.Vector as DV
+import qualified Gargantext.Core.Text.Corpus.Parsers.CSV as CSV
+import qualified Prelude     as P
+
 import Gargantext.Database.Admin.Types.Hyperdata
 import Gargantext.Prelude
 import Gargantext.Core.Text.Context (TermList)
@@ -36,15 +46,6 @@ import Gargantext.Core.Viz.Phylo.LevelMaker
 import Gargantext.Core.Viz.Phylo.Tools
 import Gargantext.Core.Viz.Phylo.View.Export
 import Gargantext.Core.Viz.Phylo.View.ViewMaker
-import System.Directory (doesFileExist)
-import System.Environment
-import qualified Data.ByteString.Lazy as L
-import qualified Data.List   as DL
-import qualified Data.Map    as DM
-import qualified Data.Text   as DT
-import qualified Data.Vector as DV
-import qualified Gargantext.Core.Text.Corpus.Parsers.CSV as CSV
-import qualified Prelude     as P
 
 
 --------------

src/Gargantext/API/Admin/Orchestrator/Types.hs

@@ -131,18 +131,6 @@ type ScrapersEnv = JobEnv JobLog JobLog
 
 type ScraperAPI  = AsyncJobsAPI JobLog ScraperInput  JobLog
 
-jobLogInit :: Int -> JobLog
-jobLogInit n = JobLog { _scst_succeeded = Just n
-                      , _scst_failed    = Just 0
-                      , _scst_remaining = Just 0
-                      , _scst_events    = Just [] }
-
-jobLogSucc :: JobLog -> JobLog
-jobLogSucc jl = over (scst_succeeded . _Just) (+ 1) $ over (scst_remaining . _Just) (\c -> c - 1) jl
-
-jobLogErr :: JobLog -> JobLog
-jobLogErr jl = over (scst_failed . _Just) (+ 1) $ over (scst_remaining . _Just) (\c -> c - 1) jl
-
 ------------------------------------------------------------------------
 type AsyncJobs event ctI input output =
   AsyncJobsAPI' 'Unsafe 'Safe ctI '[JSON] Maybe event input output

src/Gargantext/API/Job.hs

 module Gargantext.API.Job where
 
+import Control.Lens (over, _Just)
 import Data.IORef
 import Data.Maybe
 
 import Gargantext.Prelude
 
-import Gargantext.API.Admin.Orchestrator.Types (JobLog(..))
+import Gargantext.API.Admin.Orchestrator.Types
 
 
 jobLogInit :: Int -> JobLog
@@ -16,25 +17,29 @@ jobLogInit rem =
          , _scst_events = Just [] }
 
 jobLogSuccess :: JobLog -> JobLog
-jobLogSuccess (JobLog { _scst_succeeded = mSucc
-                      , _scst_remaining = mRem
-                      , _scst_failed = mFail
-                      , _scst_events = evt }) =
-  JobLog { _scst_succeeded = (+ 1) <$> mSucc
-         , _scst_remaining = (\x -> x - 1) <$> mRem
-         , _scst_failed = mFail
-         , _scst_events = evt }
-
+jobLogSuccess jl = over (scst_succeeded . _Just) (+ 1) $
+                   over (scst_remaining . _Just) (\x -> x - 1) jl
 
 jobLogFail :: JobLog -> JobLog
-jobLogFail (JobLog { _scst_succeeded = mSucc
+jobLogFail jl = over (scst_failed . _Just) (+ 1) $
+                over (scst_remaining . _Just) (\x -> x - 1) jl
+
+jobLogFailTotal :: JobLog -> JobLog
+jobLogFailTotal (JobLog { _scst_succeeded = mSucc
                         , _scst_remaining = mRem
                         , _scst_failed = mFail
                         , _scst_events = evt }) =
   JobLog { _scst_succeeded = mSucc
-         , _scst_remaining = (\x -> x - 1) <$> mRem
-         , _scst_failed = (+ 1) <$> mFail
+         , _scst_remaining = newRem
+         , _scst_failed = newFail
          , _scst_events = evt }
+  where
+    (newRem, newFail) = case mRem of
+      Nothing -> (Nothing, mFail)
+      Just rem -> (Just 0, (+ rem) <$> mFail)
+
+jobLogEvt :: JobLog -> ScraperEvent -> JobLog
+jobLogEvt jl evt = over (scst_events . _Just) (\evts -> (evt:evts)) jl
 
 runJobLog :: MonadBase IO m => Int -> (JobLog -> m ()) -> m (m (), m (), m JobLog)
 runJobLog num logStatus = do

src/Gargantext/API/Node/Corpus/New.hs

@@ -27,6 +27,8 @@ import Data.Swagger
 import Data.Text (Text)
 import qualified Data.Text as T
 import GHC.Generics (Generic)
+import qualified Prelude as Prelude
+import Protolude (readFile)
 import Servant
 import Servant.Job.Utils (jsonOptions)
 -- import Servant.Multipart
@@ -35,8 +37,9 @@ import Test.QuickCheck.Arbitrary
 
 import Gargantext.Prelude
 
-import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs, jobLogSucc)
+import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs)
 import Gargantext.API.Admin.Types (HasSettings)
+import Gargantext.API.Job (jobLogSuccess, jobLogFailTotal)
 import Gargantext.API.Node.Corpus.New.File
 import Gargantext.API.Node.Corpus.Searx
 import Gargantext.API.Node.Corpus.Types
@@ -248,9 +251,10 @@ addToCorpusWithForm user cid (NewWithForm ft d l _n) logStatus jobLog = do
       PresseRIS -> Parser.parseFormat Parser.RisPresse
 
   -- TODO granularity of the logStatus
-  docs <- liftBase $ splitEvery 500
-      <$> take 1000000
-      <$> parse (cs d)
+  eDocs <- liftBase $ parse $ cs d
+  case eDocs of
+    Right docs' -> do
+      let docs = splitEvery 500 $ take 1000000 docs'
 
       printDebug "Parsing corpus finished : " cid
       logStatus jobLog2
@@ -266,10 +270,22 @@ addToCorpusWithForm user cid (NewWithForm ft d l _n) logStatus jobLog = do
       printDebug "sending email" ("xxxxxxxxxxxxxxxxxxxxx" :: Text)
       sendMail user
 
-  pure jobLog3
+      logStatus jobLog3
+      pure $ jobLog3
+    Left e -> do
+      printDebug "Error" e
+
+      logStatus jobLogE
+      pure jobLogE
     where
-      jobLog2 = jobLogSucc jobLog
-      jobLog3 = jobLogSucc jobLog2
+      jobLog2 = jobLogSuccess jobLog
+      jobLog3 = jobLogSuccess jobLog2
+      jobLogE = jobLogFailTotal jobLog
+
+parseCsvGargV3Path :: [Char] -> IO (Either Prelude.String [HyperdataDocument])
+parseCsvGargV3Path fp = do
+  contents <- readFile fp
+  Parser.parseFormat Parser.CsvGargV3 $ cs contents
 
 {-
 addToCorpusWithFile :: FlowCmdM env err m

src/Gargantext/API/Node/FrameCalcUpload.hs

@@ -17,7 +17,8 @@ import Servant
 import Servant.Job.Async
 import Web.FormUrlEncoded (FromForm)
 
-import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs, jobLogInit, jobLogSucc, jobLogErr)
+import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs)
+import Gargantext.API.Job (jobLogInit, jobLogSuccess, jobLogFail)
 import Gargantext.API.Node.Corpus.New (addToCorpusWithForm)
 import Gargantext.API.Node.Corpus.New.File (FileType(..))
 import Gargantext.API.Node.Types (NewWithForm(..))
@@ -82,8 +83,8 @@ frameCalcUploadAsync uId nId _f logStatus jobLog = do
   -- printDebug "[frameCalcUploadAsync] mCId" mCId
 
   jobLog2 <- case mCId of
-    Nothing -> pure $ jobLogErr jobLog
+    Nothing -> pure $ jobLogFail jobLog
     Just cId ->
       addToCorpusWithForm (RootId (NodeId uId)) cId (NewWithForm CSV body Nothing "calc-upload.csv") logStatus jobLog
 
-  pure $ jobLogSucc jobLog2
+  pure $ jobLogSuccess jobLog2

src/Gargantext/API/Routes.hs

@@ -43,8 +43,8 @@ import qualified Gargantext.API.Public                   as Public
 import Gargantext.API.Admin.Auth.Types (AuthRequest, AuthResponse, AuthenticatedUser(..), PathId(..))
 import Gargantext.API.Admin.Auth (withAccess)
 import Gargantext.API.Admin.FrontEnd (FrontEndAPI)
-import Gargantext.API.Admin.Orchestrator.Types (jobLogInit)
 import Gargantext.API.Count  (CountAPI, count, Query)
+import Gargantext.API.Job (jobLogInit)
 import Gargantext.API.Ngrams (TableNgramsApi, apiNgramsTableDoc)
 import Gargantext.API.Node
 import Gargantext.API.Prelude
@@ -285,7 +285,7 @@ addCorpusWithForm user cid =
     JobFunction (\i log' ->
       let
         log'' x = do
-          printDebug "addToCorpusWithForm" x
+          printDebug "[addToCorpusWithForm] " x
           liftBase $ log' x
       in New.addToCorpusWithForm user cid i log'' (jobLogInit 3))
 
@@ -295,7 +295,7 @@ addCorpusWithFile user cid =
     JobFunction (\i log' ->
       let
         log'' x = do
-          printDebug "addToCorpusWithFile" x
+          printDebug "[addToCorpusWithFile]" x
           liftBase $ log' x
       in New.addToCorpusWithFile user cid i log'')
 

src/Gargantext/Core/Ext/IMT.hs

@@ -11,14 +11,17 @@ Portability : POSIX
 
 module Gargantext.Core.Ext.IMT where
 
-import Gargantext.Prelude
-import Data.Text (Text, splitOn)
+import Data.Either (Either(..))
 import Data.Map (Map)
+import Data.Text (Text, splitOn)
 
 import qualified Data.Set    as S
 import qualified Data.List   as DL
 import qualified Data.Vector as DV
 import qualified Data.Map    as M
+import qualified Prelude     as Prelude
+
+import Gargantext.Prelude
 
 import Gargantext.Core.Text.Metrics.Utils      as Utils
 import Gargantext.Core.Text.Corpus.Parsers.CSV as CSV
@@ -98,8 +101,10 @@ schools = [ School
 mapIdSchool :: Map Text Text
 mapIdSchool = M.fromList $ Gargantext.Prelude.map (\(School n _ i) -> (i,n)) schools
 
-hal_data :: IO (DV.Vector CsvHal)
-hal_data = snd <$> CSV.readCsvHal "doc/corpus_imt/Gargantext_Corpus.csv"
+hal_data :: IO (Either Prelude.String (DV.Vector CsvHal))
+hal_data = do
+  r <- CSV.readCsvHal "doc/corpus_imt/Gargantext_Corpus.csv"
+  pure $ snd <$> r
 
 names :: S.Set Text
 names = S.fromList $ Gargantext.Prelude.map (\s -> school_id s) schools

src/Gargantext/Core/Text/Convert.hs

@@ -16,15 +16,21 @@ Format Converter.
 module Gargantext.Core.Text.Convert (risPress2csvWrite)
     where
 
+import Data.Either (Either(..))
+import qualified Data.Text as T
 import System.FilePath (FilePath()) -- , takeExtension)
+
 import Gargantext.Prelude
 import Gargantext.Core.Text.Corpus.Parsers.CSV (writeDocs2Csv)
 import Gargantext.Core.Text.Corpus.Parsers (parseFile, FileFormat(..))
 
 
 risPress2csvWrite :: FilePath -> IO ()
-risPress2csvWrite f = parseFile RisPresse    (f <> ".ris")
-               >>= \hs -> writeDocs2Csv (f <> ".csv") hs
+risPress2csvWrite f = do
+  eContents <- parseFile RisPresse    (f <> ".ris")
+  case eContents of
+    Right contents -> writeDocs2Csv (f <> ".csv") contents
+    Left e         -> panic $ "Error: " <> (T.pack e)
 
 
 

src/Gargantext/Core/Text/Corpus/Parsers.hs

@@ -36,18 +36,20 @@ import Data.String()
 import Data.Text (Text)
 import Data.Text.Encoding (decodeUtf8)
 import Data.Tuple.Extra (both, first, second)
-import Gargantext.Core (Lang(..))
-import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
-import Gargantext.Prelude
-import Gargantext.Core.Text.Corpus.Parsers.CSV (parseHal, parseHal', parseCsv, parseCsv')
-import Gargantext.Core.Text.Corpus.Parsers.RIS.Presse (presseEnrich)
--- import Gargantext.Core.Text.Learn (detectLangDefault)
 import System.FilePath (FilePath(), takeExtension)
 import qualified Data.ByteString       as DB
 import qualified Data.ByteString.Char8 as DBC
 import qualified Data.ByteString.Lazy  as DBL
 import qualified Data.Map              as DM
 import qualified Data.Text             as DT
+import qualified Prelude as Prelude
+
+import Gargantext.Core (Lang(..))
+import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
+import Gargantext.Prelude
+import Gargantext.Core.Text.Corpus.Parsers.CSV (parseHal, parseHal', parseCsv, parseCsv')
+import Gargantext.Core.Text.Corpus.Parsers.RIS.Presse (presseEnrich)
+-- import Gargantext.Core.Text.Learn (detectLangDefault)
 import qualified Gargantext.Core.Text.Corpus.Parsers.Date as Date
 import qualified Gargantext.Core.Text.Corpus.Parsers.RIS  as RIS
 import qualified Gargantext.Core.Text.Corpus.Parsers.WOS  as WOS
@@ -75,30 +77,40 @@ data FileFormat = WOS | RIS | RisPresse
 --                | XML        -- Not Implemented / see :
 
 
-parseFormat :: FileFormat -> DB.ByteString -> IO [HyperdataDocument]
+parseFormat :: FileFormat -> DB.ByteString -> IO (Either Prelude.String [HyperdataDocument])
 parseFormat CsvGargV3 bs = pure $ parseCsv' $ DBL.fromStrict bs
 parseFormat CsvHal    bs = pure $ parseHal' $ DBL.fromStrict bs
-parseFormat RisPresse bs = mapM (toDoc RIS)
+parseFormat RisPresse bs = do
+  docs <- mapM (toDoc RIS)
           <$> snd
           <$> enrichWith RisPresse
           $ partitionEithers
           $ [runParser'  RisPresse bs]
-parseFormat WOS bs = mapM (toDoc WOS)
+  pure $ Right docs
+parseFormat WOS bs = do
+  docs <- mapM (toDoc WOS)
           <$> snd
           <$> enrichWith WOS
           $ partitionEithers
           $ [runParser'  WOS bs]
+  pure $ Right docs
 parseFormat _ _ = undefined
 
 -- | Parse file into documents
 -- TODO manage errors here
 -- TODO: to debug maybe add the filepath in error message
-parseFile :: FileFormat -> FilePath -> IO [HyperdataDocument]
+parseFile :: FileFormat -> FilePath -> IO (Either Prelude.String [HyperdataDocument])
 parseFile CsvHal    p = parseHal p
 parseFile CsvGargV3 p = parseCsv p
-parseFile RisPresse p = join $ mapM (toDoc RIS) <$> snd <$> enrichWith RisPresse <$> readFileWith RIS p
-parseFile WOS       p = join $ mapM (toDoc WOS) <$> snd <$> enrichWith WOS       <$> readFileWith WOS p
-parseFile ff        p = join $ mapM (toDoc ff)  <$> snd <$> enrichWith ff        <$> readFileWith ff  p
+parseFile RisPresse p = do
+  docs <- join $ mapM (toDoc RIS) <$> snd <$> enrichWith RisPresse <$> readFileWith RIS p
+  pure $ Right docs
+parseFile WOS       p = do
+  docs <- join $ mapM (toDoc WOS) <$> snd <$> enrichWith WOS       <$> readFileWith WOS p
+  pure $ Right docs
+parseFile ff        p = do
+  docs <- join $ mapM (toDoc ff)  <$> snd <$> enrichWith ff        <$> readFileWith ff  p
+  pure $ Right docs
 
 toDoc :: FileFormat -> [(Text, Text)] -> IO HyperdataDocument
 -- TODO use language for RIS

src/Gargantext/Core/Text/Corpus/Parsers/CSV.hs

@@ -19,7 +19,7 @@ import qualified Data.ByteString      as BS
 import qualified Data.ByteString.Lazy as BL
 import Data.Char (ord)
 import Data.Csv
-import Data.Either (Either(Left, Right))
+import Data.Either (Either(..))
 import Data.Text (Text, pack, length, intercalate)
 import Data.Time.Segment (jour)
 import qualified Data.Vector          as V
@@ -27,6 +27,8 @@ import Data.Vector (Vector)
 import GHC.IO (FilePath)
 import GHC.Word (Word8)
 
+import qualified Prelude as Prelude
+
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
 import Gargantext.Prelude hiding (length)
 import Gargantext.Core.Text
@@ -192,52 +194,47 @@ delimiter :: Word8
 delimiter = fromIntegral $ ord '\t'
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
-readCsvOn' :: [CsvDoc -> Text] -> FilePath -> IO [Text]
-readCsvOn' fields fp = V.toList
-                   <$> V.map (\l -> intercalate (pack " ") $ map (\field -> field l) fields)
-                   <$> snd
-                   <$> readFile fp
+readCsvOn' :: [CsvDoc -> Text] -> FilePath -> IO (Either Prelude.String [Text])
+readCsvOn' fields fp = do
+  r <- readFile fp
+  pure $ ( V.toList
+          . V.map (\l -> intercalate (pack " ") $ map (\field -> field l) fields)
+          . snd ) <$> r
 
 ------------------------------------------------------------------------
 
-readFileLazy :: (FromNamedRecord a) => proxy a -> FilePath -> IO (Header, Vector a)
+readFileLazy :: (FromNamedRecord a) => proxy a -> FilePath -> IO (Either Prelude.String (Header, Vector a))
 readFileLazy f = fmap (readByteStringLazy f) . BL.readFile
 
-readFileStrict :: (FromNamedRecord a) => proxy a -> FilePath -> IO (Header, Vector a)
+readFileStrict :: (FromNamedRecord a) => proxy a -> FilePath -> IO (Either Prelude.String (Header, Vector a))
 readFileStrict f = fmap (readByteStringStrict f) . BS.readFile
 
-readByteStringLazy :: (FromNamedRecord a) => proxy a -> BL.ByteString -> (Header, Vector a)
-readByteStringLazy _f bs = case decodeByNameWith csvDecodeOptions bs of
-      Left e        -> panic (pack e)
-      Right csvDocs -> csvDocs
+readByteStringLazy :: (FromNamedRecord a) => proxy a -> BL.ByteString -> Either Prelude.String (Header, Vector a)
+readByteStringLazy _f bs = decodeByNameWith csvDecodeOptions bs
 
-readByteStringStrict :: (FromNamedRecord a) => proxy a -> BS.ByteString -> (Header, Vector a)
+readByteStringStrict :: (FromNamedRecord a) => proxy a -> BS.ByteString -> Either Prelude.String (Header, Vector a)
 readByteStringStrict ff = (readByteStringLazy ff) . BL.fromStrict
 
 ------------------------------------------------------------------------
 -- | TODO use readFileLazy
-readFile :: FilePath -> IO (Header, Vector CsvDoc)
+readFile :: FilePath -> IO (Either Prelude.String (Header, Vector CsvDoc))
 readFile = fmap readCsvLazyBS . BL.readFile
 
 
 -- | TODO use readByteStringLazy
-readCsvLazyBS :: BL.ByteString -> (Header, Vector CsvDoc)
-readCsvLazyBS bs = case decodeByNameWith csvDecodeOptions bs of
-      Left e        -> panic (pack e)
-      Right csvDocs -> csvDocs
+readCsvLazyBS :: BL.ByteString -> Either Prelude.String (Header, Vector CsvDoc)
+readCsvLazyBS bs = decodeByNameWith csvDecodeOptions bs
 
 ------------------------------------------------------------------------
 -- | TODO use readFileLazy
-readCsvHal :: FilePath -> IO (Header, Vector CsvHal)
+readCsvHal :: FilePath -> IO (Either Prelude.String (Header, Vector CsvHal))
 readCsvHal = fmap readCsvHalLazyBS . BL.readFile
 
 -- | TODO use readByteStringLazy
-readCsvHalLazyBS :: BL.ByteString -> (Header, Vector CsvHal)
-readCsvHalLazyBS bs = case decodeByNameWith csvDecodeOptions bs of
-      Left e        -> panic (pack e)
-      Right csvDocs -> csvDocs
+readCsvHalLazyBS :: BL.ByteString -> Either Prelude.String (Header, Vector CsvHal)
+readCsvHalLazyBS bs = decodeByNameWith csvDecodeOptions bs
 
-readCsvHalBSStrict :: BS.ByteString -> (Header, Vector CsvHal)
+readCsvHalBSStrict :: BS.ByteString -> Either Prelude.String (Header, Vector CsvHal)
 readCsvHalBSStrict = readCsvHalLazyBS . BL.fromStrict
 
 ------------------------------------------------------------------------
@@ -382,18 +379,22 @@ csv2doc (CsvDoc title source
                                Nothing
 
 ------------------------------------------------------------------------
-parseHal :: FilePath -> IO [HyperdataDocument]
-parseHal fp = V.toList <$> V.map csvHal2doc <$> snd <$> readCsvHal fp
+parseHal :: FilePath -> IO (Either Prelude.String [HyperdataDocument])
+parseHal fp = do
+  r <- readCsvHal fp
+  pure $ (V.toList . V.map csvHal2doc . snd) <$> r
 
-parseHal' :: BL.ByteString -> [HyperdataDocument]
-parseHal' = V.toList . V.map csvHal2doc . snd . readCsvHalLazyBS 
+parseHal' :: BL.ByteString -> Either Prelude.String [HyperdataDocument]
+parseHal' bs = (V.toList . V.map csvHal2doc . snd) <$> readCsvHalLazyBS bs
 
 ------------------------------------------------------------------------
-parseCsv :: FilePath -> IO [HyperdataDocument]
-parseCsv fp = V.toList <$> V.map csv2doc <$> snd <$> readFile fp
+parseCsv :: FilePath -> IO (Either Prelude.String [HyperdataDocument])
+parseCsv fp = do
+  r <- readFile fp
+  pure $ (V.toList . V.map csv2doc . snd) <$> r
 
-parseCsv' :: BL.ByteString -> [HyperdataDocument]
-parseCsv' bs = V.toList $ V.map csv2doc $ snd $ readCsvLazyBS bs
+parseCsv' :: BL.ByteString -> Either Prelude.String [HyperdataDocument]
+parseCsv' bs = (V.toList . V.map csv2doc . snd) <$> readCsvLazyBS bs
 
 ------------------------------------------------------------------------
 -- Csv v3 weighted for phylo

src/Gargantext/Database/Action/Flow.hs

@@ -56,7 +56,7 @@ import Data.Map (Map, lookup)
 import Data.Maybe (catMaybes)
 import Data.Monoid
 import Data.Swagger
-import Data.Text (splitOn)
+import qualified Data.Text as T
 import Data.Traversable (traverse)
 import Data.Tuple.Extra (first, second)
 import GHC.Generics (Generic)
@@ -178,11 +178,12 @@ flowCorpusFile :: (FlowCmdM env err m)
            -> TermType Lang -> FileFormat -> FilePath
            -> m CorpusId
 flowCorpusFile u n l la ff fp = do
-  docs <- liftBase ( splitEvery 500
-                 <$> take l
-                 <$> parseFile ff fp
-                 )
+  eParsed <- liftBase $ parseFile ff fp
+  case eParsed of
+    Right parsed -> do
+      let docs = splitEvery 500 $ take l parsed
       flowCorpus u n la (map (map toHyperdataDocument) docs)
+    Left e       -> panic $ "Error: " <> (T.pack e)
 
 ------------------------------------------------------------------------
 -- | TODO improve the needed type to create/update a corpus
@@ -425,11 +426,11 @@ instance ExtractNgramsT HyperdataDocument
                         $ _hd_source doc
 
               institutes = map text2ngrams
-                         $ maybe ["Nothing"] (map toSchoolName . (splitOn ", "))
+                         $ maybe ["Nothing"] (map toSchoolName . (T.splitOn ", "))
                          $ _hd_institutes doc
 
               authors    = map text2ngrams
-                         $ maybe ["Nothing"] (splitOn ", ")
+                         $ maybe ["Nothing"] (T.splitOn ", ")
                          $ _hd_authors doc
 
           terms' <- map (enrichedTerms (lang' ^. tt_lang) CoreNLP NP)