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

   1 {-|
   2 Module      : Gargantext.API.Node.Corpus.New
   3 Description : New corpus API
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 New corpus means either:
  11 - new corpus
  12 - new data in existing corpus
  13 -}
  14
  15 {-# LANGUAGE TemplateHaskell    #-}
  16 {-# LANGUAGE TypeOperators      #-}
  17
  18 module Gargantext.API.Node.Corpus.New
  19       where
  20
  21 import Conduit
  22 import Control.Lens hiding (elements, Empty)
  23 import Control.Monad
  24 import Data.Aeson
  25 import Data.Aeson.TH (deriveJSON)
  26 import qualified Data.ByteString.Base64 as BSB64
  27 import Data.Conduit.Internal (zipSources)
  28 import Data.Either
  29 import Data.Maybe (fromMaybe)
  30 import Data.Swagger
  31 import Data.Text (Text)
  32 import qualified Data.Text as T
  33 import GHC.Generics (Generic)
  34 import Servant
  35 import Servant.Job.Utils (jsonOptions)
  36 -- import Servant.Multipart
  37 import qualified Data.Text.Encoding as TE
  38 -- import Test.QuickCheck (elements)
  39 import Test.QuickCheck.Arbitrary
  40
  41 import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs)
  42 import Gargantext.API.Admin.Types (HasSettings)
  43 import Gargantext.API.Node.Corpus.New.Types
  44 import Gargantext.API.Node.Corpus.Searx
  45 import Gargantext.API.Node.Corpus.Types
  46 import Gargantext.API.Node.Types
  47 import Gargantext.Core (Lang(..))
  48 import Gargantext.Core.Text.List.Social (FlowSocialListWith(..))
  49 import Gargantext.Core.Types.Individu (User(..))
  50 import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
  51 import Gargantext.Database.Action.Flow (flowCorpus, getDataText, flowDataText, TermType(..){-, allDataOrigins-})
  52 import Gargantext.Database.Action.Flow.Types (FlowCmdM)
  53 import Gargantext.Database.Action.Mail (sendMail)
  54 import Gargantext.Database.Action.Node (mkNodeWithParent)
  55 import Gargantext.Database.Action.User (getUserId)
  56 import Gargantext.Database.Admin.Types.Hyperdata
  57 import Gargantext.Database.Admin.Types.Node (CorpusId, NodeType(..), UserId)
  58 import Gargantext.Database.Prelude (hasConfig)
  59 import Gargantext.Database.Query.Table.Node (getNodeWith, updateCorpusPubmedAPIKey)
  60 import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateHyperdata)
  61 import Gargantext.Database.Schema.Node (node_hyperdata)
  62 import Gargantext.Prelude
  63 import Gargantext.Prelude.Config (gc_max_docs_parsers)
  64 import Gargantext.Utils.Jobs (JobHandle, MonadJobStatus(..))
  65 import qualified Gargantext.Core.Text.Corpus.API as API
  66 import qualified Gargantext.Core.Text.Corpus.Parsers as Parser (FileType(..), parseFormatC)
  67 import qualified Gargantext.Database.GargDB as GargDB
  68 ------------------------------------------------------------------------
  69 {-
  70 data Query = Query { query_query      :: Text
  71                    , query_node_id    :: Int
  72                    , query_lang       :: Lang
  73                    , query_databases  :: [DataOrigin]
  74                    }
  75                    deriving (Eq, Generic)
  76
  77 deriveJSON (unPrefix "query_") 'Query
  78
  79 instance Arbitrary Query where
  80     arbitrary = elements [ Query q n la fs
  81                          | q <- ["honeybee* AND collapse"
  82                                 ,"covid 19"
  83                                 ]
  84                          , n <- [0..10]
  85                          , la <- allLangs
  86                          , fs <- take 3 $ repeat allDataOrigins
  87                          ]
  88
  89 instance ToSchema Query where
  90   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "query_")
  91 -}
  92
  93 ------------------------------------------------------------------------
  94
  95 {-
  96 type Api = PostApi
  97         :<|> GetApi
  98
  99 type PostApi = Summary "New Corpus endpoint"
 100              :> ReqBody '[JSON] Query
 101              :> Post    '[JSON] CorpusId
 102 type GetApi = Get '[JSON] ApiInfo
 103 -}
 104
 105 -- | TODO manage several apis
 106 -- TODO-ACCESS
 107 -- TODO this is only the POST
 108 {-
 109 api :: (FlowCmdM env err m) => UserId -> Query -> m CorpusId
 110 api uid (Query q _ as) = do
 111   cId <- case head as of
 112     Nothing      -> flowCorpusSearchInDatabase (UserDBId uid) EN q
 113     Just API.All -> flowCorpusSearchInDatabase (UserDBId uid) EN q
 114     Just a   -> do
 115       docs <- liftBase $ API.get a q (Just 1000)
 116       cId' <- flowCorpus (UserDBId uid) (Left q) (Multi EN) [docs]
 117       pure cId'
 118
 119   pure cId
 120 -}
 121
 122 ------------------------------------------------
 123 -- TODO use this route for Client implementation
 124 data ApiInfo = ApiInfo { api_info :: [API.ExternalAPIs]}
 125   deriving (Generic)
 126 instance Arbitrary ApiInfo where
 127   arbitrary = ApiInfo <$> arbitrary
 128
 129 deriveJSON (unPrefix "") 'ApiInfo
 130
 131 instance ToSchema ApiInfo
 132
 133 info :: FlowCmdM env err m => UserId -> m ApiInfo
 134 info _u = do
 135   ext <- API.externalAPIs
 136
 137   pure $ ApiInfo ext
 138
 139 ------------------------------------------------------------------------
 140 ------------------------------------------------------------------------
 141 data WithQuery = WithQuery
 142   { _wq_query        :: !Text
 143   , _wq_databases    :: !Database
 144   , _wq_datafield    :: !(Maybe Datafield)
 145   , _wq_lang         :: !Lang
 146   , _wq_node_id      :: !Int
 147   , _wq_flowListWith :: !FlowSocialListWith
 148   }
 149   deriving Generic
 150
 151 makeLenses ''WithQuery
 152 instance FromJSON WithQuery where
 153   parseJSON = genericParseJSON $ jsonOptions "_wq_"
 154 instance ToJSON WithQuery where
 155   toJSON = genericToJSON $ jsonOptions "_wq_"
 156 instance ToSchema WithQuery where
 157   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_wq_")
 158
 159 ------------------------------------------------------------------------
 160
 161 type AddWithQuery = Summary "Add with Query to corpus endpoint"
 162    :> "corpus"
 163      :> Capture "corpus_id" CorpusId
 164    :> "query"
 165      :> AsyncJobs JobLog '[JSON] WithQuery JobLog
 166
 167 {-
 168 type AddWithFile = Summary "Add with MultipartData to corpus endpoint"
 169    :> "corpus"
 170      :> Capture "corpus_id" CorpusId
 171    :> "add"
 172    :> "file"
 173      :> MultipartForm Mem (MultipartData Mem)
 174      :> QueryParam "fileType"  FileType
 175    :> "async"
 176      :> AsyncJobs JobLog '[JSON] () JobLog
 177 -}
 178
 179
 180 ------------------------------------------------------------------------
 181 -- TODO WithQuery also has a corpus id
 182
 183
 184 addToCorpusWithQuery :: (FlowCmdM env err m, MonadJobStatus m)
 185                        => User
 186                        -> CorpusId
 187                        -> WithQuery
 188                        -> Maybe Integer
 189                        -> JobHandle m
 190                        -> m ()
 191 addToCorpusWithQuery user cid (WithQuery { _wq_query = q
 192                                          , _wq_databases = dbs
 193                                          , _wq_datafield = datafield
 194                                          , _wq_lang = l
 195                                          , _wq_flowListWith = flw }) maybeLimit jobHandle = do
 196   -- TODO ...
 197   -- printDebug "[addToCorpusWithQuery] (cid, dbs)" (cid, dbs)
 198   -- printDebug "[addToCorpusWithQuery] datafield" datafield
 199   -- printDebug "[addToCorpusWithQuery] flowListWith" flw
 200
 201   case datafield of
 202     Just Web -> do
 203       -- printDebug "[addToCorpusWithQuery] processing web request" datafield
 204
 205       markStarted 1 jobHandle
 206
 207       _ <- triggerSearxSearch user cid q l jobHandle
 208
 209       markComplete jobHandle
 210
 211     _ -> do
 212       case datafield of
 213          Just (External (PubMed { _api_key })) -> do
 214            printDebug "[addToCorpusWithQuery] pubmed api key" _api_key
 215            _ <- updateCorpusPubmedAPIKey cid _api_key
 216            pure ()
 217          _ -> pure ()
 218       markStarted 3 jobHandle
 219
 220       -- TODO add cid
 221       -- TODO if cid is folder -> create Corpus
 222       --      if cid is corpus -> add to corpus
 223       --      if cid is root   -> create corpus in Private
 224       -- printDebug "[G.A.N.C.New] getDataText with query" q
 225       db   <- database2origin dbs
 226       eTxt <- getDataText db (Multi l) q maybeLimit
 227
 228       -- printDebug "[G.A.N.C.New] lTxts" lTxts
 229       case eTxt of
 230         Right txt -> do
 231           -- TODO Sum lenghts of each txt elements
 232
 233           markProgress 1 jobHandle
 234
 235           void $ flowDataText user txt (Multi l) cid (Just flw) jobHandle
 236 -- printDebug "corpus id" cids
 237           -- printDebug "sending email" ("xxxxxxxxxxxxxxxxxxxxx" :: Text)
 238           sendMail user
 239           -- TODO ...
 240           markComplete jobHandle
 241
 242         Left err -> do
 243           -- printDebug "Error: " err
 244           markFailed (Just $ T.pack (show err)) jobHandle
 245
 246 type AddWithForm = Summary "Add with FormUrlEncoded to corpus endpoint"
 247    :> "corpus"
 248      :> Capture "corpus_id" CorpusId
 249    :> "add"
 250    :> "form"
 251    :> "async"
 252      :> AsyncJobs JobLog '[FormUrlEncoded] NewWithForm JobLog
 253
 254 addToCorpusWithForm :: (FlowCmdM env err m, MonadJobStatus m)
 255                     => User
 256                     -> CorpusId
 257                     -> NewWithForm
 258                     -> JobHandle m
 259                     -> m ()
 260 addToCorpusWithForm user cid (NewWithForm ft ff d l _n sel) jobHandle = do
 261   -- printDebug "[addToCorpusWithForm] Parsing corpus: " cid
 262   -- printDebug "[addToCorpusWithForm] fileType" ft
 263   -- printDebug "[addToCorpusWithForm] fileFormat" ff
 264   limit' <- view $ hasConfig . gc_max_docs_parsers
 265   let limit = fromIntegral limit' :: Integer
 266   let
 267     parseC = case ft of
 268       CSV_HAL   -> Parser.parseFormatC Parser.CsvHal
 269       CSV       -> Parser.parseFormatC Parser.CsvGargV3
 270       WOS       -> Parser.parseFormatC Parser.WOS
 271       PresseRIS -> Parser.parseFormatC Parser.RisPresse
 272       Iramuteq  -> Parser.parseFormatC Parser.Iramuteq
 273
 274   -- TODO granularity of the logStatus
 275   let data' = case ff of
 276         Plain -> cs d
 277         ZIP   -> case BSB64.decode $ TE.encodeUtf8 d of
 278           Left err -> panic $ T.pack "[addToCorpusWithForm] error decoding base64: " <> T.pack err
 279           Right decoded -> decoded
 280   eDocsC <- liftBase $ parseC ff data'
 281   case eDocsC of
 282     Right (mCount, docsC) -> do
 283       -- TODO Add progress (jobStatus) update for docs - this is a
 284       -- long action
 285
 286       let docsC' = zipSources (yieldMany [1..]) docsC
 287                   .| mapMC (\(idx, doc) ->
 288                         if idx > limit then do
 289                           --printDebug "[addToCorpusWithForm] number of docs exceeds the limit" (show limit)
 290                           let panicMsg' = [ "[addToCorpusWithForm] number of docs "
 291                                           , "exceeds the MAX_DOCS_PARSERS limit ("
 292                                           , show limit
 293                                           , ")" ]
 294                           let panicMsg = T.concat $ T.pack <$> panicMsg'
 295                           --logStatus $ jobLogFailTotalWithMessage panicMsg jobLog
 296                           panic panicMsg
 297                         else
 298                           pure doc)
 299                   .| mapC toHyperdataDocument
 300
 301       --printDebug "Parsing corpus finished : " cid
 302       --logStatus jobLog2
 303
 304       --printDebug "Starting extraction     : " cid
 305       -- TODO granularity of the logStatus
 306       -- printDebug "flowCorpus with (corpus_id, lang)" (cid, l)
 307
 308       _cid' <- flowCorpus user
 309                           (Right [cid])
 310                           (Multi $ fromMaybe EN l)
 311                           (Just sel)
 312                           --(Just $ fromIntegral $ length docs, docsC')
 313                           (mCount, transPipe liftBase docsC') -- TODO fix number of docs
 314                           --(map (map toHyperdataDocument) docs)
 315                           jobHandle
 316
 317       -- printDebug "Extraction finished   : " cid
 318       -- printDebug "sending email" ("xxxxxxxxxxxxxxxxxxxxx" :: Text)
 319       -- TODO uncomment this
 320       --sendMail user
 321
 322       markComplete jobHandle
 323     Left e -> do
 324       printDebug "[addToCorpusWithForm] parse error" e
 325       markFailed (Just $ T.pack e) jobHandle
 326
 327 {-
 328 addToCorpusWithFile :: FlowCmdM env err m
 329                     => CorpusId
 330                     -> MultipartData Mem
 331                     -> Maybe FileType
 332                     -> (JobLog -> m ())
 333                     -> m JobLog
 334 addToCorpusWithFile cid input filetype logStatus = do
 335   logStatus JobLog { _scst_succeeded = Just 10
 336                           , _scst_failed    = Just 2
 337                           , _scst_remaining = Just 138
 338                           , _scst_events    = Just []
 339                           }
 340   printDebug "addToCorpusWithFile" cid
 341   _h <- postUpload cid filetype input
 342
 343   pure      JobLog { _scst_succeeded = Just 137
 344                           , _scst_failed    = Just 13
 345                           , _scst_remaining = Just 0
 346                           , _scst_events    = Just []
 347                           }
 348 -}
 349
 350
 351
 352 type AddWithFile = Summary "Add with FileUrlEncoded to corpus endpoint"
 353    :> "corpus"
 354      :> Capture "corpus_id" CorpusId
 355    :> "add"
 356    :> "file"
 357    :> "async"
 358      :> AsyncJobs JobLog '[FormUrlEncoded] NewWithFile JobLog
 359
 360 addToCorpusWithFile :: (HasSettings env, FlowCmdM env err m, MonadJobStatus m)
 361                     => User
 362                     -> CorpusId
 363                     -> NewWithFile
 364                     -> JobHandle m
 365                     -> m ()
 366 addToCorpusWithFile user cid nwf@(NewWithFile _d _l fName) jobHandle = do
 367
 368   printDebug "[addToCorpusWithFile] Uploading file to corpus: " cid
 369   markStarted 1 jobHandle
 370
 371   fPath <- GargDB.writeFile nwf
 372   printDebug "[addToCorpusWithFile] File saved as: " fPath
 373
 374   uId <- getUserId user
 375   nIds <- mkNodeWithParent NodeFile (Just cid) uId fName
 376
 377   _ <- case nIds of
 378     [nId] -> do
 379         node <- getNodeWith nId (Proxy :: Proxy HyperdataFile)
 380         let hl = node ^. node_hyperdata
 381         _ <- updateHyperdata nId $ hl { _hff_name = fName
 382                                       , _hff_path = T.pack fPath }
 383
 384         printDebug "[addToCorpusWithFile] Created node with id: " nId
 385     _     -> pure ()
 386
 387   printDebug "[addToCorpusWithFile] File upload to corpus finished: " cid
 388
 389   printDebug "sending email" ("xxxxxxxxxxxxxxxxxxxxx" :: Text)
 390   sendMail user
 391
 392   markComplete jobHandle