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(..))
  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, gc_pubmed_api_key)
  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 {-
  71 data Query = Query { query_query      :: Text
  72                    , query_node_id    :: Int
  73                    , query_lang       :: Lang
  74                    , query_databases  :: [DataOrigin]
  75                    }
  76                    deriving (Eq, Generic)
  77
  78 deriveJSON (unPrefix "query_") 'Query
  79
  80 instance Arbitrary Query where
  81     arbitrary = elements [ Query q n la fs
  82                          | q <- ["honeybee* AND collapse"
  83                                 ,"covid 19"
  84                                 ]
  85                          , n <- [0..10]
  86                          , la <- allLangs
  87                          , fs <- take 3 $ repeat allDataOrigins
  88                          ]
  89
  90 instance ToSchema Query where
  91   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "query_")
  92 -}
  93
  94 ------------------------------------------------------------------------
  95
  96 {-
  97 type Api = PostApi
  98         :<|> GetApi
  99
 100 type PostApi = Summary "New Corpus endpoint"
 101              :> ReqBody '[JSON] Query
 102              :> Post    '[JSON] CorpusId
 103 type GetApi = Get '[JSON] ApiInfo
 104 -}
 105
 106 -- | TODO manage several apis
 107 -- TODO-ACCESS
 108 -- TODO this is only the POST
 109 {-
 110 api :: (FlowCmdM env err m) => UserId -> Query -> m CorpusId
 111 api uid (Query q _ as) = do
 112   cId <- case head as of
 113     Nothing      -> flowCorpusSearchInDatabase (UserDBId uid) EN q
 114     Just API.All -> flowCorpusSearchInDatabase (UserDBId uid) EN q
 115     Just a   -> do
 116       docs <- liftBase $ API.get a q (Just 1000)
 117       cId' <- flowCorpus (UserDBId uid) (Left q) (Multi EN) [docs]
 118       pure cId'
 119
 120   pure cId
 121 -}
 122
 123 ------------------------------------------------
 124 -- TODO use this route for Client implementation
 125 data ApiInfo = ApiInfo { api_info :: [API.ExternalAPIs]}
 126   deriving (Generic)
 127 instance Arbitrary ApiInfo where
 128   arbitrary = ApiInfo <$> arbitrary
 129
 130 deriveJSON (unPrefix "") 'ApiInfo
 131
 132 instance ToSchema ApiInfo
 133
 134 info :: ApiInfo
 135 info = ApiInfo API.externalAPIs
 136
 137 ------------------------------------------------------------------------
 138 ------------------------------------------------------------------------
 139 data WithQuery = WithQuery
 140   { _wq_query        :: !API.RawQuery
 141   , _wq_databases    :: !Database
 142   , _wq_datafield    :: !(Maybe Datafield)
 143   , _wq_lang         :: !Lang
 144   , _wq_node_id      :: !Int
 145   , _wq_flowListWith :: !FlowSocialListWith
 146   }
 147   deriving Generic
 148
 149 makeLenses ''WithQuery
 150 instance FromJSON WithQuery where
 151   parseJSON = genericParseJSON $ jsonOptions "_wq_"
 152 instance ToJSON WithQuery where
 153   toJSON = genericToJSON $ jsonOptions "_wq_"
 154 instance ToSchema WithQuery where
 155   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_wq_")
 156
 157 ------------------------------------------------------------------------
 158
 159 type AddWithQuery = Summary "Add with Query to corpus endpoint"
 160    :> "corpus"
 161      :> Capture "corpus_id" CorpusId
 162    :> "query"
 163      :> AsyncJobs JobLog '[JSON] WithQuery JobLog
 164
 165 {-
 166 type AddWithFile = Summary "Add with MultipartData to corpus endpoint"
 167    :> "corpus"
 168      :> Capture "corpus_id" CorpusId
 169    :> "add"
 170    :> "file"
 171      :> MultipartForm Mem (MultipartData Mem)
 172      :> QueryParam "fileType"  FileType
 173    :> "async"
 174      :> AsyncJobs JobLog '[JSON] () JobLog
 175 -}
 176
 177
 178 ------------------------------------------------------------------------
 179 -- TODO WithQuery also has a corpus id
 180
 181
 182 addToCorpusWithQuery :: (FlowCmdM env err m, MonadJobStatus m)
 183                        => User
 184                        -> CorpusId
 185                        -> WithQuery
 186                        -> Maybe API.Limit
 187                        -> JobHandle m
 188                        -> m ()
 189 addToCorpusWithQuery user cid (WithQuery { _wq_query = q
 190                                          , _wq_databases = dbs
 191                                          , _wq_datafield = datafield
 192                                          , _wq_lang = l
 193                                          , _wq_flowListWith = flw }) maybeLimit jobHandle = do
 194   -- TODO ...
 195   -- printDebug "[addToCorpusWithQuery] (cid, dbs)" (cid, dbs)
 196   -- printDebug "[addToCorpusWithQuery] datafield" datafield
 197   -- printDebug "[addToCorpusWithQuery] flowListWith" flw
 198
 199   case datafield of
 200     Just Web -> do
 201       -- printDebug "[addToCorpusWithQuery] processing web request" datafield
 202
 203       markStarted 1 jobHandle
 204
 205       _ <- triggerSearxSearch user cid q l jobHandle
 206
 207       markComplete jobHandle
 208
 209     _ -> do
 210       case datafield of
 211          Just (External PubMed) -> do
 212            _api_key <- view $ hasConfig . gc_pubmed_api_key
 213            printDebug "[addToCorpusWithQuery] pubmed api key" _api_key
 214            _ <- updateCorpusPubmedAPIKey cid _api_key
 215            pure ()
 216          _ -> pure ()
 217       markStarted 3 jobHandle
 218
 219       -- TODO add cid
 220       -- TODO if cid is folder -> create Corpus
 221       --      if cid is corpus -> add to corpus
 222       --      if cid is root   -> create corpus in Private
 223       -- printDebug "[G.A.N.C.New] getDataText with query" q
 224       let db = database2origin dbs
 225       eTxt <- getDataText db (Multi l) q maybeLimit
 226
 227       -- printDebug "[G.A.N.C.New] lTxts" lTxts
 228       case eTxt of
 229         Right txt -> do
 230           -- TODO Sum lenghts of each txt elements
 231
 232           markProgress 1 jobHandle
 233
 234           void $ flowDataText user txt (Multi l) cid (Just flw) jobHandle
 235           -- printDebug "corpus id" cids
 236           -- printDebug "sending email" ("xxxxxxxxxxxxxxxxxxxxx" :: Text)
 237           sendMail user
 238           -- TODO ...
 239           markComplete jobHandle
 240
 241         Left err -> do
 242           -- printDebug "Error: " err
 243           markFailed (Just $ T.pack (show err)) jobHandle
 244
 245 type AddWithForm = Summary "Add with FormUrlEncoded to corpus endpoint"
 246    :> "corpus"
 247      :> Capture "corpus_id" CorpusId
 248    :> "add"
 249    :> "form"
 250    :> "async"
 251      :> AsyncJobs JobLog '[FormUrlEncoded] NewWithForm JobLog
 252
 253 addToCorpusWithForm :: (FlowCmdM env err m, MonadJobStatus m)
 254                     => User
 255                     -> CorpusId
 256                     -> NewWithForm
 257                     -> JobHandle m
 258                     -> m ()
 259 addToCorpusWithForm user cid (NewWithForm ft ff d l _n sel) jobHandle = do
 260   -- printDebug "[addToCorpusWithForm] Parsing corpus: " cid
 261   -- printDebug "[addToCorpusWithForm] fileType" ft
 262   -- printDebug "[addToCorpusWithForm] fileFormat" ff
 263   limit' <- view $ hasConfig . gc_max_docs_parsers
 264   let limit = fromIntegral limit' :: Integer
 265   let
 266     parseC = case ft of
 267       CSV_HAL   -> Parser.parseFormatC Parser.CsvHal
 268       CSV       -> Parser.parseFormatC Parser.CsvGargV3
 269       WOS       -> Parser.parseFormatC Parser.WOS
 270       PresseRIS -> Parser.parseFormatC Parser.RisPresse
 271       Iramuteq  -> Parser.parseFormatC Parser.Iramuteq
 272       JSON      -> Parser.parseFormatC Parser.JSON
 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