src/Gargantext/Database/Action/Flow.hs

   1 {-|
   2 Module      : Gargantext.Database.Flow
   3 Description : Database Flow
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 -- TODO-ACCESS:
  11 --   check userId       CanFillUserCorpus   userCorpusId
  12 --   check masterUserId CanFillMasterCorpus masterCorpusId
  13
  14 -- TODO-ACCESS: check uId CanInsertDoc pId && checkDocType nodeType
  15 -- TODO-EVENTS: InsertedNodes
  16 -}
  17
  18 {-# OPTIONS_GHC -fno-warn-orphans    #-}
  19
  20 {-# LANGUAGE ConstraintKinds         #-}
  21 {-# LANGUAGE ConstrainedClassMethods #-}
  22 {-# LANGUAGE ConstraintKinds         #-}
  23 {-# LANGUAGE InstanceSigs            #-}
  24 {-# LANGUAGE TemplateHaskell         #-}
  25
  26 module Gargantext.Database.Action.Flow -- (flowDatabase, ngrams2list)
  27   ( FlowCmdM
  28   , getDataText
  29   , flowDataText
  30   , flow
  31
  32   , flowCorpusFile
  33   , flowCorpus
  34   , flowAnnuaire
  35
  36   , getOrMkRoot
  37   , getOrMk_RootWithCorpus
  38   , TermType(..)
  39   , DataOrigin(..)
  40   , allDataOrigins
  41
  42   , do_api
  43   )
  44     where
  45
  46 import Control.Lens ((^.), view, _Just, makeLenses)
  47 import Data.Aeson.TH (deriveJSON)
  48 import Data.Either
  49 import Data.List (concat)
  50 import qualified Data.Map  as Map
  51 import Data.Map (Map, lookup)
  52 import Data.Maybe (Maybe(..), catMaybes)
  53 import Data.Monoid
  54 import Data.Swagger
  55 import Data.Text (splitOn, intercalate)
  56 import Data.Traversable (traverse)
  57 import Data.Tuple.Extra (first, second)
  58 import GHC.Generics (Generic)
  59 import System.FilePath (FilePath)
  60
  61 import Gargantext.Core (Lang(..))
  62 import Gargantext.Core.Flow.Types
  63 import Gargantext.Core.Types (Terms(..))
  64 import Gargantext.Core.Types.Individu (User(..))
  65 import Gargantext.Core.Types.Main
  66 import Gargantext.Database.Action.Flow.List
  67 import Gargantext.Database.Action.Flow.Types
  68 import Gargantext.Database.Action.Flow.Utils (insertDocNgrams)
  69 import Gargantext.Database.Query.Table.Node
  70 import Gargantext.Database.Query.Table.Node.Document.Insert -- (insertDocuments, ReturnId(..), addUniqIdsDoc, addUniqIdsContact, ToDbData(..))
  71 import Gargantext.Database.Query.Tree.Root (getOrMkRoot, getOrMk_RootWithCorpus)
  72 import Gargantext.Database.Action.Search (searchDocInDatabase)
  73 import Gargantext.Database.Admin.Config (userMaster, corpusMasterName)
  74 import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..))
  75 import Gargantext.Database.Admin.Types.Hyperdata
  76 import Gargantext.Database.Admin.Types.Node -- (HyperdataDocument(..), NodeType(..), NodeId, UserId, ListId, CorpusId, RootId, MasterCorpusId, MasterUserId)
  77 import Gargantext.Database.Prelude
  78 import Gargantext.Database.Query.Table.Ngrams
  79 import Gargantext.Database.Query.Table.NodeNgrams (listInsertDb , getCgramsId)
  80 import Gargantext.Database.Query.Table.NodeNodeNgrams2
  81 import Gargantext.Core.Ext.IMT (toSchoolName)
  82 import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
  83 import Gargantext.Core.Ext.IMTUser (deserialiseImtUsersFromFile)
  84 import Gargantext.Core.Text
  85 import Gargantext.Prelude
  86 import Gargantext.Core.Text.Corpus.Parsers (parseFile, FileFormat)
  87 import Gargantext.Core.Text.List (buildNgramsLists,StopSize(..))
  88 import Gargantext.Core.Text.Terms.Mono.Stem.En (stemIt)
  89 import Gargantext.Core.Text.Terms
  90 import qualified Gargantext.Database.Query.Table.Node.Document.Add  as Doc  (add)
  91 import qualified Gargantext.Core.Text.Corpus.API as API
  92
  93 ------------------------------------------------------------------------
  94 -- TODO use internal with API name (could be old data)
  95 data DataOrigin = InternalOrigin { _do_api :: API.ExternalAPIs }
  96                 | ExternalOrigin { _do_api :: API.ExternalAPIs }
  97                -- TODO Web
  98   deriving (Generic, Eq)
  99
 100 makeLenses ''DataOrigin
 101 deriveJSON (unPrefix "_do_") ''DataOrigin
 102 instance ToSchema DataOrigin where
 103   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_do_")
 104
 105 allDataOrigins :: [DataOrigin]
 106 allDataOrigins = map InternalOrigin API.externalAPIs
 107               <> map ExternalOrigin API.externalAPIs
 108
 109 ---------------
 110 data DataText = DataOld ![NodeId]
 111               | DataNew ![[HyperdataDocument]]
 112
 113 -- TODO use the split parameter in config file
 114 getDataText :: FlowCmdM env err m
 115             => DataOrigin
 116             -> TermType Lang
 117             -> API.Query
 118             -> Maybe API.Limit
 119             -> m DataText
 120 getDataText (ExternalOrigin api) la q li = liftBase $ DataNew
 121                                   <$> splitEvery 500
 122                                   <$> API.get api (_tt_lang la) q li
 123 getDataText (InternalOrigin _) _la q _li = do
 124   (_masterUserId, _masterRootId, cId) <- getOrMk_RootWithCorpus
 125                                            (UserName userMaster)
 126                                            (Left "")
 127                                            (Nothing :: Maybe HyperdataCorpus)
 128   ids <-  map fst <$> searchDocInDatabase cId (stemIt q)
 129   pure $ DataOld ids
 130
 131 -------------------------------------------------------------------------------
 132 flowDataText :: FlowCmdM env err m
 133              => User
 134              -> DataText
 135              -> TermType Lang
 136              -> CorpusId
 137              -> m CorpusId
 138 flowDataText u (DataOld ids) tt cid = flowCorpusUser (_tt_lang tt) u (Right [cid]) corpusType ids
 139   where
 140     corpusType = (Nothing :: Maybe HyperdataCorpus)
 141 flowDataText u (DataNew txt) tt cid = flowCorpus u (Right [cid]) tt txt
 142
 143 ------------------------------------------------------------------------
 144 -- TODO use proxy
 145 flowAnnuaire :: FlowCmdM env err m
 146              => User
 147              -> Either CorpusName [CorpusId]
 148              -> (TermType Lang)
 149              -> FilePath
 150              -> m AnnuaireId
 151 flowAnnuaire u n l filePath = do
 152   docs <- liftBase $ (( splitEvery 500 <$> deserialiseImtUsersFromFile filePath) :: IO [[HyperdataContact]])
 153   flow (Nothing :: Maybe HyperdataAnnuaire) u n l docs
 154
 155 ------------------------------------------------------------------------
 156 flowCorpusFile :: FlowCmdM env err m
 157            => User
 158            -> Either CorpusName [CorpusId]
 159            -> Limit -- Limit the number of docs (for dev purpose)
 160            -> TermType Lang -> FileFormat -> FilePath
 161            -> m CorpusId
 162 flowCorpusFile u n l la ff fp = do
 163   docs <- liftBase ( splitEvery 500
 164                  <$> take l
 165                  <$> parseFile ff fp
 166                  )
 167   flowCorpus u n la (map (map toHyperdataDocument) docs)
 168
 169 ------------------------------------------------------------------------
 170 -- | TODO improve the needed type to create/update a corpus
 171 -- (For now, Either is enough)
 172 flowCorpus :: (FlowCmdM env err m, FlowCorpus a)
 173            => User
 174            -> Either CorpusName [CorpusId]
 175            -> TermType Lang
 176            -> [[a]]
 177            -> m CorpusId
 178 flowCorpus = flow (Nothing :: Maybe HyperdataCorpus)
 179
 180
 181 flow :: (FlowCmdM env err m, FlowCorpus a, MkCorpus c)
 182      => Maybe c
 183      -> User
 184      -> Either CorpusName [CorpusId]
 185      -> TermType Lang
 186      -> [[a]]
 187      -> m CorpusId
 188 flow c u cn la docs = do
 189   ids <- traverse (insertMasterDocs c la) docs
 190   flowCorpusUser (la ^. tt_lang) u cn c (concat ids)
 191
 192 ------------------------------------------------------------------------
 193 flowCorpusUser :: (FlowCmdM env err m, MkCorpus c)
 194                => Lang
 195                -> User
 196                -> Either CorpusName [CorpusId]
 197                -> Maybe c
 198                -> [NodeId]
 199                -> m CorpusId
 200 flowCorpusUser l user corpusName ctype ids = do
 201   -- User Flow
 202   (userId, _rootId, userCorpusId) <- getOrMk_RootWithCorpus user corpusName ctype
 203   listId <- getOrMkList userCorpusId userId
 204   _cooc  <- insertDefaultNode NodeListCooc listId userId
 205   -- TODO: check if present already, ignore
 206   _ <- Doc.add userCorpusId ids
 207
 208   _tId <- insertDefaultNode NodeTexts userCorpusId userId
 209   -- printDebug "Node Text Id" tId
 210
 211   -- User List Flow
 212   (masterUserId, _masterRootId, masterCorpusId) <- getOrMk_RootWithCorpus (UserName userMaster) (Left "") ctype
 213   ngs         <- buildNgramsLists l 2 3 (StopSize 3) userCorpusId masterCorpusId
 214   _userListId <- flowList_DbRepo listId ngs
 215   _mastListId <- getOrMkList masterCorpusId masterUserId
 216   -- _ <- insertOccsUpdates userCorpusId mastListId
 217   -- printDebug "userListId" userListId
 218   -- User Graph Flow
 219   _ <- insertDefaultNode NodeDashboard userCorpusId userId
 220   _ <- insertDefaultNode NodeGraph     userCorpusId userId
 221   --_ <- mkPhylo  userCorpusId userId
 222
 223   -- Annuaire Flow
 224   -- _ <- mkAnnuaire  rootUserId userId
 225   pure userCorpusId
 226
 227
 228 insertMasterDocs :: ( FlowCmdM env err m
 229                     , FlowCorpus a
 230                     , MkCorpus   c
 231                     )
 232                  => Maybe c
 233                  -> TermType Lang
 234                  -> [a]
 235                  -> m [DocId]
 236 insertMasterDocs c lang hs  =  do
 237   (masterUserId, _, masterCorpusId) <- getOrMk_RootWithCorpus (UserName userMaster) (Left corpusMasterName) c
 238
 239   -- TODO Type NodeDocumentUnicised
 240   let docs = map addUniqId hs
 241   ids <- insertDb masterUserId masterCorpusId docs
 242   let
 243     ids' = map reId ids
 244     documentsWithId = mergeData (toInserted ids) (Map.fromList $ map viewUniqId' docs)
 245   -- TODO
 246   -- create a corpus with database name (CSV or PubMed)
 247   -- add documents to the corpus (create node_node link)
 248   -- this will enable global database monitoring
 249
 250   -- maps :: IO Map Ngrams (Map NgramsType (Map NodeId Int))
 251   maps <- mapNodeIdNgrams
 252        <$> documentIdWithNgrams (extractNgramsT $ withLang lang documentsWithId) documentsWithId
 253
 254   terms2id <- insertNgrams $ Map.keys maps
 255   -- to be removed
 256   let indexedNgrams = Map.mapKeys (indexNgrams terms2id) maps
 257
 258   -- new
 259   lId      <- getOrMkList masterCorpusId masterUserId
 260   mapCgramsId <- listInsertDb lId toNodeNgramsW'
 261                 $ map (first _ngramsTerms . second Map.keys)
 262                 $ Map.toList maps
 263   -- insertDocNgrams
 264   _return <- insertNodeNodeNgrams2
 265            $ catMaybes [ NodeNodeNgrams2 <$> Just nId
 266                                          <*> getCgramsId mapCgramsId ngrams_type (_ngramsTerms terms'')
 267                                          <*> Just (fromIntegral w :: Double)
 268                        | (terms'', mapNgramsTypes) <- Map.toList maps
 269                        , (ngrams_type, mapNodeIdWeight) <- Map.toList mapNgramsTypes
 270                        , (nId, w) <- Map.toList mapNodeIdWeight
 271                        ]
 272
 273   _ <- Doc.add masterCorpusId ids'
 274   _cooc <- insertDefaultNode NodeListCooc lId masterUserId
 275   -- to be removed
 276   _   <- insertDocNgrams lId indexedNgrams
 277
 278   pure ids'
 279
 280 ------------------------------------------------------------------------
 281 ------------------------------------------------------------------------
 282 viewUniqId' :: UniqId a
 283             => a
 284             -> (HashId, a)
 285 viewUniqId' d = maybe err (\h -> (h,d)) (view uniqId d)
 286       where
 287         err = panic "[ERROR] Database.Flow.toInsert"
 288
 289
 290 toInserted :: [ReturnId]
 291            -> Map HashId ReturnId
 292 toInserted =
 293   Map.fromList . map    (\r ->  (reUniqId r, r)    )
 294                . filter (\r -> reInserted r == True)
 295
 296 mergeData :: Map HashId ReturnId
 297           -> Map HashId a
 298           -> [DocumentWithId a]
 299 mergeData rs = catMaybes . map toDocumentWithId . Map.toList
 300   where
 301     toDocumentWithId (sha,hpd) =
 302       DocumentWithId <$> fmap reId (lookup sha rs)
 303                      <*> Just hpd
 304
 305 ------------------------------------------------------------------------
 306 instance HasText HyperdataContact
 307   where
 308     hasText = undefined
 309 ------------------------------------------------------------------------
 310 ------------------------------------------------------------------------
 311 documentIdWithNgrams :: HasNodeError err
 312                      => (a
 313                      -> Cmd err (Map Ngrams (Map NgramsType Int)))
 314                      -> [DocumentWithId a]
 315                      -> Cmd err [DocumentIdWithNgrams a]
 316 documentIdWithNgrams f = traverse toDocumentIdWithNgrams
 317   where
 318     toDocumentIdWithNgrams d = do
 319       e <- f $ documentData         d
 320       pure   $ DocumentIdWithNgrams d e
 321
 322
 323 ------------------------------------------------------------------------
 324 instance ExtractNgramsT HyperdataContact
 325   where
 326     extractNgramsT l hc = filterNgramsT 255 <$> extract l hc
 327       where
 328         extract :: TermType Lang -> HyperdataContact
 329                 -> Cmd err (Map Ngrams (Map NgramsType Int))
 330         extract _l hc' = do
 331           let authors = map text2ngrams
 332                      $ maybe ["Nothing"] (\a -> [a])
 333                      $ view (hc_who . _Just . cw_lastName) hc'
 334
 335           pure $ Map.fromList $ [(a', Map.singleton Authors     1) | a' <- authors    ]
 336
 337 instance HasText HyperdataDocument
 338   where
 339     hasText h = catMaybes [ _hd_title    h
 340                           , _hd_abstract h
 341                           ]
 342
 343 instance ExtractNgramsT HyperdataDocument
 344   where
 345     extractNgramsT :: TermType Lang
 346                    -> HyperdataDocument
 347                    -> Cmd err (Map Ngrams (Map NgramsType Int))
 348     extractNgramsT lang hd = filterNgramsT 255 <$> extractNgramsT' lang hd
 349       where
 350         extractNgramsT' :: TermType Lang
 351                         -> HyperdataDocument
 352                        -> Cmd err (Map Ngrams (Map NgramsType Int))
 353         extractNgramsT' lang' doc = do
 354           let source    = text2ngrams
 355                         $ maybe "Nothing" identity
 356                         $ _hd_source doc
 357
 358               institutes = map text2ngrams
 359                          $ maybe ["Nothing"] (map toSchoolName . (splitOn ", "))
 360                          $ _hd_institutes doc
 361
 362               authors    = map text2ngrams
 363                          $ maybe ["Nothing"] (splitOn ", ")
 364                          $ _hd_authors doc
 365
 366           terms' <- map text2ngrams
 367                  <$> map (intercalate " " . _terms_label)
 368                  <$> concat
 369                  <$> liftBase (extractTerms lang' $ hasText doc)
 370
 371           pure $ Map.fromList $  [(source, Map.singleton Sources 1)]
 372                              <> [(i', Map.singleton Institutes  1) | i' <- institutes ]
 373                              <> [(a', Map.singleton Authors     1) | a' <- authors    ]
 374                              <> [(t', Map.singleton NgramsTerms 1) | t' <- terms'     ]
 375
 376