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 (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.Ext.IMT (toSchoolName)
  63 import Gargantext.Core.Ext.IMTUser (deserialiseImtUsersFromFile)
  64 import Gargantext.Core.Flow.Types
  65 import Gargantext.Core.Text
  66 import Gargantext.Core.Text.Corpus.Parsers (parseFile, FileFormat)
  67 import Gargantext.Core.Text.List (buildNgramsLists,StopSize(..))
  68 import Gargantext.Core.Text.Terms
  69 import Gargantext.Core.Text.Terms.Mono.Stem.En (stemIt)
  70 import Gargantext.Core.Types (Terms(..))
  71 import Gargantext.Core.Types.Individu (User(..))
  72 import Gargantext.Core.Types.Main
  73 import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
  74 import Gargantext.Database.Action.Flow.List
  75 import Gargantext.Database.Action.Flow.Types
  76 import Gargantext.Database.Action.Flow.Utils (insertDocNgrams)
  77 import Gargantext.Database.Action.Search (searchDocInDatabase)
  78 import Gargantext.Database.Admin.Config (userMaster, corpusMasterName)
  79 import Gargantext.Database.Admin.Types.Hyperdata
  80 import Gargantext.Database.Admin.Types.Node -- (HyperdataDocument(..), NodeType(..), NodeId, UserId, ListId, CorpusId, RootId, MasterCorpusId, MasterUserId)
  81 import Gargantext.Database.Query.Table.Node
  82 import Gargantext.Database.Query.Table.Node.Document.Insert -- (insertDocuments, ReturnId(..), addUniqIdsDoc, addUniqIdsContact, ToDbData(..))
  83 import Gargantext.Database.Query.Tree.Root (getOrMkRoot, getOrMk_RootWithCorpus)
  84 import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..))
  85 import Gargantext.Database.Query.Table.Ngrams
  86 import Gargantext.Database.Query.Table.NodeNgrams (listInsertDb , getCgramsId)
  87 import Gargantext.Database.Query.Table.NodeNodeNgrams2
  88 import Gargantext.Database.Prelude
  89 import Gargantext.Database.Schema.Node (NodePoly(..))
  90 import Gargantext.Prelude
  91 import Gargantext.Prelude.Crypto.Hash (Hash)
  92 import qualified Gargantext.Database.Query.Table.Node.Document.Add  as Doc  (add)
  93 import qualified Gargantext.Core.Text.Corpus.API as API
  94
  95 ------------------------------------------------------------------------
  96 -- TODO use internal with API name (could be old data)
  97 data DataOrigin = InternalOrigin { _do_api :: API.ExternalAPIs }
  98                 | ExternalOrigin { _do_api :: API.ExternalAPIs }
  99                -- TODO Web
 100   deriving (Generic, Eq)
 101
 102 makeLenses ''DataOrigin
 103 deriveJSON (unPrefix "_do_") ''DataOrigin
 104 instance ToSchema DataOrigin where
 105   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_do_")
 106
 107 allDataOrigins :: [DataOrigin]
 108 allDataOrigins = map InternalOrigin API.externalAPIs
 109               <> map ExternalOrigin API.externalAPIs
 110
 111 ---------------
 112 data DataText = DataOld ![NodeId]
 113               | DataNew ![[HyperdataDocument]]
 114
 115 -- TODO use the split parameter in config file
 116 getDataText :: FlowCmdM env err m
 117             => DataOrigin
 118             -> TermType Lang
 119             -> API.Query
 120             -> Maybe API.Limit
 121             -> m DataText
 122 getDataText (ExternalOrigin api) la q li = liftBase $ DataNew
 123                                   <$> splitEvery 500
 124                                   <$> API.get api (_tt_lang la) q li
 125 getDataText (InternalOrigin _) _la q _li = do
 126   (_masterUserId, _masterRootId, cId) <- getOrMk_RootWithCorpus
 127                                            (UserName userMaster)
 128                                            (Left "")
 129                                            (Nothing :: Maybe HyperdataCorpus)
 130   ids <-  map fst <$> searchDocInDatabase cId (stemIt q)
 131   pure $ DataOld ids
 132
 133 -------------------------------------------------------------------------------
 134 flowDataText :: FlowCmdM env err m
 135              => User
 136              -> DataText
 137              -> TermType Lang
 138              -> CorpusId
 139              -> m CorpusId
 140 flowDataText u (DataOld ids) tt cid = flowCorpusUser (_tt_lang tt) u (Right [cid]) corpusType ids
 141   where
 142     corpusType = (Nothing :: Maybe HyperdataCorpus)
 143 flowDataText u (DataNew txt) tt cid = flowCorpus u (Right [cid]) tt txt
 144
 145 ------------------------------------------------------------------------
 146 -- TODO use proxy
 147 flowAnnuaire :: FlowCmdM env err m
 148              => User
 149              -> Either CorpusName [CorpusId]
 150              -> (TermType Lang)
 151              -> FilePath
 152              -> m AnnuaireId
 153 flowAnnuaire u n l filePath = do
 154   docs <- liftBase $ (( splitEvery 500 <$> deserialiseImtUsersFromFile filePath) :: IO [[HyperdataContact]])
 155   flow (Nothing :: Maybe HyperdataAnnuaire) u n l docs
 156
 157 ------------------------------------------------------------------------
 158 flowCorpusFile :: FlowCmdM env err m
 159            => User
 160            -> Either CorpusName [CorpusId]
 161            -> Limit -- Limit the number of docs (for dev purpose)
 162            -> TermType Lang -> FileFormat -> FilePath
 163            -> m CorpusId
 164 flowCorpusFile u n l la ff fp = do
 165   docs <- liftBase ( splitEvery 500
 166                  <$> take l
 167                  <$> parseFile ff fp
 168                  )
 169   flowCorpus u n la (map (map toHyperdataDocument) docs)
 170
 171 ------------------------------------------------------------------------
 172 -- | TODO improve the needed type to create/update a corpus
 173 -- (For now, Either is enough)
 174 flowCorpus :: (FlowCmdM env err m, FlowCorpus a)
 175            => User
 176            -> Either CorpusName [CorpusId]
 177            -> TermType Lang
 178            -> [[a]]
 179            -> m CorpusId
 180 flowCorpus = flow (Nothing :: Maybe HyperdataCorpus)
 181
 182
 183 flow :: (FlowCmdM env err m, FlowCorpus a, MkCorpus c)
 184      => Maybe c
 185      -> User
 186      -> Either CorpusName [CorpusId]
 187      -> TermType Lang
 188      -> [[a]]
 189      -> m CorpusId
 190 flow c u cn la docs = do
 191   -- TODO if public insertMasterDocs else insertUserDocs
 192   ids <- traverse (insertMasterDocs c la) docs
 193   flowCorpusUser (la ^. tt_lang) u cn c (concat ids)
 194
 195 ------------------------------------------------------------------------
 196 flowCorpusUser :: (FlowCmdM env err m, MkCorpus c)
 197                => Lang
 198                -> User
 199                -> Either CorpusName [CorpusId]
 200                -> Maybe c
 201                -> [NodeId]
 202                -> m CorpusId
 203 flowCorpusUser l user corpusName ctype ids = do
 204   -- User Flow
 205   (userId, _rootId, userCorpusId) <- getOrMk_RootWithCorpus user corpusName ctype
 206   listId <- getOrMkList userCorpusId userId
 207   -- _cooc  <- insertDefaultNode NodeListCooc listId userId
 208   -- TODO: check if present already, ignore
 209   _ <- Doc.add userCorpusId ids
 210
 211   _tId <- insertDefaultNode NodeTexts userCorpusId userId
 212   -- printDebug "Node Text Ids:" tId
 213
 214   -- User List Flow
 215   (masterUserId, _masterRootId, masterCorpusId) <- getOrMk_RootWithCorpus (UserName userMaster) (Left "") ctype
 216   ngs         <- buildNgramsLists l 2 3 (StopSize 3) userCorpusId masterCorpusId
 217   _userListId <- flowList_DbRepo listId ngs
 218   _mastListId <- getOrMkList masterCorpusId masterUserId
 219   -- _ <- insertOccsUpdates userCorpusId mastListId
 220   -- printDebug "userListId" userListId
 221   -- User Graph Flow
 222   _ <- insertDefaultNode NodeDashboard userCorpusId userId
 223   _ <- insertDefaultNode NodeGraph     userCorpusId userId
 224   --_ <- mkPhylo  userCorpusId userId
 225   -- Annuaire Flow
 226   -- _ <- mkAnnuaire  rootUserId userId
 227   pure userCorpusId
 228
 229 -- TODO Type NodeDocumentUnicised
 230 insertDocs :: ( FlowCmdM env err m
 231               -- , FlowCorpus a
 232               , FlowInsertDB a
 233               )
 234               => UserId
 235               -> CorpusId
 236               -> [a]
 237               -> m ([DocId], [DocumentWithId a])
 238 insertDocs uId cId hs = do
 239   let docs = map addUniqId hs
 240   newIds <- insertDb uId cId docs
 241   -- printDebug "newIds" newIds
 242   let
 243     newIds' = map reId newIds
 244     documentsWithId = mergeData (toInserted newIds) (Map.fromList $ map viewUniqId' docs)
 245   _ <- Doc.add cId newIds'
 246   pure (newIds', documentsWithId)
 247
 248
 249 insertMasterDocs :: ( FlowCmdM env err m
 250                     , FlowCorpus a
 251                     , MkCorpus   c
 252                     )
 253                  => Maybe c
 254                  -> TermType Lang
 255                  -> [a]
 256                  -> m [DocId]
 257 insertMasterDocs c lang hs  =  do
 258   (masterUserId, _, masterCorpusId) <- getOrMk_RootWithCorpus (UserName userMaster) (Left corpusMasterName) c
 259   (ids', documentsWithId) <- insertDocs masterUserId masterCorpusId (map (toNode masterUserId masterCorpusId) hs )
 260   _ <- Doc.add masterCorpusId ids'
 261   -- TODO
 262   -- create a corpus with database name (CSV or PubMed)
 263   -- add documents to the corpus (create node_node link)
 264   -- this will enable global database monitoring
 265
 266   -- maps :: IO Map Ngrams (Map NgramsType (Map NodeId Int))
 267   mapNgramsDocs <- mapNodeIdNgrams
 268        <$> documentIdWithNgrams (extractNgramsT $ withLang lang documentsWithId) documentsWithId
 269
 270   terms2id <- insertNgrams $ Map.keys mapNgramsDocs
 271   -- to be removed
 272   let indexedNgrams = Map.mapKeys (indexNgrams terms2id) mapNgramsDocs
 273
 274   -- new
 275   lId      <- getOrMkList masterCorpusId masterUserId
 276   mapCgramsId <- listInsertDb lId toNodeNgramsW'
 277                 $ map (first _ngramsTerms . second Map.keys)
 278                 $ Map.toList mapNgramsDocs
 279   -- insertDocNgrams
 280   _return <- insertNodeNodeNgrams2
 281            $ catMaybes [ NodeNodeNgrams2 <$> Just nId
 282                                          <*> getCgramsId mapCgramsId ngrams_type (_ngramsTerms terms'')
 283                                          <*> Just (fromIntegral w :: Double)
 284                        | (terms'', mapNgramsTypes) <- Map.toList mapNgramsDocs
 285                        , (ngrams_type, mapNodeIdWeight) <- Map.toList mapNgramsTypes
 286                        , (nId, w) <- Map.toList mapNodeIdWeight
 287                        ]
 288
 289   -- _cooc <- insertDefaultNode NodeListCooc lId masterUserId
 290   -- to be removed
 291   _   <- insertDocNgrams lId indexedNgrams
 292   pure ids'
 293
 294 ------------------------------------------------------------------------
 295 ------------------------------------------------------------------------
 296 viewUniqId' :: UniqId a
 297             => a
 298             -> (Hash, a)
 299 viewUniqId' d = maybe err (\h -> (h,d)) (view uniqId d)
 300       where
 301         err = panic "[ERROR] Database.Flow.toInsert"
 302
 303
 304 toInserted :: [ReturnId]
 305            -> Map Hash ReturnId
 306 toInserted =
 307   Map.fromList . map    (\r -> (reUniqId r, r)     )
 308                . filter (\r -> reInserted r == True)
 309
 310 mergeData :: Map Hash ReturnId
 311           -> Map Hash a
 312           -> [DocumentWithId a]
 313 mergeData rs = catMaybes . map toDocumentWithId . Map.toList
 314   where
 315     toDocumentWithId (sha,hpd) =
 316       DocumentWithId <$> fmap reId (lookup sha rs)
 317                      <*> Just hpd
 318
 319 ------------------------------------------------------------------------
 320 instance HasText HyperdataContact
 321   where
 322     hasText = undefined
 323 ------------------------------------------------------------------------
 324 ------------------------------------------------------------------------
 325 documentIdWithNgrams :: HasNodeError err
 326                      => (a
 327                      -> Cmd err (Map Ngrams (Map NgramsType Int)))
 328                      -> [DocumentWithId a]
 329                      -> Cmd err [DocumentIdWithNgrams a]
 330 documentIdWithNgrams f = traverse toDocumentIdWithNgrams
 331   where
 332     toDocumentIdWithNgrams d = do
 333       e <- f $ documentData         d
 334       pure   $ DocumentIdWithNgrams d e
 335
 336 ------------------------------------------------------------------------
 337 instance ExtractNgramsT HyperdataContact
 338   where
 339     extractNgramsT l hc = filterNgramsT 255 <$> extract l hc
 340       where
 341         extract :: TermType Lang -> HyperdataContact
 342                 -> Cmd err (Map Ngrams (Map NgramsType Int))
 343         extract _l hc' = do
 344           let authors = map text2ngrams
 345                      $ maybe ["Nothing"] (\a -> [a])
 346                      $ view (hc_who . _Just . cw_lastName) hc'
 347
 348           pure $ Map.fromList $ [(a', Map.singleton Authors     1) | a' <- authors    ]
 349
 350 instance HasText HyperdataDocument
 351   where
 352     hasText h = catMaybes [ _hd_title    h
 353                           , _hd_abstract h
 354                           ]
 355
 356
 357 instance ExtractNgramsT HyperdataDocument
 358   where
 359     extractNgramsT :: TermType Lang
 360                    -> HyperdataDocument
 361                    -> Cmd err (Map Ngrams (Map NgramsType Int))
 362     extractNgramsT lang hd = filterNgramsT 255 <$> extractNgramsT' lang hd
 363       where
 364         extractNgramsT' :: TermType Lang
 365                         -> HyperdataDocument
 366                        -> Cmd err (Map Ngrams (Map NgramsType Int))
 367         extractNgramsT' lang' doc = do
 368           let source    = text2ngrams
 369                         $ maybe "Nothing" identity
 370                         $ _hd_source doc
 371
 372               institutes = map text2ngrams
 373                          $ maybe ["Nothing"] (map toSchoolName . (splitOn ", "))
 374                          $ _hd_institutes doc
 375
 376               authors    = map text2ngrams
 377                          $ maybe ["Nothing"] (splitOn ", ")
 378                          $ _hd_authors doc
 379
 380           terms' <- map text2ngrams
 381                  <$> map (intercalate " " . _terms_label)
 382                  <$> concat
 383                  <$> liftBase (extractTerms lang' $ hasText doc)
 384
 385           pure $ Map.fromList $  [(source, Map.singleton Sources 1)]
 386                              <> [(i', Map.singleton Institutes  1) | i' <- institutes ]
 387                              <> [(a', Map.singleton Authors     1) | a' <- authors    ]
 388                              <> [(t', Map.singleton NgramsTerms 1) | t' <- terms'     ]
 389
 390 instance (ExtractNgramsT a, HasText a) => ExtractNgramsT (Node a)
 391   where
 392     extractNgramsT l (Node _ _ _ _ _ _ _ h) = extractNgramsT l h
 393
 394 instance HasText a => HasText (Node a)
 395   where
 396     hasText (Node _ _ _ _ _ _ _ h) = hasText h
 397
 398