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
11 -- check userId CanFillUserCorpus userCorpusId
12 -- check masterUserId CanFillMasterCorpus masterCorpusId
14 -- TODO-ACCESS: check uId CanInsertDoc pId && checkDocType nodeType
15 -- TODO-EVENTS: InsertedNodes
18 {-# OPTIONS_GHC -fno-warn-orphans #-}
20 {-# LANGUAGE ConstrainedClassMethods #-}
21 {-# LANGUAGE ConstraintKinds #-}
22 {-# LANGUAGE InstanceSigs #-}
23 {-# LANGUAGE ScopedTypeVariables #-}
24 {-# LANGUAGE TemplateHaskell #-}
26 module Gargantext.Database.Action.Flow -- (flowDatabase, ngrams2list)
39 , getOrMk_RootWithCorpus
45 , indexAllDocumentsWithPosTag
50 import Control.Lens ((^.), view, _Just, makeLenses)
51 import Data.Aeson.TH (deriveJSON)
52 import Data.Conduit.Internal (zipSources)
54 import Data.HashMap.Strict (HashMap)
55 import Data.Hashable (Hashable)
56 import Data.List (concat)
57 import Data.Map (Map, lookup)
58 import Data.Maybe (catMaybes)
61 import qualified Data.Text as T
62 import Data.Traversable (traverse)
63 import Data.Tuple.Extra (first, second)
64 import GHC.Generics (Generic)
65 import Servant.Client (ClientError)
66 import System.FilePath (FilePath)
67 import qualified Data.HashMap.Strict as HashMap
68 import qualified Gargantext.Data.HashMap.Strict.Utils as HashMap
69 import qualified Data.Map as Map
71 import Gargantext.API.Admin.Orchestrator.Types (JobLog(..))
72 import Gargantext.Core (Lang(..), PosTagAlgo(..))
73 import Gargantext.Core.Ext.IMT (toSchoolName)
74 import Gargantext.Core.Ext.IMTUser (readFile_Annuaire)
75 import Gargantext.Core.Flow.Types
76 import Gargantext.Core.Text
77 import Gargantext.Core.Text.Corpus.Parsers (parseFile, FileFormat)
78 import Gargantext.Core.Text.List (buildNgramsLists)
79 import Gargantext.Core.Text.List.Group.WithStem ({-StopSize(..),-} GroupParams(..))
80 import Gargantext.Core.Text.List.Social (FlowSocialListWith)
81 import Gargantext.Core.Text.Terms
82 import Gargantext.Core.Text.Terms.Mono.Stem.En (stemIt)
83 import Gargantext.Core.Types (POS(NP))
84 import Gargantext.Core.Types.Individu (User(..))
85 import Gargantext.Core.Types.Main
86 import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
87 import Gargantext.Database.Action.Flow.List
88 import Gargantext.Database.Action.Flow.Types
89 import Gargantext.Database.Action.Flow.Utils (insertDocNgrams, DocumentIdWithNgrams(..))
90 import Gargantext.Database.Action.Search (searchDocInDatabase)
91 import Gargantext.Database.Admin.Config (userMaster, corpusMasterName)
92 import Gargantext.Database.Action.Metrics (updateNgramsOccurrences)
93 import Gargantext.Database.Admin.Types.Hyperdata
94 import Gargantext.Database.Admin.Types.Node -- (HyperdataDocument(..), NodeType(..), NodeId, UserId, ListId, CorpusId, RootId, MasterCorpusId, MasterUserId)
95 import Gargantext.Database.Prelude
96 import Gargantext.Database.Query.Table.ContextNodeNgrams2
97 import Gargantext.Database.Query.Table.Ngrams
98 import Gargantext.Database.Query.Table.Node
99 import Gargantext.Database.Query.Table.Node.Document.Insert -- (insertDocuments, ReturnId(..), addUniqIdsDoc, addUniqIdsContact, ToDbData(..))
100 import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..))
101 import Gargantext.Database.Query.Table.NodeNgrams (listInsertDb , getCgramsId)
102 import Gargantext.Database.Query.Tree.Root (getOrMkRoot, getOrMk_RootWithCorpus)
103 import Gargantext.Database.Schema.Node (NodePoly(..), node_id)
104 import Gargantext.Database.Types
105 import Gargantext.Prelude
106 import Gargantext.Prelude.Crypto.Hash (Hash)
107 import qualified Gargantext.Core.Text.Corpus.API as API
108 import qualified Gargantext.Database.Query.Table.Node.Document.Add as Doc (add)
109 import qualified Prelude as Prelude
111 ------------------------------------------------------------------------
112 -- Imports for upgrade function
113 import Gargantext.Database.Query.Tree.Root (getRootId)
114 import Gargantext.Database.Query.Tree (findNodesId)
115 import qualified Data.List as List
116 ------------------------------------------------------------------------
117 -- TODO use internal with API name (could be old data)
118 data DataOrigin = InternalOrigin { _do_api :: API.ExternalAPIs }
119 | ExternalOrigin { _do_api :: API.ExternalAPIs }
121 deriving (Generic, Eq)
123 makeLenses ''DataOrigin
124 deriveJSON (unPrefix "_do_") ''DataOrigin
125 instance ToSchema DataOrigin where
126 declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_do_")
128 allDataOrigins :: [DataOrigin]
129 allDataOrigins = map InternalOrigin API.externalAPIs
130 <> map ExternalOrigin API.externalAPIs
133 data DataText = DataOld ![NodeId]
134 | DataNew !(Maybe Integer, ConduitT () HyperdataDocument IO ())
135 -- | DataNew ![[HyperdataDocument]]
137 -- TODO use the split parameter in config file
138 getDataText :: FlowCmdM env err m
143 -> m (Either ClientError DataText)
144 getDataText (ExternalOrigin api) la q li = liftBase $ do
145 eRes <- API.get api (_tt_lang la) q li
146 pure $ DataNew <$> eRes
148 getDataText (InternalOrigin _) _la q _li = do
149 (_masterUserId, _masterRootId, cId) <- getOrMk_RootWithCorpus
150 (UserName userMaster)
152 (Nothing :: Maybe HyperdataCorpus)
153 ids <- map fst <$> searchDocInDatabase cId (stemIt q)
154 pure $ Right $ DataOld ids
156 -------------------------------------------------------------------------------
157 flowDataText :: forall env err m.
164 -> Maybe FlowSocialListWith
167 flowDataText u (DataOld ids) tt cid mfslw _ = flowCorpusUser (_tt_lang tt) u (Right [cid]) corpusType ids mfslw
169 corpusType = (Nothing :: Maybe HyperdataCorpus)
170 flowDataText u (DataNew (mLen, txtC)) tt cid mfslw logStatus =
171 flowCorpus u (Right [cid]) tt mfslw (mLen, (transPipe liftBase txtC)) logStatus
173 ------------------------------------------------------------------------
175 flowAnnuaire :: (FlowCmdM env err m)
177 -> Either CorpusName [CorpusId]
182 flowAnnuaire u n l filePath logStatus = do
183 -- TODO Conduit for file
184 docs <- liftBase $ ((readFile_Annuaire filePath) :: IO [HyperdataContact])
185 flow (Nothing :: Maybe HyperdataAnnuaire) u n l Nothing (Just $ fromIntegral $ length docs, yieldMany docs) logStatus
187 ------------------------------------------------------------------------
188 flowCorpusFile :: (FlowCmdM env err m)
190 -> Either CorpusName [CorpusId]
191 -> Limit -- Limit the number of docs (for dev purpose)
192 -> TermType Lang -> FileFormat -> FilePath
193 -> Maybe FlowSocialListWith
196 flowCorpusFile u n _l la ff fp mfslw logStatus = do
197 eParsed <- liftBase $ parseFile ff fp
200 flowCorpus u n la mfslw (Just $ fromIntegral $ length parsed, yieldMany parsed .| mapC toHyperdataDocument) logStatus
201 --let docs = splitEvery 500 $ take l parsed
202 --flowCorpus u n la mfslw (yieldMany $ map (map toHyperdataDocument) docs) logStatus
203 Left e -> panic $ "Error: " <> (T.pack e)
205 ------------------------------------------------------------------------
206 -- | TODO improve the needed type to create/update a corpus
207 -- (For now, Either is enough)
208 flowCorpus :: (FlowCmdM env err m, FlowCorpus a)
210 -> Either CorpusName [CorpusId]
212 -> Maybe FlowSocialListWith
213 -> (Maybe Integer, ConduitT () a m ())
216 flowCorpus = flow (Nothing :: Maybe HyperdataCorpus)
219 flow :: forall env err m a c.
226 -> Either CorpusName [CorpusId]
228 -> Maybe FlowSocialListWith
229 -> (Maybe Integer, ConduitT () a m ())
232 flow c u cn la mfslw (mLength, docsC) logStatus = do
233 -- TODO if public insertMasterDocs else insertUserDocs
235 zipSources (yieldMany [1..]) docsC
238 -- ids <- traverse (\(idx, doc) -> do
239 -- id <- insertMasterDocs c la doc
240 -- logStatus JobLog { _scst_succeeded = Just $ 1 + idx
241 -- , _scst_failed = Just 0
242 -- , _scst_remaining = Just $ length docs - idx
243 -- , _scst_events = Just []
246 -- ) (zip [1..] docs)
247 flowCorpusUser (la ^. tt_lang) u cn c ids mfslw
250 insertDoc :: (Integer, a) -> m NodeId
251 insertDoc (idx, doc) = do
252 id <- insertMasterDocs c la [doc]
256 logStatus JobLog { _scst_succeeded = Just $ fromIntegral $ 1 + idx
257 , _scst_failed = Just 0
258 , _scst_remaining = Just $ fromIntegral $ len - idx
259 , _scst_events = Just []
261 pure $ Prelude.head id
265 ------------------------------------------------------------------------
266 flowCorpusUser :: ( FlowCmdM env err m
271 -> Either CorpusName [CorpusId]
274 -> Maybe FlowSocialListWith
276 flowCorpusUser l user corpusName ctype ids mfslw = do
278 (userId, _rootId, userCorpusId) <- getOrMk_RootWithCorpus user corpusName ctype
279 -- NodeTexts is first
280 _tId <- insertDefaultNodeIfNotExists NodeTexts userCorpusId userId
281 -- printDebug "NodeTexts: " tId
283 -- NodeList is second
284 listId <- getOrMkList userCorpusId userId
285 -- _cooc <- insertDefaultNode NodeListCooc listId userId
286 -- TODO: check if present already, ignore
287 _ <- Doc.add userCorpusId ids
289 -- printDebug "Node Text Ids:" tId
292 (masterUserId, _masterRootId, masterCorpusId)
293 <- getOrMk_RootWithCorpus (UserName userMaster) (Left "") ctype
295 --let gp = (GroupParams l 2 3 (StopSize 3))
296 let gp = GroupWithPosTag l CoreNLP HashMap.empty
297 ngs <- buildNgramsLists user userCorpusId masterCorpusId mfslw gp
299 -- printDebug "flowCorpusUser:ngs" ngs
301 _userListId <- flowList_DbRepo listId ngs
302 _mastListId <- getOrMkList masterCorpusId masterUserId
303 -- _ <- insertOccsUpdates userCorpusId mastListId
304 -- printDebug "userListId" userListId
306 _ <- insertDefaultNodeIfNotExists NodeDashboard userCorpusId userId
307 _ <- insertDefaultNodeIfNotExists NodeGraph userCorpusId userId
308 --_ <- mkPhylo userCorpusId userId
310 -- _ <- mkAnnuaire rootUserId userId
311 _ <- updateNgramsOccurrences userCorpusId (Just listId)
316 insertMasterDocs :: ( FlowCmdM env err m
324 insertMasterDocs c lang hs = do
325 (masterUserId, _, masterCorpusId) <- getOrMk_RootWithCorpus (UserName userMaster) (Left corpusMasterName) c
326 (ids', documentsWithId) <- insertDocs masterUserId masterCorpusId (map (toNode masterUserId masterCorpusId) hs )
327 _ <- Doc.add masterCorpusId ids'
329 -- create a corpus with database name (CSV or PubMed)
330 -- add documents to the corpus (create node_node link)
331 -- this will enable global database monitoring
333 -- maps :: IO Map Ngrams (Map NgramsType (Map NodeId Int))
334 mapNgramsDocs' :: HashMap ExtractedNgrams (Map NgramsType (Map NodeId Int))
336 <$> documentIdWithNgrams
337 (extractNgramsT $ withLang lang documentsWithId)
340 lId <- getOrMkList masterCorpusId masterUserId
341 _ <- saveDocNgramsWith lId mapNgramsDocs'
343 -- _cooc <- insertDefaultNode NodeListCooc lId masterUserId
346 saveDocNgramsWith :: ( FlowCmdM env err m)
348 -> HashMap ExtractedNgrams (Map NgramsType (Map NodeId Int))
350 saveDocNgramsWith lId mapNgramsDocs' = do
351 terms2id <- insertExtractedNgrams $ HashMap.keys mapNgramsDocs'
352 --printDebug "terms2id" terms2id
354 let mapNgramsDocs = HashMap.mapKeys extracted2ngrams mapNgramsDocs'
357 mapCgramsId <- listInsertDb lId toNodeNgramsW'
358 $ map (first _ngramsTerms . second Map.keys)
359 $ HashMap.toList mapNgramsDocs
361 --printDebug "saveDocNgramsWith" mapCgramsId
363 _return <- insertContextNodeNgrams2
364 $ catMaybes [ ContextNodeNgrams2 <$> Just nId
365 <*> (getCgramsId mapCgramsId ngrams_type (_ngramsTerms terms''))
366 <*> Just (fromIntegral w :: Double)
367 | (terms'', mapNgramsTypes) <- HashMap.toList mapNgramsDocs
368 , (ngrams_type, mapNodeIdWeight) <- Map.toList mapNgramsTypes
369 , (nId, w) <- Map.toList mapNodeIdWeight
373 _ <- insertDocNgrams lId $ HashMap.mapKeys (indexNgrams terms2id) mapNgramsDocs
378 ------------------------------------------------------------------------
379 -- TODO Type NodeDocumentUnicised
380 insertDocs :: ( FlowCmdM env err m
387 -> m ([ContextId], [Indexed ContextId a])
388 insertDocs uId cId hs = do
389 let docs = map addUniqId hs
390 newIds <- insertDb uId cId docs
391 -- printDebug "newIds" newIds
393 newIds' = map reId newIds
394 documentsWithId = mergeData (toInserted newIds) (Map.fromList $ map viewUniqId' docs)
395 _ <- Doc.add cId newIds'
396 pure (newIds', documentsWithId)
399 ------------------------------------------------------------------------
400 viewUniqId' :: UniqId a
403 viewUniqId' d = maybe err (\h -> (h,d)) (view uniqId d)
405 err = panic "[ERROR] Database.Flow.toInsert"
408 toInserted :: [ReturnId]
411 Map.fromList . map (\r -> (reUniqId r, r) )
412 . filter (\r -> reInserted r == True)
414 mergeData :: Map Hash ReturnId
416 -> [Indexed NodeId a]
417 mergeData rs = catMaybes . map toDocumentWithId . Map.toList
419 toDocumentWithId (sha,hpd) =
420 Indexed <$> fmap reId (lookup sha rs)
423 ------------------------------------------------------------------------
424 ------------------------------------------------------------------------
425 ------------------------------------------------------------------------
426 documentIdWithNgrams :: HasNodeError err
428 -> Cmd err (HashMap b (Map NgramsType Int)))
429 -> [Indexed NodeId a]
430 -> Cmd err [DocumentIdWithNgrams a b]
431 documentIdWithNgrams f = traverse toDocumentIdWithNgrams
433 toDocumentIdWithNgrams d = do
435 pure $ DocumentIdWithNgrams d e
438 -- | TODO check optimization
439 mapNodeIdNgrams :: (Ord b, Hashable b)
440 => [DocumentIdWithNgrams a b]
445 mapNodeIdNgrams = HashMap.unionsWith (Map.unionWith (Map.unionWith (+))) . fmap f
447 f :: DocumentIdWithNgrams a b
448 -> HashMap b (Map NgramsType (Map NodeId Int))
449 f d = fmap (fmap (Map.singleton nId)) $ documentNgrams d
451 nId = _index $ documentWithId d
454 ------------------------------------------------------------------------
455 instance ExtractNgramsT HyperdataContact
457 extractNgramsT l hc = HashMap.mapKeys (cleanExtractedNgrams 255) <$> extract l hc
459 extract :: TermType Lang -> HyperdataContact
460 -> Cmd err (HashMap ExtractedNgrams (Map NgramsType Int))
462 let authors = map text2ngrams
463 $ maybe ["Nothing"] (\a -> [a])
464 $ view (hc_who . _Just . cw_lastName) hc'
466 pure $ HashMap.fromList $ [(SimpleNgrams a', Map.singleton Authors 1) | a' <- authors ]
469 instance ExtractNgramsT HyperdataDocument
471 extractNgramsT :: TermType Lang
473 -> Cmd err (HashMap ExtractedNgrams (Map NgramsType Int))
474 extractNgramsT lang hd = HashMap.mapKeys (cleanExtractedNgrams 255) <$> extractNgramsT' lang hd
476 extractNgramsT' :: TermType Lang
478 -> Cmd err (HashMap ExtractedNgrams (Map NgramsType Int))
479 extractNgramsT' lang' doc = do
480 let source = text2ngrams
481 $ maybe "Nothing" identity
484 institutes = map text2ngrams
485 $ maybe ["Nothing"] (map toSchoolName . (T.splitOn ", "))
488 authors = map text2ngrams
489 $ maybe ["Nothing"] (T.splitOn ", ")
492 terms' <- map (enrichedTerms (lang' ^. tt_lang) CoreNLP NP)
494 <$> liftBase (extractTerms lang' $ hasText doc)
496 pure $ HashMap.fromList
497 $ [(SimpleNgrams source, Map.singleton Sources 1) ]
498 <> [(SimpleNgrams i', Map.singleton Institutes 1) | i' <- institutes ]
499 <> [(SimpleNgrams a', Map.singleton Authors 1) | a' <- authors ]
500 <> [(EnrichedNgrams t', Map.singleton NgramsTerms 1) | t' <- terms' ]
502 instance (ExtractNgramsT a, HasText a) => ExtractNgramsT (Node a)
504 extractNgramsT l (Node _ _ _ _ _ _ _ h) = extractNgramsT l h
506 instance HasText a => HasText (Node a)
508 hasText (Node _ _ _ _ _ _ _ h) = hasText h
512 -- | TODO putelsewhere
513 -- | Upgrade function
514 -- Suppose all documents are English (this is the case actually)
515 indexAllDocumentsWithPosTag :: FlowCmdM env err m
517 indexAllDocumentsWithPosTag = do
518 rootId <- getRootId (UserName userMaster)
519 corpusIds <- findNodesId rootId [NodeCorpus]
520 docs <- List.concat <$> mapM getDocumentsWithParentId corpusIds
521 _ <- mapM extractInsert (splitEvery 1000 docs)
524 extractInsert :: FlowCmdM env err m
525 => [Node HyperdataDocument] -> m ()
526 extractInsert docs = do
527 let documentsWithId = map (\doc -> Indexed (doc ^. node_id) doc) docs
528 mapNgramsDocs' <- mapNodeIdNgrams
529 <$> documentIdWithNgrams
530 (extractNgramsT $ withLang (Multi EN) documentsWithId)
532 _ <- insertExtractedNgrams $ HashMap.keys mapNgramsDocs'