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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 ConstrainedClassMethods #-}
21 {-# LANGUAGE ConstraintKinds #-}
22 {-# LANGUAGE InstanceSigs #-}
23 {-# LANGUAGE ScopedTypeVariables #-}
24 {-# LANGUAGE TemplateHaskell #-}
25
26 module Gargantext.Database.Action.Flow -- (flowDatabase, ngrams2list)
27 ( DataText(..)
28 , getDataText
29 , flowDataText
30 , flow
31
32 , flowCorpusFile
33 , flowCorpus
34 , flowAnnuaire
35 , insertMasterDocs
36 , saveDocNgramsWith
37
38 , getOrMkRoot
39 , getOrMk_RootWithCorpus
40 , TermType(..)
41 , DataOrigin(..)
42 , allDataOrigins
43
44 , do_api
45 , indexAllDocumentsWithPosTag
46 )
47 where
48
49 import Conduit
50 import Control.Lens ((^.), view, _Just, makeLenses)
51 import Data.Aeson.TH (deriveJSON)
52 import Data.Conduit.Internal (zipSources)
53 import Data.Either
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)
59 import Data.Monoid
60 import Data.Swagger
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
70
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, FileType)
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
110
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 }
120 -- TODO Web
121 deriving (Generic, Eq)
122
123 makeLenses ''DataOrigin
124 deriveJSON (unPrefix "_do_") ''DataOrigin
125 instance ToSchema DataOrigin where
126 declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_do_")
127
128 allDataOrigins :: [DataOrigin]
129 allDataOrigins = map InternalOrigin API.externalAPIs
130 <> map ExternalOrigin API.externalAPIs
131
132 ---------------
133 data DataText = DataOld ![NodeId]
134 | DataNew !(Maybe Integer, ConduitT () HyperdataDocument IO ())
135 -- | DataNew ![[HyperdataDocument]]
136
137 -- TODO use the split parameter in config file
138 getDataText :: FlowCmdM env err m
139 => DataOrigin
140 -> TermType Lang
141 -> API.Query
142 -> Maybe API.Limit
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 <$> eRes
147
148 getDataText (InternalOrigin _) _la q _li = do
149 (_masterUserId, _masterRootId, cId) <- getOrMk_RootWithCorpus
150 (UserName userMaster)
151 (Left "")
152 (Nothing :: Maybe HyperdataCorpus)
153 ids <- map fst <$> searchDocInDatabase cId (stemIt q)
154 pure $ Right $ DataOld ids
155
156 -------------------------------------------------------------------------------
157 flowDataText :: forall env err m.
158 ( FlowCmdM env err m
159 )
160 => User
161 -> DataText
162 -> TermType Lang
163 -> CorpusId
164 -> Maybe FlowSocialListWith
165 -> (JobLog -> m ())
166 -> m CorpusId
167 flowDataText u (DataOld ids) tt cid mfslw _ = flowCorpusUser (_tt_lang tt) u (Right [cid]) corpusType ids mfslw
168 where
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
172
173 ------------------------------------------------------------------------
174 -- TODO use proxy
175 flowAnnuaire :: (FlowCmdM env err m)
176 => User
177 -> Either CorpusName [CorpusId]
178 -> (TermType Lang)
179 -> FilePath
180 -> (JobLog -> m ())
181 -> m AnnuaireId
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
186
187 ------------------------------------------------------------------------
188 flowCorpusFile :: (FlowCmdM env err m)
189 => User
190 -> Either CorpusName [CorpusId]
191 -> Limit -- Limit the number of docs (for dev purpose)
192 -> TermType Lang
193 -> FileType
194 -> FileFormat
195 -> FilePath
196 -> Maybe FlowSocialListWith
197 -> (JobLog -> m ())
198 -> m CorpusId
199 flowCorpusFile u n _l la ft ff fp mfslw logStatus = do
200 eParsed <- liftBase $ parseFile ft ff fp
201 case eParsed of
202 Right parsed -> do
203 flowCorpus u n la mfslw (Just $ fromIntegral $ length parsed, yieldMany parsed .| mapC toHyperdataDocument) logStatus
204 --let docs = splitEvery 500 $ take l parsed
205 --flowCorpus u n la mfslw (yieldMany $ map (map toHyperdataDocument) docs) logStatus
206 Left e -> panic $ "Error: " <> T.pack e
207
208 ------------------------------------------------------------------------
209 -- | TODO improve the needed type to create/update a corpus
210 -- (For now, Either is enough)
211 flowCorpus :: (FlowCmdM env err m, FlowCorpus a)
212 => User
213 -> Either CorpusName [CorpusId]
214 -> TermType Lang
215 -> Maybe FlowSocialListWith
216 -> (Maybe Integer, ConduitT () a m ())
217 -> (JobLog -> m ())
218 -> m CorpusId
219 flowCorpus = flow (Nothing :: Maybe HyperdataCorpus)
220
221
222 flow :: forall env err m a c.
223 ( FlowCmdM env err m
224 , FlowCorpus a
225 , MkCorpus c
226 )
227 => Maybe c
228 -> User
229 -> Either CorpusName [CorpusId]
230 -> TermType Lang
231 -> Maybe FlowSocialListWith
232 -> (Maybe Integer, ConduitT () a m ())
233 -> (JobLog -> m ())
234 -> m CorpusId
235 flow c u cn la mfslw (mLength, docsC) logStatus = do
236 -- TODO if public insertMasterDocs else insertUserDocs
237 ids <- runConduit $
238 zipSources (yieldMany [1..]) docsC
239 .| mapMC insertDoc
240 .| sinkList
241 -- ids <- traverse (\(idx, doc) -> do
242 -- id <- insertMasterDocs c la doc
243 -- logStatus JobLog { _scst_succeeded = Just $ 1 + idx
244 -- , _scst_failed = Just 0
245 -- , _scst_remaining = Just $ length docs - idx
246 -- , _scst_events = Just []
247 -- }
248 -- pure id
249 -- ) (zip [1..] docs)
250 flowCorpusUser (la ^. tt_lang) u cn c ids mfslw
251
252 where
253 insertDoc :: (Integer, a) -> m NodeId
254 insertDoc (idx, doc) = do
255 id <- insertMasterDocs c la [doc]
256 case mLength of
257 Nothing -> pure ()
258 Just len -> do
259 logStatus JobLog { _scst_succeeded = Just $ fromIntegral $ 1 + idx
260 , _scst_failed = Just 0
261 , _scst_remaining = Just $ fromIntegral $ len - idx
262 , _scst_events = Just []
263 }
264 pure $ Prelude.head id
265
266
267
268 ------------------------------------------------------------------------
269 flowCorpusUser :: ( FlowCmdM env err m
270 , MkCorpus c
271 )
272 => Lang
273 -> User
274 -> Either CorpusName [CorpusId]
275 -> Maybe c
276 -> [NodeId]
277 -> Maybe FlowSocialListWith
278 -> m CorpusId
279 flowCorpusUser l user corpusName ctype ids mfslw = do
280 -- User Flow
281 (userId, _rootId, userCorpusId) <- getOrMk_RootWithCorpus user corpusName ctype
282 -- NodeTexts is first
283 _tId <- insertDefaultNodeIfNotExists NodeTexts userCorpusId userId
284 -- printDebug "NodeTexts: " tId
285
286 -- NodeList is second
287 listId <- getOrMkList userCorpusId userId
288 -- _cooc <- insertDefaultNode NodeListCooc listId userId
289 -- TODO: check if present already, ignore
290 _ <- Doc.add userCorpusId ids
291
292 -- printDebug "Node Text Ids:" tId
293
294 -- User List Flow
295 (masterUserId, _masterRootId, masterCorpusId)
296 <- getOrMk_RootWithCorpus (UserName userMaster) (Left "") ctype
297
298 --let gp = (GroupParams l 2 3 (StopSize 3))
299 let gp = GroupWithPosTag l CoreNLP HashMap.empty
300 ngs <- buildNgramsLists user userCorpusId masterCorpusId mfslw gp
301
302 -- printDebug "flowCorpusUser:ngs" ngs
303
304 _userListId <- flowList_DbRepo listId ngs
305 _mastListId <- getOrMkList masterCorpusId masterUserId
306 -- _ <- insertOccsUpdates userCorpusId mastListId
307 -- printDebug "userListId" userListId
308 -- User Graph Flow
309 _ <- insertDefaultNodeIfNotExists NodeDashboard userCorpusId userId
310 _ <- insertDefaultNodeIfNotExists NodeGraph userCorpusId userId
311 --_ <- mkPhylo userCorpusId userId
312 -- Annuaire Flow
313 -- _ <- mkAnnuaire rootUserId userId
314 _ <- updateNgramsOccurrences userCorpusId (Just listId)
315
316 pure userCorpusId
317
318
319 insertMasterDocs :: ( FlowCmdM env err m
320 , FlowCorpus a
321 , MkCorpus c
322 )
323 => Maybe c
324 -> TermType Lang
325 -> [a]
326 -> m [DocId]
327 insertMasterDocs c lang hs = do
328 (masterUserId, _, masterCorpusId) <- getOrMk_RootWithCorpus (UserName userMaster) (Left corpusMasterName) c
329 (ids', documentsWithId) <- insertDocs masterUserId masterCorpusId (map (toNode masterUserId masterCorpusId) hs )
330 _ <- Doc.add masterCorpusId ids'
331 -- TODO
332 -- create a corpus with database name (CSV or PubMed)
333 -- add documents to the corpus (create node_node link)
334 -- this will enable global database monitoring
335
336 -- maps :: IO Map Ngrams (Map NgramsType (Map NodeId Int))
337 mapNgramsDocs' :: HashMap ExtractedNgrams (Map NgramsType (Map NodeId Int))
338 <- mapNodeIdNgrams
339 <$> documentIdWithNgrams
340 (extractNgramsT $ withLang lang documentsWithId)
341 documentsWithId
342
343 lId <- getOrMkList masterCorpusId masterUserId
344 _ <- saveDocNgramsWith lId mapNgramsDocs'
345
346 -- _cooc <- insertDefaultNode NodeListCooc lId masterUserId
347 pure ids'
348
349 saveDocNgramsWith :: ( FlowCmdM env err m)
350 => ListId
351 -> HashMap ExtractedNgrams (Map NgramsType (Map NodeId Int))
352 -> m ()
353 saveDocNgramsWith lId mapNgramsDocs' = do
354 terms2id <- insertExtractedNgrams $ HashMap.keys mapNgramsDocs'
355 --printDebug "terms2id" terms2id
356
357 let mapNgramsDocs = HashMap.mapKeys extracted2ngrams mapNgramsDocs'
358
359 -- new
360 mapCgramsId <- listInsertDb lId toNodeNgramsW'
361 $ map (first _ngramsTerms . second Map.keys)
362 $ HashMap.toList mapNgramsDocs
363
364 --printDebug "saveDocNgramsWith" mapCgramsId
365 -- insertDocNgrams
366 _return <- insertContextNodeNgrams2
367 $ catMaybes [ ContextNodeNgrams2 <$> Just nId
368 <*> (getCgramsId mapCgramsId ngrams_type (_ngramsTerms terms''))
369 <*> Just (fromIntegral w :: Double)
370 | (terms'', mapNgramsTypes) <- HashMap.toList mapNgramsDocs
371 , (ngrams_type, mapNodeIdWeight) <- Map.toList mapNgramsTypes
372 , (nId, w) <- Map.toList mapNodeIdWeight
373 ]
374
375 -- to be removed
376 _ <- insertDocNgrams lId $ HashMap.mapKeys (indexNgrams terms2id) mapNgramsDocs
377
378 pure ()
379
380
381 ------------------------------------------------------------------------
382 -- TODO Type NodeDocumentUnicised
383 insertDocs :: ( FlowCmdM env err m
384 -- , FlowCorpus a
385 , FlowInsertDB a
386 )
387 => UserId
388 -> CorpusId
389 -> [a]
390 -> m ([ContextId], [Indexed ContextId a])
391 insertDocs uId cId hs = do
392 let docs = map addUniqId hs
393 newIds <- insertDb uId cId docs
394 -- printDebug "newIds" newIds
395 let
396 newIds' = map reId newIds
397 documentsWithId = mergeData (toInserted newIds) (Map.fromList $ map viewUniqId' docs)
398 _ <- Doc.add cId newIds'
399 pure (newIds', documentsWithId)
400
401
402 ------------------------------------------------------------------------
403 viewUniqId' :: UniqId a
404 => a
405 -> (Hash, a)
406 viewUniqId' d = maybe err (\h -> (h,d)) (view uniqId d)
407 where
408 err = panic "[ERROR] Database.Flow.toInsert"
409
410
411 toInserted :: [ReturnId]
412 -> Map Hash ReturnId
413 toInserted =
414 Map.fromList . map (\r -> (reUniqId r, r) )
415 . filter (\r -> reInserted r == True)
416
417 mergeData :: Map Hash ReturnId
418 -> Map Hash a
419 -> [Indexed NodeId a]
420 mergeData rs = catMaybes . map toDocumentWithId . Map.toList
421 where
422 toDocumentWithId (sha,hpd) =
423 Indexed <$> fmap reId (lookup sha rs)
424 <*> Just hpd
425
426 ------------------------------------------------------------------------
427 ------------------------------------------------------------------------
428 ------------------------------------------------------------------------
429 documentIdWithNgrams :: HasNodeError err
430 => (a
431 -> Cmd err (HashMap b (Map NgramsType Int)))
432 -> [Indexed NodeId a]
433 -> Cmd err [DocumentIdWithNgrams a b]
434 documentIdWithNgrams f = traverse toDocumentIdWithNgrams
435 where
436 toDocumentIdWithNgrams d = do
437 e <- f $ _unIndex d
438 pure $ DocumentIdWithNgrams d e
439
440
441 -- | TODO check optimization
442 mapNodeIdNgrams :: (Ord b, Hashable b)
443 => [DocumentIdWithNgrams a b]
444 -> HashMap b
445 (Map NgramsType
446 (Map NodeId Int)
447 )
448 mapNodeIdNgrams = HashMap.unionsWith (Map.unionWith (Map.unionWith (+))) . fmap f
449 where
450 f :: DocumentIdWithNgrams a b
451 -> HashMap b (Map NgramsType (Map NodeId Int))
452 f d = fmap (fmap (Map.singleton nId)) $ documentNgrams d
453 where
454 nId = _index $ documentWithId d
455
456
457 ------------------------------------------------------------------------
458 instance ExtractNgramsT HyperdataContact
459 where
460 extractNgramsT l hc = HashMap.mapKeys (cleanExtractedNgrams 255) <$> extract l hc
461 where
462 extract :: TermType Lang -> HyperdataContact
463 -> Cmd err (HashMap ExtractedNgrams (Map NgramsType Int))
464 extract _l hc' = do
465 let authors = map text2ngrams
466 $ maybe ["Nothing"] (\a -> [a])
467 $ view (hc_who . _Just . cw_lastName) hc'
468
469 pure $ HashMap.fromList $ [(SimpleNgrams a', Map.singleton Authors 1) | a' <- authors ]
470
471
472 instance ExtractNgramsT HyperdataDocument
473 where
474 extractNgramsT :: TermType Lang
475 -> HyperdataDocument
476 -> Cmd err (HashMap ExtractedNgrams (Map NgramsType Int))
477 extractNgramsT lang hd = HashMap.mapKeys (cleanExtractedNgrams 255) <$> extractNgramsT' lang hd
478 where
479 extractNgramsT' :: TermType Lang
480 -> HyperdataDocument
481 -> Cmd err (HashMap ExtractedNgrams (Map NgramsType Int))
482 extractNgramsT' lang' doc = do
483 let source = text2ngrams
484 $ maybe "Nothing" identity
485 $ _hd_source doc
486
487 institutes = map text2ngrams
488 $ maybe ["Nothing"] (map toSchoolName . (T.splitOn ", "))
489 $ _hd_institutes doc
490
491 authors = map text2ngrams
492 $ maybe ["Nothing"] (T.splitOn ", ")
493 $ _hd_authors doc
494
495 terms' <- map (enrichedTerms (lang' ^. tt_lang) CoreNLP NP)
496 <$> concat
497 <$> liftBase (extractTerms lang' $ hasText doc)
498
499 pure $ HashMap.fromList
500 $ [(SimpleNgrams source, Map.singleton Sources 1) ]
501 <> [(SimpleNgrams i', Map.singleton Institutes 1) | i' <- institutes ]
502 <> [(SimpleNgrams a', Map.singleton Authors 1) | a' <- authors ]
503 <> [(EnrichedNgrams t', Map.singleton NgramsTerms 1) | t' <- terms' ]
504
505 instance (ExtractNgramsT a, HasText a) => ExtractNgramsT (Node a)
506 where
507 extractNgramsT l (Node _ _ _ _ _ _ _ h) = extractNgramsT l h
508
509 instance HasText a => HasText (Node a)
510 where
511 hasText (Node _ _ _ _ _ _ _ h) = hasText h
512
513
514
515 -- | TODO putelsewhere
516 -- | Upgrade function
517 -- Suppose all documents are English (this is the case actually)
518 indexAllDocumentsWithPosTag :: FlowCmdM env err m
519 => m ()
520 indexAllDocumentsWithPosTag = do
521 rootId <- getRootId (UserName userMaster)
522 corpusIds <- findNodesId rootId [NodeCorpus]
523 docs <- List.concat <$> mapM getDocumentsWithParentId corpusIds
524 _ <- mapM extractInsert (splitEvery 1000 docs)
525 pure ()
526
527 extractInsert :: FlowCmdM env err m
528 => [Node HyperdataDocument] -> m ()
529 extractInsert docs = do
530 let documentsWithId = map (\doc -> Indexed (doc ^. node_id) doc) docs
531 mapNgramsDocs' <- mapNodeIdNgrams
532 <$> documentIdWithNgrams
533 (extractNgramsT $ withLang (Multi EN) documentsWithId)
534 documentsWithId
535 _ <- insertExtractedNgrams $ HashMap.keys mapNgramsDocs'
536 pure ()