Skip to content

haskell-gargantext
haskell-gargantext
Commit b423c47b authored by Alexandre Delanoë's avatar Alexandre Delanoë
Browse files
Options

[FIX] merge

parents bea9480f 29fd6a4f
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 1169 additions and 1111 deletions
README.md
View file @ b423c47b
......@@ -72,6 +72,52 @@ This will take a bit of time as it has to download/build the dependencies, but t
#### With Cabal (recommanded)
##### Turning off optimization flags
Create a `cabal.project.local` file (don't commit it to git!):
```
package gargantext
ghc-options: -fwrite-ide-info -hiedir=".stack-work/hiedb" -O0
package gargantext-admin
ghc-options: -O0
package gargantext-cli
ghc-options: -O0
package gargantext-db-obfuscation
ghc-options: -O0
package gargantext-import
ghc-options: -O0
package gargantext-init
ghc-options: -O0
package gargantext-invitations
ghc-options: -O0
package gargantext-phylo
ghc-options: -O0
package gargantext-server
ghc-options: -O0
package gargantext-upgrade
ghc-options: -O0
package gargantext-graph
ghc-options: -O0
package hmatrix
ghc-options: -O0
package sparse-linear
ghc-options: -O0
```
##### Building
First, into `nix-shell`:
```shell
cabal update
......
bin/update-project-dependencies
View file @ b423c47b
......@@ -18,7 +18,7 @@ fi
# with the `sha256sum` result calculated on the `cabal.project` and
# `cabal.project.freeze`. This ensures the files stay deterministic so that CI
# cache can kick in.
expected_cabal_project_hash="3f5d6b7f26cac4aa5a7f87ba0227a7671041dfe46643ddef79512eb49bd876ec"
expected_cabal_project_hash="c9fe39301e8b60bfd183e60e7e25a14cd1c9c66d8739bf9041ca3f4db89db7c6"
expected_cabal_project_freeze_hash="db24c7d3006167102532e3101e2b49bae13d478003459c7d3f1d66590e57740a"
cabal --store-dir=$STORE_DIR v2-build --dry-run
......
cabal.project
View file @ b423c47b
......@@ -31,8 +31,8 @@ source-repository-package
source-repository-package
type: git
location: https://github.com/adinapoli/haskell-opaleye.git
tag: e9a29582ac66198dd2c2fdc3f8c8a4b1e6fbe004
location: https://github.com/garganscript/haskell-opaleye.git
tag: 6cf1bcfe215143efac17919cfd0abdd60e0f717c
source-repository-package
type: git
......@@ -183,12 +183,9 @@ allow-newer: *
package gargantext
ghc-options: -fwrite-ide-info -hiedir=".stack-work/hiedb"
package gargantext-graph
ghc-options: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal -fno-state-hack
package hmatrix
ghc-options: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal -fno-state-hack
ghc-options: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal -fno-state-hack
package sparse-linear
ghc-options: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal -fno-state-hack
ghc-options: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal -fno-state-hack
gargantext.cabal
View file @ b423c47b
This diff is collapsed.
src/Gargantext/API.hs
View file @ b423c47b
......@@ -48,10 +48,8 @@ import Gargantext.API.Admin.Settings.CORS
import Gargantext.API.Admin.Types (FireWall(..), PortNumber, cookieSettings, jwtSettings, settings, corsSettings)
import Gargantext.API.EKG
import Gargantext.API.Middleware (logStdoutDevSanitised)
import Gargantext.API.Ngrams (saveNodeStoryImmediate)
import Gargantext.API.Routes
import Gargantext.API.Server (server)
import Gargantext.Core.NodeStory
import Gargantext.Database.Prelude qualified as DB
import Gargantext.Prelude hiding (putStrLn)
import Gargantext.System.Logging
......@@ -74,7 +72,7 @@ startGargantext mode port file = withLoggerHoisted mode $ \logger -> do
app <- makeApp env
mid <- makeGargMiddleware (env ^. settings.corsSettings) mode
periodicActions <- schedulePeriodicActions env
run port (mid app) `finally` stopGargantext env periodicActions
run port (mid app) `finally` stopGargantext periodicActions
where runDbCheck env = do
r <- runExceptT (runReaderT DB.dbCheck env) `catch`
......@@ -94,11 +92,10 @@ portRouteInfo port = do
-- | Stops the gargantext server and cancels all the periodic actions
-- scheduled to run up to that point.
-- TODO clean this Monad condition (more generic) ?
stopGargantext :: HasNodeStoryImmediateSaver env => env -> [ThreadId] -> IO ()
stopGargantext env scheduledPeriodicActions = do
stopGargantext :: [ThreadId] -> IO ()
stopGargantext scheduledPeriodicActions = do
forM_ scheduledPeriodicActions killThread
putStrLn "----- Stopping gargantext -----"
runReaderT saveNodeStoryImmediate env
-- | Schedules all sorts of useful periodic actions to be run while
-- the server is alive accepting requests.
......
src/Gargantext/API/Admin/EnvTypes.hs
View file @ b423c47b
......@@ -136,9 +136,6 @@ instance HasConnectionPool Env where
instance HasNodeStoryEnv Env where
hasNodeStory = env_nodeStory
instance HasNodeStoryVar Env where
hasNodeStoryVar = hasNodeStory . nse_getter
instance HasNodeStoryImmediateSaver Env where
hasNodeStoryImmediateSaver = hasNodeStory . nse_saver_immediate
......@@ -314,9 +311,6 @@ instance HasSettings DevEnv where
instance HasNodeStoryEnv DevEnv where
hasNodeStory = dev_env_nodeStory
instance HasNodeStoryVar DevEnv where
hasNodeStoryVar = hasNodeStory . nse_getter
instance HasNodeStoryImmediateSaver DevEnv where
hasNodeStoryImmediateSaver = hasNodeStory . nse_saver_immediate
......
src/Gargantext/API/Dev.hs
View file @ b423c47b
......@@ -16,7 +16,6 @@ import Control.Monad (fail)
import Gargantext.API.Admin.EnvTypes
import Gargantext.API.Admin.Settings
import Gargantext.API.Errors.Types
import Gargantext.API.Ngrams (saveNodeStoryImmediate)
import Gargantext.API.Prelude
import Gargantext.Core.NLP (nlpServerMap)
import Gargantext.Core.NodeStory
......@@ -72,9 +71,7 @@ runCmdDev env f =
runCmdGargDev :: DevEnv -> GargM DevEnv BackendInternalError a -> IO a
runCmdGargDev env cmd =
(either (fail . show) pure =<< runExceptT (runReaderT cmd env))
`finally`
runReaderT saveNodeStoryImmediate env
either (fail . show) pure =<< runExceptT (runReaderT cmd env)
runCmdDevNoErr :: DevEnv -> Cmd' DevEnv () a -> IO a
runCmdDevNoErr = runCmdDev
......
src/Gargantext/API/Ngrams.hs
View file @ b423c47b
......@@ -60,7 +60,6 @@ module Gargantext.API.Ngrams
, r_history
, NgramsRepoElement(..)
, saveNodeStory
, saveNodeStoryImmediate
, initRepo
, TabType(..)
......@@ -87,7 +86,7 @@ module Gargantext.API.Ngrams
)
where
import Control.Lens ((.~), view, (^.), (^..), (+~), (%~), (.~), msumOf, at, _Just, Each(..), (%%~), mapped, non, ifolded, to, withIndex, over)
import Control.Lens ((.~), view, (^.), (^..), (+~), (%~), (.~), msumOf, at, _Just, Each(..), (%%~), mapped, ifolded, to, withIndex, over)
import Control.Monad.Reader
import Data.Aeson.Text qualified as DAT
import Data.Foldable
......@@ -105,10 +104,10 @@ import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs)
import Gargantext.API.Admin.Types (HasSettings)
import Gargantext.API.Errors.Types
import Gargantext.API.Metrics qualified as Metrics
import Gargantext.API.Ngrams.Tools
import Gargantext.API.Ngrams.Tools (getNodeStory)
import Gargantext.API.Ngrams.Types
import Gargantext.API.Prelude
import Gargantext.Core.NodeStory
import Gargantext.Core.NodeStory (ArchiveList, HasNodeStory, HasNodeArchiveStoryImmediateSaver(..), HasNodeStoryImmediateSaver(..), NgramsStatePatch', a_history, a_state, a_version, currentVersion)
import Gargantext.Core.Types (ListType(..), NodeId, ListId, DocId, TODO, assertValid, HasValidationError, ContextId)
import Gargantext.Core.Types.Query (Limit(..), Offset(..), MinSize(..), MaxSize(..))
import Gargantext.Database.Action.Metrics.NgramsByContext (getOccByNgramsOnlyFast)
......@@ -123,7 +122,6 @@ import Gargantext.Database.Schema.Node (node_id, node_parent_id, node_user_id)
import Gargantext.Prelude hiding (log, to, toLower, (%), isInfixOf)
import Gargantext.Prelude.Clock (hasTime, getTime)
import Gargantext.Utils.Jobs (serveJobsAPI, MonadJobStatus(..))
import GHC.Conc (readTVar, writeTVar)
import Servant hiding (Patch)
{-
......@@ -174,23 +172,10 @@ mkChildrenGroups addOrRem nt patches =
------------------------------------------------------------------------
saveNodeStory :: ( MonadReader env m, MonadBase IO m, HasNodeStoryImmediateSaver env )
=> m ()
saveNodeStory = do
=> NodeId -> ArchiveList -> m ()
saveNodeStory nId a = do
saver <- view hasNodeStoryImmediateSaver
liftBase $ do
--Gargantext.Prelude.putStrLn "---- Running node story saver ----"
saver
--Gargantext.Prelude.putStrLn "---- Node story saver finished ----"
saveNodeStoryImmediate :: ( MonadReader env m, MonadBase IO m, HasNodeStoryImmediateSaver env )
=> m ()
saveNodeStoryImmediate = do
saver <- view hasNodeStoryImmediateSaver
liftBase $ do
--Gargantext.Prelude.putStrLn "---- Running node story immediate saver ----"
saver
--Gargantext.Prelude.putStrLn "---- Node story immediate saver finished ----"
liftBase $ saver nId a
listTypeConflictResolution :: ListType -> ListType -> ListType
listTypeConflictResolution _ _ = undefined -- TODO Use Map User ListType
......@@ -256,19 +241,23 @@ setListNgrams :: HasNodeStory env err m
-> m ()
setListNgrams listId ngramsType ns = do
-- printDebug "[setListNgrams]" (listId, ngramsType)
var <- getNodeStoryVar [listId]
liftBase $ atomically $ do
nls <- readTVar var
writeTVar var $
( unNodeStory
. at listId . _Just
. a_state
. at ngramsType
%~ (\mns' -> case mns' of
Nothing -> Just ns
Just ns' -> Just $ ns <> ns')
) nls
saveNodeStory
a <- getNodeStory listId
let a' = a & a_state . at ngramsType %~ (\mns' -> case mns' of
Nothing -> Just ns
Just ns' -> Just $ ns <> ns')
saveNodeStory listId a'
-- liftBase $ atomically $ do
-- nls <- readTVar var
-- writeTVar var $
-- ( unNodeStory
-- . at listId . _Just
-- . a_state
-- . at ngramsType
-- %~ (\mns' -> case mns' of
-- Nothing -> Just ns
-- Just ns' -> Just $ ns <> ns')
-- ) nls
-- saveNodeStory
newNgramsFromNgramsStatePatch :: NgramsStatePatch' -> [Ngrams]
......@@ -292,11 +281,11 @@ commitStatePatch :: ( HasNodeStory env err m
-> m (Versioned NgramsStatePatch')
commitStatePatch listId (Versioned _p_version p) = do
-- printDebug "[commitStatePatch]" listId
var <- getNodeStoryVar [listId]
a <- getNodeStory listId
archiveSaver <- view hasNodeArchiveStoryImmediateSaver
ns <- liftBase $ atomically $ readTVar var
-- ns <- liftBase $ atomically $ readTVar var
let
a = ns ^. unNodeStory . at listId . non initArchive
-- a = ns ^. unNodeStory . at listId . non initArchive
-- apply patches from version p_version to a ^. a_version
-- TODO Check this
--q = mconcat $ take (a ^. a_version - p_version) (a ^. a_history)
......@@ -327,10 +316,12 @@ commitStatePatch listId (Versioned _p_version p) = do
-}
-- printDebug "[commitStatePatch] a version" (a ^. a_version)
-- printDebug "[commitStatePatch] a' version" (a' ^. a_version)
let newNs = ( ns & unNodeStory . at listId .~ (Just a')
, Versioned (a' ^. a_version) q'
)
-- let newNs = ( ns & unNodeStory . at listId .~ (Just a')
-- , Versioned (a' ^. a_version) q'
-- )
let newA = Versioned (a' ^. a_version) q'
-- NOTE Now is the only good time to save the archive history. We
-- have the handle to the MVar and we need to save its exact
-- snapshot. Node Story archive is a linear table, so it's only
......@@ -353,16 +344,15 @@ commitStatePatch listId (Versioned _p_version p) = do
-- archive was saved and applied)
-- newNs' <- archiveSaver $ fst newNs
liftBase $ do
newNs' <- archiveSaver $ fst newNs
atomically $ writeTVar var newNs'
-- newNs' <- archiveSaver $ fst newNs
-- atomically $ writeTVar var newNs'
void $ archiveSaver listId a'
-- Save new ngrams
_ <- insertNgrams (newNgramsFromNgramsStatePatch p)
-- NOTE State (i.e. `NodeStory` can be saved asynchronously, i.e. with debounce)
-- saveNodeStory
saveNodeStoryImmediate
saveNodeStory listId a'
pure $ snd newNs
pure newA
......@@ -374,11 +364,11 @@ tableNgramsPull :: HasNodeStory env err m
-> m (Versioned NgramsTablePatch)
tableNgramsPull listId ngramsType p_version = do
-- printDebug "[tableNgramsPull]" (listId, ngramsType)
var <- getNodeStoryVar [listId]
r <- liftBase $ atomically $ readTVar var
a <- getNodeStory listId
-- r <- liftBase $ atomically $ readTVar var
let
a = r ^. unNodeStory . at listId . non initArchive
-- a = r ^. unNodeStory . at listId . non initArchive
q = mconcat $ take (a ^. a_version - p_version) (a ^. a_history)
q_table = q ^. _PatchMap . at ngramsType . _Just
......@@ -502,10 +492,9 @@ getNgramsTableMap :: HasNodeStory env err m
-> TableNgrams.NgramsType
-> m (Versioned NgramsTableMap)
getNgramsTableMap nodeId ngramsType = do
v <- getNodeStoryVar [nodeId]
repo <- liftBase $ atomically $ readTVar v
pure $ Versioned (repo ^. unNodeStory . at nodeId . _Just . a_version)
(repo ^. unNodeStory . at nodeId . _Just . a_state . at ngramsType . _Just)
a <- getNodeStory nodeId
pure $ Versioned (a ^. a_version)
(a ^. a_state . at ngramsType . _Just)
dumpJsonTableMap :: HasNodeStory env err m
......
src/Gargantext/API/Ngrams/Tools.hs
View file @ b423c47b
......@@ -23,7 +23,7 @@ import Data.HashMap.Strict qualified as HM
import Data.Map.Strict qualified as Map
import Data.Set qualified as Set
import Data.Validity
import GHC.Conc (TVar, readTVar)
-- import GHC.Conc (TVar, readTVar)
import Gargantext.API.Ngrams.Types
import Gargantext.Core.NodeStory
import Gargantext.Core.Types (ListType(..), NodeId, ListId)
......@@ -40,10 +40,11 @@ type RootTerm = NgramsTerm
getRepo :: HasNodeStory env err m
=> [ListId] -> m NodeListStory
getRepo listIds = do
f <- getNodeListStory
v <- liftBase $ f listIds
v' <- liftBase $ atomically $ readTVar v
pure $ v'
f <- getNodeListStoryMulti
liftBase $ f listIds
-- v <- liftBase $ f listIds
-- v' <- liftBase $ atomically $ readTVar v
-- pure $ v'
repoSize :: Ord k1 => NodeStory (Map.Map k1 (Map.Map k2 a)) p
......@@ -56,21 +57,29 @@ repoSize repo node_id = Map.map Map.size state'
. a_state
getNodeStoryVar :: HasNodeStory env err m
=> [ListId] -> m (TVar NodeListStory)
getNodeStoryVar l = do
getNodeStory :: HasNodeStory env err m
=> ListId -> m ArchiveList
getNodeStory l = do
f <- getNodeListStory
v <- liftBase $ f l
pure v
liftBase $ f l
-- v <- liftBase $ f l
-- pure v
getNodeListStory :: HasNodeStory env err m
=> m ([NodeId] -> IO (TVar NodeListStory))
=> m (NodeId -> IO ArchiveList)
getNodeListStory = do
env <- view hasNodeStory
pure $ view nse_getter env
getNodeListStoryMulti :: HasNodeStory env err m
=> m ([NodeId] -> IO NodeListStory)
getNodeListStoryMulti = do
env <- view hasNodeStory
pure $ view nse_getter_multi env
listNgramsFromRepo :: [ListId]
-> NgramsType
......
src/Gargantext/Core/NodeStory.hs
View file @ b423c47b
This diff is collapsed.
src/Gargantext/Core/NodeStory/DB.hs 0 → 100644
View file @ b423c47b
{-|
Module : Gargantext.Core.NodeStory.DB
Description : NodeStory DB functions
Copyright : (c) CNRS, 2017-Present
License : AGPL + CECILL v3
Maintainer : team@gargantext.org
Stability : experimental
Portability : POSIX
-}
{-# LANGUAGE Arrows #-}
{-# LANGUAGE ConstraintKinds #-}
{-# LANGUAGE QuasiQuotes #-}
{-# LANGUAGE TemplateHaskell #-}
module Gargantext.Core.NodeStory.DB
( nodeExists
, getNodesIdWithType
, getNodesArchiveHistory
, insertNodeArchiveHistory
, nodeStoriesQuery
, insertArchiveStateList
, deleteArchiveStateList
, updateArchiveStateList
, updateNodeStoryVersion )
where
import Control.Lens ((^.))
import Control.Monad.Except
import Data.HashMap.Strict (HashMap)
import Data.HashMap.Strict qualified as HashMap
import Data.Map.Strict qualified as Map
import Data.Map.Strict.Patch qualified as PM
import Data.Monoid
import Database.PostgreSQL.Simple qualified as PGS
import Database.PostgreSQL.Simple.SqlQQ (sql)
import Database.PostgreSQL.Simple.Types (Values(..), QualifiedIdentifier(..))
import Gargantext.API.Ngrams.Types
import Gargantext.Core (toDBid)
import Gargantext.Core.NodeStory.Types
import Gargantext.Core.Types (NodeId(..), NodeType)
import Gargantext.Database.Admin.Config ()
import Gargantext.Database.Query.Table.Ngrams qualified as TableNgrams
import Gargantext.Database.Schema.Ngrams (NgramsType)
import Gargantext.Prelude hiding (to)
import Gargantext.Prelude.Database
nodeExists :: PGS.Connection -> NodeId -> IO Bool
nodeExists c nId = (== [PGS.Only True])
<$> runPGSQuery c [sql| SELECT true FROM nodes WHERE id = ? LIMIT 1 |]
(PGS.Only nId)
getNodesIdWithType :: PGS.Connection -> NodeType -> IO [NodeId]
getNodesIdWithType c nt = do
ns <- runPGSQuery c query (PGS.Only $ toDBid nt)
pure $ map (\(PGS.Only nId) -> UnsafeMkNodeId nId) ns
where
query :: PGS.Query
query = [sql| SELECT id FROM nodes WHERE typename = ? |]
-- /!\ This function is using an hard coded parameter
-- which depends on the Ngrams List Flow
-- Version > 5 is hard coded because by default
-- first version of history of manual change is 6
getNodesArchiveHistory :: PGS.Connection
-> [NodeId]
-> IO [(NodeId, (Map NgramsType [HashMap NgramsTerm NgramsPatch]))]
getNodesArchiveHistory c nodesId = do
as <- runPGSQuery c query (PGS.Only $ Values fields nodesId)
:: IO [(Int, TableNgrams.NgramsType, NgramsTerm, NgramsPatch)]
pure $ map (\(nId, ngramsType, terms, patch)
-> ( UnsafeMkNodeId nId
, Map.singleton ngramsType [HashMap.singleton terms patch]
)
) as
where
fields = [QualifiedIdentifier Nothing "int4"]
query :: PGS.Query
query = [sql| WITH nodes_id(nid) as (?)
SELECT node_id, ngrams_type_id, terms, patch
FROM node_story_archive_history
JOIN ngrams ON ngrams.id = ngrams_id
JOIN nodes_id n ON node_id = n.nid
WHERE version > 5
ORDER BY (version, node_story_archive_history.id) DESC
|]
insertNodeArchiveHistory :: PGS.Connection -> NodeId -> Version -> [NgramsStatePatch'] -> IO ()
insertNodeArchiveHistory _ _ _ [] = pure ()
insertNodeArchiveHistory c nodeId version (h:hs) = do
let tuples = mconcat $ (\(nType, NgramsTablePatch patch) ->
(\(term, p) ->
(nodeId, nType, term, p)) <$> PM.toList patch) <$> PM.toList h :: [(NodeId, TableNgrams.NgramsType, NgramsTerm, NgramsPatch)]
tuplesM <- mapM (\(nId, nType, term, patch) -> do
[PGS.Only ngramsId] <- runPGSReturning c qInsert [PGS.Only term] :: IO [PGS.Only Int]
pure (nId, nType, ngramsId, term, patch)
) tuples :: IO [(NodeId, TableNgrams.NgramsType, Int, NgramsTerm, NgramsPatch)]
_ <- runPGSExecuteMany c query $ ((\(nId, nType, termId, _term, patch) -> (nId, nType, termId, patch, version)) <$> tuplesM)
_ <- insertNodeArchiveHistory c nodeId version hs
pure ()
where
qInsert :: PGS.Query
qInsert = [sql|INSERT INTO ngrams (terms) VALUES (?)
ON CONFLICT (terms) DO UPDATE SET terms = excluded.terms
RETURNING id|]
-- https://stackoverflow.com/questions/39224438/postgresql-insert-if-foreign-key-exists
query :: PGS.Query
query = [sql| INSERT INTO node_story_archive_history(node_id, ngrams_type_id, ngrams_id, patch, version)
VALUES (?, ?, ?, ?, ?)
|]
nodeStoriesQuery :: PGS.Query
nodeStoriesQuery = [sql| SELECT version, ngrams_type_id, terms, ngrams_repo_element
FROM node_stories
JOIN ngrams ON ngrams.id = ngrams_id
WHERE node_id = ?
|]
-- Archive
insertArchiveStateList :: PGS.Connection -> NodeId -> Version -> ArchiveStateList -> IO ()
insertArchiveStateList c nodeId version as = do
mapM_ performInsert as
where
performInsert (ngramsType, ngrams, ngramsRepoElement) = do
[PGS.Only ngramsId] <- tryInsertTerms ngrams
_ <- case ngramsRepoElement ^. nre_root of
Nothing -> pure []
Just r -> tryInsertTerms r
mapM_ tryInsertTerms $ ngramsRepoElement ^. nre_children
runPGSExecute c query (nodeId, ngramsId, version, ngramsType, ngramsRepoElement)
tryInsertTerms :: NgramsTerm -> IO [PGS.Only Int]
tryInsertTerms t = runPGSReturning c qInsert [PGS.Only t]
qInsert :: PGS.Query
qInsert = [sql|INSERT INTO ngrams (terms) VALUES (?)
ON CONFLICT (terms) DO UPDATE SET terms = excluded.terms
RETURNING id|]
query :: PGS.Query
query = [sql|INSERT INTO node_stories(node_id, ngrams_id, version, ngrams_type_id, ngrams_repo_element)
VALUES (?, ?, ?, ?, ? :: jsonb)
|]
deleteArchiveStateList :: PGS.Connection -> NodeId -> ArchiveStateList -> IO ()
deleteArchiveStateList c nodeId as = do
mapM_ (\(nt, n, _) -> runPGSExecute c query (nodeId, nt, n)) as
where
query :: PGS.Query
query = [sql| DELETE FROM node_stories
WHERE node_id = ? AND ngrams_type_id = ?
AND ngrams_id IN (SELECT id FROM ngrams WHERE terms = ?)
|]
updateArchiveStateList :: PGS.Connection -> NodeId -> Version -> ArchiveStateList -> IO ()
updateArchiveStateList c nodeId version as = do
let params = (\(nt, n, nre) -> (nre, version, nodeId, nt, n)) <$> as
mapM_ (runPGSExecute c query) params
where
query :: PGS.Query
query = [sql| UPDATE node_stories
SET ngrams_repo_element = ?, version = ?
WHERE node_id = ? AND ngrams_type_id = ?
AND ngrams_id IN (SELECT id FROM ngrams WHERE terms = ?)
|]
updateNodeStoryVersion :: PGS.Connection -> NodeId -> ArchiveList -> IO ()
updateNodeStoryVersion c nodeId newArchive = do
let ngramsTypes = Map.keys $ newArchive ^. a_state
mapM_ (\nt -> runPGSExecute c query (newArchive ^. a_version, nodeId, nt)) ngramsTypes
where
query :: PGS.Query
query = [sql|UPDATE node_stories
SET version = ?
WHERE node_id = ?
AND ngrams_type_id = ?|]
src/Gargantext/Core/NodeStory/Types.hs 0 → 100644
View file @ b423c47b
{-|
Module : Gargantext.Core.NodeStory.Types
Description : Node API generation
Copyright : (c) CNRS, 2017-Present
License : AGPL + CECILL v3
Maintainer : team@gargantext.org
Stability : experimental
Portability : POSIX
-}
{-# LANGUAGE Arrows #-}
{-# LANGUAGE ConstraintKinds #-}
{-# LANGUAGE QuasiQuotes #-}
{-# LANGUAGE TemplateHaskell #-}
module Gargantext.Core.NodeStory.Types
( HasNodeStory
, HasNodeStoryEnv
, hasNodeStory
, HasNodeStoryImmediateSaver
, hasNodeStoryImmediateSaver
, HasNodeArchiveStoryImmediateSaver
, hasNodeArchiveStoryImmediateSaver
, NodeStory(..)
, NgramsState'
, NgramsStatePatch'
, NodeListStory
, ArchiveList
, initNodeListStoryMock
, NodeStoryEnv(..)
, initNodeStory
, nse_getter
, nse_getter_multi
, nse_saver_immediate
, nse_archive_saver_immediate
-- , nse_var
, unNodeStory
, Archive(..)
, initArchive
, archiveAdvance
, unionArchives
, a_history
, a_state
, a_version
, combineState
, ArchiveStateSet
, ArchiveStateList )
where
import Codec.Serialise.Class
import Control.Lens (makeLenses, Getter, (^.))
import Control.Monad.Except
import Control.Monad.Reader
import Data.Aeson hiding ((.=), decode)
import Data.Map.Strict qualified as Map
import Data.Monoid
import Data.Profunctor.Product.TH (makeAdaptorAndInstance)
import Data.Semigroup
import Data.Set qualified as Set
import Database.PostgreSQL.Simple.FromField (FromField(fromField), fromJSONField)
import Gargantext.API.Ngrams.Types
import Gargantext.Core.Types (NodeId(..))
import Gargantext.Core.Utils.Prefix (unPrefix)
import Gargantext.Database.Admin.Config ()
import Gargantext.Database.Prelude (DbCmd')
import Gargantext.Database.Query.Table.Ngrams qualified as TableNgrams
import Gargantext.Database.Query.Table.Node.Error (HasNodeError())
import Gargantext.Prelude hiding (to)
import Opaleye (DefaultFromField(..), SqlJsonb, fromPGSFromField)
------------------------------------------------------------------------
{- | Node Story for each NodeType where the Key of the Map is NodeId
TODO : generalize for any NodeType, let's start with NodeList which
is implemented already
-}
newtype NodeStory s p = NodeStory { _unNodeStory :: Map NodeId (Archive s p) }
deriving (Generic, Show, Eq)
instance (FromJSON s, FromJSON p) => FromJSON (NodeStory s p)
instance (ToJSON s, ToJSON p) => ToJSON (NodeStory s p)
instance (Serialise s, Serialise p) => Serialise (NodeStory s p)
data Archive s p = Archive
{ _a_version :: !Version
, _a_state :: !s
, _a_history :: ![p]
-- first patch in the list is the most recent
-- We use `take` in `commitStatePatch`, that's why.
-- History is immutable, we just insert things on top of existing
-- list.
-- We don't need to store the whole history in memory, this
-- structure holds only recent history, the one that will be
-- inserted to the DB.
}
deriving (Generic, Show, Eq)
instance (Serialise s, Serialise p) => Serialise (Archive s p)
type NodeListStory = NodeStory NgramsState' NgramsStatePatch'
-- NOTE: 'type NgramsTableMap = Map NgramsTerm NgramsRepoElement'
type NgramsState' = Map TableNgrams.NgramsType NgramsTableMap
type NgramsStatePatch' = PatchMap TableNgrams.NgramsType NgramsTablePatch
-- instance Serialise NgramsStatePatch'
instance FromField (Archive NgramsState' NgramsStatePatch')
where
fromField = fromJSONField
instance DefaultFromField SqlJsonb (Archive NgramsState' NgramsStatePatch')
where
defaultFromField = fromPGSFromField
-- | Combine `NgramsState'`. This is because the structure is (Map
-- NgramsType (Map ...)) and the default `(<>)` operator is
-- left-biased
-- (https://hackage.haskell.org/package/containers-0.6.6/docs/Data-Map-Internal.html#v:union)
combineState :: NgramsState' -> NgramsState' -> NgramsState'
combineState = Map.unionWith (<>)
-- This is not a typical Semigroup instance. The state is not
-- appended, instead it is replaced with the second entry. This is
-- because state changes with each version. We have to take into
-- account the removal of terms as well.
-- instance (Semigroup s, Semigroup p) => Semigroup (Archive s p) where
-- (<>) (Archive { _a_history = p }) (Archive { _a_version = v'
-- , _a_state = s'
-- , _a_history = p' }) =
-- Archive { _a_version = v'
-- , _a_state = s'
-- , _a_history = p' <> p }
-- instance (Monoid s, Semigroup p) => Monoid (Archive s p) where
-- mempty = Archive { _a_version = 0
-- , _a_state = mempty
-- , _a_history = [] }
instance (FromJSON s, FromJSON p) => FromJSON (Archive s p) where
parseJSON = genericParseJSON $ unPrefix "_a_"
instance (ToJSON s, ToJSON p) => ToJSON (Archive s p) where
toJSON = genericToJSON $ unPrefix "_a_"
toEncoding = genericToEncoding $ unPrefix "_a_"
-- | This is the normal way to update archive state, bumping the
-- version and history. Resulting state is taken directly from new
-- archive, omitting old archive completely.
archiveAdvance :: (Semigroup s, Semigroup p) => Archive s p -> Archive s p -> Archive s p
archiveAdvance aOld aNew = aNew { _a_history = _a_history aNew <> _a_history aOld }
-- | This is to merge archive states.
unionArchives :: (Semigroup s, Semigroup p) => Archive s p -> Archive s p -> Archive s p
unionArchives aOld aNew = aNew { _a_state = _a_state aOld <> _a_state aNew
, _a_history = _a_history aNew <> _a_history aOld }
------------------------------------------------------------------------
initNodeStory :: (Monoid s, Semigroup p) => NodeId -> NodeStory s p
initNodeStory ni = NodeStory $ Map.singleton ni initArchive
initArchive :: (Monoid s, Semigroup p) => Archive s p
initArchive = Archive { _a_version = 0
, _a_state = mempty
, _a_history = [] }
initNodeListStoryMock :: NodeListStory
initNodeListStoryMock = NodeStory $ Map.singleton nodeListId archive
where
nodeListId = 0
archive = Archive { _a_version = 0
, _a_state = ngramsTableMap
, _a_history = [] }
ngramsTableMap = Map.singleton TableNgrams.NgramsTerms
$ Map.fromList
[ (n ^. ne_ngrams, ngramsElementToRepo n)
| n <- mockTable ^. _NgramsTable
]
----------------------------------------------------------------------
data NodeStoryPoly nid v ngtid ngid nre =
NodeStoryDB { node_id :: !nid
, version :: !v
, ngrams_type_id :: !ngtid
, ngrams_id :: !ngid
, ngrams_repo_element :: !nre }
deriving (Eq)
data NodeStoryArchivePoly nid a =
NodeStoryArchiveDB { a_node_id :: !nid
, archive :: !a }
deriving (Eq)
$(makeAdaptorAndInstance "pNodeStory" ''NodeStoryPoly)
$(makeAdaptorAndInstance "pNodeArchiveStory" ''NodeStoryArchivePoly)
-- type NodeStoryWrite = NodeStoryPoly (Column SqlInt4) (Column SqlInt4) (Column SqlInt4) (Column SqlInt4) (Column SqlJsonb)
-- type NodeStoryRead = NodeStoryPoly (Column SqlInt4) (Column SqlInt4) (Column SqlInt4) (Column SqlInt4) (Column SqlJsonb)
-- type NodeStoryArchiveWrite = NodeStoryArchivePoly (Column SqlInt4) (Column SqlJsonb)
-- type NodeStoryArchiveRead = NodeStoryArchivePoly (Column SqlInt4) (Column SqlJsonb)
type ArchiveList = Archive NgramsState' NgramsStatePatch'
------------------------------------------------------------------------
data NodeStoryEnv = NodeStoryEnv
{ _nse_saver_immediate :: !(NodeId -> ArchiveList -> IO ())
, _nse_archive_saver_immediate :: !(NodeId -> ArchiveList -> IO ArchiveList)
, _nse_getter :: !(NodeId -> IO ArchiveList)
, _nse_getter_multi :: !([NodeId] -> IO NodeListStory)
--, _nse_cleaner :: !(IO ()) -- every 12 hours: cleans the repos of unused NodeStories
-- , _nse_lock :: !FileLock -- TODO (it depends on the option: if with database or file only)
}
deriving (Generic)
type HasNodeStory env err m = ( DbCmd' env err m
, MonadReader env m
, MonadError err m
, HasNodeStoryEnv env
, HasNodeError err
)
class (HasNodeStoryImmediateSaver env)
=> HasNodeStoryEnv env where
hasNodeStory :: Getter env NodeStoryEnv
class HasNodeStoryImmediateSaver env where
hasNodeStoryImmediateSaver :: Getter env (NodeId -> ArchiveList -> IO ())
class HasNodeArchiveStoryImmediateSaver env where
hasNodeArchiveStoryImmediateSaver :: Getter env (NodeId -> ArchiveList -> IO ArchiveList)
type ArchiveStateList = [(TableNgrams.NgramsType, NgramsTerm, NgramsRepoElement)]
type ArchiveStateSet = Set.Set (TableNgrams.NgramsType, NgramsTerm)
------------------------------------------------------------------------
------------------------------------------------------------------------
-- | Lenses at the bottom of the file because Template Haskell would reorder order of execution in others cases
makeLenses ''NodeStoryEnv
makeLenses ''NodeStory
makeLenses ''Archive
src/Gargantext/Database/Action/Flow.hs
View file @ b423c47b
This diff is collapsed.
src/Gargantext/Database/Action/Flow/Extract.hs 0 → 100644
View file @ b423c47b
{-|
Module : Gargantext.Database.Flow.Extract
Description : Database Flow
Copyright : (c) CNRS, 2017-Present
License : AGPL + CECILL v3
Maintainer : team@gargantext.org
Stability : experimental
Portability : POSIX
-}
{-# OPTIONS_GHC -fno-warn-orphans #-}
{-# LANGUAGE InstanceSigs #-}
module Gargantext.Database.Action.Flow.Extract
where
import Control.Lens ((^.), _Just, view)
import Data.HashMap.Strict qualified as HashMap
import Data.Map.Strict qualified as DM
import Gargantext.Core (Lang, NLPServerConfig, PosTagAlgo(CoreNLP))
import Gargantext.Core.Text (HasText(..))
import Gargantext.Core.Text.Corpus.Parsers (splitOn)
import Gargantext.Core.Text.Terms (ExtractNgramsT, ExtractedNgrams(..), TermType, cleanExtractedNgrams, enrichedTerms, extractNgramsT, extractTerms, tt_lang)
import Gargantext.Core.Types (POS(NP), TermsCount)
import Gargantext.Database.Admin.Types.Hyperdata (HyperdataContact, HyperdataDocument, cw_lastName, hc_who, hd_authors, hd_bdd, hd_institutes, hd_source)
import Gargantext.Database.Admin.Types.Node
import Gargantext.Database.Prelude (DBCmd)
import Gargantext.Database.Schema.Ngrams
import Gargantext.Database.Schema.Node (NodePoly(..))
import Gargantext.Prelude
------------------------------------------------------------------------
instance ExtractNgramsT HyperdataContact
where
extractNgramsT _ncs l hc = HashMap.mapKeys (cleanExtractedNgrams 255) <$> extract l hc
where
extract :: TermType Lang -> HyperdataContact
-> DBCmd err (HashMap.HashMap ExtractedNgrams (Map NgramsType Int, TermsCount))
extract _l hc' = do
let authors = map text2ngrams
$ maybe ["Nothing"] (\a -> [a])
$ view (hc_who . _Just . cw_lastName) hc'
pure $ HashMap.fromList $ [(SimpleNgrams a', (DM.singleton Authors 1, 1)) | a' <- authors ]
instance ExtractNgramsT HyperdataDocument
where
extractNgramsT :: NLPServerConfig
-> TermType Lang
-> HyperdataDocument
-> DBCmd err (HashMap.HashMap ExtractedNgrams (Map NgramsType Int, TermsCount))
extractNgramsT ncs lang hd = HashMap.mapKeys (cleanExtractedNgrams 255) <$> extractNgramsT' hd
where
extractNgramsT' :: HyperdataDocument
-> DBCmd err (HashMap.HashMap ExtractedNgrams (Map NgramsType Int, TermsCount))
extractNgramsT' doc = do
let source = text2ngrams
$ maybe "Nothing" identity
$ doc ^. hd_source
institutes = map text2ngrams
$ maybe ["Nothing"] (splitOn Institutes (doc^. hd_bdd))
$ doc ^. hd_institutes
authors = map text2ngrams
$ maybe ["Nothing"] (splitOn Authors (doc^. hd_bdd))
$ doc ^. hd_authors
termsWithCounts' <- map (\(t, cnt) -> (enrichedTerms (lang ^. tt_lang) CoreNLP NP t, cnt))
<$> concat
<$> liftBase (extractTerms ncs lang $ hasText doc)
pure $ HashMap.fromList
$ [(SimpleNgrams source, (DM.singleton Sources 1, 1)) ]
<> [(SimpleNgrams i', (DM.singleton Institutes 1, 1)) | i' <- institutes ]
<> [(SimpleNgrams a', (DM.singleton Authors 1, 1)) | a' <- authors ]
<> [(EnrichedNgrams t', (DM.singleton NgramsTerms 1, cnt')) | (t', cnt') <- termsWithCounts' ]
instance (ExtractNgramsT a, HasText a) => ExtractNgramsT (Node a)
where
extractNgramsT ncs l (Node { _node_hyperdata = h }) = extractNgramsT ncs l h
instance HasText a => HasText (Node a)
where
hasText (Node { _node_hyperdata = h }) = hasText h
-- Apparently unused functions
-- extractInsert :: ( HasNodeStory env err m
-- , HasNLPServer env )
-- => [Node HyperdataDocument] -> m ()
-- extractInsert docs = do
-- let documentsWithId = map (\doc -> Indexed (doc ^. node_id) doc) docs
-- let lang = EN
-- ncs <- view $ nlpServerGet lang
-- mapNgramsDocs' <- mapNodeIdNgrams
-- <$> documentIdWithNgrams
-- (extractNgramsT ncs $ withLang (Multi lang) documentsWithId)
-- documentsWithId
-- _ <- insertExtractedNgrams $ HashMap.keys mapNgramsDocs'
-- pure ()
src/Gargantext/Database/Action/Flow/List.hs
View file @ b423c47b
......@@ -17,16 +17,16 @@ Portability : POSIX
module Gargantext.Database.Action.Flow.List
where
import Control.Lens ((^.), (+~), (%~), at, (.~), _Just)
import Control.Lens ((^.), (+~), (%~), at, (.~))
import Control.Monad.Reader
import Data.List qualified as List
import Data.Map.Strict (toList)
import Data.Map.Strict qualified as Map
import Data.Map.Strict.Patch qualified as PM
import Gargantext.API.Ngrams (saveNodeStory)
import Gargantext.API.Ngrams.Tools (getNodeStoryVar)
import Gargantext.API.Ngrams.Tools (getNodeStory)
import Gargantext.API.Ngrams.Types
import Gargantext.Core.NodeStory
import Gargantext.Core.NodeStory (HasNodeStory, a_history, a_state, a_version)
import Gargantext.Core.Types (HasValidationError(..), assertValid)
import Gargantext.Core.Types.Main (ListType(CandidateTerm))
import Gargantext.Database.Admin.Types.Node
......@@ -34,7 +34,6 @@ import Gargantext.Database.Query.Table.Ngrams qualified as TableNgrams
import Gargantext.Database.Query.Table.NodeNgrams (NodeNgramsPoly(..), NodeNgramsW, listInsertDb,{- getCgramsId -})
import Gargantext.Database.Schema.Ngrams (NgramsType(..))
import Gargantext.Prelude hiding (toList)
import GHC.Conc (readTVar, writeTVar)
-- FLOW LIST
-- 1. select specific terms of the corpus when compared with others langs
......@@ -201,11 +200,14 @@ putListNgrams nodeId ngramsType nes = putListNgrams' nodeId ngramsType m
-- The modifyMVar_ would test the patch with applicable first.
-- If valid the rest would be atomic and no merge is required.
-}
var <- getNodeStoryVar [listId]
liftBase $ atomically $ do
r <- readTVar var
writeTVar var $
r & unNodeStory . at listId . _Just . a_version +~ 1
& unNodeStory . at listId . _Just . a_history %~ (p :)
& unNodeStory . at listId . _Just . a_state . at ngramsType' .~ Just ns
saveNodeStory
a <- getNodeStory listId
let a' = a & a_version +~ 1
& a_history %~ (p :)
& a_state . at ngramsType' .~ Just ns
-- liftBase $ atomically $ do
-- r <- readTVar var
-- writeTVar var $
-- r & unNodeStory . at listId . _Just . a_version +~ 1
-- & unNodeStory . at listId . _Just . a_history %~ (p :)
-- & unNodeStory . at listId . _Just . a_state . at ngramsType' .~ Just ns
saveNodeStory listId a'
src/Gargantext/Database/Action/Flow/Types.hs
View file @ b423c47b
......@@ -9,29 +9,40 @@ Portability : POSIX
-}
{-# OPTIONS_GHC -fno-warn-orphans #-}
{-# LANGUAGE ConstraintKinds #-}
{-# LANGUAGE ConstrainedClassMethods #-}
{-# LANGUAGE ConstraintKinds #-}
{-# LANGUAGE InstanceSigs #-}
{-# LANGUAGE TemplateHaskell #-}
module Gargantext.Database.Action.Flow.Types
where
import Conduit (ConduitT)
import Control.Lens (makeLenses)
import Data.Aeson (ToJSON)
import Gargantext.Core.Types (HasValidationError)
import Data.Aeson.TH (deriveJSON)
import Data.HashMap.Strict (HashMap)
import Data.Swagger (ToSchema(..), genericDeclareNamedSchema)
import Gargantext.Core.Flow.Types
import Gargantext.Core.Text
import Gargantext.Core.NodeStory
import Gargantext.Core.Text
import Gargantext.Core.Text.Corpus.API qualified as API
import Gargantext.Core.Text.Terms
import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
import Gargantext.Core.Types (HasValidationError, TermsCount)
import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument)
import Gargantext.Database.Admin.Types.Node (NodeId)
import Gargantext.Database.Prelude (CmdM)
import Gargantext.Database.Query.Table.Node.Document.Insert
import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
import Gargantext.Database.Query.Tree.Error (HasTreeError)
import Gargantext.Database.Schema.Ngrams (NgramsType(..))
import Gargantext.Database.Types (Indexed)
import Gargantext.Prelude
import Gargantext.System.Logging
type FlowCmdM env err m =
( CmdM env err m
, HasNodeStory env err m
......@@ -56,3 +67,27 @@ type FlowInsertDB a = ( AddUniqId a
, UniqParameters a
, InsertDb a
)
data DocumentIdWithNgrams a b =
DocumentIdWithNgrams
{ documentWithId :: Indexed NodeId a
, documentNgrams :: HashMap b (Map NgramsType Int, TermsCount)
} deriving (Show)
-- TODO use internal with API name (could be old data)
data DataOrigin = InternalOrigin { _do_api :: API.ExternalAPIs }
| ExternalOrigin { _do_api :: API.ExternalAPIs }
-- TODO Web
deriving (Generic, Eq)
makeLenses ''DataOrigin
deriveJSON (unPrefix "_do_") ''DataOrigin
instance ToSchema DataOrigin where
declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_do_")
data DataText = DataOld ![NodeId]
| DataNew !(Maybe Integer, ConduitT () HyperdataDocument IO ())
--- | DataNew ![[HyperdataDocument]]
src/Gargantext/Database/Action/Flow/Utils.hs
View file @ b423c47b
......@@ -9,30 +9,47 @@ Portability : POSIX
-}
{-# OPTIONS_GHC -fno-warn-orphans #-}
{-# LANGUAGE InstanceSigs #-}
module Gargantext.Database.Action.Flow.Utils
where
( docNgrams
, documentIdWithNgrams
, insertDocNgrams
, insertDocs
, mapNodeIdNgrams )
where
import Control.Lens ((^.))
import Data.HashMap.Strict (HashMap)
import Data.HashMap.Strict qualified as HashMap
import Data.List qualified as List
import Data.Map.Strict qualified as DM
import Data.Text qualified as T
import Gargantext.API.Ngrams.Types qualified as NT
import Gargantext.Core (Lang, toDBid)
import Gargantext.Core.Flow.Types (UniqId, uniqId)
import Gargantext.Core.Text.Terms.WithList (MatchedText, buildPatternsWith, termsInText)
import Gargantext.Core.Types (TermsCount)
import Gargantext.Core.Utils (addTuples)
import Gargantext.Data.HashMap.Strict.Utils qualified as HashMap
import Gargantext.Database.Action.Flow.Types (DocumentIdWithNgrams(..), FlowInsertDB)
import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument, hd_abstract, hd_title)
import Gargantext.Database.Admin.Types.Node
import Gargantext.Database.Prelude (DBCmd)
import Gargantext.Database.Prelude (DBCmd, DbCmd')
import Gargantext.Database.Query.Table.ContextNodeNgrams
import Gargantext.Database.Query.Table.Node.Document.Add qualified as Doc (add)
import Gargantext.Database.Query.Table.Node.Document.Insert (ReturnId, addUniqId, insertDb, reId, reInserted, reUniqId)
import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..))
import Gargantext.Database.Schema.Context (context_hyperdata, context_id)
import Gargantext.Database.Schema.Ngrams
import Gargantext.Database.Types
import Gargantext.Prelude
import Gargantext.Core (toDBid)
import Gargantext.Prelude.Crypto.Hash (Hash)
data DocumentIdWithNgrams a b =
DocumentIdWithNgrams
{ documentWithId :: Indexed NodeId a
, documentNgrams :: HashMap b (Map NgramsType Int, TermsCount)
} deriving (Show)
insertDocNgrams :: ListId
-> HashMap (Indexed NgramsId Ngrams) (Map NgramsType (Map DocId (Int, TermsCount)))
-> DBCmd err Int
......@@ -52,3 +69,122 @@ insertDocNgrams lId m = do
-- [(NodeId, {Ngrams: ({NgramsType: Int}, TermsCount)})]
-- {Ngrams: {NgramsType: {NodeId: (Int, TermsCount)}}}
docNgrams :: Lang
-> NgramsType
-> [NT.NgramsTerm]
-> Gargantext.Database.Admin.Types.Node.Context HyperdataDocument
-> [((MatchedText, TermsCount),
Map NgramsType (Map NodeId Int))]
docNgrams lang nt ts doc =
List.zip
(termsInText lang (buildPatternsWith lang ts)
$ T.unlines $ catMaybes
[ doc ^. context_hyperdata . hd_title
, doc ^. context_hyperdata . hd_abstract
]
)
(List.cycle [DM.fromList $ [(nt, DM.singleton (doc ^. context_id) 1 )]])
documentIdWithNgrams :: HasNodeError err
=> (a
-> DBCmd err (HashMap.HashMap b (Map NgramsType Int, TermsCount)))
-> [Indexed NodeId a]
-> DBCmd err [DocumentIdWithNgrams a b]
documentIdWithNgrams f = traverse toDocumentIdWithNgrams
where
toDocumentIdWithNgrams d = do
e <- f $ _unIndex d
pure $ DocumentIdWithNgrams d e
-- | TODO check optimization
mapNodeIdNgrams :: (Ord b, Hashable b)
=> [DocumentIdWithNgrams a b]
-> HashMap.HashMap b
(Map NgramsType
(Map NodeId (Int, TermsCount))
)
mapNodeIdNgrams = HashMap.unionsWith (DM.unionWith (DM.unionWith addTuples)) . fmap f
where
-- | NOTE We are somehow multiplying 'TermsCount' here: If the
-- same ngrams term has different ngrams types, the 'TermsCount'
-- for it (which is the number of times the terms appears in a
-- document) is copied over to all its types.
f :: DocumentIdWithNgrams a b
-> HashMap.HashMap b (Map NgramsType (Map NodeId (Int, TermsCount)))
f d = fmap (\(ngramsTypeMap, cnt) -> fmap (\i -> DM.singleton nId (i, cnt)) ngramsTypeMap) $ documentNgrams d
where
nId = _index $ documentWithId d
-- TODO Type NodeDocumentUnicised
insertDocs :: ( DbCmd' env err m
-- , FlowCorpus a
, FlowInsertDB a
, HasNodeError err
)
=> UserId
-> CorpusId
-> [a]
-> m ([ContextId], [Indexed ContextId a])
insertDocs uId cId hs = do
let docs = map addUniqId hs
newIds <- insertDb uId Nothing docs
-- printDebug "newIds" newIds
let
newIds' = map (nodeId2ContextId . reId) newIds
documentsWithId = mergeData (toInserted newIds) (DM.fromList $ map viewUniqId' docs)
_ <- Doc.add cId newIds'
pure (newIds', map (first nodeId2ContextId) documentsWithId)
------------------------------------------------------------------------
viewUniqId' :: UniqId a
=> a
-> (Hash, a)
viewUniqId' d = maybe err (\h -> (h,d)) (d ^. uniqId)
where
err = panicTrace "[ERROR] Database.Flow.toInsert"
mergeData :: Map Hash ReturnId
-> Map Hash a
-> [Indexed NodeId a]
mergeData rs = catMaybes . map toDocumentWithId . DM.toList
where
toDocumentWithId (sha,hpd) =
Indexed <$> fmap reId (DM.lookup sha rs)
<*> Just hpd
toInserted :: [ReturnId]
-> Map Hash ReturnId
toInserted =
DM.fromList . map (\r -> (reUniqId r, r) )
. filter (\r -> reInserted r == True)
-- Apparently unused functions
-- | TODO putelsewhere
-- | Upgrade function
-- Suppose all documents are English (this is the case actually)
-- indexAllDocumentsWithPosTag :: ( HasNodeStory env err m
-- , HasNLPServer env )
-- => m ()
-- indexAllDocumentsWithPosTag = do
-- rootId <- getRootId (UserName userMaster)
-- corpusIds <- findNodesId rootId [NodeCorpus]
-- docs <- List.concat <$> mapM getDocumentsWithParentId corpusIds
-- _ <- mapM extractInsert (splitEvery 1000 docs)
-- pure ()
src/Gargantext/Database/Action/Metrics.hs
View file @ b423c47b
......@@ -30,7 +30,7 @@ import Database.PostgreSQL.Simple.Types (Values(..), QualifiedIdentifier(..))
import Gargantext.API.Ngrams.Tools (filterListWithRoot, groupNodesByNgrams, Diagonal(..), getCoocByNgrams, mapTermListRoot, RootTerm, getRepo)
import Gargantext.API.Ngrams.Types (TabType(..), ngramsTypeFromTabType, NgramsTerm(..))
import Gargantext.Core (HasDBid(toDBid))
import Gargantext.Core.NodeStory hiding (runPGSQuery)
import Gargantext.Core.NodeStory
import Gargantext.Core.Text.Metrics (scored, Scored(..), {-localMetrics, toScored-})
import Gargantext.Core.Types (ListType(..), NodeType(..), ContextId, contextId2NodeId)
import Gargantext.Core.Types.Query (Limit(..))
......@@ -74,7 +74,8 @@ getNgramsCooc cId lId tabType maybeLimit = do
------------------------------------------------------------------------
------------------------------------------------------------------------
updateNgramsOccurrences :: (HasNodeStory env err m)
=> CorpusId -> ListId
=> CorpusId
-> ListId
-> m ()
updateNgramsOccurrences cId lId = do
_ <- mapM (updateNgramsOccurrences' cId lId Nothing) [Terms, Sources, Authors, Institutes]
......
src/Gargantext/Database/Action/Search.hs
View file @ b423c47b
......@@ -95,7 +95,7 @@ searchDocInDatabase p t = runOpaQuery (queryDocInDatabase p t)
queryDocInDatabase :: ParentId -> Text -> O.Select (Column SqlInt4, Column SqlJsonb)
queryDocInDatabase _p q = proc () -> do
row <- queryNodeSearchTable -< ()
restrict -< (_ns_search row) @@ (sqlToTSQuery (unpack q))
restrict -< (_ns_search row) @@ (sqlPlainToTSQuery (unpack q))
restrict -< (_ns_typename row) .== (sqlInt4 $ toDBid NodeDocument)
returnA -< (_ns_id row, _ns_hyperdata row)
......
stack.yaml
View file @ b423c47b
......@@ -71,10 +71,6 @@
git: "https://github.com/adinapoli/duckling.git"
subdirs:
- .
- commit: e9a29582ac66198dd2c2fdc3f8c8a4b1e6fbe004
git: "https://github.com/adinapoli/haskell-opaleye.git"
subdirs:
- .
- commit: 7533a9ccd3bfe77141745f6b61039a26aaf5c83b
git: "https://github.com/adinapoli/llvm-hs.git"
subdirs:
......@@ -119,6 +115,10 @@
git: "https://github.com/delanoe/patches-map"
subdirs:
- .
- commit: 6cf1bcfe215143efac17919cfd0abdd60e0f717c
git: "https://github.com/garganscript/haskell-opaleye.git"
subdirs:
- .
- commit: 4fd2edf30c141600ffad6d730cc4c1c08a6dbce4
git: "https://github.com/robstewart57/rdf4h.git"
subdirs:
......
test/Test/Database/Operations.hs
View file @ b423c47b
......@@ -68,6 +68,7 @@ tests = sequential $ aroundAll withTestDB $ describe "Database" $ do
it "Can perform search by author in documents" corpusSearch02
it "Can perform more complex searches using the boolean API" corpusSearch03
it "Can correctly count doc score" corpusScore01
it "Can perform search with spaces for doc in db" corpusSearchDB01
nodeStoryTests :: Spec
nodeStoryTests = sequential $
......
test/Test/Database/Operations/DocumentSearch.hs
View file @ b423c47b
......@@ -208,3 +208,16 @@ corpusScore01 env = do
liftIO $ do
map facetDoc_score results `shouldBe` [Just 0.0, Just 0.0]
-- | Check that we support search with tsquery
corpusSearchDB01 :: TestEnv -> Assertion
corpusSearchDB01 env = do
flip runReaderT env $ runTestMonad $ do
parentId <- getRootId (UserName userMaster)
[corpus] <- getCorporaWithParentId parentId
results <- searchDocInDatabase (_node_id corpus) ("first second")
liftIO $ do
length results `shouldBe` 0 -- doesn't exist, we just check that proper to_tsquery is called
test/Test/Database/Operations/NodeStory.hs
View file @ b423c47b
......@@ -20,9 +20,9 @@ import Data.Map.Strict.Patch qualified as PM
import Data.Set qualified as Set
import Database.PostgreSQL.Simple qualified as PSQL
import Database.PostgreSQL.Simple.SqlQQ
import Gargantext.API.Ngrams (commitStatePatch, mSetFromList, setListNgrams, saveNodeStoryImmediate)
import Gargantext.API.Ngrams (commitStatePatch, mSetFromList, setListNgrams, saveNodeStory)
import Gargantext.API.Ngrams.Types (MSet(..), NgramsPatch(..), NgramsRepoElement(..), NgramsTerm(..), Versioned(..), mkNgramsTablePatch, nre_children, nre_list, nre_parent, nre_root)
import Gargantext.API.Ngrams.Tools (getNodeStoryVar)
import Gargantext.API.Ngrams.Tools (getNodeStory)
import Gargantext.Core.NodeStory hiding (runPGSQuery)
import Gargantext.Core.Types.Individu
import Gargantext.Core.Types (ListType(..), ListId, NodeId, UserId)
......@@ -35,13 +35,12 @@ import Gargantext.Database.Query.Tree.Root
import Gargantext.Database.Schema.Ngrams (NgramsType(..))
import Gargantext.Database.Schema.Node (NodePoly(..))
import Gargantext.Prelude
import GHC.Conc (TVar, readTVar)
import Test.Database.Types
import Test.Hspec.Expectations
import Test.Tasty.HUnit
commonInitialization :: TestMonad ( UserId, NodeId, ListId, TVar NodeListStory )
commonInitialization :: TestMonad ( UserId, NodeId, ListId, ArchiveList )
commonInitialization = do
let user = UserName userMaster
parentId <- getRootId user
......@@ -52,9 +51,9 @@ commonInitialization = do
listId <- getOrMkList corpusId userId
v <- getNodeStoryVar [listId]
a <- getNodeStory listId
pure $ (userId, corpusId, listId, v)
pure $ (userId, corpusId, listId, a)
initArchiveList :: ArchiveList
......@@ -90,7 +89,7 @@ simpleChildTerm = ( simpleChildTerm'
createListTest :: TestEnv -> Assertion
createListTest env = do
flip runReaderT env $ runTestMonad $ do
(userId, corpusId, listId, _v) <- commonInitialization
(userId, corpusId, listId, _a) <- commonInitialization
listId' <- getOrMkList corpusId userId
......@@ -100,28 +99,32 @@ createListTest env = do
queryNodeStoryTest :: TestEnv -> Assertion
queryNodeStoryTest env = do
flip runReaderT env $ runTestMonad $ do
(_userId, _corpusId, listId, v) <- commonInitialization
(_userId, _corpusId, listId, a) <- commonInitialization
liftIO $ do
a `shouldBe` initArchiveList
saveNodeStory listId a
a' <- getNodeStory listId
saveNodeStoryImmediate
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId initArchiveList)
a' `shouldBe` a
insertNewTermsToNodeStoryTest :: TestEnv -> Assertion
insertNewTermsToNodeStoryTest env = do
flip runReaderT env $ runTestMonad $ do
(_userId, _corpusId, listId, v) <- commonInitialization
(_userId, _corpusId, listId, _a) <- commonInitialization
let (terms, nre) = simpleTerm
let nls = Map.singleton terms nre
setListNgrams listId NgramsTerms nls
a <- getNodeStory listId
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId
(initArchiveList { _a_state = Map.singleton NgramsTerms nls }))
a `shouldBe` (initArchiveList { _a_state = Map.singleton NgramsTerms nls })
-- check that the ngrams are in the DB as well
ngramsMap <- selectNgramsId [unNgramsTerm terms]
liftIO $ (snd <$> Map.toList ngramsMap) `shouldBe` [unNgramsTerm terms]
......@@ -139,7 +142,7 @@ insertNewTermsToNodeStoryTest env = do
insertNewTermsWithChildrenToNodeStoryTest :: TestEnv -> Assertion
insertNewTermsWithChildrenToNodeStoryTest env = do
flip runReaderT env $ runTestMonad $ do
(_userId, _corpusId, listId, v) <- commonInitialization
(_userId, _corpusId, listId, _a) <- commonInitialization
let (tParent, nreParent) = simpleParentTerm
let (tChild, nreChild) = simpleChildTerm
......@@ -148,10 +151,10 @@ insertNewTermsWithChildrenToNodeStoryTest env = do
let nls = Map.fromList [(tParent, nreParent), (tChild, nreChild)]
setListNgrams listId NgramsTerms nls
a <- getNodeStory listId
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId
(initArchiveList { _a_state = Map.singleton NgramsTerms nls }))
a `shouldBe` (initArchiveList { _a_state = Map.singleton NgramsTerms nls })
-- `setListNgrams` calls saveNodeStory already so we should have
-- the terms in the DB by now
......@@ -178,7 +181,7 @@ insertNewTermsWithChildrenToNodeStoryTest env = do
insertNodeStoryChildrenWithDifferentNgramsTypeThanParentTest :: TestEnv -> Assertion
insertNodeStoryChildrenWithDifferentNgramsTypeThanParentTest env = do
flip runReaderT env $ runTestMonad $ do
(_userId, _corpusId, listId, v) <- commonInitialization
(_userId, _corpusId, listId, _a) <- commonInitialization
let (tParent, nreParent) = simpleParentTerm
let (tChild, nreChildGoodType) = simpleChildTerm
......@@ -190,10 +193,10 @@ insertNodeStoryChildrenWithDifferentNgramsTypeThanParentTest env = do
setListNgrams listId NgramsTerms nls
a <- getNodeStory listId
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId
(initArchiveList { _a_state = Map.singleton NgramsTerms nlsWithChildFixed }))
a `shouldBe` (initArchiveList { _a_state = Map.singleton NgramsTerms nlsWithChildFixed })
ngramsMap <- selectNgramsId terms
liftIO $ (snd <$> Map.toList ngramsMap) `shouldBe` terms
......@@ -216,16 +219,16 @@ insertNodeStoryChildrenWithDifferentNgramsTypeThanParentTest env = do
setListNgramsUpdatesNodeStoryTest :: TestEnv -> Assertion
setListNgramsUpdatesNodeStoryTest env = do
flip runReaderT env $ runTestMonad $ do
(_userId, _corpusId, listId, v) <- commonInitialization
(_userId, _corpusId, listId, _a) <- commonInitialization
let (terms, nre) = simpleTerm
let nls = Map.singleton terms nre
setListNgrams listId NgramsTerms nls
a <- getNodeStory listId
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId
(initArchiveList { _a_state = Map.singleton NgramsTerms nls }))
a `shouldBe` (initArchiveList { _a_state = Map.singleton NgramsTerms nls })
-- check that the ngrams are in the DB as well
ngramsMap <- selectNgramsId [unNgramsTerm terms]
liftIO $ (snd <$> Map.toList ngramsMap) `shouldBe` [unNgramsTerm terms]
......@@ -238,27 +241,27 @@ setListNgramsUpdatesNodeStoryTest env = do
let terms2 = "WORLD"
let nls2 = Map.singleton (NgramsTerm terms2) nre2
setListNgrams listId NgramsTerms nls2
a' <- getNodeStory listId
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId
(initArchiveList { _a_state = Map.singleton NgramsTerms $ nls <> nls2 }))
a' `shouldBe` (initArchiveList { _a_state = Map.singleton NgramsTerms $ nls <> nls2 })
setListNgramsUpdatesNodeStoryWithChildrenTest :: TestEnv -> Assertion
setListNgramsUpdatesNodeStoryWithChildrenTest env = do
flip runReaderT env $ runTestMonad $ do
(_userId, _corpusId, listId, v) <- commonInitialization
(_userId, _corpusId, listId, _a) <- commonInitialization
let (tChild, nreChild) = simpleChildTerm
let (tParent, nreParent) = simpleParentTerm
let nls = Map.fromList [(tParent, nreParent), (tChild, nreChild)]
setListNgrams listId NgramsTerms nls
a <- getNodeStory listId
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId
(initArchiveList { _a_state = Map.singleton NgramsTerms nls }))
a `shouldBe` (initArchiveList { _a_state = Map.singleton NgramsTerms nls })
-- OK, now we substitute parent with no children, the parent of
-- 'nreChild' should become Nothing
......@@ -270,22 +273,20 @@ setListNgramsUpdatesNodeStoryWithChildrenTest env = do
, _nre_root = Nothing }
let nlsNew = Map.fromList [(tParent, nreParentNew), (tChild, nreChildNew)]
a' <- getNodeStory listId
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId
(initArchiveList { _a_state = Map.singleton NgramsTerms nlsNew }))
a' `shouldBe` (initArchiveList { _a_state = Map.singleton NgramsTerms nlsNew })
commitPatchSimpleTest :: TestEnv -> Assertion
commitPatchSimpleTest env = do
flip runReaderT env $ runTestMonad $ do
(_userId, _corpusId, listId, v) <- commonInitialization
(_userId, _corpusId, listId, a) <- commonInitialization
-- initially, the node story table is empty
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId
(initArchiveList { _a_state = Map.empty }))
a `shouldBe` (initArchiveList { _a_state = Map.empty })
let (term, nre) = simpleTerm
let tPatch = NgramsReplace { _patch_old = Nothing
......@@ -298,9 +299,9 @@ commitPatchSimpleTest env = do
_patchApplied <- commitStatePatch listId patch
let nls = Map.fromList [(term, nre)]
a' <- getNodeStory listId
liftIO $ do
ns <- atomically $ readTVar v
ns `shouldBe` (NodeStory $ Map.singleton listId
(initArchiveList { _a_state = Map.singleton NgramsTerms nls
, _a_version = ver + 1 }))
a' `shouldBe` (initArchiveList { _a_state = Map.singleton NgramsTerms nls
, _a_version = ver + 1 })
test/Test/Database/Types.hs
View file @ b423c47b
......@@ -115,10 +115,6 @@ instance HasMail TestEnv where
instance HasNodeStoryEnv TestEnv where
hasNodeStory = to test_nodeStory
instance HasNodeStoryVar TestEnv where
hasNodeStoryVar = hasNodeStory . nse_getter
instance HasNodeStoryImmediateSaver TestEnv where
hasNodeStoryImmediateSaver = hasNodeStory . nse_saver_immediate
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment