]> Git — Sourcephile - gargantext.git/blob - src/Gargantext/Database/Prelude.hs
[node] fix pubmed JSON serialization
[gargantext.git] / src / Gargantext / Database / Prelude.hs
1 {-|
2 Module : Gargantext.Database.Prelude
3 Description : Specific Prelude for Database management
4 Copyright : (c) CNRS, 2017-Present
5 License : AGPL + CECILL v3
6 Maintainer : team@gargantext.org
7 Stability : experimental
8 Portability : POSIX
9
10 -}
11
12 {-# LANGUAGE Arrows #-}
13 {-# LANGUAGE ConstraintKinds, ScopedTypeVariables #-}
14 {-# LANGUAGE LambdaCase #-}
15
16 module Gargantext.Database.Prelude where
17
18 --import Control.Monad.Logger (MonadLogger)
19 import Control.Exception
20 import Control.Lens (Getter, view)
21 import Control.Monad.Except
22 import Control.Monad.Random
23 import Control.Monad.Reader
24 import Control.Monad.Trans.Control (MonadBaseControl)
25 import Data.Aeson (Result(Error,Success), fromJSON, FromJSON)
26 import Data.ByteString.Char8 (hPutStrLn)
27 import Data.Either.Extra (Either)
28 import Data.Pool (Pool, withResource)
29 import Data.Profunctor.Product.Default (Default)
30 import Data.Text (pack, unpack, Text)
31 import Data.Word (Word16)
32 import Database.PostgreSQL.Simple (Connection, connect)
33 import Database.PostgreSQL.Simple.FromField ( Conversion, ResultError(ConversionFailed), fromField, returnError)
34 import Database.PostgreSQL.Simple.Internal (Field)
35 import Database.PostgreSQL.Simple.Types (Query(..))
36 import Gargantext.Core.Mail.Types (HasMail)
37 import Gargantext.Core.NLP (HasNLPServer)
38 import Gargantext.Prelude
39 import Gargantext.Prelude.Config (GargConfig(), readIniFile', val)
40 import Opaleye (Unpackspec, showSql, FromFields, Select, runSelect, SqlJsonb, DefaultFromField, toFields, matchMaybe, MaybeFields)
41 import Opaleye.Aggregate (countRows)
42 import System.IO (FilePath, stderr)
43 import Text.Read (readMaybe)
44 import qualified Data.ByteString as DB
45 import qualified Data.List as DL
46 import qualified Database.PostgreSQL.Simple as PGS
47 import qualified Opaleye.Internal.Constant
48 import qualified Opaleye.Internal.Operators
49
50 -------------------------------------------------------
51 class HasConnectionPool env where
52 connPool :: Getter env (Pool Connection)
53
54 instance HasConnectionPool (Pool Connection) where
55 connPool = identity
56
57 class HasConfig env where
58 hasConfig :: Getter env GargConfig
59
60 instance HasConfig GargConfig where
61 hasConfig = identity
62
63 -------------------------------------------------------
64 type JSONB = DefaultFromField SqlJsonb
65 -------------------------------------------------------
66
67 type CmdM'' env err m =
68 ( MonadReader env m
69 , MonadError err m
70 , MonadBaseControl IO m
71 , MonadRandom m
72 --, MonadLogger m
73 )
74
75 type CmdM' env err m =
76 ( MonadReader env m
77 , MonadError err m
78 , MonadBaseControl IO m
79 --, MonadLogger m
80 -- , MonadRandom m
81 )
82
83 type CmdCommon env =
84 ( HasConnectionPool env
85 , HasConfig env
86 , HasMail env
87 , HasNLPServer env )
88
89 type CmdM env err m =
90 ( CmdM' env err m
91 , CmdCommon env
92 )
93
94 type CmdRandom env err m =
95 ( CmdM' env err m
96 , HasConnectionPool env
97 , HasConfig env
98 , MonadRandom m
99 , HasMail env
100 )
101
102 type Cmd'' env err a = forall m. CmdM'' env err m => m a
103 type Cmd' env err a = forall m. CmdM' env err m => m a
104 type Cmd err a = forall m env. CmdM env err m => m a
105 type CmdR err a = forall m env. CmdRandom env err m => m a
106
107
108
109 fromInt64ToInt :: Int64 -> Int
110 fromInt64ToInt = fromIntegral
111
112 -- TODO: ideally there should be very few calls to this functions.
113 mkCmd :: (Connection -> IO a) -> Cmd err a
114 mkCmd k = do
115 pool <- view connPool
116 withResource pool (liftBase . k)
117
118 runCmd :: (HasConnectionPool env)
119 => env
120 -> Cmd'' env err a
121 -> IO (Either err a)
122 runCmd env m = runExceptT $ runReaderT m env
123
124 runOpaQuery :: Default FromFields fields haskells
125 => Select fields
126 -> Cmd err [haskells]
127 runOpaQuery q = mkCmd $ \c -> runSelect c q
128
129 runCountOpaQuery :: Select a -> Cmd err Int
130 runCountOpaQuery q = do
131 counts <- mkCmd $ \c -> runSelect c $ countRows q
132 -- countRows is guaranteed to return a list with exactly one row so DL.head is safe here
133 pure $ fromInt64ToInt $ DL.head counts
134
135 formatPGSQuery :: PGS.ToRow a => PGS.Query -> a -> Cmd err DB.ByteString
136 formatPGSQuery q a = mkCmd $ \conn -> PGS.formatQuery conn q a
137
138 -- TODO use runPGSQueryDebug everywhere
139 runPGSQuery' :: (PGS.ToRow a, PGS.FromRow b) => PGS.Query -> a -> Cmd err [b]
140 runPGSQuery' q a = mkCmd $ \conn -> PGS.query conn q a
141
142 runPGSQuery :: ( CmdM env err m
143 , PGS.FromRow r, PGS.ToRow q
144 )
145 => PGS.Query -> q -> m [r]
146 runPGSQuery q a = mkCmd $ \conn -> catch (PGS.query conn q a) (printError conn)
147 where
148 printError c (SomeException e) = do
149 q' <- PGS.formatQuery c q a
150 hPutStrLn stderr q'
151 throw (SomeException e)
152
153 {-
154 -- TODO
155 runPGSQueryFold :: ( CmdM env err m
156 , PGS.FromRow r
157 )
158 => PGS.Query -> a -> (a -> r -> IO a) -> m a
159 runPGSQueryFold q initialState consume = mkCmd $ \conn -> catch (PGS.fold_ conn initialState consume) (printError conn)
160 where
161 printError c (SomeException e) = do
162 q' <- PGS.formatQuery c q
163 hPutStrLn stderr q'
164 throw (SomeException e)
165 -}
166
167
168
169 -- | TODO catch error
170 runPGSQuery_ :: ( CmdM env err m
171 , PGS.FromRow r
172 )
173 => PGS.Query -> m [r]
174 runPGSQuery_ q = mkCmd $ \conn -> catch (PGS.query_ conn q) printError
175 where
176 printError (SomeException e) = do
177 hPutStrLn stderr (fromQuery q)
178 throw (SomeException e)
179
180 execPGSQuery :: PGS.ToRow a => PGS.Query -> a -> Cmd err Int64
181 execPGSQuery q a = mkCmd $ \conn -> PGS.execute conn q a
182
183 ------------------------------------------------------------------------
184 databaseParameters :: FilePath -> IO PGS.ConnectInfo
185 databaseParameters fp = do
186 ini <- readIniFile' fp
187 let val' key = unpack $ val ini "database" key
188 let dbPortRaw = val' "DB_PORT"
189 let dbPort = case (readMaybe dbPortRaw :: Maybe Word16) of
190 Nothing -> panic $ "DB_PORT incorrect: " <> (pack dbPortRaw)
191 Just d -> d
192
193 pure $ PGS.ConnectInfo { PGS.connectHost = val' "DB_HOST"
194 , PGS.connectPort = dbPort
195 , PGS.connectUser = val' "DB_USER"
196 , PGS.connectPassword = val' "DB_PASS"
197 , PGS.connectDatabase = val' "DB_NAME"
198 }
199
200 connectGargandb :: FilePath -> IO Connection
201 connectGargandb fp = databaseParameters fp >>= \params -> connect params
202
203 fromField' :: (Typeable b, FromJSON b) => Field -> Maybe DB.ByteString -> Conversion b
204 fromField' field mb = do
205 v <- fromField field mb
206 valueToHyperdata v
207 where
208 valueToHyperdata v = case fromJSON v of
209 Success a -> pure a
210 Error _err -> returnError ConversionFailed field
211 $ DL.intercalate " " [ "cannot parse hyperdata for JSON: "
212 , show v
213 ]
214
215 printSqlOpa :: Default Unpackspec a a => Select a -> IO ()
216 printSqlOpa = putStrLn . maybe "Empty query" identity . showSql
217
218 dbCheck :: CmdM env err m => m Bool
219 dbCheck = do
220 r :: [PGS.Only Text] <- runPGSQuery_ "select username from public.auth_user"
221 case r of
222 [] -> return False
223 _ -> return True
224
225 restrictMaybe :: ( Default Opaleye.Internal.Operators.IfPP b b
226 , (Default Opaleye.Internal.Constant.ToFields Bool b))
227 => MaybeFields a -> (a -> b) -> b
228 restrictMaybe v cond = matchMaybe v $ \case
229 Nothing -> toFields True
230 Just v' -> cond v'