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haskell-gargantext
haskell-gargantext
Commit a43c33d0 authored by qlobbe's avatar qlobbe
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Merge branch 'dev-phylo' of https://gitlab.iscpif.fr/gargantext/haskell-gargantext into dev-phylo

parents c77a8b8d 8873a848
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    CHANGELOG.md
    View file @ a43c33d0
    ## Version 0.0.5.6.7
    * [BACK] fix limit with MAX_DOCS_SCRAPERS
    * [FEAT] Users Password Sugar function : in repl, runCmdReplEasy $ updateUsersPassword ["user@mail.com"]
    ## Version 0.0.5.6.6
    * [BACK] CSV List post and reindex after (for both CSV and JSON)
    ## Version 0.0.5.6.5
    * [BACK] HAL parser with Conduit
    ## Version 0.0.5.6.4
    * [FRONT] Forest Tooltip + Async progress bar fix
    ## Version 0.0.5.6.3
    * [BACK][EXPORT][GEXF] node size
    ......
    bin/gargantext-client/Auth.hs
    View file @ a43c33d0
    module Auth where
    import Prelude
    import Data.Maybe
    import Core
    import Options
    ......
    bin/gargantext-client/Core.hs
    View file @ a43c33d0
    module Core (problem, whenVerbose) where
    import Prelude
    import Options
    import Options.Generic
    ......
    bin/gargantext-client/Main.hs
    View file @ a43c33d0
    ......@@ -2,11 +2,11 @@ module Main where
    import Control.Monad
    import Network.HTTP.Client
    import Options.Generic
    import Servant.Client
    import Options
    import Options.Generic
    import Prelude
    import Script (script)
    import Servant.Client
    main :: IO ()
    main = do
    ......
    bin/gargantext-client/Options.hs
    View file @ a43c33d0
    {-# LANGUAGE TypeOperators #-}
    module Options where
    import Prelude
    import Options.Generic
    -- | Some general options to be specified on the command line.
    ......
    bin/gargantext-client/Script.hs
    View file @ a43c33d0
    module Script (script) where
    import Control.Monad.IO.Class
    import Gargantext.API.Client
    import Servant.Client
    import Auth
    import Control.Monad.IO.Class
    import Core
    import Gargantext.API.Client
    import Options
    import Prelude
    import Servant.Client
    import Tracking
    -- | An example script. Tweak, rebuild and re-run the executable to see the
    ......
    bin/gargantext-client/Tracking.hs
    View file @ a43c33d0
    ......@@ -8,6 +8,7 @@ module Tracking
    import Core
    import Options
    import Prelude
    import Control.Monad.IO.Class
    import Data.List (intersperse)
    ......
    bin/gargantext-import/Main.hs
    View file @ a43c33d0
    ......@@ -17,10 +17,11 @@ module Main where
    import Control.Exception (finally)
    import Data.Either
    import Data.Maybe (Maybe(..))
    import Data.Text (Text)
    import Prelude (read)
    import System.Environment (getArgs)
    import qualified Data.Text as Text
    import Text.Read (readMaybe)
    import Gargantext.API.Dev (withDevEnv, runCmdDev)
    import Gargantext.API.Admin.EnvTypes (DevEnv(..))
    ......@@ -46,11 +47,14 @@ main = do
    --tt = (Unsupervised EN 6 0 Nothing)
    tt = (Multi EN)
    format = CsvGargV3 -- CsvHal --WOS
    limit' = case (readMaybe limit :: Maybe Int) of
    Nothing -> panic $ "Cannot read limit: " <> (Text.pack limit)
    Just l -> l
    corpus :: forall m. FlowCmdM DevEnv GargError m => m CorpusId
    corpus = flowCorpusFile (UserName $ cs user) (Left (cs name :: Text)) (read limit :: Int) tt format corpusPath Nothing (\_ -> pure ())
    corpus = flowCorpusFile (UserName $ cs user) (Left (cs name :: Text)) limit' tt format corpusPath Nothing (\_ -> pure ())
    corpusCsvHal :: forall m. FlowCmdM DevEnv GargError m => m CorpusId
    corpusCsvHal = flowCorpusFile (UserName $ cs user) (Left (cs name :: Text)) (read limit :: Int) tt CsvHal corpusPath Nothing (\_ -> pure ())
    corpusCsvHal = flowCorpusFile (UserName $ cs user) (Left (cs name :: Text)) limit' tt CsvHal corpusPath Nothing (\_ -> pure ())
    annuaire :: forall m. FlowCmdM DevEnv GargError m => m CorpusId
    annuaire = flowAnnuaire (UserName $ cs user) (Left "Annuaire") (Multi EN) corpusPath (\_ -> pure ())
    ......
    devops/postgres/create
    View file @ a43c33d0
    ......@@ -16,16 +16,17 @@ HOST=$(getter "DB_HOST")
    PORT=$(getter "DB_PORT")
    #psql -c "CREATE USER \"${USER}\""
    #psql -c "ALTER USER \"${USER}\" with PASSWORD '${PW}'"
    psql -c "CREATE USER \"${USER}\""
    psql -c "ALTER USER \"${USER}\" with PASSWORD '${PW}'"
    psql -c "DROP DATABASE IF EXISTS \"${NAME}\""
    createdb "${NAME}"
    psql "${NAME}" < extensions.sql
    #psql "${NAME}" < schema.sql
    # if new
    #psql "${NAME}" < schema.sql
    #../../bin/psql ../../gargantext.ini < gargandb.dump
    psql ${NAME} < $2
    psql -c "ALTER DATABASE \"${NAME}\" OWNER to \"${USER}\""
    ......
    package.yaml
    View file @ a43c33d0
    name: gargantext
    version: '0.0.5.6.3'
    version: '0.0.5.6.7'
    synopsis: Search, map, share
    description: Please see README.md
    category: Data
    ......@@ -57,6 +57,7 @@ library:
    - Gargantext.API.Ngrams.Prelude
    - Gargantext.API.Admin.Settings
    - Gargantext.API.Admin.EnvTypes
    - Gargantext.API.Admin.Auth.Types
    - Gargantext.API.Admin.Types
    - Gargantext.API.Prelude
    - Gargantext.API.Client
    ......@@ -327,6 +328,42 @@ executables:
    - unordered-containers
    - full-text-search
    gargantext-client:
    main: Main.hs
    source-dirs: bin/gargantext-client
    ghc-options:
    - -Wall
    - -threaded
    - -rtsopts
    - -with-rtsopts=-N
    - -O2
    - -Wmissing-signatures
    default-extensions:
    - DataKinds
    - DeriveGeneric
    - FlexibleContexts
    - FlexibleInstances
    - GeneralizedNewtypeDeriving
    - MultiParamTypeClasses
    - NamedFieldPuns
    - NoImplicitPrelude
    - OverloadedStrings
    - RankNTypes
    - RecordWildCards
    dependencies:
    - base
    - extra
    - servant
    - text
    - optparse-generic
    - exceptions
    - servant-client
    - servant-auth-client
    - gargantext
    - ekg-json
    - http-client
    gargantext-phylo:
    main: Main.hs
    source-dirs: bin/gargantext-phylo
    ......
    src/Gargantext/API/Ngrams/List.hs
    View file @ a43c33d0
    ......@@ -20,16 +20,16 @@ import Data.Aeson
    import Data.Either (Either(..))
    import Data.HashMap.Strict (HashMap)
    import Data.Map (Map, toList)
    import Data.Maybe (catMaybes)
    import Data.Maybe (catMaybes, fromMaybe)
    import Data.Set (Set)
    import Data.Text (Text, concat, pack)
    import Data.Text (Text, concat, pack, splitOn)
    import Data.Vector (Vector)
    import Gargantext.API.Admin.Orchestrator.Types
    import Gargantext.API.Ngrams (setListNgrams)
    import Gargantext.API.Ngrams.List.Types
    import Gargantext.API.Ngrams.Prelude (getNgramsList)
    import Gargantext.API.Ngrams.Tools (getTermsWith)
    import Gargantext.API.Ngrams.Types
    import Gargantext.API.Ngrams.Prelude (getNgramsList)
    import Gargantext.API.Ngrams.List.Types
    import Gargantext.API.Prelude (GargServer)
    import Gargantext.Core.NodeStory
    import Gargantext.Core.Text.Terms (ExtractedNgrams(..))
    ......@@ -40,9 +40,11 @@ import Gargantext.Database.Action.Flow.Types (FlowCmdM)
    import Gargantext.Database.Action.Metrics.NgramsByContext (getOccByNgramsOnlyFast')
    import Gargantext.Database.Admin.Types.Hyperdata.Document
    import Gargantext.Database.Admin.Types.Node
    import Gargantext.Database.Query.Table.Node (getNode)
    import Gargantext.Database.Query.Table.NodeContext (selectDocNodes)
    import Gargantext.Database.Schema.Ngrams
    import Gargantext.Database.Schema.Context
    import Gargantext.Database.Schema.Ngrams
    import Gargantext.Database.Schema.Node (_node_parent_id)
    import Gargantext.Database.Types (Indexed(..))
    import Gargantext.Prelude
    import Network.HTTP.Media ((//), (/:))
    ......@@ -53,22 +55,12 @@ import qualified Data.Csv as Csv
    import qualified Data.HashMap.Strict as HashMap
    import qualified Data.List as List
    import qualified Data.Map as Map
    import qualified Data.Set as Set
    import qualified Data.Text as Text
    import qualified Data.Vector as Vec
    import qualified Prelude as Prelude
    import qualified Protolude as P
    ------------------------------------------------------------------------
    -- | TODO refactor
    {-
    type API = Get '[JSON, HTML] (Headers '[Header "Content-Disposition" Text] NgramsList)
    -- :<|> ReqBody '[JSON] NgramsList :> Post '[JSON] Bool
    :<|> PostAPI
    :<|> CSVPostAPI
    api :: ListId -> GargServer API
    api l = get l :<|> postAsync l :<|> csvPostAsync l
    -}
    ----------------------
    type GETAPI = Summary "Get List"
    :> "lists"
    :> Capture "listId" ListId
    ......@@ -122,11 +114,11 @@ get lId = do
    ------------------------------------------------------------------------
    -- TODO : purge list
    -- TODO talk
    post :: FlowCmdM env err m
    setList :: FlowCmdM env err m
    => ListId
    -> NgramsList
    -> m Bool
    post l m = do
    setList l m = do
    -- TODO check with Version for optim
    printDebug "New list as file" l
    _ <- mapM (\(nt, Versioned _v ns) -> setListNgrams l nt ns) $ toList m
    ......@@ -150,12 +142,12 @@ reIndexWith cId lId nt lts = do
    <$> HashMap.toList
    <$> getTermsWith identity [lId] nt lts
    printDebug "ts" ts
    -- printDebug "ts" ts
    -- Taking the ngrams with 0 occurrences only (orphans)
    occs <- getOccByNgramsOnlyFast' cId lId nt ts
    printDebug "occs" occs
    -- printDebug "occs" occs
    let orphans = List.concat
    $ map (\t -> case HashMap.lookup t occs of
    ......@@ -163,11 +155,11 @@ reIndexWith cId lId nt lts = do
    Just n -> if n <= 1 then [t] else [ ]
    ) ts
    printDebug "orphans" orphans
    -- printDebug "orphans" orphans
    -- Get all documents of the corpus
    docs <- selectDocNodes cId
    printDebug "docs length" (List.length docs)
    -- printDebug "docs length" (List.length docs)
    -- Checking Text documents where orphans match
    -- TODO Tests here
    ......@@ -184,7 +176,7 @@ reIndexWith cId lId nt lts = do
    (List.cycle [Map.fromList $ [(nt, Map.singleton (doc ^. context_id) 1 )]])
    ) docs
    printDebug "ngramsByDoc" ngramsByDoc
    -- printDebug "ngramsByDoc" ngramsByDoc
    -- Saving the indexation in database
    _ <- mapM (saveDocNgramsWith lId) ngramsByDoc
    ......@@ -210,7 +202,7 @@ postAsync lId =
    JobFunction (\f log' ->
    let
    log'' x = do
    printDebug "postAsync ListId" x
    -- printDebug "postAsync ListId" x
    liftBase $ log' x
    in postAsync' lId f log'')
    ......@@ -223,20 +215,32 @@ postAsync' l (WithFile _ m _) logStatus = do
    logStatus JobLog { _scst_succeeded = Just 0
    , _scst_failed = Just 0
    , _scst_remaining = Just 1
    , _scst_remaining = Just 2
    , _scst_events = Just []
    }
    printDebug "New list as file" l
    _ <- post l m
    _ <- setList l m
    -- printDebug "Done" r
    pure JobLog { _scst_succeeded = Just 1
    logStatus JobLog { _scst_succeeded = Just 1
    , _scst_failed = Just 0
    , _scst_remaining = Just 1
    , _scst_events = Just []
    }
    corpus_node <- getNode l -- (Proxy :: Proxy HyperdataList)
    let corpus_id = fromMaybe (panic "") (_node_parent_id corpus_node)
    _ <- reIndexWith corpus_id l NgramsTerms (Set.fromList [MapTerm, CandidateTerm])
    pure JobLog { _scst_succeeded = Just 2
    , _scst_failed = Just 0
    , _scst_remaining = Just 0
    , _scst_events = Just []
    }
    ------------------------------------------------------------------------
    ------------------------------------------------------------------------
    type CSVPostAPI = Summary "Update List (legacy v3 CSV)"
    :> "csv"
    :> "add"
    ......@@ -257,12 +261,22 @@ readCsvText t = case eDec of
    parseCsvData :: [(Text, Text, Text)] -> Map NgramsTerm NgramsRepoElement
    parseCsvData lst = Map.fromList $ conv <$> lst
    where
    conv (_status, label, _forms) =
    conv (status, label, forms) =
    (NgramsTerm label, NgramsRepoElement { _nre_size = 1
    , _nre_list = CandidateTerm
    , _nre_list = case status == "map" of
    True -> MapTerm
    False -> case status == "main" of
    True -> CandidateTerm
    False -> StopTerm
    , _nre_root = Nothing
    , _nre_parent = Nothing
    , _nre_children = MSet Map.empty })
    , _nre_children = MSet
    $ Map.fromList
    $ map (\form -> (NgramsTerm form, ()))
    $ filter (/= "")
    $ splitOn "|&|" forms
    }
    )
    csvPost :: FlowCmdM env err m
    => ListId
    ......@@ -277,11 +291,14 @@ csvPost l m = do
    --printDebug "[csvPost] lst" lst
    printDebug "[csvPost] p" p
    _ <- setListNgrams l NgramsTerms p
    pure True
    ------------------------------------------------------------------------
    printDebug "ReIndexing List" l
    corpus_node <- getNode l -- (Proxy :: Proxy HyperdataList)
    let corpus_id = fromMaybe (panic "") (_node_parent_id corpus_node)
    _ <- reIndexWith corpus_id l NgramsTerms (Set.fromList [MapTerm, CandidateTerm])
    pure True
    ------------------------------------------------------------------------
    csvPostAsync :: GargServer CSVAPI
    csvPostAsync lId =
    serveJobsAPI $
    ......
    src/Gargantext/API/Node/Contact.hs
    View file @ a43c33d0
    ......@@ -22,6 +22,7 @@ Portability : POSIX
    module Gargantext.API.Node.Contact
    where
    import Conduit
    import Data.Aeson
    import Data.Either (Either(Right))
    import Data.Maybe (Maybe(..))
    ......@@ -93,7 +94,7 @@ addContact u nId (AddContactParams fn ln) logStatus = do
    , _scst_remaining = Just 1
    , _scst_events = Just []
    }
    _ <- flow (Nothing :: Maybe HyperdataAnnuaire) u (Right [nId]) (Multi EN) Nothing [[hyperdataContact fn ln]] logStatus
    _ <- flow (Nothing :: Maybe HyperdataAnnuaire) u (Right [nId]) (Multi EN) Nothing (Just 1, yield $ hyperdataContact fn ln) logStatus
    pure JobLog { _scst_succeeded = Just 2
    , _scst_failed = Just 0
    ......
    src/Gargantext/API/Node/Corpus/New.hs
    View file @ a43c33d0
    ......@@ -18,6 +18,8 @@ New corpus means either:
    module Gargantext.API.Node.Corpus.New
    where
    import Conduit
    import Control.Lens hiding (elements, Empty)
    import Data.Aeson
    import Data.Aeson.TH (deriveJSON)
    ......@@ -39,7 +41,7 @@ import Gargantext.Prelude
    import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs, ScraperEvent(..), scst_events)
    import Gargantext.API.Admin.Types (HasSettings)
    import Gargantext.API.Job (jobLogSuccess, jobLogFailTotal, jobLogFailTotalWithMessage)
    import Gargantext.API.Job (addEvent, jobLogSuccess, jobLogFailTotal, jobLogFailTotalWithMessage)
    import Gargantext.API.Node.Corpus.New.File
    import Gargantext.API.Node.Corpus.Searx
    import Gargantext.API.Node.Corpus.Types
    ......@@ -213,15 +215,20 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
    -- TODO if cid is folder -> create Corpus
    -- if cid is corpus -> add to corpus
    -- if cid is root -> create corpus in Private
    txts <- mapM (\db -> getDataText db (Multi l) q maybeLimit) [database2origin dbs]
    logStatus JobLog { _scst_succeeded = Just 2
    eTxts <- mapM (\db -> getDataText db (Multi l) q maybeLimit) [database2origin dbs]
    let lTxts = lefts eTxts
    case lTxts of
    [] -> do
    let txts = rights eTxts
    -- TODO Sum lenghts of each txt elements
    logStatus $ JobLog { _scst_succeeded = Just 2
    , _scst_failed = Just 0
    , _scst_remaining = Just $ 1 + length txts
    , _scst_events = Just []
    }
    cids <- mapM (\txt -> flowDataText user txt (Multi l) cid Nothing logStatus) txts
    cids <- mapM (\txt -> do
    flowDataText user txt (Multi l) cid Nothing logStatus) txts
    printDebug "corpus id" cids
    printDebug "sending email" ("xxxxxxxxxxxxxxxxxxxxx" :: Text)
    sendMail user
    ......@@ -232,6 +239,14 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
    , _scst_events = Just []
    }
    (err:_) -> do
    pure $ addEvent "ERROR" (T.pack $ show err) $
    JobLog { _scst_succeeded = Just 2
    , _scst_failed = Just 1
    , _scst_remaining = Just 0
    , _scst_events = Just []
    }
    type AddWithForm = Summary "Add with FormUrlEncoded to corpus endpoint"
    :> "corpus"
    ......@@ -268,15 +283,16 @@ addToCorpusWithForm user cid (NewWithForm ft d l _n) logStatus jobLog = do
    _ -> cs d
    eDocs <- liftBase $ parse data'
    case eDocs of
    Right docs' -> do
    Right docs -> do
    -- TODO Add progress (jobStatus) update for docs - this is a
    -- long action
    limit' <- view $ hasConfig . gc_max_docs_parsers
    let limit = fromIntegral limit'
    if length docs' > limit then do
    printDebug "[addToCorpusWithForm] number of docs exceeds the limit" (show $ length docs')
    if length docs > limit then do
    printDebug "[addToCorpusWithForm] number of docs exceeds the limit" (show $ length docs)
    let panicMsg' = [ "[addToCorpusWithForm] number of docs ("
    , show $ length docs'
    , show $ length docs
    , ") exceeds the MAX_DOCS_PARSERS limit ("
    , show limit
    , ")" ]
    ......@@ -285,7 +301,6 @@ addToCorpusWithForm user cid (NewWithForm ft d l _n) logStatus jobLog = do
    panic panicMsg
    else
    pure ()
    let docs = splitEvery 500 $ take limit docs'
    printDebug "Parsing corpus finished : " cid
    logStatus jobLog2
    ......@@ -296,7 +311,8 @@ addToCorpusWithForm user cid (NewWithForm ft d l _n) logStatus jobLog = do
    (Right [cid])
    (Multi $ fromMaybe EN l)
    Nothing
    (map (map toHyperdataDocument) docs)
    (Just $ fromIntegral $ length docs, yieldMany docs .| mapC toHyperdataDocument)
    --(map (map toHyperdataDocument) docs)
    logStatus
    printDebug "Extraction finished : " cid
    ......
    src/Gargantext/API/Node/DocumentUpload.hs
    View file @ a43c33d0
    ......@@ -69,21 +69,32 @@ api :: UserId -> NodeId -> GargServer API
    api uId nId =
    serveJobsAPI $
    JobFunction (\q log' -> do
    documentUpload uId nId q (liftBase . log')
    documentUploadAsync uId nId q (liftBase . log')
    )
    documentUpload :: (FlowCmdM env err m)
    documentUploadAsync :: (FlowCmdM env err m)
    => UserId
    -> NodeId
    -> DocumentUpload
    -> (JobLog -> m ())
    -> m JobLog
    documentUpload _uId nId doc logStatus = do
    documentUploadAsync _uId nId doc logStatus = do
    let jl = JobLog { _scst_succeeded = Just 0
    , _scst_failed = Just 0
    , _scst_remaining = Just 1
    , _scst_events = Just [] }
    logStatus jl
    docIds <- documentUpload nId doc
    printDebug "documentUploadAsync" docIds
    pure $ jobLogSuccess jl
    documentUpload :: (FlowCmdM env err m)
    => NodeId
    -> DocumentUpload
    -> m [DocId]
    documentUpload nId doc = do
    mcId <- getClosestParentIdByType' nId NodeCorpus
    let cId = case mcId of
    Just c -> c
    ......@@ -116,5 +127,6 @@ documentUpload _uId nId doc logStatus = do
    docIds <- insertMasterDocs (Nothing :: Maybe HyperdataCorpus) (Multi EN) [hd]
    _ <- Doc.add cId docIds
    pure docIds
    pure $ jobLogSuccess jl
    src/Gargantext/API/Node/DocumentsFromWriteNodes.hs
    View file @ a43c33d0
    ......@@ -16,6 +16,7 @@ Portability : POSIX
    module Gargantext.API.Node.DocumentsFromWriteNodes
    where
    import Conduit
    import Control.Lens ((^.))
    import Data.Aeson
    import Data.Either (Either(..), rights)
    ......@@ -100,7 +101,7 @@ documentsFromWriteNodes uId nId _p logStatus = do
    let parsedE = (\(node, contents) -> hyperdataDocumentFromFrameWrite (node ^. node_hyperdata, contents)) <$> frameWritesWithContents
    let parsed = rights parsedE
    _ <- flowDataText (RootId (NodeId uId)) (DataNew [parsed]) (Multi EN) cId Nothing logStatus
    _ <- flowDataText (RootId (NodeId uId)) (DataNew (Just $ fromIntegral $ length parsed, yieldMany parsed)) (Multi EN) cId Nothing logStatus
    pure $ jobLogSuccess jobLog
    ------------------------------------------------------------------------
    ......
    src/Gargantext/API/Node/Update.hs
    View file @ a43c33d0
    ......@@ -36,7 +36,8 @@ import Gargantext.Database.Action.Flow.Types (FlowCmdM)
    import Gargantext.Database.Action.Metrics (updateNgramsOccurrences, updateContextScore)
    import Gargantext.Database.Admin.Types.Hyperdata
    import Gargantext.Database.Admin.Types.Node
    import Gargantext.Database.Query.Table.Node (defaultList, getNode, insertNodes, node)
    import Gargantext.Database.Query.Table.Node (defaultList, getNode)
    import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateHyperdata)
    import Gargantext.Database.Schema.Ngrams (NgramsType(NgramsTerms))
    import Gargantext.Database.Schema.Node (node_parent_id)
    import Gargantext.Prelude (Bool(..), Ord, Eq, (<$>), ($), liftBase, (.), printDebug, pure, show, cs, (<>), panic, (<*>))
    ......@@ -191,7 +192,7 @@ updateNode _uId lId (UpdateNodeParamsList _mode) logStatus = do
    , _scst_events = Just []
    }
    updateNode userId phyloId (UpdateNodePhylo config) logStatus = do
    updateNode _userId phyloId (UpdateNodePhylo config) logStatus = do
    logStatus JobLog { _scst_succeeded = Just 1
    , _scst_failed = Just 0
    , _scst_remaining = Just 2
    ......@@ -210,7 +211,7 @@ updateNode userId phyloId (UpdateNodePhylo config) logStatus = do
    , _scst_events = Just []
    }
    _phyloId <- insertNodes [node NodePhylo "Phylo" (HyperdataPhylo Nothing (Just phy)) (Just corpusId) userId]
    _ <- updateHyperdata phyloId (HyperdataPhylo Nothing (Just phy))
    pure JobLog { _scst_succeeded = Just 3
    , _scst_failed = Just 0
    ......
    src/Gargantext/Core/Text/Corpus/API.hs
    View file @ a43c33d0
    ......@@ -18,6 +18,8 @@ module Gargantext.Core.Text.Corpus.API
    )
    where
    import Conduit
    import Data.Either (Either(..))
    import Data.Maybe
    import Gargantext.API.Admin.Orchestrator.Types (ExternalAPIs(..), externalAPIs)
    import Gargantext.Core (Lang(..))
    ......@@ -27,21 +29,25 @@ import qualified Gargantext.Core.Text.Corpus.API.Hal as HAL
    import qualified Gargantext.Core.Text.Corpus.API.Isidore as ISIDORE
    import qualified Gargantext.Core.Text.Corpus.API.Istex as ISTEX
    import qualified Gargantext.Core.Text.Corpus.API.Pubmed as PUBMED
    -- | TODO put in gargantext.init
    default_limit :: Maybe Integer
    default_limit = Just 10000
    import Servant.Client (ClientError)
    -- | Get External API metadata main function
    get :: ExternalAPIs
    -> Lang
    -> Query
    -> Maybe Limit
    -> IO [HyperdataDocument]
    get PubMed _la q _l = PUBMED.get q default_limit -- EN only by default
    get HAL la q _l = HAL.get la q default_limit
    get IsTex la q _l = ISTEX.get la q default_limit
    get Isidore la q _l = ISIDORE.get la (fromIntegral <$> default_limit) (Just q) Nothing
    -- -> IO [HyperdataDocument]
    -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
    get PubMed _la q limit = PUBMED.get q limit
    --docs <- PUBMED.get q default_limit -- EN only by default
    --pure (Just $ fromIntegral $ length docs, yieldMany docs)
    get HAL la q limit = HAL.getC la q limit
    get IsTex la q limit = do
    docs <- ISTEX.get la q limit
    pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
    get Isidore la q limit = do
    docs <- ISIDORE.get la (fromIntegral <$> limit) (Just q) Nothing
    pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
    get _ _ _ _ = undefined
    -- | Some Sugar for the documentation
    ......
    src/Gargantext/Core/Text/Corpus/API/Hal.hs
    View file @ a43c33d0
    ......@@ -12,8 +12,11 @@ Portability : POSIX
    module Gargantext.Core.Text.Corpus.API.Hal
    where
    import Conduit
    import Data.Either
    import Data.Maybe
    import Data.Text (Text, pack, intercalate)
    import Servant.Client (ClientError)
    import Gargantext.Core (Lang(..))
    import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
    ......@@ -25,8 +28,16 @@ import qualified HAL.Doc.Corpus as HAL
    get :: Lang -> Text -> Maybe Integer -> IO [HyperdataDocument]
    get la q ml = do
    docs <- HAL.getMetadataWith q (Just 0) (fromIntegral <$> ml)
    either (panic . pack . show) (\d -> mapM (toDoc' la) $ HAL._docs d) docs
    eDocs <- HAL.getMetadataWith q (Just 0) ml
    either (panic . pack . show) (\d -> mapM (toDoc' la) $ HAL._docs d) eDocs
    getC :: Lang -> Text -> Maybe Integer -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
    getC la q ml = do
    eRes <- HAL.getMetadataWithC q (Just 0) ml
    pure $ (\(len, docsC) -> (len, docsC .| mapMC (toDoc' la))) <$> eRes
    -- case eRes of
    -- Left err -> panic $ pack $ show err
    -- Right (len, docsC) -> pure (len, docsC .| mapMC (toDoc' la))
    toDoc' :: Lang -> HAL.Corpus -> IO HyperdataDocument
    toDoc' la (HAL.Corpus i t ab d s aus affs struct_id) = do
    ......
    src/Gargantext/Core/Text/Corpus/API/Pubmed.hs
    View file @ a43c33d0
    ......@@ -13,9 +13,12 @@ Portability : POSIX
    module Gargantext.Core.Text.Corpus.API.Pubmed
    where
    import Conduit
    import Data.Either (Either)
    import Data.Maybe
    import Data.Text (Text)
    import qualified Data.Text as Text
    import Servant.Client (ClientError)
    import Gargantext.Prelude
    import Gargantext.Core (Lang(..))
    ......@@ -31,17 +34,21 @@ type Limit = PubMed.Limit
    -- | TODO put default pubmed query in gargantext.ini
    -- by default: 10K docs
    get :: Query -> Maybe Limit -> IO [HyperdataDocument]
    get q l = either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN))
    <$> PubMed.getMetadataWith q l
    get :: Query -> Maybe Limit -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
    get q l = do
    eRes <- PubMed.getMetadataWithC q l
    pure $ (\(len, docsC) -> (len, docsC .| mapC (toDoc EN))) <$> eRes
    --either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN))
    -- <$> PubMed.getMetadataWithC q l
    toDoc :: Lang -> PubMedDoc.PubMed -> HyperdataDocument
    toDoc l (PubMedDoc.PubMed (PubMedDoc.PubMedArticle t j as aus)
    (PubMedDoc.PubMedDate a y m d)
    toDoc l (PubMedDoc.PubMed { pubmed_id
    , pubmed_article = PubMedDoc.PubMedArticle t j as aus
    , pubmed_date = PubMedDoc.PubMedDate a y m d }
    ) = HyperdataDocument { _hd_bdd = Just "PubMed"
    , _hd_doi = Nothing
    , _hd_url = Nothing
    , _hd_uniqId = Nothing
    , _hd_uniqId = Just $ Text.pack $ show pubmed_id
    , _hd_uniqIdBdd = Nothing
    , _hd_page = Nothing
    , _hd_title = t
    ......
    src/Gargantext/Core/Types/Main.hs
    View file @ a43c33d0
    ......@@ -34,7 +34,7 @@ import Gargantext.Prelude
    import Servant.API (FromHttpApiData(..), ToHttpApiData(..))
    import Test.QuickCheck (elements)
    import Test.QuickCheck.Arbitrary (Arbitrary, arbitrary)
    import Text.Read (read)
    import Text.Read (readMaybe)
    type CorpusName = Text
    ------------------------------------------------------------------------
    ......@@ -74,7 +74,11 @@ instance Semigroup ListType
    instance FromHttpApiData ListType where
    parseUrlPiece = Right . read . unpack
    parseUrlPiece s = Right s'
    where
    s' = case (readMaybe $ unpack s) of
    Nothing -> panic $ "Cannot read url piece: " <> s
    Just s'' -> s''
    instance ToHttpApiData ListType where
    toUrlPiece = pack . show
    ......
    src/Gargantext/Core/Viz/Phylo.hs
    View file @ a43c33d0
    ......@@ -203,23 +203,23 @@ data PhyloConfig =
    ------------------------------------------------------------------------
    data PhyloSubConfig =
    PhyloSubConfig { _sc_phyloProximity :: Proximity
    , _sc_phyloSynchrony :: Synchrony
    , _sc_phyloQuality :: Quality
    PhyloSubConfig { _sc_phyloProximity :: Double
    , _sc_phyloSynchrony :: Double
    , _sc_phyloQuality :: Double
    , _sc_timeUnit :: TimeUnit
    , _sc_clique :: Clique
    , _sc_exportFilter :: [Filter]
    , _sc_exportFilter :: Double
    }
    deriving (Show,Generic,Eq)
    subConfig2config :: PhyloSubConfig -> PhyloConfig
    subConfig2config subConfig = defaultConfig { phyloProximity = _sc_phyloProximity subConfig
    , phyloSynchrony = _sc_phyloSynchrony subConfig
    , phyloQuality = _sc_phyloQuality subConfig
    subConfig2config subConfig = defaultConfig { phyloProximity = WeightedLogJaccard $ _sc_phyloProximity subConfig
    , phyloSynchrony = ByProximityThreshold (_sc_phyloSynchrony subConfig) 0 AllBranches MergeAllGroups
    , phyloQuality = Quality (_sc_phyloQuality subConfig) 1
    , timeUnit = _sc_timeUnit subConfig
    , clique = _sc_clique subConfig
    , exportFilter = _sc_exportFilter subConfig
    , exportFilter = [ByBranchSize $ _sc_exportFilter subConfig]
    }
    ------------------------------------------------------------------------
    ......
    src/Gargantext/Core/Viz/Phylo/API.hs
    View file @ a43c33d0
    ......@@ -30,7 +30,8 @@ import Gargantext.Core.Viz.Phylo.Example (phyloExample)
    import Gargantext.Core.Viz.Phylo.Legacy.LegacyMain
    import Gargantext.Database.Admin.Types.Hyperdata
    import Gargantext.Database.Admin.Types.Node -- (PhyloId, ListId, CorpusId, UserId, NodeId(..))
    import Gargantext.Database.Query.Table.Node (insertNodes, node)
    import Gargantext.Database.Query.Table.Node (getClosestParentIdByType)
    import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateHyperdata)
    import Gargantext.Prelude
    import Network.HTTP.Media ((//), (/:))
    import Servant
    ......@@ -90,7 +91,10 @@ type GetPhylo = QueryParam "listId" ListId
    -- Fix Filter parameters
    -- TODO fix parameters to default config that should be in Node
    getPhylo :: PhyloId -> GargServer GetPhylo
    getPhylo phyloId _lId _level _minSizeBranch = getPhyloDataJson phyloId
    getPhylo phyloId _lId _level _minSizeBranch = do
    theData <- getPhyloDataJson phyloId
    -- printDebug "getPhylo" theData
    pure theData
    getPhyloDataJson :: PhyloId -> GargNoServer Value
    getPhyloDataJson phyloId = do
    ......@@ -118,17 +122,19 @@ type PostPhylo = QueryParam "listId" ListId
    -- :> ReqBody '[JSON] PhyloQueryBuild
    :> (Post '[JSON] NodeId)
    postPhylo :: CorpusId -> UserId -> GargServer PostPhylo
    postPhylo corpusId userId _lId = do
    postPhylo :: PhyloId -> UserId -> GargServer PostPhylo
    postPhylo phyloId _userId _lId = do
    -- TODO get Reader settings
    -- s <- ask
    -- let
    -- _vrs = Just ("1" :: Text)
    -- _sft = Just (Software "Gargantext" "4")
    -- _prm = initPhyloParam vrs sft (Just q)
    phy <- flowPhyloAPI defaultConfig corpusId -- params
    phyloId <- insertNodes [node NodePhylo "Phylo" (HyperdataPhylo Nothing (Just phy)) (Just corpusId) userId]
    pure $ NodeId (fromIntegral phyloId)
    corpusId <- getClosestParentIdByType phyloId NodeCorpus
    phy <- flowPhyloAPI defaultConfig (fromMaybe (panic "[G.C.V.P.API] no corpus ID found") corpusId) -- params
    -- phyloId <- insertNodes [node NodePhylo "Phylo" (HyperdataPhylo Nothing (Just phy)) (Just corpusId) userId]
    _ <- updateHyperdata phyloId (HyperdataPhylo Nothing (Just phy))
    pure phyloId
    ------------------------------------------------------------------------
    -- | DELETE Phylo == delete a node
    ......
    src/Gargantext/Core/Viz/Phylo/API/Tools.hs
    View file @ a43c33d0
    ......@@ -9,7 +9,6 @@ Portability : POSIX
    -}
    module Gargantext.Core.Viz.Phylo.API.Tools
    where
    ......
    src/Gargantext/Core/Viz/Phylo/PhyloExport.hs
    View file @ a43c33d0
    ......@@ -209,6 +209,7 @@ exportToDot phylo export =
    graphAttrs ( [ Label (toDotLabel $ (phyloName $ getConfig phylo))]
    <> [ FontSize 30, LabelLoc VTop, NodeSep 1, RankSep [1], Rank SameRank, Splines SplineEdges, Overlap ScaleOverlaps
    , Ratio FillRatio
    -- , Ratio AutoRatio
    , Style [SItem Filled []],Color [toWColor White]]
    {-- home made attributes -}
    <> [(toAttr (fromStrict "phyloFoundations") $ pack $ show (length $ Vector.toList $ getRoots phylo))
    ......
    src/Gargantext/Database/Action/Flow.hs
    View file @ a43c33d0
    ......@@ -46,8 +46,10 @@ module Gargantext.Database.Action.Flow -- (flowDatabase, ngrams2list)
    )
    where
    import Conduit
    import Control.Lens ((^.), view, _Just, makeLenses)
    import Data.Aeson.TH (deriveJSON)
    import Data.Conduit.Internal (zipSources)
    import Data.Either
    import Data.HashMap.Strict (HashMap)
    import Data.Hashable (Hashable)
    ......@@ -60,6 +62,7 @@ import qualified Data.Text as T
    import Data.Traversable (traverse)
    import Data.Tuple.Extra (first, second)
    import GHC.Generics (Generic)
    import Servant.Client (ClientError)
    import System.FilePath (FilePath)
    import qualified Data.HashMap.Strict as HashMap
    import qualified Gargantext.Data.HashMap.Strict.Utils as HashMap
    ......@@ -103,6 +106,7 @@ import Gargantext.Prelude
    import Gargantext.Prelude.Crypto.Hash (Hash)
    import qualified Gargantext.Core.Text.Corpus.API as API
    import qualified Gargantext.Database.Query.Table.Node.Document.Add as Doc (add)
    import qualified Prelude as Prelude
    ------------------------------------------------------------------------
    -- Imports for upgrade function
    ......@@ -127,7 +131,8 @@ allDataOrigins = map InternalOrigin API.externalAPIs
    ---------------
    data DataText = DataOld ![NodeId]
    | DataNew ![[HyperdataDocument]]
    | DataNew !(Maybe Integer, ConduitT () HyperdataDocument IO ())
    -- | DataNew ![[HyperdataDocument]]
    -- TODO use the split parameter in config file
    getDataText :: FlowCmdM env err m
    ......@@ -135,10 +140,10 @@ getDataText :: FlowCmdM env err m
    -> TermType Lang
    -> API.Query
    -> Maybe API.Limit
    -> m DataText
    getDataText (ExternalOrigin api) la q li = liftBase $ DataNew
    <$> splitEvery 500
    <$> API.get api (_tt_lang la) q li
    -> m (Either ClientError DataText)
    getDataText (ExternalOrigin api) la q li = liftBase $ do
    eRes <- API.get api (_tt_lang la) q li
    pure $ DataNew <$> eRes
    getDataText (InternalOrigin _) _la q _li = do
    (_masterUserId, _masterRootId, cId) <- getOrMk_RootWithCorpus
    ......@@ -146,10 +151,11 @@ getDataText (InternalOrigin _) _la q _li = do
    (Left "")
    (Nothing :: Maybe HyperdataCorpus)
    ids <- map fst <$> searchDocInDatabase cId (stemIt q)
    pure $ DataOld ids
    pure $ Right $ DataOld ids
    -------------------------------------------------------------------------------
    flowDataText :: ( FlowCmdM env err m
    flowDataText :: forall env err m.
    ( FlowCmdM env err m
    )
    => User
    -> DataText
    ......@@ -161,7 +167,8 @@ flowDataText :: ( FlowCmdM env err m
    flowDataText u (DataOld ids) tt cid mfslw _ = flowCorpusUser (_tt_lang tt) u (Right [cid]) corpusType ids mfslw
    where
    corpusType = (Nothing :: Maybe HyperdataCorpus)
    flowDataText u (DataNew txt) tt cid mfslw logStatus = flowCorpus u (Right [cid]) tt mfslw txt logStatus
    flowDataText u (DataNew (mLen, txtC)) tt cid mfslw logStatus =
    flowCorpus u (Right [cid]) tt mfslw (mLen, (transPipe liftBase txtC)) logStatus
    ------------------------------------------------------------------------
    -- TODO use proxy
    ......@@ -173,8 +180,9 @@ flowAnnuaire :: (FlowCmdM env err m)
    -> (JobLog -> m ())
    -> m AnnuaireId
    flowAnnuaire u n l filePath logStatus = do
    docs <- liftBase $ (( splitEvery 500 <$> readFile_Annuaire filePath) :: IO [[HyperdataContact]])
    flow (Nothing :: Maybe HyperdataAnnuaire) u n l Nothing docs logStatus
    -- TODO Conduit for file
    docs <- liftBase $ ((readFile_Annuaire filePath) :: IO [HyperdataContact])
    flow (Nothing :: Maybe HyperdataAnnuaire) u n l Nothing (Just $ fromIntegral $ length docs, yieldMany docs) logStatus
    ------------------------------------------------------------------------
    flowCorpusFile :: (FlowCmdM env err m)
    ......@@ -185,12 +193,13 @@ flowCorpusFile :: (FlowCmdM env err m)
    -> Maybe FlowSocialListWith
    -> (JobLog -> m ())
    -> m CorpusId
    flowCorpusFile u n l la ff fp mfslw logStatus = do
    flowCorpusFile u n _l la ff fp mfslw logStatus = do
    eParsed <- liftBase $ parseFile ff fp
    case eParsed of
    Right parsed -> do
    let docs = splitEvery 500 $ take l parsed
    flowCorpus u n la mfslw (map (map toHyperdataDocument) docs) logStatus
    flowCorpus u n la mfslw (Just $ fromIntegral $ length parsed, yieldMany parsed .| mapC toHyperdataDocument) logStatus
    --let docs = splitEvery 500 $ take l parsed
    --flowCorpus u n la mfslw (yieldMany $ map (map toHyperdataDocument) docs) logStatus
    Left e -> panic $ "Error: " <> (T.pack e)
    ------------------------------------------------------------------------
    ......@@ -201,13 +210,14 @@ flowCorpus :: (FlowCmdM env err m, FlowCorpus a)
    -> Either CorpusName [CorpusId]
    -> TermType Lang
    -> Maybe FlowSocialListWith
    -> [[a]]
    -> (Maybe Integer, ConduitT () a m ())
    -> (JobLog -> m ())
    -> m CorpusId
    flowCorpus = flow (Nothing :: Maybe HyperdataCorpus)
    flow :: ( FlowCmdM env err m
    flow :: forall env err m a c.
    ( FlowCmdM env err m
    , FlowCorpus a
    , MkCorpus c
    )
    ......@@ -216,22 +226,39 @@ flow :: ( FlowCmdM env err m
    -> Either CorpusName [CorpusId]
    -> TermType Lang
    -> Maybe FlowSocialListWith
    -> [[a]]
    -> (Maybe Integer, ConduitT () a m ())
    -> (JobLog -> m ())
    -> m CorpusId
    flow c u cn la mfslw docs logStatus = do
    flow c u cn la mfslw (mLength, docsC) logStatus = do
    -- TODO if public insertMasterDocs else insertUserDocs
    ids <- traverse (\(idx, doc) -> do
    id <- insertMasterDocs c la doc
    logStatus JobLog { _scst_succeeded = Just $ 1 + idx
    ids <- runConduit $
    zipSources (yieldMany [1..]) docsC
    .| mapMC insertDoc
    .| sinkList
    -- ids <- traverse (\(idx, doc) -> do
    -- id <- insertMasterDocs c la doc
    -- logStatus JobLog { _scst_succeeded = Just $ 1 + idx
    -- , _scst_failed = Just 0
    -- , _scst_remaining = Just $ length docs - idx
    -- , _scst_events = Just []
    -- }
    -- pure id
    -- ) (zip [1..] docs)
    flowCorpusUser (la ^. tt_lang) u cn c ids mfslw
    where
    insertDoc :: (Integer, a) -> m NodeId
    insertDoc (idx, doc) = do
    id <- insertMasterDocs c la [doc]
    case mLength of
    Nothing -> pure ()
    Just len -> do
    logStatus JobLog { _scst_succeeded = Just $ fromIntegral $ 1 + idx
    , _scst_failed = Just 0
    , _scst_remaining = Just $ length docs - idx
    , _scst_remaining = Just $ fromIntegral $ len - idx
    , _scst_events = Just []
    }
    pure id
    ) (zip [1..] docs)
    flowCorpusUser (la ^. tt_lang) u cn c (concat ids) mfslw
    pure $ Prelude.head id
    ......@@ -250,7 +277,7 @@ flowCorpusUser l user corpusName ctype ids mfslw = do
    -- User Flow
    (userId, _rootId, userCorpusId) <- getOrMk_RootWithCorpus user corpusName ctype
    -- NodeTexts is first
    _tId <- insertDefaultNode NodeTexts userCorpusId userId
    _tId <- insertDefaultNodeIfNotExists NodeTexts userCorpusId userId
    -- printDebug "NodeTexts: " tId
    -- NodeList is second
    ......@@ -276,8 +303,8 @@ flowCorpusUser l user corpusName ctype ids mfslw = do
    -- _ <- insertOccsUpdates userCorpusId mastListId
    -- printDebug "userListId" userListId
    -- User Graph Flow
    _ <- insertDefaultNode NodeDashboard userCorpusId userId
    _ <- insertDefaultNode NodeGraph userCorpusId userId
    _ <- insertDefaultNodeIfNotExists NodeDashboard userCorpusId userId
    _ <- insertDefaultNodeIfNotExists NodeGraph userCorpusId userId
    --_ <- mkPhylo userCorpusId userId
    -- Annuaire Flow
    -- _ <- mkAnnuaire rootUserId userId
    ......@@ -322,7 +349,7 @@ saveDocNgramsWith :: ( FlowCmdM env err m)
    -> m ()
    saveDocNgramsWith lId mapNgramsDocs' = do
    terms2id <- insertExtractedNgrams $ HashMap.keys mapNgramsDocs'
    printDebug "terms2id" terms2id
    --printDebug "terms2id" terms2id
    let mapNgramsDocs = HashMap.mapKeys extracted2ngrams mapNgramsDocs'
    ......@@ -331,7 +358,7 @@ saveDocNgramsWith lId mapNgramsDocs' = do
    $ map (first _ngramsTerms . second Map.keys)
    $ HashMap.toList mapNgramsDocs
    printDebug "saveDocNgramsWith" mapCgramsId
    --printDebug "saveDocNgramsWith" mapCgramsId
    -- insertDocNgrams
    _return <- insertContextNodeNgrams2
    $ catMaybes [ ContextNodeNgrams2 <$> Just nId
    ......@@ -504,5 +531,3 @@ extractInsert docs = do
    documentsWithId
    _ <- insertExtractedNgrams $ HashMap.keys mapNgramsDocs'
    pure ()
    src/Gargantext/Database/Action/User/New.hs
    View file @ a43c33d0
    ......@@ -27,7 +27,7 @@ import Gargantext.Database.Query.Table.User
    import Gargantext.Prelude
    import Gargantext.Prelude.Crypto.Pass.User (gargPass)
    import Gargantext.Prelude.Mail.Types (MailConfig)
    ------------------------------------------------------------------------
    ------------------------------------------------------------------------
    newUsers :: (CmdM env err m, MonadRandom m, HasNodeError err, HasMail env)
    => [EmailAddress] -> m Int64
    ......@@ -35,6 +35,18 @@ newUsers us = do
    us' <- mapM newUserQuick us
    config <- view $ mailSettings
    newUsers' config us'
    ------------------------------------------------------------------------
    updateUsersPassword :: (CmdM env err m, MonadRandom m, HasNodeError err, HasMail env)
    => [EmailAddress] -> m Int64
    updateUsersPassword us = do
    us' <- mapM newUserQuick us
    config <- view $ mailSettings
    _ <- mapM (\u -> updateUser (SendEmail True) config u) us'
    pure 1
    ------------------------------------------------------------------------
    ------------------------------------------------------------------------
    newUserQuick :: (MonadRandom m)
    => Text -> m (NewUser GargPassword)
    ......@@ -44,6 +56,7 @@ newUserQuick n = do
    Just (u', _m) -> u'
    Nothing -> panic "[G.D.A.U.N.newUserQuick]: Email invalid"
    pure (NewUser u n (GargPassword pass))
    ------------------------------------------------------------------------
    ------------------------------------------------------------------------
    -- | guessUserName
    ......@@ -68,7 +81,6 @@ newUsers' cfg us = do
    printDebug "newUsers'" us
    pure r
    ------------------------------------------------------------------------
    updateUser :: HasNodeError err
    => SendEmail -> MailConfig -> NewUser GargPassword -> Cmd err Int64
    updateUser (SendEmail send) cfg u = do
    ......
    src/Gargantext/Database/Prelude.hs
    View file @ a43c33d0
    ......@@ -24,7 +24,7 @@ import Data.ByteString.Char8 (hPutStrLn)
    import Data.Either.Extra (Either)
    import Data.Pool (Pool, withResource)
    import Data.Profunctor.Product.Default (Default)
    import Data.Text (unpack, Text)
    import Data.Text (pack, unpack, Text)
    import Data.Word (Word16)
    import Database.PostgreSQL.Simple (Connection, connect)
    import Database.PostgreSQL.Simple.FromField ( Conversion, ResultError(ConversionFailed), fromField, returnError)
    ......@@ -36,7 +36,7 @@ import Opaleye (Unpackspec, showSql, FromFields, Select, runSelect, SqlJsonb, De
    import Opaleye.Aggregate (countRows)
    import System.IO (FilePath)
    import System.IO (stderr)
    import Text.Read (read)
    import Text.Read (readMaybe)
    import qualified Data.ByteString as DB
    import qualified Data.List as DL
    import qualified Database.PostgreSQL.Simple as PGS
    ......@@ -176,9 +176,13 @@ databaseParameters :: FilePath -> IO PGS.ConnectInfo
    databaseParameters fp = do
    ini <- readIniFile' fp
    let val' key = unpack $ val ini "database" key
    let dbPortRaw = val' "DB_PORT"
    let dbPort = case (readMaybe dbPortRaw :: Maybe Word16) of
    Nothing -> panic $ "DB_PORT incorrect: " <> (pack dbPortRaw)
    Just d -> d
    pure $ PGS.ConnectInfo { PGS.connectHost = val' "DB_HOST"
    , PGS.connectPort = read (val' "DB_PORT") :: Word16
    , PGS.connectPort = dbPort
    , PGS.connectUser = val' "DB_USER"
    , PGS.connectPassword = val' "DB_PASS"
    , PGS.connectDatabase = val' "DB_NAME"
    ......
    src/Gargantext/Database/Query/Table/Node.hs
    View file @ a43c33d0
    ......@@ -255,6 +255,14 @@ insertDefaultNode :: HasDBid NodeType
    => NodeType -> ParentId -> UserId -> Cmd err [NodeId]
    insertDefaultNode nt p u = insertNode nt Nothing Nothing p u
    insertDefaultNodeIfNotExists :: HasDBid NodeType
    => NodeType -> ParentId -> UserId -> Cmd err [NodeId]
    insertDefaultNodeIfNotExists nt p u = do
    children <- getChildrenByType p nt
    case children of
    [] -> insertDefaultNode nt p u
    xs -> pure xs
    insertNode :: HasDBid NodeType
    => NodeType -> Maybe Name -> Maybe DefaultHyperdata -> ParentId -> UserId -> Cmd err [NodeId]
    insertNode nt n h p u = insertNodesR [nodeW nt n h p u]
    ......
    stack.yaml
    View file @ a43c33d0
    ......@@ -69,11 +69,11 @@ extra-deps:
    # External Data API connectors
    - git: https://gitlab.iscpif.fr/gargantext/crawlers/pubmed.git
    commit: 9cdba6423decad5acfacb0f274212fd8723ce734
    commit: 12cb16c391577bff4295e3dd1b126281d78037b4
    - git: https://gitlab.iscpif.fr/gargantext/crawlers/istex.git
    commit: daeae80365250c4bd539f0a65e271f9aa37f731f
    - git: https://gitlab.iscpif.fr/gargantext/crawlers/hal.git
    commit: 020f5f9b308f5c23c925aedf5fb11f8b4728fb19
    commit: 3bf77f28d3dc71d2e8349cbf422a34cf4c23cd11
    - git: https://gitlab.iscpif.fr/gargantext/crawlers/isidore.git
    commit: 3db385e767d2100d8abe900833c6e7de3ac55e1b
    ......
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