Merge branch 'dev' into 224-dev-uniform-ngrams-creation

CHANGELOG.md

-## Version 0.0.6.9.9.9.4.3
+## Version 0.0.6.9.9.9.4.4
+
+* [FRONT][FIX][trim / deblank missing in invitations modal box (#618)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/618)
+* [FRONT][FIX][[Breadcrumb] Remove unnecessary informations (#616)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/616)
 
+## Version 0.0.6.9.9.9.4.3
 
 * [BACK][LOGS][A consistent error format for Gargantext (#267)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/267)
 * [BACK][ADM] Build Deps / test / cabal

bench/Main.hs

@@ -2,18 +2,54 @@
 {-# LANGUAGE TypeApplications  #-}
 module Main where
 
+import Control.DeepSeq
 import Gargantext.Core.Types.Individu
+import Gargantext.Core.Viz.Phylo
+import Gargantext.Core.Viz.Phylo.API.Tools (readPhylo)
+import Gargantext.Core.Viz.Phylo.PhyloMaker (toPhylo)
+import Gargantext.Core.Viz.Phylo.PhyloTools
 import Gargantext.Prelude.Crypto.Auth (createPasswordHash)
 
 import Test.Tasty.Bench
+import Paths_gargantext
+
+phyloConfig :: PhyloConfig
+phyloConfig = PhyloConfig {
+    corpusPath = "corpus.csv"
+  , listPath = "list.csv"
+  , outputPath = "data/"
+  , corpusParser = Csv {_csv_limit = 150000}
+  , listParser = V4
+  , phyloName = "Phylo Name"
+  , phyloScale = 2
+  , similarity = WeightedLogJaccard {_wlj_sensibility = 0.5, _wlj_minSharedNgrams = 2}
+  , seaElevation = Constante {_cons_start = 0.1, _cons_gap = 0.1}
+  , defaultMode = True
+  , findAncestors = True
+  , phyloSynchrony = ByProximityThreshold {_bpt_threshold = 0.5, _bpt_sensibility = 0.0, _bpt_scope = AllBranches, _bpt_strategy = MergeAllGroups}
+  , phyloQuality = Quality {_qua_granularity = 0.8, _qua_minBranch = 3}
+  , timeUnit = Year {_year_period = 3, _year_step = 1, _year_matchingFrame = 5}
+  , clique = MaxClique {_mcl_size = 5, _mcl_threshold = 1.0e-4, _mcl_filter = ByThreshold}
+  , exportLabel = [ BranchLabel {_branch_labelTagger = MostEmergentTfIdf, _branch_labelSize = 2}
+                  , GroupLabel {_group_labelTagger = MostEmergentInclusive, _group_labelSize = 2}
+                  ]
+  , exportSort = ByHierarchy {_sort_order = Desc}
+  , exportFilter = [ByBranchSize {_branch_size = 3.0}]
+  }
 
 main :: IO ()
-main = defaultMain
-  [ bgroup "Benchmarks"
-    [ bgroup "User creation" [
-      bench "createPasswordHash"  $ whnfIO (createPasswordHash "rabbit")
-    , bench "toUserHash"  $
-        whnfIO (toUserHash $ NewUser "alfredo" "alfredo@well-typed.com" (GargPassword "rabbit"))
-    ]
+main = do
+  _issue290Phylo     <- force . setConfig phyloConfig <$> (readPhylo =<< getDataFileName "bench-data/phylo/issue-290.json")
+  issue290PhyloSmall <- force . setConfig phyloConfig <$> (readPhylo =<< getDataFileName "bench-data/phylo/issue-290-small.json")
+  defaultMain
+    [ bgroup "Benchmarks"
+      [ bgroup "User creation" [
+        bench "createPasswordHash"  $ whnfIO (createPasswordHash "rabbit")
+      , bench "toUserHash"  $
+          whnfIO (toUserHash $ NewUser "alfredo" "alfredo@well-typed.com" (GargPassword "rabbit"))
+      ]
+      , bgroup "Phylo" [
+          bench "toPhylo (small)" $ nf toPhylo issue290PhyloSmall
+      ]
+      ]
     ]
-  ]

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 2.0
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.6.9.9.9.4.3
+version: 0.0.6.9.9.9.4.4
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data
@@ -17,6 +17,8 @@ license:        AGPL-3
 license-file:   LICENSE
 build-type:     Simple
 data-files:
+    bench-data/phylo/issue-290.json
+    bench-data/phylo/issue-290-small.json
     devops/postgres/extensions.sql
     devops/postgres/schema.sql
     ekg-assets/index.html
@@ -32,6 +34,7 @@ data-files:
     test-data/ngrams/simple.csv
     test-data/phylo/bpa_phylo_test.json
     test-data/phylo/open_science.json
+    test-data/phylo/issue-290-small.golden.json
     test-data/test_config.ini
     .clippy.dhall
 
@@ -957,6 +960,7 @@ test-suite garg-test-tasty
       Test.Ngrams.Query.PaginationCorpus
       Test.Offline.Errors
       Test.Offline.JSON
+      Test.Offline.Phylo
       Test.Parsers.Date
       Test.Parsers.Types
       Test.Parsers.WOS
@@ -1161,11 +1165,14 @@ benchmark garg-bench
   main-is:       Main.hs
   hs-source-dirs: bench
   type:          exitcode-stdio-1.0
+  other-modules:
+      Paths_gargantext
   build-depends: base
                , bytestring
+               , deepseq
                , gargantext
                , gargantext-prelude
                , tasty-bench
-  ghc-options:   "-with-rtsopts=-A32m"
+  ghc-options:   "-with-rtsopts=-T -A32m"
   if impl(ghc >= 8.6)
     ghc-options: "-with-rtsopts=--nonmoving-gc"

nix/pkgs.nix

@@ -15,6 +15,15 @@ rec {
                           ];
                 })
            else pkgs.haskell.compiler.ghc8107;
+  graphviz = pkgs.graphviz.overrideAttrs (finalAttrs: previousAttrs: {
+                # Increase the YY_BUF_SIZE, see https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/290#note_9015
+                patches = [
+                            (pkgs.fetchpatch {
+                              url = "https://gist.githubusercontent.com/adinapoli/e93ca7b1d714d27f4af537716b03e3bb/raw/b9cc297c3465878da2d18ee92a3f9b8273923493/graphviz-yy-buf-size.patch";
+                              sha256 = "sha256-8Q3tf37iYaPV50P+Vf/n263ordECiu5eKwONCy3ynV8=";
+                            })
+                          ];
+                });
   haskell1 = pkgs.haskell // {
       packages = pkgs.haskell.packages // {
         ghc8107 = pkgs.haskell.packages.ghc8107.override {

src/Gargantext/API/Node/Update.hs

@@ -50,6 +50,8 @@ import Gargantext.Utils.Jobs (serveJobsAPI, MonadJobStatus(..))
 import Servant
 import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary
+import Gargantext.Utils.UTCTime (timeMeasured)
+import Gargantext.System.Logging
 
 ------------------------------------------------------------------------
 type API = Summary " Update node according to NodeType params"
@@ -94,7 +96,11 @@ api nId =
   serveJobsAPI UpdateNodeJob $ \jHandle p ->
     updateNode nId p jHandle
 
-updateNode :: (HasNodeStory env err m, HasSettings env, MonadJobStatus m)
+updateNode :: (HasNodeStory env err m
+              , HasSettings env
+              , MonadJobStatus m
+              , MonadLogger m
+              )
            => NodeId
            -> UpdateNodeParams
            -> JobHandle m
@@ -156,7 +162,7 @@ updateNode phyloId (UpdateNodePhylo config) jobHandle = do
 
   let corpusId = fromMaybe (panicTrace "no corpus id") corpusId'
 
-  phy <- flowPhyloAPI (subConfigAPI2config config) corpusId
+  phy <- timeMeasured "updateNode.flowPhyloAPI" $ flowPhyloAPI (subConfigAPI2config config) corpusId
   markProgress 2 jobHandle
 
 {-
@@ -166,7 +172,7 @@ updateNode phyloId (UpdateNodePhylo config) jobHandle = do
                    , _scst_events    = Just []
                    }
 -}
-  _ <- updateHyperdata phyloId (HyperdataPhylo Nothing (Just phy))
+  _ <- timeMeasured "updateNode.updateHyperdataPhylo" $ updateHyperdata phyloId (HyperdataPhylo Nothing (Just phy))
 
   -- TODO: catch the error of sendMail if userId is not found, then debug
   -- sendMail (UserDBId userId)

src/Gargantext/Core/Types/Phylo.hs

@@ -26,6 +26,7 @@ Phylomemy was first described in Chavalarias, D., Cointet, J.-P., 2013. Phylomem
 
 module Gargantext.Core.Types.Phylo where
 
+import Control.DeepSeq
 import Control.Lens (makeLenses)
 import Control.Monad.Fail (fail)
 import Data.Aeson
@@ -51,6 +52,8 @@ data Phylo = Phylo { _phylo_Duration :: (Start, End)
                    , _phylo_Periods  :: [PhyloPeriod]
                    } deriving (Generic)
 
+instance NFData Phylo
+
 -- | UTCTime in seconds since UNIX epoch
 type Start   = POSIXTime
 type End     = POSIXTime
@@ -66,6 +69,8 @@ data PhyloPeriod = PhyloPeriod { _phylo_PeriodId     :: PhyloPeriodId
                                , _phylo_PeriodLevels :: [PhyloLevel]
                                } deriving (Generic)
 
+instance NFData PhyloPeriod
+
 type PhyloPeriodId = (Start, End)
 
 -- | PhyloLevel : levels of phylomemy on level axis
@@ -78,6 +83,8 @@ data PhyloLevel = PhyloLevel { _phylo_LevelId     :: PhyloLevelId
                              , _phylo_LevelGroups :: [PhyloGroup]
                              } deriving (Generic)
 
+instance NFData PhyloLevel
+
 type PhyloLevelId = (PhyloPeriodId, Int)
 
 -- | PhyloGroup : group of ngrams at each level and step
@@ -88,14 +95,16 @@ type PhyloLevelId = (PhyloPeriodId, Int)
 data PhyloGroup = PhyloGroup { _phylo_GroupId            :: PhyloGroupId
                              , _phylo_GroupLabel         :: Maybe Text
                              , _phylo_GroupNgrams        :: [NgramId]
-                   
+
                              , _phylo_GroupPeriodParents :: [Edge]
                              , _phylo_GroupPeriodChilds  :: [Edge]
-                   
+
                              , _phylo_GroupLevelParents  :: [Edge]
                              , _phylo_GroupLevelChilds   :: [Edge]
                              } deriving (Generic)
 
+instance NFData PhyloGroup
+
 type PhyloGroupId = (PhyloLevelId, Int)
 type Edge         = (PhyloGroupId, Weight)
 type Weight       = Double

src/Gargantext/Core/Viz/Phylo.hs

@@ -26,6 +26,7 @@ one 8, e54847.
 
 module Gargantext.Core.Viz.Phylo where
 
+import Control.DeepSeq
 import Control.Lens (makeLenses)
 import Data.Aeson
 import Data.Aeson.TH (deriveJSON)
@@ -62,7 +63,7 @@ data SeaElevation =
     | Adaptative
       { _adap_steps :: Double }
     | Evolving
-      { _evol_neighborhood :: Bool }      
+      { _evol_neighborhood :: Bool }
     deriving (Show,Generic,Eq)
 
 instance ToSchema SeaElevation
@@ -74,8 +75,8 @@ data PhyloSimilarity =
     | WeightedLogSim
       { _wls_sensibility     :: Double
       , _wls_minSharedNgrams :: Int }
-    | Hamming 
-      { _hmg_sensibility     :: Double 
+    | Hamming
+      { _hmg_sensibility     :: Double
       , _hmg_minSharedNgrams :: Int}
 
     deriving (Show,Generic,Eq)
@@ -188,7 +189,6 @@ data PhyloConfig =
             , exportFilter   :: [Filter]
             } deriving (Show,Generic,Eq)
 
-
 --------------------------------
 -- | SubConfig API & 1Click | --
 --------------------------------
@@ -205,8 +205,8 @@ data PhyloSubConfigAPI =
 
 
 subConfigAPI2config :: PhyloSubConfigAPI -> PhyloConfig
-subConfigAPI2config subConfig = defaultConfig 
-                                           { similarity     = WeightedLogJaccard (_sc_phyloProximity subConfig) 2 
+subConfigAPI2config subConfig = defaultConfig
+                                           { similarity     = WeightedLogJaccard (_sc_phyloProximity subConfig) 2
                                            , phyloSynchrony = ByProximityThreshold (_sc_phyloSynchrony subConfig) 0 AllBranches MergeAllGroups
                                            , phyloQuality   = Quality (_sc_phyloQuality   subConfig) 3
                                            , timeUnit       = _sc_timeUnit       subConfig
@@ -217,7 +217,7 @@ subConfigAPI2config subConfig = defaultConfig
 
 --------------------------
 -- | SubConfig 1Click | --
---------------------------  
+--------------------------
 
 defaultConfig :: PhyloConfig
 defaultConfig =
@@ -474,7 +474,6 @@ data PhyloScale =
 instance ToSchema PhyloScale where
   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 
-
 type PhyloGroupId  = (PhyloScaleId, Int)
 
 -- | BranchId : (a scale, a sequence of branch index)
@@ -552,19 +551,16 @@ data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq)
 instance ToSchema Filter where
   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 
-
 data Order = Asc | Desc deriving (Show,Generic,Eq, ToSchema)
 
 data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy {_sort_order :: Order } deriving (Show,Generic,Eq)
 instance ToSchema Sort where
   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_sort_")
 
-
 data Tagger = MostInclusive | MostEmergentInclusive | MostEmergentTfIdf deriving (Show,Generic,Eq)
 instance ToSchema Tagger where
   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 
-
 data PhyloLabel =
       BranchLabel
       { _branch_labelTagger :: Tagger
@@ -654,3 +650,30 @@ instance FromJSON PhyloGroup
 instance ToJSON PhyloGroup
 
 $(deriveJSON (unPrefix "_foundations_"  ) ''PhyloFoundations)
+
+-- NFData instances
+
+instance NFData CorpusParser
+instance NFData ListParser
+instance NFData SeaElevation
+instance NFData PhyloSimilarity
+instance NFData SynchronyScope
+instance NFData SynchronyStrategy
+instance NFData Synchrony
+instance NFData MaxCliqueFilter
+instance NFData Cluster
+instance NFData Quality
+instance NFData PhyloConfig
+instance NFData Software
+instance NFData PhyloParam
+instance NFData PhyloFoundations
+instance NFData PhyloCounts
+instance NFData PhyloSources
+instance NFData Phylo
+instance NFData PhyloPeriod
+instance NFData PhyloScale
+instance NFData Filter
+instance NFData Order
+instance NFData Sort
+instance NFData Tagger
+instance NFData PhyloLabel

src/Gargantext/Core/Viz/Phylo/API/Tools.hs

@@ -12,12 +12,14 @@ Portability : POSIX
 {-# OPTIONS_GHC -fno-warn-deprecations #-}
 
 {-# LANGUAGE TypeApplications #-}
+{-# LANGUAGE TemplateHaskell  #-}
+{-# LANGUAGE BangPatterns #-}
 
 module Gargantext.Core.Viz.Phylo.API.Tools
   where
 
 import Control.Lens hiding (Context)
-import Data.Aeson (Value, decodeFileStrict, eitherDecode, encode)
+import Data.Aeson (Value, decodeFileStrict, encode, eitherDecodeFileStrict')
 import Data.ByteString.Lazy qualified as Lazy
 import Data.Map.Strict qualified as Map
 import Data.Proxy
@@ -47,10 +49,12 @@ import Gargantext.Database.Schema.Context
 import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.Database.Schema.Node
 import Gargantext.Prelude hiding (to)
+import Gargantext.System.Logging
 import Prelude qualified
 import System.FilePath ((</>))
 import System.IO.Temp (withTempDirectory)
 import System.Process qualified as Shell
+import Gargantext.Utils.UTCTime (timeMeasured)
 
 --------------------------------------------------------------------
 getPhyloData :: HasNodeError err
@@ -88,15 +92,20 @@ phylo2dot2json phylo = do
       Just v  -> pure v
 
 
-flowPhyloAPI :: (HasNodeStory env err m, HasNodeError err)
+flowPhyloAPI :: (HasNodeStory env err m, HasNodeError err, MonadLogger m)
              => PhyloConfig -> CorpusId -> m Phylo
 flowPhyloAPI config cId = do
   corpus <- corpusIdtoDocuments (timeUnit config) cId
-  let phyloWithCliques = toPhyloWithoutLink corpus config
+  let !phyloWithCliques = toPhyloWithoutLink corpus config
   -- writePhylo phyloWithCliquesFile phyloWithCliques
-  printDebug "PhyloConfig old: " config
+  $(logLocM) DEBUG $ "PhyloConfig old: " <> show config
 
-  pure $ toPhylo $ setConfig config phyloWithCliques
+  _ <- timeMeasured "flowPhyloAPI.phyloWithCliques" (pure $! phyloWithCliques)
+
+  let !phyloConfigured = setConfig config phyloWithCliques
+  _ <- timeMeasured "flowPhyloAPI.phyloConfigured" (pure $! phyloConfigured)
+
+  pure $! toPhylo phyloConfigured
 
 --------------------------------------------------------------------
 corpusIdtoDocuments :: (HasNodeStory env err m, HasNodeError err)
@@ -192,13 +201,8 @@ writePhylo path phylo = Lazy.writeFile path $ encode phylo
 
 readPhylo :: [Char] -> IO Phylo
 readPhylo path = do
-  phyloJson <- (eitherDecode <$> readJson path) :: IO (Either Prelude.String Phylo)
-  case phyloJson of
-    Left err -> do
-      putStrLn err
-      undefined
-    Right phylo -> pure phylo
-
+  phyloJson <- eitherDecodeFileStrict' @Phylo path
+  either errorTrace pure phyloJson
 
 -- | To read and decode a Json file
 readJson :: FilePath -> IO Lazy.ByteString

src/Gargantext/Utils/UTCTime.hs

@@ -11,6 +11,7 @@ Portability : POSIX
 
 {-# LANGUAGE DeriveAnyClass             #-}
 {-# LANGUAGE DeriveGeneric              #-}
+{-# LANGUAGE TemplateHaskell            #-}
 {-# LANGUAGE TypeFamilies               #-}
 
 module Gargantext.Utils.UTCTime where
@@ -19,10 +20,14 @@ import Data.Aeson (FromJSON, ToJSON)
 import Data.Morpheus.Kind (SCALAR)
 import Data.Morpheus.Types (GQLType(..), DecodeScalar(..), EncodeScalar(..))
 import Data.Morpheus.Types qualified as DMT
+import Data.String (fromString)
 import Data.Swagger (ToSchema)
 import Data.Text qualified as T
 import Data.Time (UTCTime)
+import Data.Time.Clock.POSIX (getPOSIXTime)
 import Gargantext.Prelude
+import Gargantext.System.Logging
+import Prelude (String)
 
 
 newtype NUTCTime = NUTCTime UTCTime
@@ -39,3 +44,27 @@ instance GQLType NUTCTime where
 instance FromJSON NUTCTime
 instance ToJSON NUTCTime
 instance ToSchema NUTCTime
+
+timeMeasured :: (MonadLogger m, MonadBase IO m, HasCallStack)
+             => String
+             -- ^ A label
+             -> m a
+             -- ^ The action to run
+             -> m a
+timeMeasured = withFrozenCallStack $ timeMeasured' DEBUG
+
+timeMeasured' :: (MonadLogger m, MonadBase IO m, HasCallStack)
+             => LogLevel
+             -- ^ The severity of the log
+             -> String
+             -- ^ A label to identify the action.
+             -> m a
+             -- ^ The action to run
+             -> m a
+timeMeasured' severity label action = withFrozenCallStack $ do
+  startTime <- liftBase getPOSIXTime
+  res       <- action
+  endTime   <- liftBase getPOSIXTime
+  let msg = label <> " took " <> (show $ endTime - startTime) <> " seconds to execute."
+  $(logLocM) severity (fromString msg)
+  return res

test/Test/API/UpdateList.hs

@@ -7,6 +7,9 @@
 
 module Test.API.UpdateList (
     tests
+  , newCorpusForUser
+  , JobPollHandle(..)
+  , pollUntilFinished
   ) where
 
 import Data.Aeson qualified as JSON

test/Test/Offline/Phylo.hs

+{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE TypeApplications #-}
+{-# LANGUAGE ScopedTypeVariables #-}
+{-# LANGUAGE QuasiQuotes #-}
+
+module Test.Offline.Phylo (tests) where
+
+import Gargantext.Core.Viz.Phylo
+import Gargantext.Core.Viz.Phylo.API.Tools (readPhylo, writePhylo)
+import Gargantext.Core.Viz.Phylo.PhyloMaker (toPhylo)
+import Gargantext.Core.Viz.Phylo.PhyloTools
+import Prelude
+import Test.Tasty
+import Test.Tasty.HUnit
+import Test.Tasty.QuickCheck
+
+import Paths_gargantext
+
+phyloConfig :: PhyloConfig
+phyloConfig = PhyloConfig {
+    corpusPath = "corpus.csv"
+  , listPath = "list.csv"
+  , outputPath = "data/"
+  , corpusParser = Csv {_csv_limit = 150000}
+  , listParser = V4
+  , phyloName = "Phylo Name"
+  , phyloScale = 2
+  , similarity = WeightedLogJaccard {_wlj_sensibility = 0.5, _wlj_minSharedNgrams = 2}
+  , seaElevation = Constante {_cons_start = 0.1, _cons_gap = 0.1}
+  , defaultMode = True
+  , findAncestors = True
+  , phyloSynchrony = ByProximityThreshold {_bpt_threshold = 0.5, _bpt_sensibility = 0.0, _bpt_scope = AllBranches, _bpt_strategy = MergeAllGroups}
+  , phyloQuality = Quality {_qua_granularity = 0.8, _qua_minBranch = 3}
+  , timeUnit = Year {_year_period = 3, _year_step = 1, _year_matchingFrame = 5}
+  , clique = MaxClique {_mcl_size = 5, _mcl_threshold = 1.0e-4, _mcl_filter = ByThreshold}
+  , exportLabel = [ BranchLabel {_branch_labelTagger = MostEmergentTfIdf, _branch_labelSize = 2}
+                  , GroupLabel {_group_labelTagger = MostEmergentInclusive, _group_labelSize = 2}
+                  ]
+  , exportSort = ByHierarchy {_sort_order = Desc}
+  , exportFilter = [ByBranchSize {_branch_size = 3.0}]
+  }
+
+tests :: TestTree
+tests = testGroup "Phylo" [
+  testCase "returns expected data" testSmallPhyloExpectedOutput
+  ]
+
+testSmallPhyloExpectedOutput :: Assertion
+testSmallPhyloExpectedOutput = do
+  issue290PhyloSmall <- setConfig phyloConfig <$> (readPhylo =<< getDataFileName "bench-data/phylo/issue-290-small.json")
+  expected <- readPhylo =<< getDataFileName "test-data/phylo/issue-290-small.golden.json"
+  let actual = toPhylo issue290PhyloSmall
+  expected @?= actual

test/drivers/hspec/Main.hs

+{-# LANGUAGE TypeApplications #-}
 
 module Main where
 
 import Gargantext.Prelude
 
+import Control.Monad
+import Data.Text (isInfixOf)
 import Shelly hiding (FilePath)
 import System.IO
 import System.Process
+import Test.Hspec
+import qualified Data.Text as T
 import qualified Test.API                     as API
 import qualified Test.Database.Operations     as DB
 
-import Test.Hspec
 
 startCoreNLPServer :: IO ProcessHandle
 startCoreNLPServer = do
   devNull <- openFile "/dev/null" WriteMode
   let p = proc "./startServer.sh" []
-  (_, _, _, hdl) <- createProcess $ p { cwd = Just "devops/coreNLP/stanford-corenlp-current"
+  (_, _, _, hdl) <- (createProcess $ p { cwd = Just "devops/coreNLP/stanford-corenlp-current"
                     , delegate_ctlc = True
                     , create_group = True
                     , std_out = UseHandle devNull
                     , std_err = UseHandle devNull
-                    }
+                    }) `catch` \e -> case e of
+                                           _ | True <- "does not exist" `isInfixOf` (T.pack . show @SomeException $ e)
+                                             -> fail $ "Cannot execute the 'startServer.sh' script. If this is the " <>
+                                                       "first time you are running the tests, you have to run " <>
+                                                       "cd devops/coreNLP && ./build.sh first. You have to run it only once, " <>
+                                                       "and then you are good to go for the time being."
+                                             | otherwise -> throwIO e
   pure hdl
 
 stopCoreNLPServer :: ProcessHandle -> IO ()

test/drivers/tasty/Main.hs

@@ -20,6 +20,7 @@ import qualified Test.Ngrams.NLP              as NLP
 import qualified Test.Ngrams.Query            as NgramsQuery
 import qualified Test.Offline.JSON            as JSON
 import qualified Test.Offline.Errors          as Errors
+import qualified Test.Offline.Phylo           as Phylo
 import qualified Test.Parsers.Date            as PD
 import qualified Test.Utils.Crypto            as Crypto
 import qualified Test.Utils.Jobs              as Jobs
@@ -51,4 +52,5 @@ main = do
     , CorpusQuery.tests
     , JSON.tests
     , Errors.tests
+    , Phylo.tests
     ]