[BREAKING phylo] refactor to use uniform TimeUnitCriteria

NOTE: Golden tests don't pass

This is a proposal

Should go together with

https://gitlab.iscpif.fr/gargantext/purescript-gargantext/tree/dev-phylo-document-dates-with-hh-mm-ss

README.md

@@ -478,7 +478,7 @@ Sometimes, however, we genuinely want to modify the output so that it's the new
 golden reference). To do so, it's enough to run the testsuite passing the `--accept` flag, for example:
 
 ```shell
-cabal v2-test garg-test-tasty --test-show-details=streaming --flags 'test-crypto no-phylo-debug-logs' --test-option=--pattern='/Phylo/' --test-option=--accept"
+cabal v2-test --test-show-details=streaming --flags 'test-crypto no-phylo-debug-logs' --test-option=--match='/Phylo/' --test-option=--accept
 ```
 
 # Async workers <a name="async-workers"></a>

bin/gargantext-cli/CLI/Phylo.hs

@@ -45,7 +45,18 @@ phyloCLI (PhyloArgs configPath) = do
       mapList <-  fileToList (listParser config) (listPath config)
 
       corpus  <- if (defaultMode config)
-                  then fileToDocsDefault (corpusParser config) (corpusPath config) [Year 3 1 5,Month 3 1 5,Week 4 2 5] mapList
+                 then
+                   fileToDocsDefault (corpusParser config)
+                                     (corpusPath config)
+                                     [Year $ TimeUnitCriteria { _tuc_step = 3
+                                                              , _tuc_period = 1
+                                                              , _tuc_matchingFrame = 5 }
+                                     , Month $ TimeUnitCriteria { _tuc_step = 3
+                                                                , _tuc_period = 1
+                                                                , _tuc_matchingFrame = 5 }
+                                     , Week $ TimeUnitCriteria { _tuc_step = 4
+                                                               , _tuc_period = 2
+                                                               , _tuc_matchingFrame = 5 } ] mapList
                   else fileToDocsAdvanced (corpusParser config) (corpusPath config) (timeUnit config)  mapList
 
       printIOComment (show (length corpus) <> " parsed docs from the corpus")

bin/gargantext-cli/CLI/Phylo/Common.hs

@@ -157,11 +157,14 @@ fileToList parser path =
 -- Config time parameters to label
 timeToLabel :: PhyloConfig -> [Char]
 timeToLabel config = case (timeUnit config) of
-      Epoch p s f -> ("time_epochs" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
-      Year  p s f -> ("time_years"  <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
-      Month p s f -> ("time_months" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
-      Week  p s f -> ("time_weeks"  <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
-      Day   p s f -> ("time_days"   <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
+      Epoch tuc -> "time_epochs" <> toLabel tuc
+      Year  tuc -> "time_years"  <> toLabel tuc
+      Month tuc -> "time_months" <> toLabel tuc
+      Week  tuc -> "time_weeks"  <> toLabel tuc
+      Day   tuc -> "time_days"   <> toLabel tuc
+      where
+        toLabel (TimeUnitCriteria { .. }) =
+          show _tuc_period <> "_" <> show _tuc_step <> "_" <> show _tuc_matchingFrame
 
 
 seaToLabel :: PhyloConfig -> [Char]

bin/gargantext-cli/CLI/Phylo/Profile.hs

@@ -36,7 +36,9 @@ phyloConfig outdir = PhyloConfig {
   , findAncestors = False
   , 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}
+  , timeUnit = Year $ TimeUnitCriteria { _tuc_period = 3
+                                       , _tuc_step = 1
+                                       , _tuc_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}
@@ -65,9 +67,22 @@ phyloProfileCLI = do
 
         mapList <-  liftIO $ fileToList (listParser config) (listPath config)
 
-        corpus  <- liftIO $ if (defaultMode config)
-                    then fileToDocsDefault (corpusParser config) (corpusPath config) [Year 3 1 5,Month 3 1 5,Week 4 2 5] mapList
-                    else fileToDocsAdvanced (corpusParser config) (corpusPath config) (timeUnit config)  mapList
+        corpus  <- liftIO $
+          if (defaultMode config)
+          then
+            fileToDocsDefault (corpusParser config)
+                              (corpusPath config)
+                              [ Year $ TimeUnitCriteria { _tuc_period = 3
+                                                        , _tuc_step = 1
+                                                        , _tuc_matchingFrame = 5 }
+                              , Month $ TimeUnitCriteria { _tuc_period = 3
+                                                         , _tuc_step = 1
+                                                         , _tuc_matchingFrame = 5 }
+                              , Week $ TimeUnitCriteria { _tuc_period = 4
+                                                        , _tuc_step = 2
+                                                        , _tuc_matchingFrame = 5 } ] mapList
+          else
+            fileToDocsAdvanced (corpusParser config) (corpusPath config) (timeUnit config)  mapList
 
         liftIO $ do
           printIOComment (show (length corpus) <> " parsed docs from the corpus")

gargantext.cabal

@@ -844,6 +844,7 @@ test-suite garg-test
       Test.API.UpdateList
       Test.API.UpdateList
       Test.API.Worker
+      Test.Core.Aeson
       Test.Core.LinearAlgebra
       Test.Core.Notifications
       Test.Core.Orchestrator

src/Gargantext/Core/Viz/Phylo.hs

@@ -21,19 +21,22 @@ in science evolution — the rise and fall of scientific fields. PloS
 one 8, e54847.
 -}
 
-{-# LANGUAGE DeriveAnyClass   #-}
-{-# LANGUAGE DerivingStrategies #-}
-{-# LANGUAGE LambdaCase #-}
-{-# LANGUAGE TemplateHaskell   #-}
-{-# LANGUAGE TypeApplications #-}
+{-# LANGUAGE DeriveAnyClass      #-}
+{-# LANGUAGE DerivingStrategies  #-}
+{-# LANGUAGE LambdaCase          #-}
+{-# LANGUAGE ScopedTypeVariables #-}
+{-# LANGUAGE TemplateHaskell     #-}
+{-# LANGUAGE TypeApplications    #-}
 
 module Gargantext.Core.Viz.Phylo where
 
 import Control.Lens (over)
+import Control.Monad.Fail (fail)
+import Data.Aeson (object, withObject, (.=), (.:))
 import Data.Aeson.Types qualified as JS
 import Data.List.NonEmpty qualified as NE
 import Data.Swagger (ToSchema(..), genericDeclareNamedSchema)
-import Data.Text (pack)
+import Data.Text (pack, unpack)
 import Data.Text.Lazy qualified as TextLazy
 import Data.TreeDiff (ToExpr (..))
 import Data.Vector (Vector)
@@ -109,33 +112,33 @@ data Synchrony =
     | ByProximityDistribution
       { _bpd_sensibility :: Double
       , _bpd_strategy :: SynchronyStrategy }
-    deriving (Show,Generic,Eq,ToExpr)
+    deriving (Show, Generic, Eq, ToExpr)
 
 instance ToSchema Synchrony where
   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 
+
+data TimeUnitCriteria =
+  TimeUnitCriteria { _tuc_period        :: Int
+                   , _tuc_step          :: Int
+                   , _tuc_matchingFrame :: Int }
+      deriving (Show, Generic, Eq, NFData, ToExpr)
+instance ToSchema TimeUnitCriteria where
+  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_tuc")
+
+defaultTimeUnitCriteria :: TimeUnitCriteria
+defaultTimeUnitCriteria = TimeUnitCriteria { _tuc_period = 3
+                                           , _tuc_step = 1
+                                           , _tuc_matchingFrame = 5 }
+
+
 data TimeUnit =
-      Epoch
-      { _epoch_period :: Int
-      , _epoch_step   :: Int
-      , _epoch_matchingFrame :: Int }
-    | Year
-      { _year_period :: Int
-      , _year_step   :: Int
-      , _year_matchingFrame :: Int }
-    | Month
-      { _month_period :: Int
-      , _month_step   :: Int
-      , _month_matchingFrame :: Int }
-    | Week
-      { _week_period :: Int
-      , _week_step   :: Int
-      , _week_matchingFrame :: Int }
-    | Day
-      { _day_period :: Int
-      , _day_step   :: Int
-      , _day_matchingFrame :: Int }
-      deriving (Show,Generic,Eq,NFData,ToExpr)
+      Epoch TimeUnitCriteria
+    | Year TimeUnitCriteria
+    | Month TimeUnitCriteria
+    | Week TimeUnitCriteria
+    | Day TimeUnitCriteria
+      deriving (Show, Generic, Eq, NFData, ToExpr)
 
 instance ToSchema TimeUnit where
   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
@@ -146,6 +149,13 @@ data MaxCliqueFilter = ByThreshold | ByNeighbours deriving (Show,Generic,Eq,ToEx
 instance ToSchema MaxCliqueFilter where
   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 
+timeUnitTUC :: TimeUnit -> TimeUnitCriteria
+timeUnitTUC (Epoch tuc) = tuc
+timeUnitTUC (Year tuc) = tuc
+timeUnitTUC (Month tuc) = tuc
+timeUnitTUC (Week tuc) = tuc
+timeUnitTUC (Day tuc) = tuc
+
 
 
 data Cluster =
@@ -237,7 +247,7 @@ defaultConfig =
             , findAncestors  = False
             , phyloSynchrony = ByProximityThreshold 0.6 0 AllBranches MergeAllGroups
             , phyloQuality   = Quality 0.5 3
-            , timeUnit       = Year 3 1 5
+            , timeUnit       = Year defaultTimeUnitCriteria
             , clique         = Fis 2 3
             , exportLabel    = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2]
             , exportSort     = ByHierarchy Desc
@@ -266,8 +276,51 @@ instance ToJSON PhyloSimilarity
 instance FromJSON SeaElevation
 instance ToJSON SeaElevation
 
-instance FromJSON TimeUnit
-instance ToJSON TimeUnit
+instance FromJSON TimeUnitCriteria where
+  parseJSON = withObject "TimeUnitCriteria" $ \o -> do
+    _tuc_period <- o .: "period"
+    _tuc_step <- o .: "step"
+    _tuc_matchingFrame <- o .: "matchingFrame"
+    pure $ TimeUnitCriteria { .. }
+instance ToJSON TimeUnitCriteria where
+  toJSON (TimeUnitCriteria { .. }) =
+    object [ ("period" .= toJSON _tuc_period)
+           , ("step" .= toJSON _tuc_step)
+           , ("matchingFrame" .= toJSON _tuc_matchingFrame) ]
+
+
+instance FromJSON TimeUnit where
+  parseJSON = withObject "TimeUnit" $ \o -> do
+    tag :: Text <- o .: "tag"
+    tuc :: TimeUnitCriteria <- o .: "time_unit_criteria"
+    case tag of
+      "Epoch" -> do
+        pure $ Epoch tuc
+      "Year" -> do
+        pure $ Year tuc
+      "Month" -> do
+        pure $ Month tuc
+      "Week" -> do
+        pure $ Week tuc
+      "Day" -> do
+        pure $ Day tuc
+      s -> fail $ "Unknown tag " <> unpack s
+instance ToJSON TimeUnit where
+  toJSON (Epoch tuc) =
+    object [ ("tag" .= toJSON ("Epoch" :: Text))
+           , ("time_unit_criteria") .= toJSON tuc ]
+  toJSON (Year tuc) =
+    object [ ("tag" .= toJSON ("Year" :: Text))
+           , ("time_unit_criteria") .= toJSON tuc ]
+  toJSON (Month tuc) =
+    object [ ("tag" .= toJSON ("Month" :: Text))
+           , ("time_unit_criteria") .= toJSON tuc ]
+  toJSON (Week tuc) =
+    object [ ("tag" .= toJSON ("Week" :: Text))
+           , ("time_unit_criteria") .= toJSON tuc ]
+  toJSON (Day tuc) =
+    object [ ("tag" .= toJSON ("Day" :: Text))
+           , ("time_unit_criteria") .= toJSON tuc ]
 
 instance FromJSON MaxCliqueFilter
 instance ToJSON MaxCliqueFilter

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

@@ -33,7 +33,7 @@ import Gargantext.Core.NodeStory.Types (HasNodeStory, NodeStoryEnv, HasNodeStory
 import Gargantext.Core.Text.Ngrams (NgramsType(..))
 import Gargantext.Core.Text.Terms.WithList (Patterns, buildPatterns, termsInText)
 import Gargantext.Core.Types.Main (ListType(MapTerm))
-import Gargantext.Core.Viz.Phylo (TimeUnit(..), Date, Document(..), PhyloConfig(..), Phylo (_phylo_computeTime), trackComputeTime, ComputeTimeHistory)
+import Gargantext.Core.Viz.Phylo (TimeUnit(..), Date, Document(..), PhyloConfig(..), Phylo (_phylo_computeTime), trackComputeTime, ComputeTimeHistory, defaultTimeUnitCriteria)
 import Gargantext.Core.Viz.Phylo.PhyloExport (toPhyloExport, dotToFile)
 import Gargantext.Core.Viz.Phylo.PhyloMaker  (toPhylo, toPhyloWithoutLink)
 import Gargantext.Core.Viz.Phylo.PhyloTools  ({-printIOMsg, printIOComment,-} setConfig)
@@ -181,7 +181,7 @@ context2phyloDocument timeUnit context (ngs_terms, ngs_sources) = do
     text'    = maybe [] toText $ Map.lookup (nodeId2ContextId contextId) ngs_terms
     sources' = maybe [] toText $ Map.lookup (nodeId2ContextId contextId) ngs_sources
 
-  pure $ Document date date' text' Nothing sources' (Year 3 1 5)
+  pure $ Document date date' text' Nothing sources' (Year defaultTimeUnitCriteria)
 
 
 -- TODO better default date and log the errors to improve data quality

src/Gargantext/Core/Viz/Phylo/Example.hs

@@ -110,7 +110,7 @@ docs = map (\(d,t)
                 (filter (\n -> isRoots n (foundations ^. foundations_roots)) $ monoTexts t) 
                 Nothing
                 []
-                (Year 3 1 5)
+                (Year defaultTimeUnitCriteria)
             ) corpus
 
 

src/Gargantext/Core/Viz/Phylo/PhyloTools.hs

@@ -189,28 +189,13 @@ toTimeScale dates step =
 
 
 getTimeStep :: TimeUnit -> Int
-getTimeStep time = case time of
-    Epoch { .. } -> _epoch_step
-    Year  { .. } -> _year_step
-    Month { .. } -> _month_step
-    Week  { .. } -> _week_step
-    Day   { .. } -> _day_step
+getTimeStep time = _tuc_step $ timeUnitTUC time
 
 getTimePeriod :: TimeUnit -> Int
-getTimePeriod time = case time of
-    Epoch { .. } -> _epoch_period
-    Year  { .. } -> _year_period
-    Month { .. } -> _month_period
-    Week  { .. } -> _week_period
-    Day   { .. } -> _day_period
+getTimePeriod time = _tuc_period $ timeUnitTUC time
 
 getTimeFrame :: TimeUnit -> Int
-getTimeFrame time = case time of
-    Epoch { .. } -> _epoch_matchingFrame
-    Year  { .. } -> _year_matchingFrame
-    Month { .. } -> _month_matchingFrame
-    Week  { .. } -> _week_matchingFrame
-    Day   { .. } -> _day_matchingFrame
+getTimeFrame time = _tuc_matchingFrame $ timeUnitTUC time
 
 -------------
 -- | Fis | --

src/Gargantext/Core/Worker/Types.hs

-{-# LANGUAGE StandaloneDeriving #-}
 {-# LANGUAGE DerivingStrategies #-}
+{-# LANGUAGE StandaloneDeriving #-}
+
 {-|
 Module      : Gargantext.Core.Worker.Types
 Description : Some useful worker types

test/Main.hs

@@ -15,6 +15,7 @@ import Test.Database.Operations qualified as DB
 import Test.Database.Transactions qualified as DBT
 import Test.Hspec
 import Test.Server.ReverseProxy qualified as ReverseProxy
+import Test.Core.Aeson                 qualified as AesonTest
 import Test.Core.LinearAlgebra         qualified as LinearAlgebra
 import Test.Core.Notifications         qualified as Notifications
 import Test.Core.Orchestrator          qualified as Orchestrator
@@ -93,6 +94,7 @@ main = do
       DBT.tests
       DB.nodeStoryTests
       describe "Utils" $ Utils.test
+      describe "Aeson" $ AesonTest.tests
       describe "Graph Clustering" $ Clustering.test
       describe "Graph Distance" $ Distance.test
       describe "Date split" $ PD.testDateSplit

test/Test/Core/Text.hs

 {-|
-Module      : Graph.Clustering
+Module      : Test.Core.Text
 Description : Basic tests to avoid quick regression
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3

test/Test/Core/Worker.hs

@@ -11,19 +11,15 @@ Portability : POSIX
 
 module Test.Core.Worker where
 
-import Data.Aeson qualified as Aeson
-import Gargantext.Core.Worker.Jobs.Types (Job(..))
 import Gargantext.Prelude
 import Test.Instances ()
 import Test.Hspec
-import Test.Hspec.QuickCheck
 
 
 
 tests :: Spec
-tests = describe "worker unit tests" $
-    prop "Worker Job to/from JSON serialization is correct" $
-      \job -> Aeson.decode (Aeson.encode (job :: Job)) == Just job
+tests =
+  describe "worker unit tests" $ pure ()
 
   -- , testProperty "JobInfo to/from JSON serialization is correct" $
   --     \ji -> Aeson.decode (Aeson.encode (ji :: JobInfo)) == Just ji

test/Test/Instances.hs

@@ -273,6 +273,7 @@ instance Arbitrary Phylo.Synchrony where arbitrary = genericArbitrary
 instance Arbitrary Phylo.SynchronyScope where arbitrary = genericArbitrary
 instance Arbitrary Phylo.SynchronyStrategy where arbitrary = genericArbitrary
 instance Arbitrary Phylo.Tagger where arbitrary = genericArbitrary
+instance Arbitrary Phylo.TimeUnitCriteria where arbitrary = genericArbitrary
 instance Arbitrary Phylo.TimeUnit where arbitrary = genericArbitrary
 instance Arbitrary PhyloData where arbitrary = genericArbitrary
 

test/Test/Offline/Phylo.hs

-{-# LANGUAGE TypeApplications #-}
 {-# LANGUAGE ScopedTypeVariables #-}
 {-# LANGUAGE QuasiQuotes #-}
 {-# LANGUAGE TupleSections #-}
+{-# LANGUAGE TypeApplications #-}
 
 module Test.Offline.Phylo (tests) where
 
@@ -45,7 +45,7 @@ phyloTestConfig = PhyloConfig {
   , findAncestors = False
   , 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}
+  , timeUnit = Year defaultTimeUnitCriteria
   , 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}
@@ -136,7 +136,15 @@ testNadalWithoutLinkExpectedOutput = do
   mapList <- fileToList (listParser config) (listPath config)
   corpus <- fileToDocsDefault (corpusParser config)
                         (corpusPath config)
-                        [Year 3 1 5,Month 3 1 5,Week 4 2 5]
+                        [ Year $ TimeUnitCriteria { _tuc_period = 3
+                                                  , _tuc_step = 1
+                                                  , _tuc_matchingFrame = 5 }
+                        , Month $ TimeUnitCriteria { _tuc_period = 3
+                                                   , _tuc_step = 1
+                                                   , _tuc_matchingFrame = 5 }
+                        , Week $ TimeUnitCriteria { _tuc_period = 4
+                                                  , _tuc_step = 2
+                                                  , _tuc_matchingFrame = 5 } ]
                         mapList
   pure ( "test-data/phylo/nadal.golden.json"
        , JSON.encodePretty $ setConfig phyloTestConfig $ toPhyloWithoutLink corpus config
@@ -153,7 +161,15 @@ testSmallPhyloWithoutLinkExpectedOutput = do
   mapList <- fileToList (listParser config) (listPath config)
   corpus <- fileToDocsDefault (corpusParser config)
                         (corpusPath config)
-                        [Year 3 1 5,Month 3 1 5,Week 4 2 5]
+                        [ Year $ TimeUnitCriteria { _tuc_period = 3
+                                                  , _tuc_step = 1
+                                                  , _tuc_matchingFrame = 5 }
+                        , Month $ TimeUnitCriteria { _tuc_period = 3
+                                                   , _tuc_step = 1
+                                                   , _tuc_matchingFrame = 5 }
+                        , Week $ TimeUnitCriteria { _tuc_period = 4
+                                                  , _tuc_step = 2
+                                                  , _tuc_matchingFrame = 5 } ]
                         mapList
   let actual = setConfig phyloTestConfig $ toPhyloWithoutLink corpus config
   expected   <- setConfig phyloTestConfig <$> (readPhylo =<< getDataFileName "test-data/phylo/small-phylo.golden.json")
@@ -286,7 +302,15 @@ testToPhyloDeterminism = do
   mapList <- tsvMapTermList (listPath config)
   corpus <- fileToDocsDefault (corpusParser config)
                               (corpusPath config)
-                              [Year 3 1 5,Month 3 1 5,Week 4 2 5]
+                              [ Year $ TimeUnitCriteria { _tuc_period = 3
+                                                        , _tuc_step = 1
+                                                        , _tuc_matchingFrame = 5 }
+                              , Month $ TimeUnitCriteria { _tuc_period = 3
+                                                         , _tuc_step = 1
+                                                         , _tuc_matchingFrame = 5 }
+                              , Week $ TimeUnitCriteria { _tuc_period = 4
+                                                        , _tuc_step = 2
+                                                        , _tuc_matchingFrame = 5 } ]
                               mapList
   let actual = setConfig phyloTestConfig $ toPhylo $ toPhyloWithoutLink corpus config
   pure ( "test-data/phylo/187481.json"