src/Gargantext/Core/Viz/AdaptativePhylo.hs

   1 {-|
   2 Module      : Gargantext.Core.Viz.AdaptativePhylo
   3 Description : Phylomemy definitions and types.
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 Specifications of Phylomemy export format.
  11
  12 Phylomemy can be described as a Temporal Graph with different scale of
  13 granularity of group of ngrams (terms and multi-terms).
  14
  15 The main type is Phylo which is synonym of Phylomemy (only difference is
  16 the number of chars).
  17
  18 References:
  19 Chavalarias, D., Cointet, J.-P., 2013. Phylomemetic patterns
  20 in science evolution — the rise and fall of scientific fields. PloS
  21 one 8, e54847.
  22 -}
  23
  24 {-# LANGUAGE DeriveAnyClass   #-}
  25 {-# LANGUAGE TemplateHaskell   #-}
  26
  27 module Gargantext.Core.Viz.AdaptativePhylo where
  28
  29 import Data.Aeson
  30 import Data.Aeson.TH (deriveJSON)
  31 import Data.Text   (Text, pack)
  32 import Data.Vector (Vector)
  33 import Data.Map (Map)
  34
  35 import Gargantext.Core.Utils.Prefix (unPrefix)
  36 import Gargantext.Prelude
  37 import Gargantext.Core.Text.Context (TermList)
  38
  39 import GHC.Generics
  40 import GHC.IO (FilePath)
  41 import Control.DeepSeq (NFData)
  42 import Control.Lens (makeLenses)
  43
  44 import qualified Data.Text.Lazy as TextLazy
  45
  46
  47 ----------------
  48 -- | Config | --
  49 ----------------
  50
  51
  52 data CorpusParser =
  53       Wos {_wos_limit :: Int}
  54     | Csv {_csv_limit :: Int}
  55     deriving (Show,Generic,Eq)
  56
  57 data SeaElevation =
  58       Constante
  59       { _cons_start :: Double
  60       , _cons_step  :: Double }
  61     | Adaptative
  62       { _adap_granularity :: Double }
  63     deriving (Show,Generic,Eq)
  64
  65 data Proximity =
  66       WeightedLogJaccard
  67       { _wlj_sensibility   :: Double
  68 {-
  69       -- , _wlj_thresholdInit :: Double
  70       -- , _wlj_thresholdStep :: Double
  71       -- | max height for sea level in temporal matching
  72       -- , _wlj_elevation     :: Double
  73 -}
  74       }
  75     | WeightedLogSim
  76       { _wlj_sensibility   :: Double
  77 {-
  78       -- , _wlj_thresholdInit :: Double
  79       -- , _wlj_thresholdStep :: Double
  80       -- | max height for sea level in temporal matching
  81       -- , _wlj_elevation     :: Double
  82 -}
  83       }
  84     | Hamming
  85     deriving (Show,Generic,Eq)
  86
  87
  88 data SynchronyScope = SingleBranch | SiblingBranches | AllBranches deriving (Show,Generic,Eq)
  89
  90 data SynchronyStrategy = MergeRegularGroups | MergeAllGroups deriving (Show,Generic,Eq)
  91
  92 data Synchrony =
  93       ByProximityThreshold
  94       { _bpt_threshold :: Double
  95       , _bpt_sensibility :: Double
  96       , _bpt_scope :: SynchronyScope
  97       , _bpt_strategy :: SynchronyStrategy }
  98     | ByProximityDistribution
  99       { _bpd_sensibility :: Double
 100       , _bpd_strategy :: SynchronyStrategy }
 101     deriving (Show,Generic,Eq)
 102
 103
 104 data TimeUnit =
 105       Year
 106       { _year_period :: Int
 107       , _year_step   :: Int
 108       , _year_matchingFrame :: Int }
 109       deriving (Show,Generic,Eq)
 110
 111 data CliqueFilter = ByThreshold | ByNeighbours deriving (Show,Generic,Eq)
 112
 113 data Clique =
 114       Fis
 115       { _fis_support :: Int
 116       , _fis_size    :: Int }
 117     | MaxClique
 118       { _mcl_size      :: Int
 119       , _mcl_threshold :: Double
 120       , _mcl_filter    :: CliqueFilter }
 121       deriving (Show,Generic,Eq)
 122
 123
 124 data Quality =
 125      Quality { _qua_granularity :: Double
 126              , _qua_minBranch   :: Int }
 127       deriving (Show,Generic,Eq)
 128
 129
 130 data Config =
 131      Config { corpusPath     :: FilePath
 132             , listPath       :: FilePath
 133             , outputPath     :: FilePath
 134             , corpusParser   :: CorpusParser
 135             , phyloName      :: Text
 136             , phyloLevel     :: Int
 137             , phyloProximity :: Proximity
 138             , seaElevation   :: SeaElevation
 139             , findAncestors  :: Bool
 140             , phyloSynchrony :: Synchrony
 141             , phyloQuality   :: Quality
 142             , timeUnit       :: TimeUnit
 143             , clique         :: Clique
 144             , exportLabel    :: [PhyloLabel]
 145             , exportSort     :: Sort
 146             , exportFilter   :: [Filter]
 147             } deriving (Show,Generic,Eq)
 148
 149
 150 defaultConfig :: Config
 151 defaultConfig =
 152      Config { corpusPath     = ""
 153             , listPath       = ""
 154             , outputPath     = ""
 155             , corpusParser   = Csv 1000
 156             , phyloName      = pack "Default Phylo"
 157             , phyloLevel     = 2
 158             , phyloProximity = WeightedLogJaccard 10
 159             , seaElevation   = Constante 0.1 0.1
 160             , findAncestors  = True
 161             , phyloSynchrony = ByProximityThreshold 0.1 10 SiblingBranches MergeAllGroups
 162             , phyloQuality   = Quality 0 1
 163             , timeUnit       = Year 3 1 5
 164             , clique         = MaxClique 0 3 ByNeighbours
 165             , exportLabel    = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2]
 166             , exportSort     = ByHierarchy
 167             , exportFilter   = [ByBranchSize 2]
 168             }
 169
 170 instance FromJSON Config
 171 instance ToJSON Config
 172 instance FromJSON CorpusParser
 173 instance ToJSON CorpusParser
 174 instance FromJSON Proximity
 175 instance ToJSON Proximity
 176 instance FromJSON SeaElevation
 177 instance ToJSON SeaElevation
 178 instance FromJSON TimeUnit
 179 instance ToJSON TimeUnit
 180 instance FromJSON CliqueFilter
 181 instance ToJSON CliqueFilter
 182 instance FromJSON Clique
 183 instance ToJSON Clique
 184 instance FromJSON PhyloLabel
 185 instance ToJSON PhyloLabel
 186 instance FromJSON Tagger
 187 instance ToJSON Tagger
 188 instance FromJSON Sort
 189 instance ToJSON Sort
 190 instance FromJSON Order
 191 instance ToJSON Order
 192 instance FromJSON Filter
 193 instance ToJSON Filter
 194 instance FromJSON SynchronyScope
 195 instance ToJSON SynchronyScope
 196 instance FromJSON SynchronyStrategy
 197 instance ToJSON SynchronyStrategy
 198 instance FromJSON Synchrony
 199 instance ToJSON Synchrony
 200 instance FromJSON Quality
 201 instance ToJSON Quality
 202
 203
 204 -- | Software parameters
 205 data Software =
 206      Software { _software_name    :: Text
 207               , _software_version :: Text
 208      } deriving (Generic, Show, Eq)
 209
 210 defaultSoftware :: Software
 211 defaultSoftware =
 212       Software { _software_name    = pack "Gargantext"
 213                , _software_version = pack "v4" }
 214
 215
 216 -- | Global parameters of a Phylo
 217 data PhyloParam =
 218      PhyloParam { _phyloParam_version  :: Text
 219                 , _phyloParam_software :: Software
 220                 , _phyloParam_config   :: Config
 221      } deriving (Generic, Show, Eq)
 222
 223 defaultPhyloParam :: PhyloParam
 224 defaultPhyloParam =
 225       PhyloParam { _phyloParam_version  = pack "v2.adaptative"
 226                  , _phyloParam_software = defaultSoftware
 227                  , _phyloParam_config   = defaultConfig }
 228
 229
 230 ------------------
 231 -- | Document | --
 232 ------------------
 233
 234
 235 -- | Date : a simple Integer
 236 type Date = Int
 237
 238 -- | Ngrams : a contiguous sequence of n terms
 239 type Ngrams = Text
 240
 241 -- | Document : a piece of Text linked to a Date
 242 data Document = Document
 243       { date :: Date
 244       , text :: [Ngrams]
 245       } deriving (Eq,Show,Generic,NFData)
 246
 247
 248 --------------------
 249 -- | Foundation | --
 250 --------------------
 251
 252
 253 -- | The Foundations of a Phylo created from a given TermList
 254 data PhyloFoundations = PhyloFoundations
 255       { _foundations_roots   :: !(Vector Ngrams)
 256       , _foundations_mapList :: TermList
 257       } deriving (Generic, Show, Eq)
 258
 259
 260 ---------------------------
 261 -- | Coocurency Matrix | --
 262 ---------------------------
 263
 264
 265 -- | Cooc : a coocurency matrix between two ngrams
 266 type Cooc =  Map (Int,Int) Double
 267
 268
 269 -------------------
 270 -- | Phylomemy | --
 271 -------------------
 272
 273
 274 -- | Phylo datatype of a phylomemy
 275 --  foundations : the foundations of the phylo
 276 --  timeCooc : a Map of coocurency by minimal unit of time (ex: by year)
 277 --  timeDocs : a Map with the numbers of docs by minimal unit of time (ex: by year)
 278 --  param : the parameters of the phylomemy (with the user's configuration)
 279 --  periods : the temporal steps of a phylomemy
 280 data Phylo =
 281      Phylo { _phylo_foundations  :: PhyloFoundations
 282            , _phylo_timeCooc     :: !(Map Date Cooc)
 283            , _phylo_timeDocs     :: !(Map Date Double)
 284            , _phylo_termFreq     :: !(Map Int Double)
 285            , _phylo_lastTermFreq :: !(Map Int Double)
 286            , _phylo_horizon      :: !(Map (PhyloGroupId,PhyloGroupId) Double)
 287            , _phylo_groupsProxi  :: !(Map (PhyloGroupId,PhyloGroupId) Double)
 288            , _phylo_param        :: PhyloParam
 289            , _phylo_periods      :: Map PhyloPeriodId PhyloPeriod
 290            }
 291            deriving (Generic, Show, Eq)
 292
 293
 294 -- | PhyloPeriodId : the id of a given period
 295 type PhyloPeriodId = (Date,Date)
 296
 297 -- | PhyloPeriod : steps of a phylomemy on a temporal axis
 298 --  id: tuple (start date, end date) of the temporal step of the phylomemy
 299 --  levels: levels of granularity
 300 data PhyloPeriod =
 301      PhyloPeriod { _phylo_periodPeriod :: (Date,Date)
 302                  , _phylo_periodLevels :: Map PhyloLevelId PhyloLevel
 303                  } deriving (Generic, Show, Eq)
 304
 305
 306 -- | Level : a level of clustering
 307 type Level = Int
 308
 309 -- | PhyloLevelId : the id of a level of clustering in a given period
 310 type PhyloLevelId  = (PhyloPeriodId,Level)
 311
 312 -- | PhyloLevel : levels of phylomemy on a synchronic axis
 313 -- Levels description:
 314 -- Level 0: The foundations and the base of the phylo
 315 -- Level 1: First level of clustering (the Fis)
 316 -- Level [2..N]: Nth level of synchronic clustering (cluster of Fis)
 317 data PhyloLevel =
 318      PhyloLevel { _phylo_levelPeriod :: (Date,Date)
 319                 , _phylo_levelLevel  :: Level
 320                 , _phylo_levelGroups :: Map PhyloGroupId PhyloGroup
 321                 }
 322                 deriving (Generic, Show, Eq)
 323
 324
 325 type PhyloGroupId  = (PhyloLevelId, Int)
 326
 327 -- | BranchId : (a level, a sequence of branch index)
 328 -- the sequence is a path of heritage from the most to the less specific branch
 329 type PhyloBranchId = (Level, [Int])
 330
 331 -- | PhyloGroup : group of ngrams at each level and period
 332 data PhyloGroup =
 333       PhyloGroup { _phylo_groupPeriod   :: (Date,Date)
 334                  , _phylo_groupLevel    :: Level
 335                  , _phylo_groupIndex    :: Int
 336                  , _phylo_groupLabel    :: Text
 337                  , _phylo_groupSupport  :: Support
 338                  , _phylo_groupNgrams   :: [Int]
 339                  , _phylo_groupCooc     :: !(Cooc)
 340                  , _phylo_groupBranchId :: PhyloBranchId
 341                  , _phylo_groupMeta     :: Map Text [Double]
 342                  , _phylo_groupLevelParents  :: [Pointer]
 343                  , _phylo_groupLevelChilds   :: [Pointer]
 344                  , _phylo_groupPeriodParents :: [Pointer]
 345                  , _phylo_groupPeriodChilds  :: [Pointer]
 346                  , _phylo_groupAncestors     :: [Pointer]
 347                  }
 348                  deriving (Generic, Show, Eq, NFData)
 349
 350 -- | Weight : A generic mesure that can be associated with an Id
 351 type Weight = Double
 352
 353 -- | Pointer : A weighted pointer to a given PhyloGroup
 354 type Pointer = (PhyloGroupId, Weight)
 355
 356 data Filiation = ToParents | ToChilds deriving (Generic, Show)
 357 data PointerType = TemporalPointer | LevelPointer deriving (Generic, Show)
 358
 359
 360 ----------------------
 361 -- | Phylo Clique | --
 362 ----------------------
 363
 364 -- | Support : Number of Documents where a Clique occurs
 365 type Support  = Int
 366
 367 data PhyloClique = PhyloClique
 368   { _phyloClique_nodes   :: [Int]
 369   , _phyloClique_support :: Support
 370   , _phyloClique_period  :: (Date,Date)
 371   } deriving (Generic,NFData,Show,Eq)
 372
 373 ----------------
 374 -- | Export | --
 375 ----------------
 376
 377 type DotId = TextLazy.Text
 378
 379 data EdgeType = GroupToGroup | BranchToGroup | BranchToBranch | GroupToAncestor | PeriodToPeriod deriving (Show,Generic,Eq)
 380
 381 data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq)
 382
 383 data Order = Asc | Desc deriving (Show,Generic,Eq)
 384
 385 data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy deriving (Show,Generic,Eq)
 386
 387 data Tagger = MostInclusive | MostEmergentInclusive | MostEmergentTfIdf deriving (Show,Generic,Eq)
 388
 389 data PhyloLabel =
 390       BranchLabel
 391       { _branch_labelTagger :: Tagger
 392       , _branch_labelSize   :: Int }
 393     | GroupLabel
 394       { _group_labelTagger  :: Tagger
 395       , _group_labelSize    :: Int }
 396     deriving (Show,Generic,Eq)
 397
 398 data PhyloBranch =
 399       PhyloBranch
 400       { _branch_id :: PhyloBranchId
 401       , _branch_canonId  :: [Int]
 402       , _branch_seaLevel :: [Double]
 403       , _branch_x        :: Double
 404       , _branch_y        :: Double
 405       , _branch_w        :: Double
 406       , _branch_t        :: Double
 407       , _branch_label    :: Text
 408       , _branch_meta     :: Map Text [Double]
 409       } deriving (Generic, Show, Eq)
 410
 411 data PhyloExport =
 412       PhyloExport
 413       { _export_groups    :: [PhyloGroup]
 414       , _export_branches  :: [PhyloBranch]
 415       } deriving (Generic, Show)
 416
 417 ----------------
 418 -- | Lenses | --
 419 ----------------
 420
 421 makeLenses ''Config
 422 makeLenses ''Proximity
 423 makeLenses ''SeaElevation
 424 makeLenses ''Quality
 425 makeLenses ''Clique
 426 makeLenses ''PhyloLabel
 427 makeLenses ''TimeUnit
 428 makeLenses ''PhyloFoundations
 429 makeLenses ''PhyloClique
 430 makeLenses ''Phylo
 431 makeLenses ''PhyloPeriod
 432 makeLenses ''PhyloLevel
 433 makeLenses ''PhyloGroup
 434 makeLenses ''PhyloParam
 435 makeLenses ''PhyloExport
 436 makeLenses ''PhyloBranch
 437
 438 ------------------------
 439 -- | JSON instances | --
 440 ------------------------
 441
 442 instance FromJSON Phylo
 443 instance ToJSON Phylo
 444 instance FromJSON PhyloParam
 445 instance ToJSON PhyloParam
 446 instance FromJSON PhyloPeriod
 447 instance ToJSON PhyloPeriod
 448 instance FromJSON PhyloLevel
 449 instance ToJSON PhyloLevel
 450 instance FromJSON Software
 451 instance ToJSON Software
 452 instance FromJSON PhyloGroup
 453 instance ToJSON PhyloGroup
 454
 455 $(deriveJSON (unPrefix "_foundations_"  ) ''PhyloFoundations)