src/Gargantext/Viz/Phylo.hs

   1 {-|
   2 Module      : Gargantext.Viz.Phylo
   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
  25 {-# LANGUAGE DeriveGeneric     #-}
  26 {-# LANGUAGE NoImplicitPrelude #-}
  27 {-# LANGUAGE TemplateHaskell   #-}
  28
  29 module Gargantext.Viz.Phylo where
  30
  31 import Control.Lens (makeLenses)
  32 import Data.Aeson.TH (deriveJSON)
  33 import Data.Maybe   (Maybe)
  34 import Data.Text    (Text)
  35 import Data.Set     (Set)
  36 import Data.Map     (Map)
  37 import Data.Vector  (Vector)
  38 import Data.Time.Clock.POSIX  (POSIXTime)
  39 import GHC.Generics (Generic)
  40 import Gargantext.Database.Schema.Ngrams (NgramsId)
  41 import Gargantext.Core.Utils.Prefix (unPrefix)
  42 import Gargantext.Prelude
  43
  44 ------------------------------------------------------------------------
  45 data PhyloExport =
  46      PhyloExport { _phyloExport_param :: PhyloParam
  47                  , _phyloExport_data :: Phylo
  48      } deriving (Generic)
  49
  50 -- | .phylo parameters
  51 data PhyloParam =
  52      PhyloParam { _phyloParam_version     :: Text -- Double ?
  53                 , _phyloParam_software    :: Software
  54                 , _phyloParam_params      :: Hash
  55      } deriving (Generic)
  56
  57 type Hash = Text
  58
  59 -- | Software
  60 -- TODO move somewhere since it is generic
  61 data Software =
  62      Software { _software_name    :: Text
  63               , _software_version :: Text
  64      } deriving (Generic)
  65
  66 ------------------------------------------------------------------------
  67 -- | Phylo datatype descriptor of a phylomemy
  68 -- Duration : time Segment of the whole phylomemy (start,end)
  69 -- Ngrams   : list of all (possible) terms contained in the phylomemy (with their id)
  70 -- Steps    : list of all steps to build the phylomemy
  71 data Phylo =
  72      Phylo { _phylo_duration :: (Start, End)
  73            , _phylo_ngrams   :: PhyloNgrams
  74            , _phylo_periods  :: [PhyloPeriod]
  75            }
  76            deriving (Generic, Show)
  77
  78
  79 -- | Date : a simple Integer
  80 type Date = Int
  81
  82 -- | UTCTime in seconds since UNIX epoch
  83 -- type Start   = POSIXTime
  84 -- type End     = POSIXTime
  85 type Start   = Date
  86 type End     = Date
  87
  88 -- | PhyloStep : steps of phylomemy on temporal axis
  89 -- Period: tuple (start date, end date) of the step of the phylomemy
  90 -- Levels: levels of granularity
  91 data PhyloPeriod =
  92      PhyloPeriod { _phylo_periodId     :: PhyloPeriodId
  93                  , _phylo_periodLevels :: [PhyloLevel]
  94                  }
  95                  deriving (Generic, Show)
  96
  97 type PhyloPeriodId = (Start, End)
  98
  99 -- | PhyloLevel : levels of phylomemy on level axis
 100 -- Levels description:
 101 -- Level -1: Ngram equals itself         (by identity) == _phylo_Ngrams
 102 -- Level  0: Group of synonyms           (by stems + by qualitative expert meaning)
 103 -- Level  1: First level of clustering
 104 -- Level  N: Nth   level of clustering
 105 data PhyloLevel =
 106      PhyloLevel { _phylo_levelId     :: PhyloLevelId
 107                 , _phylo_levelGroups :: [PhyloGroup]
 108                 }
 109                 deriving (Generic, Show)
 110
 111 type PhyloLevelId = (PhyloPeriodId, Int)
 112
 113 -- | PhyloGroup : group of ngrams at each level and step
 114 -- Label : maybe has a label as text
 115 -- Ngrams: set of terms that build the group
 116 -- Quality : map of measures (support, etc.) that depict some qualitative aspects of a phylo
 117 -- Period Parents|Childs: weighted link to Parents|Childs (Temporal Period   axis)
 118 -- Level  Parents|Childs: weighted link to Parents|Childs (Level Granularity axis)
 119 -- Pointers are directed link from Self to any PhyloGroup (/= Self ?)
 120 data PhyloGroup =
 121      PhyloGroup { _phylo_groupId            :: PhyloGroupId
 122                 , _phylo_groupLabel         :: Text
 123                 , _phylo_groupNgrams        :: [Int]
 124                 , _phylo_groupQuality       :: Map Text Double
 125
 126                 , _phylo_groupPeriodParents :: [Pointer]
 127                 , _phylo_groupPeriodChilds  :: [Pointer]
 128
 129                 , _phylo_groupLevelParents  :: [Pointer]
 130                 , _phylo_groupLevelChilds   :: [Pointer]
 131                 }
 132                 deriving (Generic, Show, Eq)
 133
 134 type PhyloGroupId = (PhyloLevelId, Int)
 135 type Pointer      = (PhyloGroupId, Weight)
 136 type Weight       = Double
 137
 138
 139
 140
 141 -- | Ngrams : a contiguous sequence of n terms
 142 type Ngrams = Text
 143 -- | PhyloNgrams : Vector of all the Ngrams (PhyloGroup of level -1) used within a Phylo
 144 type PhyloNgrams = Vector Ngrams
 145
 146
 147 -- | Clique : Set of ngrams cooccurring in the same Document
 148 type Clique  = Set Ngrams
 149 -- | Support : Number of Documents where a Clique occurs
 150 type Support = Int
 151 -- | Fis : Frequent Items Set (ie: the association between a Clique and a Support)
 152 type Fis = Map Clique Support
 153
 154
 155 data Direction = From | To
 156     deriving (Show, Eq)
 157
 158 data LevelLabel = Level_m1 | Level_0 | Level_1 | Level_mN | Level_N | Level_pN
 159   deriving (Show, Eq, Enum, Bounded)
 160
 161 data Level =
 162      Level { _levelLabel :: LevelLabel
 163            , _levelValue :: Int
 164            } deriving (Show)
 165
 166 data LevelLink =
 167      LevelLink { _levelFrom :: Level
 168                , _levelTo   :: Level
 169                } deriving (Show)
 170
 171 -- | Document : a piece of Text linked to a Date
 172 data Document = Document
 173       { date :: Date
 174       , text :: Text
 175       } deriving (Show)
 176
 177 data PhyloError = LevelDoesNotExist
 178                 | LevelUnassigned
 179           deriving (Show)
 180
 181
 182 data Proximity  = WeightedLogJaccard | Other
 183
 184
 185 data PairTo = Childs | Parents
 186
 187 -- | Lenses
 188 makeLenses ''Phylo
 189 makeLenses ''PhyloParam
 190 makeLenses ''PhyloExport
 191 makeLenses ''Software
 192 makeLenses ''PhyloGroup
 193 makeLenses ''PhyloLevel
 194 makeLenses ''PhyloPeriod
 195 makeLenses ''Level
 196 makeLenses ''LevelLink
 197
 198 -- | JSON instances
 199 $(deriveJSON (unPrefix "_phylo_"       ) ''Phylo       )
 200 $(deriveJSON (unPrefix "_phylo_period" ) ''PhyloPeriod )
 201 $(deriveJSON (unPrefix "_phylo_level"  ) ''PhyloLevel  )
 202 $(deriveJSON (unPrefix "_phylo_group"  ) ''PhyloGroup  )
 203 --
 204 $(deriveJSON (unPrefix "_software_"    ) ''Software    )
 205 $(deriveJSON (unPrefix "_phyloParam_"  ) ''PhyloParam  )
 206 $(deriveJSON (unPrefix "_phyloExport_" ) ''PhyloExport )
 207
 208 -- | TODO XML instances
 209