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            , _phylo_branches :: [PhyloBranch]
  76            }
  77            deriving (Generic, Show)
  78
  79
  80 -- | Date : a simple Integer
  81 type Date = Int
  82
  83 -- | UTCTime in seconds since UNIX epoch
  84 -- type Start   = POSIXTime
  85 -- type End     = POSIXTime
  86 type Start   = Date
  87 type End     = Date
  88
  89 -- | PhyloStep : steps of phylomemy on temporal axis
  90 -- Period: tuple (start date, end date) of the step of the phylomemy
  91 -- Levels: levels of granularity
  92 data PhyloPeriod =
  93      PhyloPeriod { _phylo_periodId     :: PhyloPeriodId
  94                  , _phylo_periodLevels :: [PhyloLevel]
  95                  }
  96                  deriving (Generic, Show)
  97
  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
 112 -- | PhyloGroup : group of ngrams at each level and step
 113 -- Label : maybe has a label as text
 114 -- Ngrams: set of terms that build the group
 115 -- Quality : map of measures (support, etc.) that depict some qualitative aspects of a phylo
 116 -- Period Parents|Childs: weighted link to Parents|Childs (Temporal Period   axis)
 117 -- Level  Parents|Childs: weighted link to Parents|Childs (Level Granularity axis)
 118 -- Pointers are directed link from Self to any PhyloGroup (/= Self ?)
 119 data PhyloGroup =
 120      PhyloGroup { _phylo_groupId            :: PhyloGroupId
 121                 , _phylo_groupLabel         :: Text
 122                 , _phylo_groupNgrams        :: [Int]
 123                 , _phylo_groupQuality       :: Map Text Double
 124                 , _phylo_groupCooc          :: Map (Int, Int) 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 data PhyloBranch =
 135      PhyloBranch { _phylo_branchId     :: (Int,Int)
 136                  , _phylo_branchLabel  :: Text
 137                  , _phylo_branchGroups :: [PhyloGroupId]
 138                  }
 139                  deriving (Generic, Show)
 140
 141 type PhyloPeriodId = (Start, End)
 142 type PhyloLevelId  = (PhyloPeriodId, Int)
 143 type PhyloGroupId  = (PhyloLevelId, Int)
 144
 145 type Pointer       = (PhyloGroupId, Weight)
 146 type Weight        = Double
 147
 148 type PhyloBranchId = (Int, Int)
 149
 150
 151 -- | Ngrams : a contiguous sequence of n terms
 152 type Ngrams = Text
 153 -- | PhyloNgrams : Vector of all the Ngrams (PhyloGroup of level -1) used within a Phylo
 154 type PhyloNgrams = Vector Ngrams
 155
 156
 157 -- | Clique : Set of ngrams cooccurring in the same Document
 158 type Clique  = Set Ngrams
 159 -- | Support : Number of Documents where a Clique occurs
 160 type Support = Int
 161 -- | Fis : Frequent Items Set (ie: the association between a Clique and a Support)
 162 type Fis = Map Clique Support
 163
 164
 165 data Direction = From | To
 166     deriving (Show, Eq)
 167
 168 data LevelLabel = Level_m1 | Level_0 | Level_1 | Level_mN | Level_N | Level_pN
 169   deriving (Show, Eq, Enum, Bounded)
 170
 171 data Level =
 172      Level { _levelLabel :: LevelLabel
 173            , _levelValue :: Int
 174            } deriving (Show, Eq)
 175
 176 data LevelLink =
 177      LevelLink { _levelFrom :: Level
 178                , _levelTo   :: Level
 179                } deriving (Show)
 180
 181 -- | Document : a piece of Text linked to a Date
 182 data Document = Document
 183       { date :: Date
 184       , text :: Text
 185       } deriving (Show)
 186
 187 data PhyloError = LevelDoesNotExist
 188                 | LevelUnassigned
 189           deriving (Show)
 190
 191
 192 type PhyloGraph = (PhyloNodes,PhyloEdges)
 193 type PhyloNodes = [PhyloGroup]
 194 type PhyloEdges = [(((PhyloGroup,PhyloGroup)),Double)]
 195
 196
 197 data Proximity  = WeightedLogJaccard | Hamming | FromPairs
 198
 199 data Clustering  = Louvain | RelatedComponents
 200
 201
 202 data PairTo = Childs | Parents
 203
 204 -- | Lenses
 205 makeLenses ''Phylo
 206 makeLenses ''PhyloParam
 207 makeLenses ''PhyloExport
 208 makeLenses ''Software
 209 makeLenses ''PhyloGroup
 210 makeLenses ''PhyloLevel
 211 makeLenses ''PhyloPeriod
 212 makeLenses ''Level
 213 makeLenses ''LevelLink
 214 makeLenses ''PhyloBranch
 215
 216 -- | JSON instances
 217 $(deriveJSON (unPrefix "_phylo_"       ) ''Phylo       )
 218 $(deriveJSON (unPrefix "_phylo_period" ) 'PhyloPeriod  )
 219 $(deriveJSON (unPrefix "_phylo_level"  ) ''PhyloLevel  )
 220 $(deriveJSON (unPrefix "_phylo_group"  ) ''PhyloGroup  )
 221 $(deriveJSON (unPrefix "_phylo_branch" ) ''PhyloBranch )
 222 --
 223 $(deriveJSON (unPrefix "_software_"    ) ''Software    )
 224 $(deriveJSON (unPrefix "_phyloParam_"  ) ''PhyloParam  )
 225 $(deriveJSON (unPrefix "_phyloExport_" ) ''PhyloExport )
 226
 227 -- | TODO XML instances
 228