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 -- | UTCTime in seconds since UNIX epoch
  79 -- type Start   = POSIXTime
  80 -- type End     = POSIXTime
  81 type Start   = Int
  82 type End     = Int
  83
  84
  85 -- | PhyloStep : steps of phylomemy on temporal axis
  86 -- Period: tuple (start date, end date) of the step of the phylomemy
  87 -- Levels: levels of granularity
  88 data PhyloPeriod =
  89      PhyloPeriod { _phylo_periodId     :: PhyloPeriodId
  90                  , _phylo_periodLevels :: [PhyloLevel]
  91                  }
  92                  deriving (Generic, Show)
  93
  94 type PhyloPeriodId = (Start, End)
  95
  96 -- | PhyloLevel : levels of phylomemy on level axis
  97 -- Levels description:
  98 -- Level -1: Ngram equals itself         (by identity) == _phylo_Ngrams
  99 -- Level  0: Group of synonyms           (by stems + by qualitative expert meaning)
 100 -- Level  1: First level of clustering
 101 -- Level  N: Nth   level of clustering
 102 data PhyloLevel =
 103      PhyloLevel { _phylo_levelId     :: PhyloLevelId
 104                 , _phylo_levelGroups :: [PhyloGroup]
 105                 }
 106                 deriving (Generic, Show)
 107
 108 type PhyloLevelId = (PhyloPeriodId, Int)
 109
 110 -- | PhyloGroup : group of ngrams at each level and step
 111 -- Label : maybe has a label as text
 112 -- Ngrams: set of terms that build the group
 113 -- Period Parents|Childs: weighted link to Parents|Childs (Temporal Period   axis)
 114 -- Level  Parents|Childs: weighted link to Parents|Childs (Level Granularity axis)
 115 -- Pointers are directed link from Self to any PhyloGroup (/= Self ?)
 116 data PhyloGroup =
 117      PhyloGroup { _phylo_groupId    :: PhyloGroupId
 118                 , _phylo_groupLabel :: Text
 119                 , _phylo_groupNgrams        :: [Int]
 120
 121                 , _phylo_groupPeriodParents :: [Pointer]
 122                 , _phylo_groupPeriodChilds  :: [Pointer]
 123
 124                 , _phylo_groupLevelParents  :: [Pointer]
 125                 , _phylo_groupLevelChilds   :: [Pointer]
 126                 }
 127                 deriving (Generic, Show)
 128
 129 type PhyloGroupId = (PhyloLevelId, Int)
 130 type Pointer      = (PhyloGroupId, Weight)
 131 type Weight       = Double
 132
 133
 134
 135 -- | Ngrams : a contiguous sequence of n terms
 136 type Ngrams = Text
 137 -- | PhyloNgrams : Vector of all the Ngrams (PhyloGroup of level -1) used within a Phylo
 138 type PhyloNgrams = Vector Ngrams
 139
 140
 141 -- | Clique : Set of ngrams cooccurring in the same Document
 142 type Clique  = Set Ngrams
 143 -- | Support : Number of Documents where a Clique occurs
 144 type Support = Int
 145 -- | Fis : Frequent Items Set (ie: the association between a Clique and a Support)
 146 type Fis = Map Clique Support
 147
 148
 149 -- | Lenses
 150 makeLenses ''Phylo
 151 makeLenses ''PhyloParam
 152 makeLenses ''PhyloExport
 153 makeLenses ''Software
 154 makeLenses ''PhyloGroup
 155 makeLenses ''PhyloLevel
 156 makeLenses ''PhyloPeriod
 157
 158 -- | JSON instances
 159 $(deriveJSON (unPrefix "_phylo_"       ) ''Phylo       )
 160 $(deriveJSON (unPrefix "_phylo_period" ) ''PhyloPeriod )
 161 $(deriveJSON (unPrefix "_phylo_level"  ) ''PhyloLevel  )
 162 $(deriveJSON (unPrefix "_phylo_group"  ) ''PhyloGroup  )
 163 --
 164 $(deriveJSON (unPrefix "_software_"    ) ''Software    )
 165 $(deriveJSON (unPrefix "_phyloParam_"  ) ''PhyloParam  )
 166 $(deriveJSON (unPrefix "_phyloExport_" ) ''PhyloExport )
 167
 168 -- | TODO XML instances
 169