{-| Module : Gargantext.Viz.AdaptativePhylo Description : Phylomemy definitions and types. Copyright : (c) CNRS, 2017-Present License : AGPL + CECILL v3 Maintainer : team@gargantext.org Stability : experimental Portability : POSIX Specifications of Phylomemy export format. Phylomemy can be described as a Temporal Graph with different scale of granularity of group of ngrams (terms and multi-terms). The main type is Phylo which is synonym of Phylomemy (only difference is the number of chars). References: Chavalarias, D., Cointet, J.-P., 2013. Phylomemetic patterns in science evolution — the rise and fall of scientific fields. PloS one 8, e54847. -} {-# LANGUAGE DeriveAnyClass #-} {-# LANGUAGE TemplateHaskell #-} module Gargantext.Viz.AdaptativePhylo where import Data.Aeson import Data.Aeson.TH (deriveJSON) import Data.Text (Text, pack) import Data.Vector (Vector) import Data.Map (Map) import Gargantext.Core.Utils.Prefix (unPrefix) import Gargantext.Prelude import Gargantext.Core.Text.Context (TermList) import GHC.Generics import GHC.IO (FilePath) import Control.DeepSeq (NFData) import Control.Lens (makeLenses) import qualified Data.Text.Lazy as TextLazy ---------------- -- | Config | -- ---------------- data CorpusParser = Wos {_wos_limit :: Int} | Csv {_csv_limit :: Int} deriving (Show,Generic,Eq) data SeaElevation = Constante { _cons_start :: Double , _cons_step :: Double } | Adaptative { _adap_granularity :: Double } deriving (Show,Generic,Eq) data Proximity = WeightedLogJaccard { _wlj_sensibility :: Double {- -- , _wlj_thresholdInit :: Double -- , _wlj_thresholdStep :: Double -- | max height for sea level in temporal matching -- , _wlj_elevation :: Double -} } | Hamming deriving (Show,Generic,Eq) data SynchronyScope = SingleBranch | SiblingBranches | AllBranches deriving (Show,Generic,Eq) data SynchronyStrategy = MergeRegularGroups | MergeAllGroups deriving (Show,Generic,Eq) data Synchrony = ByProximityThreshold { _bpt_threshold :: Double , _bpt_sensibility :: Double , _bpt_scope :: SynchronyScope , _bpt_strategy :: SynchronyStrategy } | ByProximityDistribution { _bpd_sensibility :: Double , _bpd_strategy :: SynchronyStrategy } deriving (Show,Generic,Eq) data TimeUnit = Year { _year_period :: Int , _year_step :: Int , _year_matchingFrame :: Int } deriving (Show,Generic,Eq) data Clique = Fis { _fis_support :: Int , _fis_size :: Int } | MaxClique { _mcl_size :: Int } deriving (Show,Generic,Eq) data Quality = Quality { _qua_granularity :: Double , _qua_minBranch :: Int } deriving (Show,Generic,Eq) data Config = Config { corpusPath :: FilePath , listPath :: FilePath , outputPath :: FilePath , corpusParser :: CorpusParser , phyloName :: Text , phyloLevel :: Int , phyloProximity :: Proximity , seaElevation :: SeaElevation , phyloSynchrony :: Synchrony , phyloQuality :: Quality , timeUnit :: TimeUnit , clique :: Clique , exportLabel :: [PhyloLabel] , exportSort :: Sort , exportFilter :: [Filter] } deriving (Show,Generic,Eq) defaultConfig :: Config defaultConfig = Config { corpusPath = "" , listPath = "" , outputPath = "" , corpusParser = Csv 1000 , phyloName = pack "Default Phylo" , phyloLevel = 2 , phyloProximity = WeightedLogJaccard 10 , seaElevation = Constante 0.6 1 , phyloSynchrony = ByProximityThreshold 0.5 10 SiblingBranches MergeAllGroups , phyloQuality = Quality 100 1 , timeUnit = Year 3 1 5 , clique = MaxClique 0 , exportLabel = [BranchLabel MostInclusive 2, GroupLabel MostEmergentInclusive 2] , exportSort = ByHierarchy , exportFilter = [ByBranchSize 2] } instance FromJSON Config instance ToJSON Config instance FromJSON CorpusParser instance ToJSON CorpusParser instance FromJSON Proximity instance ToJSON Proximity instance FromJSON SeaElevation instance ToJSON SeaElevation instance FromJSON TimeUnit instance ToJSON TimeUnit instance FromJSON Clique instance ToJSON Clique instance FromJSON PhyloLabel instance ToJSON PhyloLabel instance FromJSON Tagger instance ToJSON Tagger instance FromJSON Sort instance ToJSON Sort instance FromJSON Order instance ToJSON Order instance FromJSON Filter instance ToJSON Filter instance FromJSON SynchronyScope instance ToJSON SynchronyScope instance FromJSON SynchronyStrategy instance ToJSON SynchronyStrategy instance FromJSON Synchrony instance ToJSON Synchrony instance FromJSON Quality instance ToJSON Quality -- | Software parameters data Software = Software { _software_name :: Text , _software_version :: Text } deriving (Generic, Show, Eq) defaultSoftware :: Software defaultSoftware = Software { _software_name = pack "Gargantext" , _software_version = pack "v4" } -- | Global parameters of a Phylo data PhyloParam = PhyloParam { _phyloParam_version :: Text , _phyloParam_software :: Software , _phyloParam_config :: Config } deriving (Generic, Show, Eq) defaultPhyloParam :: PhyloParam defaultPhyloParam = PhyloParam { _phyloParam_version = pack "v2.adaptative" , _phyloParam_software = defaultSoftware , _phyloParam_config = defaultConfig } ------------------ -- | Document | -- ------------------ -- | Date : a simple Integer type Date = Int -- | Ngrams : a contiguous sequence of n terms type Ngrams = Text -- | Document : a piece of Text linked to a Date data Document = Document { date :: Date , text :: [Ngrams] } deriving (Eq,Show,Generic,NFData) -------------------- -- | Foundation | -- -------------------- -- | The Foundations of a Phylo created from a given TermList data PhyloFoundations = PhyloFoundations { _foundations_roots :: !(Vector Ngrams) , _foundations_mapList :: TermList } deriving (Generic, Show, Eq) --------------------------- -- | Coocurency Matrix | -- --------------------------- -- | Cooc : a coocurency matrix between two ngrams type Cooc = Map (Int,Int) Double ------------------- -- | Phylomemy | -- ------------------- -- | Phylo datatype of a phylomemy -- foundations : the foundations of the phylo -- timeCooc : a Map of coocurency by minimal unit of time (ex: by year) -- timeDocs : a Map with the numbers of docs by minimal unit of time (ex: by year) -- param : the parameters of the phylomemy (with the user's configuration) -- periods : the temporal steps of a phylomemy data Phylo = Phylo { _phylo_foundations :: PhyloFoundations , _phylo_timeCooc :: !(Map Date Cooc) , _phylo_timeDocs :: !(Map Date Double) , _phylo_termFreq :: !(Map Int Double) , _phylo_horizon :: !(Map (PhyloGroupId,PhyloGroupId) Double) , _phylo_groupsProxi :: !(Map (PhyloGroupId,PhyloGroupId) Double) , _phylo_param :: PhyloParam , _phylo_periods :: Map PhyloPeriodId PhyloPeriod } deriving (Generic, Show, Eq) -- | PhyloPeriodId : the id of a given period type PhyloPeriodId = (Date,Date) -- | PhyloPeriod : steps of a phylomemy on a temporal axis -- id: tuple (start date, end date) of the temporal step of the phylomemy -- levels: levels of granularity data PhyloPeriod = PhyloPeriod { _phylo_periodPeriod :: (Date,Date) , _phylo_periodLevels :: Map PhyloLevelId PhyloLevel } deriving (Generic, Show, Eq) -- | Level : a level of clustering type Level = Int -- | PhyloLevelId : the id of a level of clustering in a given period type PhyloLevelId = (PhyloPeriodId,Level) -- | PhyloLevel : levels of phylomemy on a synchronic axis -- Levels description: -- Level 0: The foundations and the base of the phylo -- Level 1: First level of clustering (the Fis) -- Level [2..N]: Nth level of synchronic clustering (cluster of Fis) data PhyloLevel = PhyloLevel { _phylo_levelPeriod :: (Date,Date) , _phylo_levelLevel :: Level , _phylo_levelGroups :: Map PhyloGroupId PhyloGroup } deriving (Generic, Show, Eq) type PhyloGroupId = (PhyloLevelId, Int) -- | BranchId : (a level, a sequence of branch index) -- the sequence is a path of heritage from the most to the less specific branch type PhyloBranchId = (Level, [Int]) -- | PhyloGroup : group of ngrams at each level and period data PhyloGroup = PhyloGroup { _phylo_groupPeriod :: (Date,Date) , _phylo_groupLevel :: Level , _phylo_groupIndex :: Int , _phylo_groupLabel :: Text , _phylo_groupSupport :: Support , _phylo_groupNgrams :: [Int] , _phylo_groupCooc :: !(Cooc) , _phylo_groupBranchId :: PhyloBranchId , _phylo_groupMeta :: Map Text [Double] , _phylo_groupLevelParents :: [Pointer] , _phylo_groupLevelChilds :: [Pointer] , _phylo_groupPeriodParents :: [Pointer] , _phylo_groupPeriodChilds :: [Pointer] } deriving (Generic, Show, Eq, NFData) -- | Weight : A generic mesure that can be associated with an Id type Weight = Double -- | Pointer : A weighted pointer to a given PhyloGroup type Pointer = (PhyloGroupId, Weight) data Filiation = ToParents | ToChilds deriving (Generic, Show) data PointerType = TemporalPointer | LevelPointer deriving (Generic, Show) ---------------------- -- | Phylo Clique | -- ---------------------- -- | Support : Number of Documents where a Clique occurs type Support = Int data PhyloClique = PhyloClique { _phyloClique_nodes :: [Int] , _phyloClique_support :: Support , _phyloClique_period :: (Date,Date) } deriving (Generic,NFData,Show,Eq) ------------------------ -- | Phylo Ancestor | -- ------------------------ data PhyloAncestor = PhyloAncestor { _phyloAncestor_id :: Int , _phyloAncestor_ngrams :: [Int] , _phyloAncestor_groups :: [PhyloGroupId] } deriving (Generic,NFData,Show,Eq) ---------------- -- | Export | -- ---------------- type DotId = TextLazy.Text data EdgeType = GroupToGroup | BranchToGroup | BranchToBranch | PeriodToPeriod deriving (Show,Generic,Eq) data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq) data Order = Asc | Desc deriving (Show,Generic,Eq) data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy deriving (Show,Generic,Eq) data Tagger = MostInclusive | MostEmergentInclusive deriving (Show,Generic,Eq) data PhyloLabel = BranchLabel { _branch_labelTagger :: Tagger , _branch_labelSize :: Int } | GroupLabel { _group_labelTagger :: Tagger , _group_labelSize :: Int } deriving (Show,Generic,Eq) data PhyloBranch = PhyloBranch { _branch_id :: PhyloBranchId , _branch_canonId :: [Int] , _branch_seaLevel :: [Double] , _branch_x :: Double , _branch_y :: Double , _branch_w :: Double , _branch_t :: Double , _branch_label :: Text , _branch_meta :: Map Text [Double] } deriving (Generic, Show, Eq) data PhyloExport = PhyloExport { _export_groups :: [PhyloGroup] , _export_branches :: [PhyloBranch] , _export_ancestors :: [PhyloAncestor] } deriving (Generic, Show) ---------------- -- | Lenses | -- ---------------- makeLenses ''Config makeLenses ''Proximity makeLenses ''SeaElevation makeLenses ''Quality makeLenses ''Clique makeLenses ''PhyloLabel makeLenses ''TimeUnit makeLenses ''PhyloFoundations makeLenses ''PhyloClique makeLenses ''Phylo makeLenses ''PhyloPeriod makeLenses ''PhyloLevel makeLenses ''PhyloGroup makeLenses ''PhyloParam makeLenses ''PhyloExport makeLenses ''PhyloBranch ------------------------ -- | JSON instances | -- ------------------------ $(deriveJSON (unPrefix "_foundations_" ) ''PhyloFoundations)