{- Module : Gargantext.Core.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.Core.Viz.Phylo where import Control.DeepSeq (NFData) import Control.Lens (makeLenses) import Data.Aeson import Data.Aeson.TH (deriveJSON) import Data.Map (Map) import Data.Swagger import Data.Text (Text, pack) import Data.Vector (Vector) import GHC.Generics import GHC.IO (FilePath) import Gargantext.Core.Utils.Prefix (unPrefix) import Gargantext.Core.Utils.Prefix (unPrefixSwagger) import Gargantext.Prelude import qualified Data.Text.Lazy as TextLazy ---------------- -- | PhyloConfig | -- ---------------- data CorpusParser = Wos {_wos_limit :: Int} | Csv {_csv_limit :: Int} | Csv' {_csv'_limit :: Int} deriving (Show,Generic,Eq) instance ToSchema CorpusParser where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_") data ListParser = V3 | V4 deriving (Show,Generic,Eq) instance ToSchema ListParser data SeaElevation = Constante { _cons_start :: Double , _cons_gap :: Double } | Adaptative { _adap_steps :: Double } | Evolving { _evol_neighborhood :: Bool } deriving (Show,Generic,Eq) instance ToSchema SeaElevation data PhyloSimilarity = WeightedLogJaccard { _wlj_sensibility :: Double , _wlj_minSharedNgrams :: Int } | WeightedLogSim { _wls_sensibility :: Double , _wls_minSharedNgrams :: Int } | Hamming { _hmg_sensibility :: Double , _hmg_minSharedNgrams :: Int} deriving (Show,Generic,Eq) instance ToSchema PhyloSimilarity where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "") data SynchronyScope = SingleBranch | SiblingBranches | AllBranches deriving (Show,Generic,Eq, ToSchema) data SynchronyStrategy = MergeRegularGroups | MergeAllGroups deriving (Show,Generic,Eq) instance ToSchema SynchronyStrategy where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "") 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) instance ToSchema Synchrony where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_") data TimeUnit = Epoch { _epoch_period :: Int , _epoch_step :: Int , _epoch_matchingFrame :: Int } | Year { _year_period :: Int , _year_step :: Int , _year_matchingFrame :: Int } | Month { _month_period :: Int , _month_step :: Int , _month_matchingFrame :: Int } | Week { _week_period :: Int , _week_step :: Int , _week_matchingFrame :: Int } | Day { _day_period :: Int , _day_step :: Int , _day_matchingFrame :: Int } deriving (Show,Generic,Eq,NFData) instance ToSchema TimeUnit where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "") data MaxCliqueFilter = ByThreshold | ByNeighbours deriving (Show,Generic,Eq) instance ToSchema MaxCliqueFilter where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "") data Cluster = Fis { _fis_support :: Int , _fis_size :: Int } | MaxClique { _mcl_size :: Int , _mcl_threshold :: Double , _mcl_filter :: MaxCliqueFilter } deriving (Show,Generic,Eq) instance ToSchema Cluster where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "") data Quality = Quality { _qua_granularity :: Double , _qua_minBranch :: Int } deriving (Show,Generic,Eq) instance ToSchema Quality where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_qua_") data PhyloConfig = PhyloConfig { corpusPath :: FilePath , listPath :: FilePath , outputPath :: FilePath , corpusParser :: CorpusParser , listParser :: ListParser , phyloName :: Text , phyloScale :: Int , similarity :: PhyloSimilarity , seaElevation :: SeaElevation , defaultMode :: Bool , findAncestors :: Bool , phyloSynchrony :: Synchrony , phyloQuality :: Quality , timeUnit :: TimeUnit , clique :: Cluster , exportLabel :: [PhyloLabel] , exportSort :: Sort , exportFilter :: [Filter] } deriving (Show,Generic,Eq) ------------------------------------------------------------------------ data PhyloSubConfig = PhyloSubConfig { _sc_phyloProximity :: Double , _sc_phyloSynchrony :: Double , _sc_phyloQuality :: Double , _sc_timeUnit :: TimeUnit , _sc_clique :: Cluster , _sc_exportFilter :: Double , _sc_defaultMode :: Bool } deriving (Show,Generic,Eq) subConfig2config :: PhyloSubConfig -> PhyloConfig subConfig2config subConfig = defaultConfig { similarity = WeightedLogJaccard (_sc_phyloProximity subConfig) 1 , phyloSynchrony = ByProximityThreshold (_sc_phyloSynchrony subConfig) 0 AllBranches MergeAllGroups , phyloQuality = Quality (_sc_phyloQuality subConfig) 1 , timeUnit = _sc_timeUnit subConfig , clique = _sc_clique subConfig , exportFilter = [ByBranchSize $ _sc_exportFilter subConfig] } ------------------------------------------------------------------------ defaultConfig :: PhyloConfig defaultConfig = PhyloConfig { corpusPath = "corpus.csv" -- useful for commandline only , listPath = "list.csv" -- useful for commandline only , outputPath = "data/" , corpusParser = Csv 100000 , listParser = V4 , phyloName = pack "Phylo Name" , phyloScale = 2 , similarity = WeightedLogJaccard 0.5 1 , seaElevation = Constante 0.1 0.1 , defaultMode = False , findAncestors = False , phyloSynchrony = ByProximityThreshold 0.5 0 AllBranches MergeAllGroups , phyloQuality = Quality 0.5 1 , timeUnit = Year 3 1 5 , clique = MaxClique 5 0.0001 ByThreshold , exportLabel = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2] , exportSort = ByHierarchy Desc , exportFilter = [ByBranchSize 3] } -- Main Instances instance ToSchema PhyloConfig instance ToSchema PhyloSubConfig instance FromJSON PhyloConfig instance ToJSON PhyloConfig instance FromJSON PhyloSubConfig instance ToJSON PhyloSubConfig instance FromJSON CorpusParser instance ToJSON CorpusParser instance FromJSON ListParser instance ToJSON ListParser instance FromJSON PhyloSimilarity instance ToJSON PhyloSimilarity instance FromJSON SeaElevation instance ToJSON SeaElevation instance FromJSON TimeUnit instance ToJSON TimeUnit instance FromJSON MaxCliqueFilter instance ToJSON MaxCliqueFilter instance FromJSON Cluster instance ToJSON Cluster 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) instance ToSchema Software where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_software_") defaultSoftware :: Software defaultSoftware = Software { _software_name = pack "GarganText" , _software_version = pack "v5" } -- | Global parameters of a Phylo data PhyloParam = PhyloParam { _phyloParam_version :: Text , _phyloParam_software :: Software , _phyloParam_config :: PhyloConfig } deriving (Generic, Show, Eq) instance ToSchema PhyloParam where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phyloParam_") defaultPhyloParam :: PhyloParam defaultPhyloParam = PhyloParam { _phyloParam_version = pack "v3" , _phyloParam_software = defaultSoftware , _phyloParam_config = defaultConfig } ------------------ -- | Document | -- ------------------ -- | Date : a simple Integer type Date = Int -- | DateStr : the string version of a Date type DateStr = Text -- | Ngrams : a contiguous sequence of n terms type Ngrams = Text -- Document : a piece of Text linked to a Date -- date = computational date; date' = original string date yyyy-mm-dd -- Export Database to Document data Document = Document { date :: Date -- datatype Date {unDate :: Int} , date' :: DateStr -- show date , text :: [Ngrams] , weight :: Maybe Double , sources :: [Text] , docTime :: TimeUnit } deriving (Eq,Show,Generic,NFData) -------------------- -- | Foundation | -- -------------------- -- | The Foundations of a Phylo created from a given TermList data PhyloFoundations = PhyloFoundations { _foundations_roots :: (Vector Ngrams) , _foundations_rootsInGroups :: Map Int [PhyloGroupId] -- map of roots associated to groups } deriving (Generic, Show, Eq) data PhyloCounts = PhyloCounts { coocByDate :: !(Map Date Cooc) , docsByDate :: !(Map Date Double) , rootsCountByDate :: !(Map Date (Map Int Double)) , rootsCount :: !(Map Int Double) , rootsFreq :: !(Map Int Double) , lastRootsFreq :: !(Map Int Double) } deriving (Generic, Show, Eq) data PhyloSources = PhyloSources { _sources :: !(Vector Text) } deriving (Generic, Show, Eq) instance ToSchema PhyloFoundations where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_foundations_") instance ToSchema PhyloCounts where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_") instance ToSchema PhyloSources where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_") --------------------------- -- | Coocurency Matrix | -- --------------------------- -- | Cooc : a coocurency matrix between two ngrams type Cooc = Map (Int,Int) Double ------------------- -- | Phylomemy | -- ------------------- -- | Period : a tuple of Dates type Period = (Date,Date) -- | PeriodStr : a tuple of DateStr type PeriodStr = (DateStr,DateStr) -- | 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_sources :: PhyloSources , _phylo_counts :: PhyloCounts , _phylo_seaLadder :: [Double] , _phylo_param :: PhyloParam , _phylo_periods :: Map Period PhyloPeriod , _phylo_quality :: Double , _phylo_level :: Double } deriving (Generic, Show, Eq) instance ToSchema Phylo where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_") ---------------- -- | Period | -- ---------------- -- | PhyloPeriod : steps of a phylomemy on a temporal axis -- id: tuple (start date, end date) of the temporal step of the phylomemy -- scales: scales of synchronic description data PhyloPeriod = PhyloPeriod { _phylo_periodPeriod :: Period , _phylo_periodPeriodStr :: PeriodStr , _phylo_periodScales :: Map PhyloScaleId PhyloScale } deriving (Generic, Show, Eq) instance ToSchema PhyloPeriod where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_") --------------- -- | Scale | -- --------------- -- | Scale : a scale of synchronic description type Scale = Int -- | PhyloScaleId : the id of a scale of synchronic description type PhyloScaleId = (Period,Scale) -- | PhyloScale : sub-structure of the phylomemy in scale of synchronic description data PhyloScale = PhyloScale { _phylo_scalePeriod :: Period , _phylo_scalePeriodStr :: PeriodStr , _phylo_scaleScale :: Scale , _phylo_scaleGroups :: Map PhyloGroupId PhyloGroup } deriving (Generic, Show, Eq) instance ToSchema PhyloScale where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_") type PhyloGroupId = (PhyloScaleId, Int) -- | BranchId : (a scale, a sequence of branch index) -- the sequence is a path of heritage from the most to the less specific branch type PhyloBranchId = (Scale, [Int]) -- | PhyloGroup : group of ngrams at each scale and period data PhyloGroup = PhyloGroup { _phylo_groupPeriod :: Period , _phylo_groupPeriod' :: (Text,Text) , _phylo_groupScale :: Scale , _phylo_groupIndex :: Int , _phylo_groupLabel :: Text , _phylo_groupSupport :: Support , _phylo_groupWeight :: Maybe Double , _phylo_groupSources :: [Int] , _phylo_groupNgrams :: [Int] , _phylo_groupCooc :: !(Cooc) , _phylo_groupDensity :: Double , _phylo_groupBranchId :: PhyloBranchId , _phylo_groupMeta :: Map Text [Double] , _phylo_groupRootsCount :: Map Int Double , _phylo_groupScaleParents :: [Pointer] , _phylo_groupScaleChilds :: [Pointer] , _phylo_groupPeriodParents :: [Pointer] , _phylo_groupPeriodChilds :: [Pointer] , _phylo_groupAncestors :: [Pointer] , _phylo_groupPeriodMemoryParents :: [Pointer'] , _phylo_groupPeriodMemoryChilds :: [Pointer'] } deriving (Generic, Show, Eq, NFData) instance ToSchema PhyloGroup where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_") -- | Weight : A generic mesure that can be associated with an Id type Weight = Double type Thr = Double -- | Pointer : A weighted pointer to a given PhyloGroup type Pointer = (PhyloGroupId, Weight) -- | Pointer' : A weighted pointer to a given PhyloGroup with a lower bounded threshold type Pointer' = (PhyloGroupId, (Thr,Weight)) data Filiation = ToParents | ToChilds | ToParentsMemory | ToChildsMemory deriving (Generic, Show) data PointerType = TemporalPointer | ScalePointer deriving (Generic, Show) -------------------------- -- | Phylo Clustering | -- -------------------------- -- | Support : Number of Documents where a Cluster occurs type Support = Int data Clustering = Clustering { _clustering_roots :: [Int] , _clustering_support :: Support , _clustering_period :: Period -- additional materials for visualization , _clustering_visWeighting :: Maybe Double , _clustering_visFiltering :: [Int] } deriving (Generic,NFData,Show,Eq) ---------------- -- | Export | -- ---------------- type DotId = TextLazy.Text data EdgeType = GroupToGroup | GroupToGroupMemory | BranchToGroup | BranchToBranch | GroupToAncestor | PeriodToPeriod deriving (Show,Generic,Eq) data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq) instance ToSchema Filter where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "") data Order = Asc | Desc deriving (Show,Generic,Eq, ToSchema) data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy {_sort_order :: Order } deriving (Show,Generic,Eq) instance ToSchema Sort where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_sort_") data Tagger = MostInclusive | MostEmergentInclusive | MostEmergentTfIdf deriving (Show,Generic,Eq) instance ToSchema Tagger where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "") data PhyloLabel = BranchLabel { _branch_labelTagger :: Tagger , _branch_labelSize :: Int } | GroupLabel { _group_labelTagger :: Tagger , _group_labelSize :: Int } deriving (Show,Generic,Eq) instance ToSchema PhyloLabel where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_") 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) instance ToSchema PhyloBranch where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_branch_") data PhyloExport = PhyloExport { _export_groups :: [PhyloGroup] , _export_branches :: [PhyloBranch] } deriving (Generic, Show) instance ToSchema PhyloExport where declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_export_") ---------------- -- | Lenses | -- ---------------- makeLenses ''PhyloConfig makeLenses ''PhyloSubConfig makeLenses ''PhyloSimilarity makeLenses ''SeaElevation makeLenses ''Quality makeLenses ''Cluster makeLenses ''PhyloLabel makeLenses ''TimeUnit makeLenses ''PhyloFoundations makeLenses ''Clustering makeLenses ''Phylo makeLenses ''PhyloPeriod makeLenses ''PhyloScale makeLenses ''PhyloGroup makeLenses ''PhyloParam makeLenses ''PhyloExport makeLenses ''PhyloBranch ------------------------ -- | JSON instances | -- ------------------------ instance FromJSON Phylo instance ToJSON Phylo instance FromJSON PhyloSources instance ToJSON PhyloSources instance FromJSON PhyloParam instance ToJSON PhyloParam instance FromJSON PhyloCounts instance ToJSON PhyloCounts instance FromJSON PhyloPeriod instance ToJSON PhyloPeriod instance FromJSON PhyloScale instance ToJSON PhyloScale instance FromJSON Software instance ToJSON Software instance FromJSON PhyloGroup instance ToJSON PhyloGroup $(deriveJSON (unPrefix "_foundations_" ) ''PhyloFoundations)