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haskell-gargantext
haskell-gargantext
Commit 815ab543 authored by qlobbe's avatar qlobbe
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add parallelism

parent 7832afe9
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    package.yaml
    View file @ 815ab543
    ......@@ -103,6 +103,7 @@ library:
    - contravariant
    - crawlerPubMed
    - data-time-segment
    - deepseq
    - directory
    - duckling
    - exceptions
    ......@@ -138,6 +139,7 @@ library:
    - natural-transformation
    - opaleye
    - pandoc
    - parallel
    - parsec
    - patches-class
    - patches-map
    ......
    src/Gargantext/Viz/Phylo.hs
    View file @ 815ab543
    ......@@ -22,7 +22,7 @@ one 8, e54847.
    -}
    {-# LANGUAGE DeriveGeneric #-}
    {-# LANGUAGE DeriveGeneric, DeriveAnyClass #-}
    {-# LANGUAGE NoImplicitPrelude #-}
    {-# LANGUAGE TemplateHaskell #-}
    {-# LANGUAGE MultiParamTypeClasses #-}
    ......@@ -44,6 +44,8 @@ import Gargantext.Core.Utils.Prefix (unPrefix)
    import Gargantext.Text.Context (TermList)
    import Gargantext.Prelude
    import Control.DeepSeq
    --------------------
    -- | PhyloParam | --
    --------------------
    ......@@ -161,7 +163,9 @@ data PhyloGroup =
    , _phylo_groupLevelParents :: [Pointer]
    , _phylo_groupLevelChilds :: [Pointer]
    }
    deriving (Generic, Show, Eq, Ord)
    deriving (Generic, NFData, Show, Eq, Ord)
    -- instance NFData PhyloGroup
    -- | Level : A level of aggregation (-1 = Txt, 0 = Ngrams, 1 = Fis, [2..] = Cluster)
    ......
    src/Gargantext/Viz/Phylo/Aggregates/Cluster.hs
    View file @ 815ab543
    ......@@ -13,11 +13,13 @@ Portability : POSIX
    {-# LANGUAGE NoImplicitPrelude #-}
    {-# LANGUAGE FlexibleContexts #-}
    {-# LANGUAGE OverloadedStrings #-}
    {-# LANGUAGE TemplateHaskell #-}
    module Gargantext.Viz.Phylo.Aggregates.Cluster
    where
    import Data.List (null,tail,concat,sort,intersect)
    import Control.Parallel.Strategies
    import Data.List (null,concat,sort,intersect,(++))
    import Data.Map (Map)
    import Data.Tuple (fst)
    import Gargantext.Prelude
    ......@@ -44,17 +46,19 @@ getCandidates gs = filter (\(g,g') -> (not . null) $ intersect (getGroupNgrams g
    graphToClusters :: Cluster -> GroupGraph -> [PhyloCluster]
    graphToClusters clust (nodes,edges) = case clust of
    Louvain (LouvainParams _) -> undefined
    RelatedComponents (RCParams _) -> relatedComp 0 (head' "graphToClusters" nodes) (tail nodes,edges) [] []
    RelatedComponents (RCParams _) -> relatedComp $ ((map (\((g,g'),_) -> [g,g']) edges) ++ (map (\g -> [g]) nodes))
    _ -> panic "[ERR][Viz.Phylo.Aggregates.Cluster.graphToClusters] not implemented"
    -- | To transform a list of PhyloGroups into a Graph of Proximity
    groupsToGraph :: Double -> Proximity -> [PhyloGroup] -> ([GroupNode],[GroupEdge])
    groupsToGraph nbDocs prox gs = case prox of
    WeightedLogJaccard (WLJParams _ sens) -> (gs, map (\(x,y) -> ((x,y), weightedLogJaccard sens nbDocs (getGroupCooc x) (getGroupCooc y) (getGroupNgrams x) (getGroupNgrams y)))
    $ getCandidates gs)
    WeightedLogJaccard (WLJParams _ sens) -> (gs, let candidates = map (\(x,y) -> ((x,y), weightedLogJaccard sens nbDocs (getGroupCooc x) (getGroupCooc y) (getGroupNgrams x) (getGroupNgrams y)))
    $ getCandidates gs
    candidates' = candidates `using` parList rdeepseq
    in candidates' )
    Hamming (HammingParams _) -> (gs, map (\(x,y) -> ((x,y), hamming (getGroupCooc x) (getGroupCooc y))) $ getCandidates gs)
    _ -> undefined
    _ -> undefined
    -- | To filter a Graph of Proximity using a given threshold
    ......@@ -78,9 +82,11 @@ phyloToClusters lvl clus p = Map.fromList
    graphs' = traceGraphFiltered lvl
    $ map (\g -> filterGraph prox g) graphs
    --------------------------------------
    graphs :: [([GroupNode],[GroupEdge])]
    graphs = traceGraph lvl (getThreshold prox)
    $ map (\prd -> groupsToGraph (periodsToNbDocs [prd] p) prox (getGroupsWithFilters lvl prd p)) periods
    graphs :: [([GroupNode],[GroupEdge])]
    graphs = traceGraph lvl (getThreshold prox)
    $ let gs = map (\prd -> groupsToGraph (periodsToNbDocs [prd] p) prox (getGroupsWithFilters lvl prd p)) periods
    gs' = gs `using` parList rdeepseq
    in gs'
    --------------------------------------
    prox :: Proximity
    prox = getProximity clus
    ......@@ -115,7 +121,3 @@ traceGraphFiltered lvl g = trace ( "----\nClustering in Phylo" <> show (lvl) <>
    <> show (percentile 90 (VS.fromList lst)) <> " (90%)\n") g
    where
    lst = sort $ map snd $ concat $ map snd g
    -- traceSim :: PhyloGroup -> PhyloGroup -> Phylo -> Double -> Double
    -- traceSim g g' p sim = trace (show (getGroupText g p) <> " [vs] " <> show (getGroupText g' p) <> " = " <> show (sim) <> "\n") sim
    src/Gargantext/Viz/Phylo/BranchMaker.hs
    View file @ 815ab543
    ......@@ -17,6 +17,7 @@ Portability : POSIX
    module Gargantext.Viz.Phylo.BranchMaker
    where
    import Control.Parallel.Strategies
    import Control.Lens hiding (both, Level)
    import Data.List (concat,nub,(++),tail,sortOn,take,reverse,sort,null,intersect,union)
    import Data.Map (Map)
    ......@@ -82,13 +83,14 @@ findSimBranches frame thr nth p (id,gs) bs
    pks = getGroupsPeaks gs nth p
    --------------------------------------
    findBestPointer :: Phylo -> Proximity -> [PhyloGroup] -> [PhyloGroup] -> [(PhyloGroupId,Pointer)]
    findBestPointer p prox gs gs' = take 1
    $ reverse
    $ sortOn (snd . snd)
    $ concat
    $ map (\g -> let pts = findBestCandidates' prox gs' g p
    in map (\pt -> (getGroupId g,pt)) pts) gs
    findBestPointer p prox gs gs' =
    let candidates = map (\g -> let pts = findBestCandidates' prox gs' g p
    in map (\pt -> (getGroupId g,pt)) pts) gs
    candidates' = candidates `using` parList rdeepseq
    in take 1 $ reverse $ sortOn (snd . snd) $ concat candidates'
    makeBranchLinks :: Phylo -> Proximity -> (PhyloBranchId,[PhyloGroup]) -> [(PhyloBranchId,[PhyloGroup])] -> [(PhyloGroupId,Pointer)] -> [(PhyloGroupId,Pointer)]
    makeBranchLinks p prox (id,gs) bs pts
    ......@@ -126,34 +128,22 @@ linkPhyloBranches lvl prox p = setPhyloBranches lvl
    -- | To transform a PhyloGraph into a list of PhyloBranches by using the relatedComp clustering
    graphToBranches :: Level -> GroupGraph -> Phylo -> [(Int,PhyloGroupId)]
    graphToBranches _lvl (nodes,edges) _p = concat
    $ map (\(idx,gs) -> map (\g -> (idx,getGroupId g)) gs)
    $ zip [1..]
    $ relatedComp 0 (head' "branchMaker" nodes) (tail nodes,edges) [] []
    -- | To build a graph using the parents and childs pointers
    makeGraph :: [PhyloGroup] -> Phylo -> GroupGraph
    makeGraph gs p = (gs,edges)
    where
    edges :: [GroupEdge]
    edges = (nub . concat)
    $ map (\g -> (map (\g' -> ((g',g),1)) $ getGroupParents g p)
    ++
    (map (\g' -> ((g,g'),1)) $ getGroupChilds g p)) gs
    graphToBranches :: [PhyloGroup] -> Phylo -> [(Int,PhyloGroupId)]
    graphToBranches groups p = concat
    $ map (\(idx,gs) -> map (\g -> (idx,getGroupId g)) gs)
    $ zip [1..]
    $ relatedComp
    $ map (\g -> nub $ [g] ++ (getGroupParents g p) ++ (getGroupChilds g p)) groups
    -- | To set all the PhyloBranches for a given Level in a Phylo
    setPhyloBranches :: Level -> Phylo -> Phylo
    setPhyloBranches lvl p = alterGroupWithLevel (\g -> let bIdx = (fst $ head' "branchMaker" $ filter (\b -> snd b == getGroupId g) bs)
    in over (phylo_groupBranchId) (\_ -> Just (lvl,bIdx)) g) lvl p
    where
    --------------------------------------
    bs :: [(Int,PhyloGroupId)]
    bs = graphToBranches lvl graph p
    setPhyloBranches lvl p = alterGroupWithLevel (\g ->
    let bIdx = (fst $ head' "branchMaker"
    $ filter (\b -> snd b == getGroupId g) branches)
    in over (phylo_groupBranchId) (\_ -> Just (lvl,bIdx)) g) lvl p
    where
    --------------------------------------
    graph :: GroupGraph
    graph = makeGraph (getGroupsWithLevel lvl p) p
    branches :: [(Int,PhyloGroupId)]
    branches = graphToBranches (getGroupsWithLevel lvl p) p
    --------------------------------------
    src/Gargantext/Viz/Phylo/Example.hs
    View file @ 815ab543
    ......@@ -105,7 +105,7 @@ queryEx = "title=Cesar et Cleôpatre"
    phyloQueryBuild :: PhyloQueryBuild
    phyloQueryBuild = PhyloQueryBuild "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)"
    5 3 defaultFis [] [] (WeightedLogJaccard $ WLJParams 0.1 20) 5 0.5 4 2 (RelatedComponents $ RCParams $ WeightedLogJaccard $ WLJParams 0.3 0)
    5 3 defaultFis [] [] (WeightedLogJaccard $ WLJParams 0.6 20) 5 0.5 4 2 (RelatedComponents $ RCParams $ WeightedLogJaccard $ WLJParams 0.4 0)
    ......
    src/Gargantext/Viz/Phylo/LevelMaker.hs
    View file @ 815ab543
    ......@@ -19,6 +19,7 @@ Portability : POSIX
    module Gargantext.Viz.Phylo.LevelMaker
    where
    import Control.Parallel.Strategies
    import Control.Lens hiding (both, Level)
    import Data.List ((++), sort, concat, nub, zip, last)
    import Data.Map (Map, (!), empty, singleton)
    ......@@ -61,7 +62,10 @@ instance PhyloLevelMaker PhyloCluster
    | otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Clusters at level < 2")
    --------------------------------------
    -- | Level -> (Date,Date) -> [Cluster] -> Map (Date,Date) [Cluster] -> Phylo -> [PhyloGroup]
    toPhyloGroups lvl (d,d') l m p = map (\(idx,cluster) -> clusterToGroup (d,d') lvl idx "" cluster m p) $ zip [1..] l
    toPhyloGroups lvl (d,d') l m p =
    let clusters = map (\(idx,cluster) -> clusterToGroup (d,d') lvl idx "" cluster m p) $ zip [1..] l
    clusters' = clusters `using` parList rdeepseq
    in clusters'
    --------------------------------------
    ......@@ -74,7 +78,10 @@ instance PhyloLevelMaker PhyloFis
    | otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Fis at level <> 1")
    --------------------------------------
    -- | Level -> (Date,Date) -> [Fis] -> Map (Date,Date) [Fis] -> Phylo -> [PhyloGroup]
    toPhyloGroups lvl (d,d') l _ p = map (\(idx,fis) -> cliqueToGroup (d,d') lvl idx "" fis p) $ zip [1..] l
    toPhyloGroups lvl (d,d') l _ p =
    let groups = map (\(idx,fis) -> cliqueToGroup (d,d') lvl idx "" fis p) $ zip [1..] l
    groups' = groups `using` parList rdeepseq
    in groups'
    --------------------------------------
    ......@@ -87,8 +94,7 @@ instance PhyloLevelMaker Document
    | otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Documents at level <> 0")
    --------------------------------------
    -- | Level -> (Date,Date) -> [Document] -> Map (Date,Date) [Fis] -> Phylo -> [PhyloGroup]
    toPhyloGroups lvl (d,d') l _m p = map (\(idx,ngram) -> ngramsToGroup (d,d') lvl idx ngram [ngram] p)
    $ zip [1..]
    toPhyloGroups lvl (d,d') l _m p = map (\ngram -> ngramsToGroup (d,d') lvl (getIdxInRoots ngram p) ngram [ngram] p)
    $ (nub . concat)
    $ map text l
    --------------------------------------
    ......@@ -100,11 +106,13 @@ clusterToGroup prd lvl idx lbl groups _m p =
    PhyloGroup ((prd, lvl), idx) lbl ngrams empty
    Nothing
    (getMiniCooc (listToFullCombi ngrams) (periodsToYears [prd]) (getPhyloCooc p))
    [] [] [] childs
    ascLink desLink [] childs
    where
    --------------------------------------
    childs :: [Pointer]
    childs = map (\g -> (getGroupId g, 1)) groups
    ascLink = concat $ map getGroupPeriodParents groups
    desLink = concat $ map getGroupPeriodChilds groups
    --------------------------------------
    ngrams :: [Int]
    ngrams = (sort . nub . concat) $ map getGroupNgrams groups
    ......@@ -116,7 +124,7 @@ cliqueToGroup :: PhyloPeriodId -> Level -> Int -> Text -> PhyloFis -> Phylo -> P
    cliqueToGroup prd lvl idx lbl fis p =
    PhyloGroup ((prd, lvl), idx) lbl ngrams (singleton "support" (fromIntegral $ getSupport fis)) Nothing
    (getMiniCooc (listToFullCombi ngrams) (periodsToYears [prd]) (getPhyloCooc p))
    [] [] [] []
    [] [] [] childs
    where
    --------------------------------------
    ngrams :: [Int]
    ......@@ -124,6 +132,9 @@ cliqueToGroup prd lvl idx lbl fis p =
    $ Set.toList
    $ getClique fis
    --------------------------------------
    childs :: [Pointer]
    childs = map (\n -> (((prd, lvl - 1), n),1)) ngrams
    --------------------------------------
    -- | To transform a list of Ngrams into a PhyloGroup
    ......@@ -152,6 +163,7 @@ toNthLevel lvlMax prox clus p
    $ traceBranches (lvl + 1)
    $ setPhyloBranches (lvl + 1)
    $ transposePeriodLinks (lvl + 1)
    $ tracePhyloN (lvl + 1)
    $ setLevelLinks (lvl, lvl + 1)
    $ addPhyloLevel (lvl + 1)
    (clusters) p
    ......@@ -169,15 +181,15 @@ toNthLevel lvlMax prox clus p
    toPhylo1 :: Cluster -> Proximity -> Map (Date, Date) [Document] -> Phylo -> Phylo
    toPhylo1 clus prox d p = case clus of
    Fis (FisParams k s t) -> traceReBranches 1
    $ linkPhyloBranches 1 prox
    -- $ linkPhyloBranches 1 prox
    $ traceBranches 1
    $ setPhyloBranches 1
    $ traceTempoMatching Descendant 1
    $ interTempoMatching Descendant 1 prox
    $ traceTempoMatching Ascendant 1
    $ interTempoMatching Ascendant 1 prox
    $ tracePhylo1
    $ setLevelLinks (0,1)
    $ setLevelLinks (1,0)
    $ addPhyloLevel 1 phyloFis phylo'
    where
    --------------------------------------
    ......@@ -212,7 +224,7 @@ instance PhyloMaker [(Date, Text)]
    phylo1 = toPhylo1 (getContextualUnit q) (getInterTemporalMatching q) phyloDocs phylo0
    --------------------------------------
    phylo0 :: Phylo
    phylo0 = toPhylo0 phyloDocs phyloBase
    phylo0 = tracePhylo0 $ toPhylo0 phyloDocs phyloBase
    --------------------------------------
    phyloDocs :: Map (Date, Date) [Document]
    phyloDocs = corpusToDocs c phyloBase
    ......@@ -251,7 +263,7 @@ instance PhyloMaker [Document]
    phylo1 = toPhylo1 (getContextualUnit q) (getInterTemporalMatching q) phyloDocs phylo0
    --------------------------------------
    phylo0 :: Phylo
    phylo0 = toPhylo0 phyloDocs phyloBase
    phylo0 = tracePhylo0 $ toPhylo0 phyloDocs phyloBase
    --------------------------------------
    phyloDocs :: Map (Date, Date) [Document]
    phyloDocs = corpusToDocs c phyloBase
    ......@@ -286,13 +298,16 @@ instance PhyloMaker [Document]
    tracePhylo0 :: Phylo -> Phylo
    tracePhylo0 p = trace ("\n---------------\n--| Phylo 0 |--\n---------------\n\n") p
    tracePhylo0 p = trace ("\n---------------\n--| Phylo 0 |--\n---------------\n\n"
    <> show (length $ getGroupsWithLevel 0 p) <> " groups created \n") p
    tracePhylo1 :: Phylo -> Phylo
    tracePhylo1 p = trace ("\n---------------\n--| Phylo 1 |--\n---------------\n\n") p
    tracePhylo1 p = trace ("\n---------------\n--| Phylo 1 |--\n---------------\n\n"
    <> show (length $ getGroupsWithLevel 1 p) <> " groups created \n") p
    tracePhyloN :: Level -> Phylo -> Phylo
    tracePhyloN lvl p = trace ("\n---------------\n--| Phylo " <> show (lvl) <> " |--\n---------------\n\n") p
    tracePhyloN lvl p = trace ("\n---------------\n--| Phylo " <> show (lvl) <> " |--\n---------------\n\n"
    <> show (length $ getGroupsWithLevel lvl p) <> " groups created \n") p
    tracePhyloBase :: Phylo -> Phylo
    ......
    src/Gargantext/Viz/Phylo/LinkMaker.hs
    View file @ 815ab543
    This diff is collapsed.
    src/Gargantext/Viz/Phylo/Metrics/Clustering.hs
    View file @ 815ab543
    ......@@ -18,36 +18,20 @@ module Gargantext.Viz.Phylo.Metrics.Clustering
    where
    import Data.Graph.Clustering.Louvain.CplusPlus
    import Data.List (last,concat,null,nub,(++),init,tail,elemIndex,groupBy,(!!))
    import Data.List (concat,null,nub,(++),elemIndex,groupBy,(!!), (\\), union, intersect)
    import Data.Map (fromList,mapKeys)
    import Gargantext.Prelude
    import Gargantext.Viz.Phylo
    import Gargantext.Viz.Phylo.Tools
    -- | To apply the related components method to a PhyloGraph
    -- curr = the current PhyloGroup
    -- (nodes,edges) = the initial PhyloGraph minus the current PhyloGroup
    -- next = the next PhyloGroups to be added in the cluster
    -- memo = the memory of the allready created clusters
    relatedComp :: Int -> PhyloGroup -> GroupGraph -> [PhyloGroup] -> [[PhyloGroup]] -> [[PhyloGroup]]
    relatedComp idx curr (nodes,edges) next memo
    | null nodes' && null next' = memo'
    | (not . null) next' = relatedComp idx (head' "relatedComp1" next' ) (nodes' ,edges) (tail next') memo'
    | otherwise = relatedComp (idx + 1) (head' "relatedComp2" nodes') (tail nodes',edges) [] memo'
    where
    --------------------------------------
    memo' :: [[PhyloGroup]]
    memo'
    | null memo = [[curr]]
    | idx == ((length memo) - 1) = (init memo) ++ [(last memo) ++ [curr]]
    | otherwise = memo ++ [[curr]]
    --------------------------------------
    next' :: [PhyloGroup]
    next' = filter (\x -> not $ elem x $ concat memo) $ nub $ next ++ (getNeighbours False curr edges)
    --------------------------------------
    nodes' :: [PhyloGroup]
    nodes' = filter (\x -> not $ elem x next') nodes
    --------------------------------------
    relatedComp :: [[PhyloGroup]] -> [[PhyloGroup]]
    relatedComp graphs = foldl' (\mem groups ->
    if (null mem)
    then mem ++ [groups]
    else
    let related = filter (\groups' -> (not . null) $ intersect groups groups') mem
    in if (null related)
    then mem ++ [groups]
    else (mem \\ related) ++ [union groups (nub $ concat related)] ) [] graphs
    louvain :: ([GroupNode],[GroupEdge]) -> IO [[PhyloGroup]]
    ......
    src/Gargantext/Viz/Phylo/Tools.hs
    View file @ 815ab543
    ......@@ -110,6 +110,13 @@ listToDirectedCombi :: Eq a => [a] -> [(a,a)]
    listToDirectedCombi l = [(x,y) | x <- l, y <- l, x /= y]
    listToEqualCombi :: Eq a => [a] -> [(a,a)]
    listToEqualCombi l = [(x,y) | x <- l, y <- l, x == y]
    listToPairs :: Eq a => [a] -> [(a,a)]
    listToPairs l = (listToEqualCombi l) ++ (listToUnDirectedCombi l)
    -- | To get all combinations of a list and apply a function to the resulting list of pairs
    listToDirectedCombiWith :: Eq a => forall b. (a -> b) -> [a] -> [(b,b)]
    listToDirectedCombiWith f l = [(f x,f y) | x <- l, y <- l, x /= y]
    ......@@ -195,6 +202,9 @@ getPhyloDescription p = _q_phyloTitle $ _phyloParam_query $ getPhyloParams p
    getPhyloMatchingFrame :: Phylo -> Int
    getPhyloMatchingFrame p = _q_interTemporalMatchingFrame $ _phyloParam_query $ getPhyloParams p
    getPhyloProximity :: Phylo -> Proximity
    getPhyloProximity p = _q_interTemporalMatching $ _phyloParam_query $ getPhyloParams p
    getPhyloReBranchThr :: Phylo -> Double
    getPhyloReBranchThr p = _q_reBranchThr $ _phyloParam_query $ getPhyloParams p
    ......@@ -243,7 +253,7 @@ alterGroupWithLevel f lvl p = over ( phylo_periods
    . traverse
    ) (\g -> if getGroupLevel g == lvl
    then f g
    else g ) p
    else g ) p
    -- | To alter each list of PhyloGroups following a given function
    ......
    stack.yaml
    View file @ 815ab543
    ......@@ -35,6 +35,7 @@ extra-deps:
    - KMP-0.1.0.2
    - accelerate-1.2.0.0
    - aeson-lens-0.5.0.0
    - deepseq-th-0.1.0.4
    - duckling-0.1.3.0
    - full-text-search-0.2.1.4
    - fullstop-0.1.4
    ......
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