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haskell-gargantext
Commit 63e3a6fd authored by Alexandre Delanoë's avatar Alexandre Delanoë
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[FIX] Haddock documentation ok

parent 43fe729b
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    src/Gargantext/API/Admin/Orchestrator/Types.hs
    View file @ 63e3a6fd
    ......@@ -27,13 +27,13 @@ instance Arbitrary a => Arbitrary (JobOutput a) where
    arbitrary = JobOutput <$> arbitrary
    -- | Main Types
    -- TODO IsidoreAuth
    data ExternalAPIs = All
    | PubMed
    | HAL
    | IsTex
    | Isidore
    deriving (Show, Eq, Enum, Bounded, Generic)
    -- | IsidoreAuth
    -- | Main Instances
    ......
    src/Gargantext/Text/Terms.hs
    View file @ 63e3a6fd
    ......@@ -175,6 +175,6 @@ newTries n t = buildTries n (fmap toToken $ uniText t)
    uniText :: Text -> [[Text]]
    uniText = map (List.filter (not . isPunctuation))
    . map tokenize
    . sentences -- | TODO get sentences according to lang
    . sentences -- TODO get sentences according to lang
    . Text.toLower
    src/Gargantext/Text/Terms/Eleve.hs
    View file @ 63e3a6fd
    ......@@ -73,12 +73,12 @@ subst (src, dst) x | sim src x = dst
    | otherwise = x
    ------------------------------------------------------------------------
    -- | TODO: Show Instance only used for debugging
    type Entropy e =
    ( Fractional e
    , Floating e
    , P.RealFloat e
    , Show e
    -- ^ TODO: only used for debugging
    )
    ------------------------------------------------------------------------
    -- | Example and tests for development
    ......
    src/Gargantext/Viz/AdaptativePhylo.hs
    View file @ 63e3a6fd
    ......@@ -65,11 +65,13 @@ data SeaElevation =
    data Proximity =
    WeightedLogJaccard
    { _wlj_sensibility :: Double
    { _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)
    ......
    src/Gargantext/Viz/Graph/Distances/Matrice.hs
    View file @ 63e3a6fd
    ......@@ -235,13 +235,16 @@ conditional' m = ( run $ ie $ map fromIntegral $ use m
    -- \[N_{m} = \sum_{i,i \neq i}^{m} \sum_{j, j \neq j}^{m} S_{ij}\]
    --
    distributional :: Matrix Int -> Matrix Double
    distributional m = run -- $ matMiniMax
    distributional m = run {- -- $ matMiniMax
    -- $ ri
    -- $ myMin
    -- $ myMin
    -}
    $ filter' 0
    $ s_mi
    $ map fromIntegral -- ^ from Int to Double
    $ use m -- ^ push matrix in Accelerate type
    $ map fromIntegral
    {- from Int to Double -}
    $ use m
    {- push matrix in Accelerate type -}
    where
    -- filter m = zipWith (\a b -> max a b) m (transpose m)
    ......
    src/Gargantext/Viz/Phylo/LevelMaker.hs
    View file @ 63e3a6fd
    ......@@ -207,7 +207,7 @@ toNthLevel lvlMax prox clus p
    | otherwise = toNthLevel lvlMax prox clus
    $ traceBranches (lvl + 1)
    $ setPhyloBranches (lvl + 1)
    -- $ transposePeriodLinks (lvl + 1)
    -- \$ transposePeriodLinks (lvl + 1)
    $ traceTranspose (lvl + 1) Descendant
    $ transposeLinks (lvl + 1) Descendant
    $ traceTranspose (lvl + 1) Ascendant
    ......@@ -230,15 +230,15 @@ 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) -> traceBranches 1
    -- $ reLinkPhyloBranches 1
    -- $ traceBranches 1
    -- \$ reLinkPhyloBranches 1
    -- \$ traceBranches 1
    $ setPhyloBranches 1
    $ traceTempoMatching Descendant 1
    $ interTempoMatching Descendant 1 prox
    $ traceTempoMatching Ascendant 1
    $ interTempoMatching Ascendant 1 prox
    $ tracePhyloN 1
    -- $ setLevelLinks (0,1)
    -- \$ setLevelLinks (0,1)
    $ addPhyloLevel 1 (getPhyloFis phyloFis)
    $ trace (show (size $ getPhyloFis phyloFis) <> " Fis created") $ phyloFis
    where
    ......
    src/Gargantext/Viz/Phylo/LinkMaker.hs
    View file @ 63e3a6fd
    ......@@ -126,15 +126,15 @@ phyloGroupMatching :: [PhyloPeriodId] -> PhyloGroup -> Phylo -> [Pointer]
    phyloGroupMatching periods g p = case pointers of
    Nothing -> []
    Just pts -> head' "phyloGroupMatching"
    -- | Keep only the best set of pointers grouped by proximity
    -- Keep only the best set of pointers grouped by proximity
    $ groupBy (\pt pt' -> snd pt == snd pt')
    $ reverse $ sortOn snd pts
    -- | Find the first time frame where at leats one pointer satisfies the proximity threshold
    -- Find the first time frame where at leats one pointer satisfies the proximity threshold
    where
    --------------------------------------
    pointers :: Maybe [Pointer]
    pointers = find (not . null)
    -- | For each time frame, process the Proximity on relevant pairs of targeted groups
    -- For each time frame, process the Proximity on relevant pairs of targeted groups
    $ scanl (\acc frame ->
    let pairs = makePairs frame g p
    in acc ++ ( filter (\(_,proxi) -> filterProximity proxi (getPhyloProximity p))
    ......@@ -145,7 +145,7 @@ phyloGroupMatching periods g p = case pointers of
    if (t == t')
    then [(getGroupId t,proxi)]
    else [(getGroupId t,proxi),(getGroupId t',proxi)] ) pairs ) ) []
    -- | [[1900],[1900,1901],[1900,1901,1902],...] | length max => + 5 years
    -- [[1900],[1900,1901],[1900,1901,1902],...] | length max => + 5 years
    $ inits periods
    --------------------------------------
    ......@@ -218,8 +218,6 @@ interTempoMatching fil lvl _ p = updateGroups fil lvl (Map.fromList pointers) p
    ------------------------------------------------------------------------
    -- | Make links from Period to Period after level 1
    listToTuple :: (a -> b) -> [a] -> [(b,a)]
    listToTuple f l = map (\x -> (f x, x)) l
    ......
    src/Gargantext/Viz/Phylo/Metrics.hs
    View file @ 63e3a6fd
    ......@@ -90,13 +90,13 @@ findDynamics n pv pn m =
    bid = fromJust $ (pn ^. pn_bid)
    end = last' "dynamics" (sort $ map snd $ elems m)
    in if (((snd prd) == (snd $ m ! n)) && (snd prd /= end))
    -- | emergence
    -- emergence
    then 2
    else if ((fst prd) == (fst $ m ! n))
    -- | recombination
    -- recombination
    then 0
    else if (not $ sharedWithParents (fst prd) bid n pv)
    -- | decrease
    -- decrease
    then 1
    else 3
    ......@@ -175,9 +175,3 @@ hamming f1 f2 = fromIntegral $ max ((size inter) - (size f1)) ((size inter) - (s
    inter :: Map (Int, Int) Double
    inter = intersection f1 f2
    --------------------------------------
    src/Gargantext/Viz/Phylo/PhyloExport.hs
    View file @ 63e3a6fd
    ......@@ -171,12 +171,12 @@ exportToDot phylo export =
    <> "##########################") $
    digraph ((Str . fromStrict) $ (phyloName $ getConfig phylo)) $ do
    -- | 1) init the dot graph
    {- 1) init the dot graph -}
    graphAttrs ( [ Label (toDotLabel $ (phyloName $ getConfig phylo))]
    <> [ FontSize 30, LabelLoc VTop, NodeSep 1, RankSep [1], Rank SameRank, Splines SplineEdges, Overlap ScaleOverlaps
    , Ratio FillRatio
    , Style [SItem Filled []],Color [toWColor White]]
    -- | home made attributes
    {-- home made attributes -}
    <> [(toAttr (fromStrict "phyloFoundations") $ pack $ show (length $ Vector.toList $ getRoots phylo))
    ,(toAttr (fromStrict "phyloTerms") $ pack $ show (length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) $ export ^. export_groups))
    ,(toAttr (fromStrict "phyloDocs") $ pack $ show (sum $ elems $ phylo ^. phylo_timeDocs))
    ......@@ -185,36 +185,36 @@ exportToDot phylo export =
    ,(toAttr (fromStrict "phyloGroups") $ pack $ show (length $ export ^. export_groups))
    ])
    {-
    -- toAttr (fromStrict k) $ (pack . unwords) $ map show v
    -- | 2) create a layer for the branches labels
    -- 2) create a layer for the branches labels -}
    subgraph (Str "Branches peaks") $ do
    graphAttrs [Rank SameRank]
    -- | 3) group the branches by hierarchy
    {-
    -- 3) group the branches by hierarchy
    -- mapM (\branches ->
    -- subgraph (Str "Branches clade") $ do
    -- graphAttrs [Rank SameRank]
    -- -- | 4) create a node for each branch
    -- -- 4) create a node for each branch
    -- mapM branchToDotNode branches
    -- ) $ elems $ fromListWith (++) $ map (\b -> ((init . snd) $ b ^. branch_id,[b])) $ export ^. export_branches
    -}
    mapM (\b -> branchToDotNode b (fromJust $ elemIndex b (export ^. export_branches))) $ export ^. export_branches
    -- | 5) create a layer for each period
    {-- 5) create a layer for each period -}
    _ <- mapM (\period ->
    subgraph ((Str . fromStrict . Text.pack) $ ("Period" <> show (fst period) <> show (snd period))) $ do
    graphAttrs [Rank SameRank]
    periodToDotNode period
    -- | 6) create a node for each group
    {-- 6) create a node for each group -}
    mapM (\g -> groupToDotNode (getRoots phylo) g (toBid g (export ^. export_branches))) (filter (\g -> g ^. phylo_groupPeriod == period) $ export ^. export_groups)
    ) $ getPeriodIds phylo
    -- | 7) create the edges between a branch and its first groups
    {-- 7) create the edges between a branch and its first groups -}
    _ <- mapM (\(bId,groups) ->
    mapM (\g -> toDotEdge (branchIdToDotId bId) (groupIdToDotId $ getGroupId g) "" BranchToGroup) groups
    )
    ......@@ -224,31 +224,29 @@ exportToDot phylo export =
    $ sortOn (fst . _phylo_groupPeriod) groups)
    $ fromListWith (++) $ map (\g -> (g ^. phylo_groupBranchId,[g])) $ export ^. export_groups
    -- | 8) create the edges between the groups
    {- 8) create the edges between the groups -}
    _ <- mapM (\((k,k'),_) ->
    toDotEdge (groupIdToDotId k) (groupIdToDotId k') "" GroupToGroup
    ) $ (toList . mergePointers) $ export ^. export_groups
    -- | 7) create the edges between the periods
    {- 7) create the edges between the periods -}
    _ <- mapM (\(prd,prd') ->
    toDotEdge (periodIdToDotId prd) (periodIdToDotId prd') "" PeriodToPeriod
    ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ getPeriodIds phylo
    -- | 8) create the edges between the branches
    {- 8) create the edges between the branches
    -- _ <- mapM (\(bId,bId') ->
    -- toDotEdge (branchIdToDotId bId) (branchIdToDotId bId')
    -- (Text.pack $ show(branchIdsToProximity bId bId'
    -- (getThresholdInit $ phyloProximity $ getConfig phylo)
    -- (getThresholdStep $ phyloProximity $ getConfig phylo))) BranchToBranch
    -- ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ map _branch_id $ export ^. export_branches
    -}
    graphAttrs [Rank SameRank]
    ----------------
    -- | Filter | --
    ----------------
    ......@@ -439,13 +437,13 @@ toDynamics n parents g m =
    let prd = g ^. phylo_groupPeriod
    end = last' "dynamics" (sort $ map snd $ elems m)
    in if (((snd prd) == (snd $ m ! n)) && (snd prd /= end))
    -- | decrease
    {- decrease -}
    then 2
    else if ((fst prd) == (fst $ m ! n))
    -- | recombination
    {- recombination -}
    then 0
    else if isNew
    -- | emergence
    {- emergence -}
    then 1
    else 3
    where
    ......
    src/Gargantext/Viz/Phylo/PhyloMaker.hs
    View file @ 63e3a6fd
    ......@@ -115,7 +115,7 @@ cliqueToGroup fis pId lvl idx fdt coocs =
    (fis ^. phyloClique_support)
    ngrams
    (ngramsToCooc ngrams coocs)
    (1,[0]) -- | branchid (lvl,[path in the branching tree])
    (1,[0]) -- branchid (lvl,[path in the branching tree])
    (fromList [("breaks",[0]),("seaLevels",[0])])
    [] [] [] []
    ......@@ -142,24 +142,24 @@ toPhylo1 docs phyloBase = case (getSeaElevation phyloBase) of
    ---------------------------
    -- | To apply a filter with the possibility of keeping some periods non empty (keep : True|False)
    -- To apply a filter with the possibility of keeping some periods non empty (keep : True|False)
    filterClique :: Bool -> Int -> (Int -> [PhyloClique] -> [PhyloClique]) -> Map (Date, Date) [PhyloClique] -> Map (Date, Date) [PhyloClique]
    filterClique keep thr f m = case keep of
    False -> map (\l -> f thr l) m
    True -> map (\l -> keepFilled (f) thr l) m
    -- | To filter Fis with small Support
    -- To filter Fis with small Support
    filterCliqueBySupport :: Int -> [PhyloClique] -> [PhyloClique]
    filterCliqueBySupport thr l = filter (\clq -> (clq ^. phyloClique_support) >= thr) l
    -- | To filter Fis with small Clique size
    -- To filter Fis with small Clique size
    filterCliqueBySize :: Int -> [PhyloClique] -> [PhyloClique]
    filterCliqueBySize thr l = filter (\clq -> (size $ clq ^. phyloClique_nodes) >= thr) l
    -- | To filter nested Fis
    -- To filter nested Fis
    filterCliqueByNested :: Map (Date, Date) [PhyloClique] -> Map (Date, Date) [PhyloClique]
    filterCliqueByNested m =
    let clq = map (\l ->
    ......@@ -173,16 +173,16 @@ filterCliqueByNested m =
    in fromList $ zip (keys m) clq'
    -- | To transform a time map of docs innto a time map of Fis with some filters
    -- To transform a time map of docs innto a time map of Fis with some filters
    toPhyloClique :: Phylo -> Map (Date, Date) [Document] -> Map (Date,Date) [PhyloClique]
    toPhyloClique phylo phyloDocs = case (clique $ getConfig phylo) of
    Fis s s' -> -- traceFis "Filtered Fis"
    filterCliqueByNested
    -- $ traceFis "Filtered by clique size"
    {- \$ traceFis "Filtered by clique size" -}
    $ filterClique True s' (filterCliqueBySize)
    -- $ traceFis "Filtered by support"
    {- \$ traceFis "Filtered by support" -}
    $ filterClique True s (filterCliqueBySupport)
    -- $ traceFis "Unfiltered Fis"
    {- \$ traceFis "Unfiltered Fis" -}
    phyloClique
    MaxClique _ -> undefined
    where
    ......@@ -204,7 +204,7 @@ toPhyloClique phylo phyloDocs = case (clique $ getConfig phylo) of
    --------------------
    -- | To transform the docs into a time map of coocurency matrix
    -- To transform the docs into a time map of coocurency matrix
    docsToTimeScaleCooc :: [Document] -> Vector Ngrams -> Map Date Cooc
    docsToTimeScaleCooc docs fdt =
    let mCooc = fromListWith sumCooc
    ......@@ -221,7 +221,7 @@ docsToTimeScaleCooc docs fdt =
    -- | to Phylo Base | --
    -----------------------
    -- | To group a list of Documents by fixed periods
    -- To group a list of Documents by fixed periods
    groupDocsByPeriod' :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc]
    groupDocsByPeriod' f pds docs =
    let docs' = groupBy (\d d' -> f d == f d') $ sortOn f docs
    ......@@ -237,7 +237,7 @@ groupDocsByPeriod' f pds docs =
    -- | To group a list of Documents by fixed periods
    -- To group a list of Documents by fixed periods
    groupDocsByPeriod :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc]
    groupDocsByPeriod _ _ [] = panic "[ERR][Viz.Phylo.PhyloMaker] Empty [Documents] can not have any periods"
    groupDocsByPeriod f pds es =
    ......@@ -265,7 +265,7 @@ docsToTermFreq docs fdt =
    in map (/sumFreqs) freqs
    -- | To count the number of docs by unit of time
    -- To count the number of docs by unit of time
    docsToTimeScaleNb :: [Document] -> Map Date Double
    docsToTimeScaleNb docs =
    let docs' = fromListWith (+) $ map (\d -> (date d,1)) docs
    ......@@ -279,7 +279,7 @@ initPhyloLevels lvlMax pId =
    fromList $ map (\lvl -> ((pId,lvl),PhyloLevel pId lvl empty)) [1..lvlMax]
    -- | To init the basic elements of a Phylo
    -- To init the basic elements of a Phylo
    toPhyloBase :: [Document] -> TermList -> Config -> Phylo
    toPhyloBase docs lst conf =
    let foundations = PhyloFoundations (Vector.fromList $ nub $ concat $ map text docs) lst
    ......
    src/Gargantext/Viz/Phylo/SynchronicClustering.hs
    View file @ 63e3a6fd
    ......@@ -36,13 +36,13 @@ import qualified Data.Set as Set
    mergeBranchIds :: [[Int]] -> [Int]
    mergeBranchIds ids = (head' "mergeBranchIds" . sort . mostFreq') ids
    where
    -- | 2) find the most Up Left ids in the hierarchy of similarity
    -- 2) find the most Up Left ids in the hierarchy of similarity
    -- mostUpLeft :: [[Int]] -> [[Int]]
    -- mostUpLeft ids' =
    -- let groupIds = (map (\gIds -> (length $ head' "gIds" gIds, head' "gIds" gIds)) . groupBy (\id id' -> length id == length id') . sortOn length) ids'
    -- inf = (fst . minimum) groupIds
    -- in map snd $ filter (\gIds -> fst gIds == inf) groupIds
    -- | 1) find the most frequent ids
    -- 1) find the most frequent ids
    mostFreq' :: [[Int]] -> [[Int]]
    mostFreq' ids' =
    let groupIds = (map (\gIds -> (length gIds, head' "gIds" gIds)) . group . sort) ids'
    ......@@ -58,12 +58,12 @@ mergeMeta bId groups =
    groupsToBranches' :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]]
    groupsToBranches' groups =
    -- | run the related component algorithm
    -- run the related component algorithm
    let egos = map (\g -> [getGroupId g]
    ++ (map fst $ g ^. phylo_groupPeriodParents)
    ++ (map fst $ g ^. phylo_groupPeriodChilds) ) $ elems groups
    graph = relatedComponents egos
    -- | update each group's branch id
    -- update each group's branch id
    in map (\ids ->
    let groups' = elems $ restrictKeys groups (Set.fromList ids)
    bId = mergeBranchIds $ map (\g -> snd $ g ^. phylo_groupBranchId) groups'
    ......@@ -103,26 +103,26 @@ toNextLevel' phylo groups =
    newGroups = concat $ groupsToBranches'
    $ fromList $ map (\g -> (getGroupId g, g))
    $ foldlWithKey (\acc id groups' ->
    -- | 4) create the parent group
    -- 4) create the parent group
    let parent = mergeGroups (elems $ restrictKeys (phylo ^. phylo_timeCooc) $ periodsToYears [(fst . fst) id]) id oldGroups groups'
    in acc ++ [parent]) []
    -- | 3) group the current groups by parentId
    -- 3) group the current groups by parentId
    $ fromListWith (++) $ map (\g -> (getLevelParentId g, [g])) groups
    newPeriods = fromListWith (++) $ map (\g -> (g ^. phylo_groupPeriod, [g])) newGroups
    in traceSynchronyEnd
    $ over ( phylo_periods . traverse . phylo_periodLevels . traverse
    -- | 6) update each period at curLvl + 1
    -- 6) update each period at curLvl + 1
    . filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == (curLvl + 1)))
    -- | 7) by adding the parents
    -- 7) by adding the parents
    (\phyloLvl ->
    if member (phyloLvl ^. phylo_levelPeriod) newPeriods
    then phyloLvl & phylo_levelGroups
    .~ fromList (map (\g -> (getGroupId g, g)) $ newPeriods ! (phyloLvl ^. phylo_levelPeriod))
    else phyloLvl)
    -- | 2) add the curLvl + 1 phyloLevel to the phylo
    -- 2) add the curLvl + 1 phyloLevel to the phylo
    $ addPhyloLevel (curLvl + 1)
    -- | 1) update the current groups (with level parent pointers) in the phylo
    -- 1) update the current groups (with level parent pointers) in the phylo
    $ updatePhyloGroups curLvl (fromList $ map (\g -> (getGroupId g, g)) groups) phylo
    --------------------
    ......@@ -187,19 +187,19 @@ toParentId child = ((child ^. phylo_groupPeriod, child ^. phylo_groupLevel + 1),
    reduceGroups :: Proximity -> Synchrony -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
    reduceGroups prox sync docs diagos branch =
    -- | 1) reduce a branch as a set of periods & groups
    -- 1) reduce a branch as a set of periods & groups
    let periods = fromListWith (++)
    $ map (\g -> (g ^. phylo_groupPeriod,[g])) branch
    in (concat . concat . elems)
    $ mapWithKey (\prd groups ->
    -- | 2) for each period, transform the groups as a proximity graph filtered by a threshold
    -- 2) for each period, transform the groups as a proximity graph filtered by a threshold
    let diago = reduceDiagos $ filterDiago diagos [prd]
    edges = groupsToEdges prox sync ((sum . elems) $ restrictKeys docs $ periodsToYears [prd]) diago groups
    in map (\comp ->
    -- | 4) add to each groups their futur level parent group
    -- 4) add to each groups their futur level parent group
    let parentId = toParentId (head' "parentId" comp)
    in map (\g -> g & phylo_groupLevelParents %~ (++ [(parentId,1)]) ) comp )
    -- |3) reduce the graph a a set of related components
    -- 3) reduce the graph a a set of related components
    $ toRelatedComponents groups edges) periods
    ......@@ -251,4 +251,4 @@ synchronicClustering phylo =
    -- <> "\n"
    -- ) "" edges
    -- ) "" $ elems $ groupByField _phylo_groupPeriod branch)
    -- ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo
    \ No newline at end of file
    -- ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo
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