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gargantext
haskell-gargantext
Commits
aaf48a73
Commit
aaf48a73
authored
Nov 08, 2021
by
Alexandre Delanoë
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[Merge]
parents
1b1b4a07
d63bc5be
Pipeline
#2044
failed with stage
in 10 minutes and 6 seconds
Changes
9
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1
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9 changed files
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43 additions
and
26 deletions
+43
-26
package.yaml
package.yaml
+1
-0
Mail.hs
src/Gargantext/Core/Mail.hs
+1
-1
Parsers.hs
src/Gargantext/Core/Text/Corpus/Parsers.hs
+5
-8
Date.hs
src/Gargantext/Core/Text/Corpus/Parsers/Date.hs
+1
-1
Wikidata.hs
src/Gargantext/Core/Text/Corpus/Parsers/Wikidata.hs
+6
-5
Bridgeness.hs
src/Gargantext/Core/Viz/Graph/Bridgeness.hs
+1
-1
Tools.hs
src/Gargantext/Core/Viz/Graph/Tools.hs
+4
-4
IGraph.hs
src/Gargantext/Core/Viz/Graph/Tools/IGraph.hs
+1
-4
stack.yaml
stack.yaml
+23
-2
No files found.
package.yaml
View file @
aaf48a73
...
@@ -158,6 +158,7 @@ library:
...
@@ -158,6 +158,7 @@ library:
-
full-text-search
-
full-text-search
-
fullstop
-
fullstop
-
gargantext-prelude
-
gargantext-prelude
-
gargantext-graph >= 0.1.0.0
-
graphviz
-
graphviz
-
hashable
-
hashable
-
haskell-igraph
-
haskell-igraph
...
...
src/Gargantext/Core/Mail.hs
View file @
aaf48a73
...
@@ -64,7 +64,7 @@ email_to' (NewUser u m _) = (m,u)
...
@@ -64,7 +64,7 @@ email_to' (NewUser u m _) = (m,u)
------------------------------------------------------------------------
------------------------------------------------------------------------
bodyWith
::
ServerAddress
->
MailModel
->
[
Text
]
bodyWith
::
ServerAddress
->
MailModel
->
[
Text
]
bodyWith
server
(
Invitation
u
)
=
[
"Congratulation, you have been granted a
beta
user account to test the"
bodyWith
server
(
Invitation
u
)
=
[
"Congratulation, you have been granted a user account to test the"
,
"new GarganText platform!"
,
"new GarganText platform!"
]
<>
(
email_credentials
server
u
)
]
<>
(
email_credentials
server
u
)
...
...
src/Gargantext/Core/Text/Corpus/Parsers.hs
View file @
aaf48a73
...
@@ -25,9 +25,8 @@ module Gargantext.Core.Text.Corpus.Parsers (FileFormat(..), clean, parseFile, cl
...
@@ -25,9 +25,8 @@ module Gargantext.Core.Text.Corpus.Parsers (FileFormat(..), clean, parseFile, cl
import
"zip"
Codec.Archive.Zip
(
withArchive
,
getEntry
,
getEntries
)
import
"zip"
Codec.Archive.Zip
(
withArchive
,
getEntry
,
getEntries
)
import
Control.Concurrent.Async
as
CCA
(
mapConcurrently
)
import
Control.Concurrent.Async
as
CCA
(
mapConcurrently
)
import
Control.Monad
(
join
,
sequence
)
import
Control.Monad.IO.Class
(
liftIO
)
import
Data.Attoparsec.ByteString
(
parseOnly
,
Parser
)
import
Data.Attoparsec.ByteString
(
parseOnly
,
Parser
)
import
Control.Monad
(
join
)
import
Data.Either
(
Either
(
..
))
import
Data.Either
(
Either
(
..
))
import
Data.Either.Extra
(
partitionEithers
)
import
Data.Either.Extra
(
partitionEithers
)
import
Data.List
(
concat
,
lookup
)
import
Data.List
(
concat
,
lookup
)
...
@@ -98,13 +97,11 @@ parseFormat WOS bs = do
...
@@ -98,13 +97,11 @@ parseFormat WOS bs = do
$
[
runParser'
WOS
bs
]
$
[
runParser'
WOS
bs
]
pure
$
Right
docs
pure
$
Right
docs
parseFormat
ZIP
bs
=
do
parseFormat
ZIP
bs
=
do
path
<-
emptySystemTempFile
"parsed
.
zip"
path
<-
emptySystemTempFile
"parsed
-
zip"
DB
.
writeFile
path
bs
DB
.
writeFile
path
bs
withArchive
path
$
do
parsedZip
<-
withArchive
path
$
do
files
<-
DM
.
keys
<$>
getEntries
DM
.
keys
<$>
getEntries
filesContents
<-
mapM
getEntry
files
pure
$
Left
$
"Not implemented for ZIP, parsedZip"
<>
show
parsedZip
ddocs
<-
liftIO
$
mapM
(
parseFormat
CsvGargV3
)
filesContents
pure
$
concat
<$>
sequence
ddocs
parseFormat
_
_
=
undefined
parseFormat
_
_
=
undefined
-- | Parse file into documents
-- | Parse file into documents
...
...
src/Gargantext/Core/Text/Corpus/Parsers/Date.hs
View file @
aaf48a73
...
@@ -119,7 +119,7 @@ getTimeValue rt = case head rt of
...
@@ -119,7 +119,7 @@ getTimeValue rt = case head rt of
Nothing
Nothing
Just
x
->
case
rval
x
of
Just
x
->
case
rval
x
of
RVal
Time
t
->
Just
$
toJSON
t
RVal
Time
t
->
Just
$
toJSON
t
_
->
do
_
->
do
Nothing
Nothing
extractValue
::
Maybe
Value
->
Maybe
Text
extractValue
::
Maybe
Value
->
Maybe
Text
...
...
src/Gargantext/Core/Text/Corpus/Parsers/Wikidata.hs
View file @
aaf48a73
{-|
{-|
Module : Gargantext.Core.Text.Corpus.Parsers.Wikidata
Module : Gargantext.Core.Text.Corpus.Parsers.Wikidata
<<<<<<< HEAD
Description : To query Wikidata
Description : To query Wikidata
=======
Description : To query Wikidata
>>>>>>> dev-clustering
Copyright : (c) CNRS, 2019-Present
Copyright : (c) CNRS, 2019-Present
License : AGPL + CECILL v3
License : AGPL + CECILL v3
Maintainer : team@gargantext.org
Maintainer : team@gargantext.org
...
@@ -29,7 +33,7 @@ import Gargantext.Core.Text.Corpus.Parsers.Date (dateSplit)
...
@@ -29,7 +33,7 @@ import Gargantext.Core.Text.Corpus.Parsers.Date (dateSplit)
data
WikiResult
=
WikiResult
{
_wr_cid
::
Maybe
Text
data
WikiResult
=
WikiResult
{
_wr_cid
::
Maybe
Text
,
_wr_title
::
Maybe
Text
,
_wr_title
::
Maybe
Text
,
_wr_url
::
Maybe
Text
,
_wr_url
::
Maybe
Text
,
_wr_yearStart
::
Maybe
Text
,
_wr_yearStart
::
Maybe
Text
...
@@ -48,10 +52,9 @@ wikidataGet n m = do
...
@@ -48,10 +52,9 @@ wikidataGet n m = do
wikiPageToDocument
::
NumberOfSections
->
WikiResult
->
IO
HyperdataDocument
wikiPageToDocument
::
NumberOfSections
->
WikiResult
->
IO
HyperdataDocument
wikiPageToDocument
m
wr
=
do
wikiPageToDocument
m
wr
=
do
sections
<-
case
wr
^.
wr_url
of
sections
<-
case
wr
^.
wr_url
of
Nothing
->
pure
[]
Nothing
->
pure
[]
Just
u
->
crawlPage
u
Just
u
->
crawlPage
u
let
bdd
=
Just
"wikidata"
let
bdd
=
Just
"wikidata"
doi
=
Nothing
doi
=
Nothing
...
@@ -129,5 +132,3 @@ wikidataQuery n = List.unlines
...
@@ -129,5 +132,3 @@ wikidataQuery n = List.unlines
,
" LIMIT "
<>
(
cs
$
show
n
)
,
" LIMIT "
<>
(
cs
$
show
n
)
]
]
src/Gargantext/Core/Viz/Graph/Bridgeness.hs
View file @
aaf48a73
...
@@ -24,7 +24,7 @@ import Data.Maybe (catMaybes)
...
@@ -24,7 +24,7 @@ import Data.Maybe (catMaybes)
import
Data.Ord
(
Down
(
..
))
import
Data.Ord
(
Down
(
..
))
import
Gargantext.Prelude
import
Gargantext.Prelude
import
qualified
Data.Map
as
DM
import
qualified
Data.Map
as
DM
import
G
argantext.Core.Viz.Graph.Tools.IGraph
(
ClusterNode
(
..
))
import
G
raph.Types
(
ClusterNode
(
..
))
----------------------------------------------------------------------
----------------------------------------------------------------------
type
Partitions
a
=
Map
(
Int
,
Int
)
Double
->
IO
[
a
]
type
Partitions
a
=
Map
(
Int
,
Int
)
Double
->
IO
[
a
]
...
...
src/Gargantext/Core/Viz/Graph/Tools.hs
View file @
aaf48a73
...
@@ -27,8 +27,10 @@ import Gargantext.Core.Statistics
...
@@ -27,8 +27,10 @@ import Gargantext.Core.Statistics
import
Gargantext.Core.Viz.Graph
import
Gargantext.Core.Viz.Graph
import
Gargantext.Core.Viz.Graph.Bridgeness
(
bridgeness
,
Partitions
,
ToComId
(
..
))
import
Gargantext.Core.Viz.Graph.Bridgeness
(
bridgeness
,
Partitions
,
ToComId
(
..
))
import
Gargantext.Core.Viz.Graph.Index
(
createIndices
,
toIndex
,
map2mat
,
mat2map
,
Index
,
MatrixShape
(
..
))
import
Gargantext.Core.Viz.Graph.Index
(
createIndices
,
toIndex
,
map2mat
,
mat2map
,
Index
,
MatrixShape
(
..
))
import
Gargantext.Core.Viz.Graph.Tools.IGraph
(
mkGraphUfromEdges
,
spinglass
,
ClusterNode
)
import
Gargantext.Core.Viz.Graph.Tools.IGraph
(
mkGraphUfromEdges
,
spinglass
)
import
Gargantext.Prelude
import
Gargantext.Prelude
import
Graph.Types
(
ClusterNode
)
import
qualified
Graph.BAC.ProxemyOptim
as
BAC
import
IGraph.Random
-- (Gen(..))
import
IGraph.Random
-- (Gen(..))
import
qualified
Data.HashMap.Strict
as
HashMap
import
qualified
Data.HashMap.Strict
as
HashMap
import
qualified
Data.List
as
List
import
qualified
Data.List
as
List
...
@@ -40,12 +42,10 @@ import qualified IGraph.Algorithms.Layout as Layout
...
@@ -40,12 +42,10 @@ import qualified IGraph.Algorithms.Layout as Layout
-------------------------------------------------------------
-------------------------------------------------------------
defaultClustering
::
Map
(
Int
,
Int
)
Double
->
IO
[
ClusterNode
]
defaultClustering
::
Map
(
Int
,
Int
)
Double
->
IO
[
ClusterNode
]
defaultClustering
=
spinglass
1
defaultClustering
x
=
pure
$
BAC
.
defaultClustering
x
-------------------------------------------------------------
-------------------------------------------------------------
type
Threshold
=
Double
type
Threshold
=
Double
cooc2graph'
::
Ord
t
=>
Distance
cooc2graph'
::
Ord
t
=>
Distance
...
...
src/Gargantext/Core/Viz/Graph/Tools/IGraph.hs
View file @
aaf48a73
...
@@ -20,6 +20,7 @@ import Data.Singletons (SingI)
...
@@ -20,6 +20,7 @@ import Data.Singletons (SingI)
import
IGraph
hiding
(
mkGraph
,
neighbors
,
edges
,
nodes
,
Node
,
Graph
)
import
IGraph
hiding
(
mkGraph
,
neighbors
,
edges
,
nodes
,
Node
,
Graph
)
import
Protolude
import
Protolude
import
Gargantext.Core.Viz.Graph.Index
import
Gargantext.Core.Viz.Graph.Index
import
Graph.Types
import
qualified
Data.List
as
List
import
qualified
Data.List
as
List
import
qualified
IGraph
as
IG
import
qualified
IGraph
as
IG
import
qualified
IGraph.Algorithms.Clique
as
IG
import
qualified
IGraph.Algorithms.Clique
as
IG
...
@@ -82,10 +83,6 @@ partitions_spinglass' s g = do
...
@@ -82,10 +83,6 @@ partitions_spinglass' s g = do
IG
.
findCommunity
g
Nothing
Nothing
IG
.
spinglass
gen
IG
.
findCommunity
g
Nothing
Nothing
IG
.
spinglass
gen
data
ClusterNode
=
ClusterNode
{
cl_node_id
::
Int
,
cl_community_id
::
Int
}
toClusterNode
::
[[
Int
]]
->
[
ClusterNode
]
toClusterNode
::
[[
Int
]]
->
[
ClusterNode
]
toClusterNode
ns
=
List
.
concat
toClusterNode
ns
=
List
.
concat
$
map
(
\
(
cId
,
ns'
)
->
map
(
\
n
->
ClusterNode
n
cId
)
ns'
)
$
map
(
\
(
cId
,
ns'
)
->
map
(
\
n
->
ClusterNode
n
cId
)
ns'
)
...
...
stack.yaml
View file @
aaf48a73
...
@@ -4,7 +4,7 @@ flags: {}
...
@@ -4,7 +4,7 @@ flags: {}
extra-package-dbs
:
[]
extra-package-dbs
:
[]
packages
:
packages
:
-
.
-
.
#- 'deps/patches-class
'
#- 'deps/gargantext-graph
'
#- 'deps/patches-map'
#- 'deps/patches-map'
#- 'deps/accelerate'
#- 'deps/accelerate'
#- 'deps/accelerate-utility'
#- 'deps/accelerate-utility'
...
@@ -30,6 +30,9 @@ extra-deps:
...
@@ -30,6 +30,9 @@ extra-deps:
-
#git: https://gitlab.iscpif.fr/gargantext/haskell-gargantext-prelude.git
-
#git: https://gitlab.iscpif.fr/gargantext/haskell-gargantext-prelude.git
git
:
https://gitlab.iscpif.fr/cgenie/haskell-gargantext-prelude.git
git
:
https://gitlab.iscpif.fr/cgenie/haskell-gargantext-prelude.git
commit
:
35b09629a658fc16cc9ff63e7591e58511cd98a7
commit
:
35b09629a658fc16cc9ff63e7591e58511cd98a7
#git: ssh://git@gitlab.iscpif.fr:20022/gargantext/gargantext-graph.git
-
git
:
ssh://gitolite3@delanoe.org/gargantext-graph
commit
:
294887a220460bd0c114638fff9ea53306cd2f18
# Data Mining Libs
# Data Mining Libs
-
git
:
https://github.com/delanoe/data-time-segment.git
-
git
:
https://github.com/delanoe/data-time-segment.git
commit
:
10a416b9f6c443866b36479c3441ebb3bcdeb7ef
commit
:
10a416b9f6c443866b36479c3441ebb3bcdeb7ef
...
@@ -88,7 +91,18 @@ extra-deps:
...
@@ -88,7 +91,18 @@ extra-deps:
-
git
:
https://github.com/rspeer/wikiparsec.git
-
git
:
https://github.com/rspeer/wikiparsec.git
commit
:
9637a82344bb70f7fa8f02e75db3c081ccd434ce
commit
:
9637a82344bb70f7fa8f02e75db3c081ccd434ce
# Others dependencies (using stack resolver)
# Gargantext-graph
-
eigen-3.3.7.0@sha256:7c24a86426b238e02ba0ac2179cc44997518b443a13828ed7a791fe49a6dffa5,82060
-
git
:
https://github.com/alpmestan/sparse-linear.git
commit
:
bc6ca8058077b0b5702ea4b88bd4189cfcad267a
subdirs
:
-
sparse-linear
-
git
:
https://github.com/alpmestan/hmatrix.git
commit
:
b9fca8beee0f23c17a6b2001ec834d071709e6e7
subdirs
:
-
packages/base
# Others dependencies (using stack resolver)
-
constraints-extras-0.3.1.0@sha256:12016ebb91ad5ed2c82bf7e48c6bd6947d164d33c9dca5ac3965de1bb6c780c0,1777
-
constraints-extras-0.3.1.0@sha256:12016ebb91ad5ed2c82bf7e48c6bd6947d164d33c9dca5ac3965de1bb6c780c0,1777
-
KMP-0.2.0.0@sha256:6dfbac03ef00ebd9347234732cb86a40f62ab5a80c0cc6bedb8eb51766f7df28,2562
-
KMP-0.2.0.0@sha256:6dfbac03ef00ebd9347234732cb86a40f62ab5a80c0cc6bedb8eb51766f7df28,2562
-
Unique-0.4.7.8@sha256:9661f45aa31dde119a2114566166ea38b011a45653337045ee4ced75636533c0,2067
-
Unique-0.4.7.8@sha256:9661f45aa31dde119a2114566166ea38b011a45653337045ee4ced75636533c0,2067
...
@@ -122,3 +136,10 @@ extra-deps:
...
@@ -122,3 +136,10 @@ extra-deps:
-
taggy-0.2.1@sha256:7bc55ddba178971dc6052163597f0445a0a2b5b0ca0e84ce651d53d722e3c265,4662
-
taggy-0.2.1@sha256:7bc55ddba178971dc6052163597f0445a0a2b5b0ca0e84ce651d53d722e3c265,4662
-
servant-ekg-0.3.1@sha256:19bd9dc3943983da8e79d6f607614c68faea4054fb889d508c8a2b67b6bdd448,2203
-
servant-ekg-0.3.1@sha256:19bd9dc3943983da8e79d6f607614c68faea4054fb889d508c8a2b67b6bdd448,2203
# For the graph clustering
ghc-options
:
hmatrix
:
-O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal -fno-state-hack
sparse-linear
:
-O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal -fno-state-hack
gargantext-graph
:
-O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal -fno-state-hack
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