[ghc] more deps fixes, also test small fix

README.md

@@ -166,6 +166,10 @@ If you want to see the detailed build info for a given dependency:
 cabal v2-build -v servant-server
 ```
 
+Also, you might use the `-Wunused-packages` GHC option, to get a
+warning about unused packages (make sure though you build all targets
+with `cabal v2-build all`).
+
 Also, here is a relevant discussion:
 https://discourse.haskell.org/t/whats-your-workflow-to-update-cabal-dependencies/9475
 

bin/update-project-dependencies

@@ -18,8 +18,8 @@ fi
 # with the `sha256sum` result calculated on the `cabal.project` and
 # `cabal.project.freeze`. This ensures the files stay deterministic so that CI
 # cache can kick in.
-expected_cabal_project_hash="641c87fb990ef95f861805e11c76663f075516af845c5dab458bf82b3ba5fd7d"
-expected_cabal_project_freeze_hash="6ca9d2c298827a05d873e30aaac5db3cf6648c7ca9118f13f1b109c13479f38b"
+expected_cabal_project_hash="967fee2ed28f46b12a629ad9821301854d3159975b7297653e50d7fc1f3b8919"
+expected_cabal_project_freeze_hash="af825192f1ec47b07e6001dd2556b59991c9e6c50094dc732ee933a41f0dc9bd"
 
 
 cabal --store-dir=$STORE_DIR v2-build --dry-run

cabal.project

@@ -90,7 +90,7 @@ source-repository-package
 source-repository-package
     type: git
     location: https://gitlab.iscpif.fr/gargantext/crawlers/epo-proxy-api.git
-    tag: 9225d046083853200b9045c8d71161e6a234fc5c
+    tag: cf4e5004f3b002bdef3fcab95e3559d65cdcd858
 
 source-repository-package
     type: git
@@ -110,7 +110,7 @@ source-repository-package
 source-repository-package
     type: git
     location: https://gitlab.iscpif.fr/gargantext/crawlers/openalex.git
-    tag: d2df0130575cfd32d6863d77e2ce34c48a1c32fa
+    tag: 4eec15855207dc74afc75b94c3764eede4de7b55
 
 source-repository-package
     type: git
@@ -199,8 +199,6 @@ source-repository-package
     tag: 02f5ed9ee2d6cce45161addf945b88bc6adf9059
 
         
 allow-newer:
              accelerate-arithmetic:accelerate
            , MissingH:base
@@ -210,10 +208,6 @@ allow-newer:
            , crawlerISTEX:servant
            , crawlerPubMed:servant
            , crawlerPubMed:servant-client-core
-           , epo-api-client:base
-           , epo-api-client:aeson
-           , epo-api-client:servant
-           , epo-api-client:text
            , iso639:aeson
            , iso639:text
            , morpheus-graphql-app:text
@@ -224,9 +218,6 @@ allow-newer:
            , morpheus-graphql-server:text
            , morpheus-graphql-subscriptions:text
            , morpheus-graphql:text
-           , openalex:servant
-           , openalex:servant-client-core
-           , openalex:time
            , servant-client:servant
            , servant-client:servant-client-core
            , servant-ekg:base
@@ -240,11 +231,8 @@ allow-newer:
            , stemmer:base
 allow-older: aeson:hashable
            , crawlerHAL:servant-client
-           , epo-api-client:http-client-tls
            , haskell-throttle:time
            , hsparql:rdf4h
-           , openalex:http-client-tls
-           , openalex:vector
 
 package gargantext
     ghc-options: -fwrite-ide-info -hiedir=".stack-work/hiedb"

gargantext.cabal

@@ -472,8 +472,7 @@ library
   if flag(no-phylo-debug-logs)
     cpp-options: -DNO_PHYLO_DEBUG_LOGS
   build-depends:
-      HSvm ^>= 0.1.1.3.22
-    , KMP ^>= 0.2.0.0
+      KMP ^>= 0.2.0.0
     , MissingH ^>= 1.4.3.0
     , MonadRandom ^>= 0.6
     , QuickCheck ^>= 2.14.2
@@ -502,7 +501,6 @@ library
     , crawlerPubMed
     , cron ^>= 0.7.0
     , data-time-segment ^>= 0.1.0.0
-    , deepseq ^>= 1.4.4.0
     , deferred-folds >= 0.9.18 && < 0.10
     , directory ^>= 1.3.6.0
     , discrimination >= 0.5
@@ -516,7 +514,6 @@ library
     , filepath ^>= 1.4.2.1
     , fmt
     , formatting ^>= 7.2.0
-    , full-text-search ^>= 0.2.1.4
     , fullstop ^>= 0.1.4
     , gargantext-graph >=0.1.0.0
     , gargantext-prelude
@@ -530,11 +527,10 @@ library
     , http-api-data >= 0.5 && < 0.6
     , http-client ^>= 0.7.14
     , http-client-tls == 0.3.6.1
-    , http-conduit ^>= 2.3.8
+    , http-conduit >= 2.3.8 && < 2.3.9
     , http-media ^>= 0.8.0.0
     , http-types ^>= 0.12.3
     , http-reverse-proxy >= 0.6.1.0
-    , hxt ^>= 9.3.1.22
     , ini ^>= 0.4.1
     , insert-ordered-containers ^>= 0.2.5.1
     , iso639 ^>= 0.1.0.3
@@ -542,8 +538,6 @@ library
     , json-stream ^>= 0.4.2.4
     , lens >= 5.2.2 && < 5.3
     , lens-aeson < 1.3
-    , lifted-base ^>= 0.2.3.12
-    , listsafe ^>= 0.1.0.1
     , matrix ^>= 0.3.6.1
     , mime-mail >= 0.5.1
     , monad-control ^>= 1.0.3.1
@@ -553,13 +547,11 @@ library
     , morpheus-graphql-subscriptions >= 0.24.3 && < 0.25
     , mtl ^>= 2.2.2
     , nanomsg-haskell >= 0.2.4 && < 0.3
-    , natural-transformation ^>= 0.4
     , network >= 3.1.4.0
     , network-uri ^>= 2.6.4.1
     , opaleye ^>= 0.9.6.1
     , opaleye-textsearch >= 0.2.0.0
     , openalex
-    , pandoc ^>= 3.0.1
     , parallel ^>= 3.2.2.0
     , parsec ^>= 3.1.14.0
     , patches-class ^>= 0.1.0.1
@@ -586,7 +578,6 @@ library
     , servant-client-core >= 0.20 && < 0.21
     , servant-ekg ^>= 0.3.1
     , servant-job >= 0.2.0.0
-    , servant-multipart ^>= 0.12.1
     , servant-routes < 0.2
     , servant-server >= 0.18.3 && < 0.21
     , servant-swagger ^>= 1.2
@@ -602,7 +593,6 @@ library
     , stm-containers >= 1.2.0.3 && < 1.3
     , stringsearch >= 0.3.6.6
     , swagger2 ^>= 2.8.7
-    , taggy-lens ^>= 0.1.2
     , tagsoup ^>= 0.14.8
     , template-haskell ^>= 2.19.0.0
     , temporary ^>= 1.3
@@ -624,7 +614,6 @@ library
     , wai-cors ^>= 0.2.7
     , wai-extra ^>= 3.1.8
     , wai-util >= 0.8
-    , wai-websockets ^>= 3.0.1.2
     , warp ^>= 3.3.20
     , websockets ^>= 0.12.7.3
     , wreq ^>= 0.5.3.3
@@ -667,7 +656,6 @@ executable gargantext-cli
     , cryptohash ^>= 0.11.9
     , directory ^>= 1.3.6.0
     , extra ^>= 1.7.9
-    , full-text-search ^>= 0.2.1.4
     , gargantext
     , gargantext-prelude
     , ini ^>= 0.4.1
@@ -704,7 +692,6 @@ executable gargantext-server
       cassava ^>= 0.5.2.0
     , containers ^>= 0.6.5.1
     , extra ^>= 1.7.9
-    , full-text-search ^>= 0.2.1.4
     , gargantext
     , gargantext-prelude
     , ini ^>= 0.4.1
@@ -892,7 +879,6 @@ benchmark garg-bench
       Paths_gargantext
   build-depends: base
                , bytestring ^>= 0.11.5.2
-               , deepseq
                , gargantext
                , gargantext-prelude
                , tasty-bench

src/Gargantext/MicroServices/ReverseProxy.hs

@@ -51,7 +51,7 @@ import Network.Wai
 import Network.Wai.Util (redirect')
 import Servant hiding (Header)
 import Servant.Auth.Server
-import Servant.Auth.Server.Internal.AddSetCookie
+import Servant.Auth.Server.Internal.AddSetCookie ()
 import Servant.Auth.Swagger ()
 import Servant.Client.Core.BaseUrl
 import Servant.Server.Generic
@@ -59,13 +59,13 @@ import Text.RE.Replace hiding (Capture)
 import Text.RE.TDFA.ByteString
 
 
--- See https://github.com/haskell-servant/servant/issues/1601#issue-1338013029
-instance {-# OVERLAPPING #-}
-  ( AddSetCookies ('S n) a a
-  , AddSetCookies ('S n) b b'
-  )
-  => AddSetCookies ('S n) (a :<|> b) (a :<|> b') where
-  addSetCookies cookies ( a :<|> b) = addSetCookies cookies a :<|> addSetCookies cookies b
+-- -- See https://github.com/haskell-servant/servant/issues/1601#issue-1338013029
+-- instance {-# OVERLAPPING #-}
+--   ( AddSetCookies ('S n) a a
+--   , AddSetCookies ('S n) b b'
+--   )
+--   => AddSetCookies ('S n) (a :<|> b) (a :<|> b') where
+--   addSetCookies cookies ( a :<|> b) = addSetCookies cookies a :<|> addSetCookies cookies b
 
 --
 -- Types

stack.yaml

-#"allow-newer": true
+"allow-newer": false
 "extra-deps":
-- "HSvm-0.1.1.3.22"
+- "JuicyPixels-3.3.9"
 - "KMP-0.2.0.0"
-- "MissingH-1.4.3.0"
+- "MissingH-1.4.3.1"
+- "OneTuple-0.4.2"
+- "aeson-pretty-0.8.10"
+- "alex-3.5.1.0"
+- "ansi-terminal-1.0.2"
+- "assoc-1.1.1"
+- "async-2.2.5"
+- "atomic-primops-0.8.8"
+- "barbies-2.1.1.0"
+- "base-compat-0.13.1"
+- "base-compat-batteries-0.13.1"
+- "base-orphans-0.9.2"
+- "base64-1.0"
+- "bifunctors-5.6.2"
+- "binary-orphans-1.0.5"
+- "blaze-html-0.9.2.0"
+- "boring-0.2.2"
+- "bzlib-conduit-0.3.0.3"
+- "cabal-doctest-1.0.10"
+- "cassava-0.5.3.2"
+- "cassava-conduit-0.6.6"
+- "cborg-0.2.10.0"
+- "concurrent-output-1.10.21"
+- "conduit-1.3.6"
+- "criterion-measurement-0.2.2.0"
+- "cron-0.7.1"
+- "crypton-1.0.0"
+- "crypton-x509-1.7.7"
+- "data-fix-0.3.4"
+- "dec-0.0.6"
 - "deferred-folds-0.9.18.6"
-- "full-text-search-0.2.1.4"
+- "digest-0.0.2.1"
+- "double-conversion-2.0.5.0"
+- "extra-1.7.16"
+- "fast-logger-3.2.3"
+- "fgl-5.8.2.0"
+- "file-embed-0.0.16.0"
+- "file-embed-lzma-0.1"
+- "foldl-1.4.17"
+- "free-5.2"
 - "fullstop-0.1.4"
-- "hgal-2.0.0.2"
+- "graphviz-2999.20.2.0"
+- "hashable-1.4.4.0"
+- "haskell-src-meta-0.8.14"
+- "hedgehog-1.5"
+- "hslogger-1.3.1.1"
 - "hsparql-0.3.8"
-- "hspec-2.11.1"
-- "hspec-core-2.11.1"
-- "hspec-discover-2.11.1"
-- "hspec-expectations-0.8.3"
+- "hspec-2.11.9"
+- "hspec-api-2.11.9"
+- "hspec-core-2.11.9"
+- "hspec-discover-2.11.9"
+- "hspec-expectations-0.8.4"
 - "http-accept-0.2"
+- "http-api-data-0.5.1"
+- "http-conduit-2.3.8.3"
+- "http-types-0.12.4"
+- "http2-5.0.1"
+- "indexed-traversable-0.1.4"
+- "invariant-0.6.3"
+- "iproute-1.7.14"
+- "jose-0.10.0.1"
+- "json-stream-0.4.6.0"
+- "kan-extensions-5.2.6"
+- "language-c-0.9.3"
+- "libyaml-0.1.4"
+- "libyaml-clib-0.2.5"
+- "lifted-async-0.10.2.5"
+- "logict-0.8.1.0"
+- "lzma-0.0.1.1"
+- "math-functions-0.3.4.4"
+- "matrix-0.3.6.3"
+- "megaparsec-9.6.1"
+- "microlens-th-0.4.3.15"
+- "mono-traversable-1.0.17.0"
+- "monoid-extras-0.6.3"
 - "morpheus-graphql-0.24.3"
 - "morpheus-graphql-app-0.24.3"
 - "morpheus-graphql-client-0.24.3"
@@ -21,25 +85,78 @@
 - "morpheus-graphql-core-0.24.3"
 - "morpheus-graphql-server-0.24.3"
 - "morpheus-graphql-subscriptions-0.24.3"
-- "opaleye-0.9.6.1"
+- "mwc-random-0.15.1.0"
+- "network-control-0.0.2"
+- "old-time-1.1.0.4"
+- "ordered-containers-0.2.4"
+- "os-string-2.0.6"
+- "password-3.0.4.0"
+- "postgres-options-0.2.2.0"
+- "primitive-0.7.4.0"
+- "primitive-extras-0.10.2"
 - "primitive-unlifted-2.1.0.0"
+- "protolude-0.3.4"
+- "psqueues-0.2.8.0"
 - "rake-0.0.1"
-- "random-1.2.1"
+- "random-1.2.1.2"
 - "recover-rtti-0.4.3"
-- "servant-0.20.1"
-- "servant-auth-server-0.4.8.0"
-- "servant-auth-swagger-0.2.10.2"
-- "servant-client-core-0.20"
+- "reflection-2.1.8"
+- "resourcet-1.3.0"
+- "safe-0.3.21"
+- "serialise-0.2.6.1"
+- "servant-0.20.2"
+- "servant-auth-0.4.2.0"
+- "servant-auth-client-0.4.2.0"
+- "servant-auth-server-0.4.9.0"
+- "servant-auth-swagger-0.2.11.0"
+- "servant-client-core-0.20.2"
 - "servant-ekg-0.3.1"
 - "servant-flatten-0.2"
-- "servant-server-0.20"
-- "servant-swagger-1.2"
+- "servant-server-0.20.2"
+- "servant-swagger-1.2.1"
+- "servant-swagger-ui-0.3.5.5.0.1"
+- "singleton-bool-0.1.8"
+- "singletons-3.0.3"
+- "some-1.0.6"
+- "split-0.2.5"
 - "stemmer-0.5.2"
+- "stm-containers-1.2.1"
+- "stm-hamt-1.2.1"
+- "swagger2-2.8.9"
+- "tagged-0.8.8"
 - "taggy-0.2.1"
 - "taggy-lens-0.1.2"
-- "vector-0.12.3.0"
+- "tasty-1.5"
+- "tasty-bench-0.4"
+- "tasty-hspec-1.2.0.4"
+- "tasty-hunit-0.10.2"
+- "tasty-quickcheck-0.11"
+- "text-short-0.1.6"
+- "th-compat-0.1.5"
+- "these-1.2.1"
+- "time-compat-1.9.7"
+- "type-equality-1.0.1"
+- "typed-process-0.2.12.0"
+- "unicode-collation-0.1.3.6"
+- "unix-compat-0.7.2"
+- "unix-time-0.4.15"
+- "unordered-containers-0.2.20"
+- "utility-ht-0.0.17.2"
+- "uuid-1.3.16"
+- "uuid-types-1.0.6"
+- "validity-0.12.1.0"
+- "vector-0.12.3.1"
+- "vector-algorithms-0.9.0.2"
 - "wai-3.2.4"
+- "wai-app-static-3.1.9"
+- "wai-extra-3.1.15"
+- "wai-logger-2.4.1"
 - "wai-util-0.8"
+- "warp-3.3.31"
+- "wreq-0.5.4.3"
+- "zip-2.0.1"
+- "zip-archive-0.4.3.2"
+- "zlib-0.7.1.0"
 - commit: 2b5d69448557e89002c0179ea1aaf59bb757a6e3
   git: "https://github.com/AccelerateHS/accelerate-llvm.git"
   subdirs:
@@ -88,7 +205,7 @@
   git: "https://github.com/boolexpr/boolexpr.git"
   subdirs:
   - .
-- commit: 8fff32a43df743c8c83428a86dd566a0936a4fba
+- commit: 1790fdf9138970dde0dbabf8b270698145a4a88c
   git: "https://github.com/chessai/eigen.git"
   subdirs:
   - .
@@ -124,7 +241,7 @@
   git: "https://gitlab.iscpif.fr/gargantext/crawlers/arxiv-api.git"
   subdirs:
   - .
-- commit: 9225d046083853200b9045c8d71161e6a234fc5c
+- commit: cf4e5004f3b002bdef3fcab95e3559d65cdcd858
   git: "https://gitlab.iscpif.fr/gargantext/crawlers/epo-proxy-api.git"
   subdirs:
   - .
@@ -140,7 +257,7 @@
   git: "https://gitlab.iscpif.fr/gargantext/crawlers/istex.git"
   subdirs:
   - .
-- commit: d2df0130575cfd32d6863d77e2ce34c48a1c32fa
+- commit: 4eec15855207dc74afc75b94c3764eede4de7b55
   git: "https://gitlab.iscpif.fr/gargantext/crawlers/openalex.git"
   subdirs:
   - .
@@ -218,11 +335,10 @@ flags:
     "lib-only": false
   "ansi-terminal":
     example: false
-    "win32-2-13-1": false
   "ansi-wl-pprint":
     example: false
   assoc:
-    tagged: true
+    tagged: false
   async:
     bench: false
   "atomic-primops":
@@ -233,7 +349,6 @@ flags:
     "base-4-8": true
     "old-base": false
   bifunctors:
-    semigroups: true
     tagged: true
   bitvec:
     simd: true
@@ -244,8 +359,6 @@ flags:
   c2hs:
     base3: true
     regression: false
-  cassava:
-    "bytestring--lt-0_10_4": false
   "cassava-conduit":
     small_base: true
   cborg:
@@ -254,9 +367,6 @@ flags:
     "bytestring-builder": false
   "cipher-aes":
     support_aesni: true
-  citeproc:
-    executable: false
-    icu: false
   clock:
     llvm: false
   cmdargs:
@@ -300,6 +410,12 @@ flags:
     support_sse: false
     use_target_attributes: true
   digest:
+    have_arm64_crc32c: false
+    have_builtin_prefetch: false
+    have_mm_prefetch: false
+    have_sse42: false
+    have_strong_getauxval: false
+    have_weak_getauxval: false
     "pkg-config": true
   distributive:
     semigroups: true
@@ -316,9 +432,7 @@ flags:
   "foldable1-classes-compat":
     tagged: true
   formatting:
-    "no-double-conversion": true
-  "full-text-search":
-    "build-search-demo": false
+    "no-double-conversion": false
   gargantext:
     "no-phylo-debug-logs": false
     "test-crypto": false
@@ -354,7 +468,7 @@ flags:
     devel: false
     h2spec: false
   hxt:
-    "network-uri": true
+    "network-uri": false
     profile: false
   "hxt-charproperties":
     profile: false
@@ -408,6 +522,8 @@ flags:
   "mtl-compat":
     "two-point-one": false
     "two-point-two": false
+  "mwc-random":
+    benchpapi: false
   network:
     devel: false
   "optics-core":
@@ -416,8 +532,6 @@ flags:
     process: true
   "optparse-simple":
     "build-example": false
-  pandoc:
-    embed_data_files: false
   "parser-combinators":
     dev: false
   parsers:
@@ -427,6 +541,8 @@ flags:
   password:
     argon2: true
     bcrypt: true
+    crypton: false
+    cryptonite: false
     pbkdf2: true
     scrypt: true
   "postgresql-libpq":
@@ -483,10 +599,6 @@ flags:
   "simple-sendfile":
     "allow-bsd": true
     fallback: false
-  skylighting:
-    executable: false
-  "skylighting-core":
-    executable: false
   some:
     "newtype-unsafe": true
   splitmix:
@@ -502,21 +614,15 @@ flags:
   tasty:
     unix: true
   "tasty-bench":
-    debug: false
     tasty: true
   "tasty-golden":
     "build-example": false
-  texmath:
-    executable: false
-    server: false
   "text-format":
     developer: false
   "text-metrics":
     dev: false
   "text-short":
     asserts: false
-  "time-compat":
-    "old-locale": false
   "time-locale-compat":
     "old-locale": false
   tls:
@@ -536,16 +642,6 @@ flags:
   "unicode-collation":
     doctests: false
     executable: false
-  "unicode-data":
-    ucd2haskell: false
-  "unicode-transforms":
-    "bench-show": false
-    dev: false
-    "has-icu": false
-    "has-llvm": false
-    "use-gauge": false
-  "unix-compat":
-    "old-time": false
   "unordered-containers":
     debug: false
   "uri-bytestring":
@@ -601,8 +697,8 @@ flags:
     executable: false
   zlib:
     "bundled-c-zlib": false
-    "non-blocking-ffi": false
-    "pkg-config": false
+    "non-blocking-ffi": true
+    "pkg-config": true
   zstd:
     standalone: true
 packages:

test/Test/Utils/Jobs.hs

@@ -362,19 +362,24 @@ testFetchJobStatusNoContention = do
 testMarkProgress :: IO ()
 testMarkProgress = do
   myEnv <- newTestEnv
-  evts  <- newTBQueueIO 7
+  -- evts  <- newTBQueueIO 7
+  evts <- newTVarIO []
   let getStatus hdl = do
         liftIO $ threadDelay 100_000
         st <- getLatestJobStatus hdl
-        liftIO $ atomically $ writeTBQueue evts st
+        -- liftIO $ atomically $ writeTBQueue evts st
+        liftIO $ atomically $ modifyTVar evts (\xs -> st:xs)
       readAllEvents = do  
         -- We will get thread blocking if there is ANY error in the job
         -- Hence we assert the `readAllEvents` test doesn't take too long
-        mRet <- timeout 2_000_000 $ atomically $ do
-          allEventsArrived <- isFullTBQueue evts
+        mRet <- timeout 1_000_000 $ atomically $ do
+          -- allEventsArrived <- isFullTBQueue evts
+          evts' <- readTVar evts
           -- STM retry if things failed
-          check allEventsArrived
-          flushTBQueue evts
+          -- check allEventsArrived
+          check (length evts' == 7)
+          -- flushTBQueue evts
+          return evts'
         return $ fromMaybe [] mRet
 
   withJob_ myEnv $ \hdl _input -> do
@@ -401,7 +406,8 @@ testMarkProgress = do
 
     getStatus hdl
 
-  [jl0, jl1, jl2, jl3, jl4, jl5, jl6] <- readAllEvents
+  evts' <- readAllEvents
+  let [jl0, jl1, jl2, jl3, jl4, jl5, jl6] = evts'
 
   -- Check the events are what we expect
   jl0 `shouldBe` JobLog { _scst_succeeded = Just 0