[FIX] merge

.gitignore

@@ -33,7 +33,6 @@ deps
 _darcs
 *.pdf
 *.png
-*.sql
 *.ini
 *.toml
 !test-data/test_config.ini

.gitlab-ci.yml

 # Optimising CI speed by using tips from https://blog.nimbleways.com/let-s-make-faster-gitlab-ci-cd-pipelines/
-image: adinapoli/gargantext:v3.4
+#image: adinapoli/gargantext:v3.4
+image: cgenie/gargantext:9.4.8
 
 variables:
   STACK_ROOT: "${CI_PROJECT_DIR}/.stack-root"

CHANGELOG.md

+## Version 0.0.7.3.1
+
+* [FRONT][FIX][Cannot build the project on latest `dev` (#701)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/701)
+* [FRONT][FIX][Phylomemy  panel reload after first query (#674)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/674)
+* [BACK][FIX][Various test failures (#408)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/408)
+* [BACK][FIX][Swagger documentation is down (#407)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/407)
+* [BACK][ADMIN][Improve startup error from
+  `runDbCheck`](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/347)
+* [BACK][CLEAN] removing unused SQL function in schema.sql
+* [BACK][TESTS][Terms are calculated over all documents, even those in trash (#385)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/385)
+
+## Version 0.0.7.3 [/!\ Maintenance command inside]
+
+* [BACK][FIX][Upgrade to GHC 9.4.8][Switch from .ini to TOML? (#304)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/304)
+* [BACK][CLEAN][Unused trigger](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/345)
+  * ``` $ ./bin/psql gargantext.ini < devops/postgres/upgrade/0.0.7.3.sql```
+* [BACK][Update Readme](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/346)
+* [FRONT][FIX][[Node document] Display the db source of a document (with authors, etc.) (#695)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/695)
+* [FRONT][FIX][Add separators between keywords in phylo (#696)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/696)
+* [FRONT][FIX][[Node Terms] In settings, on the download tab, put JSON as default selectbox choice, instead of the current JSON (zipped) (#691)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/691)
+* [BACK][FIX][Order 2] Back to previous parameter WIP
+
+## Version 0.0.7.2.8
+
+* [BACK][FEAT][Switch from .ini to TOML? (#304)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/304)
+* [BACK][SCRIPTS][Improve conversion script
+  ](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/341)
+* [BACK][FIX][Remove obsolete GHC option (#388)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/388)
+* [DOC][README][Little update to README, docs and .gitignore
+  interface](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/343)
+
 ## Version 0.0.7.2.7
 
 * [BACK][FEAT][Switch from .ini to TOML? (#304)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/304)

README.md

@@ -190,9 +190,11 @@ The initialization schema should be loaded automatically from `devops/postgres/s
 $ cp gargantext-settings.toml_toModify gargantext-settings.toml
 ```
 
-**NOTE** If you had the `gargantext.ini` file before, you can automatically generate toml with:
+**NOTE** If you had the `gargantext.ini` file before, you can automatically
+convert it into a file `gargantext-settings.toml` by running the following
+from a Nix shell:
 ```shell
-n$ cabal run gargantext-cli -- ini --ini-path gargantext.ini --toml-path gargantext-settings.toml
+n$ cabal v2-run gargantext-cli -- ini
 ```
 
 > `.gitignore` excludes this file, so you don't need to worry about
@@ -236,6 +238,27 @@ If you want to run particular tests, use:
 cabal v2-test garg-test-tasty --test-show-details=streaming --test-option=--pattern='/job status update and tracking/
 ```
 
+### CI
+
+The CI is on gitlab and is controlled by the `.gitlab-ci.yml` file.
+
+The Docker image that is used can be built with:
+```shell
+podman build -t cgenie/gargantext:9.4.8 -f ./devops/docker/Dockerfile --format=docker .
+```
+or
+```shell
+docker build -t cgenie/gargantext:9.4.8 -f ./devops/docker/Dockerfile .
+```
+
+NOTE: if podman/docker complains about not enough space, it's probably
+about tmpfs. In that case you can set
+```shell
+mkdir _build
+export TMPDIR=$(pwd)/_build
+```
+(https://stackoverflow.com/questions/75845647/changing-podman-build-to-path-with-more-space).
+
 ### Working on libraries
 
 When a devlopment is needed on libraries (for instance, the HAL crawler in https://gitlab.iscpif.fr/gargantext/crawlers):

bin/update-project-dependencies

@@ -18,13 +18,12 @@ 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="3943da8b9f3ae918afadf2b302875b3b395b31b2f69c3d42135af2ac800b7a0c"
-expected_cabal_project_freeze_hash="af825192f1ec47b07e6001dd2556b59991c9e6c50094dc732ee933a41f0dc9bd"
+expected_cabal_project_hash="3afb11e01938b74ae8419caa160180d8f8628a67315a2d689c3a42a76463071e"
+expected_cabal_project_freeze_hash="de1726d350936da5f5e15140e3be29bb4f44757c5702defe995c2386f1b4a741"
 
 
 cabal --store-dir=$STORE_DIR v2-build --dry-run
-cabal2stack --system-ghc --allow-newer --resolver lts-21.17 --resolver-file devops/stack/lts-21.17.yaml -o stack.yaml
-cabal --store-dir=$STORE_DIR v2-freeze
+cabal2stack --system-ghc --allow-newer --resolver lts-21.25 --resolver-file devops/stack/lts-21.25.yaml -o stack.yaml
 
 # Run 'sed' to remove the constraint for 'gargantext', as it doesn't make sense and
 # for the test we need to run this with a different flag.

cabal.project

@@ -3,7 +3,7 @@
 -- index-state: 2023-12-10T10:34:46Z
 index-state: 2024-09-12T03:02:26Z
 
-with-compiler: ghc-9.4.7
+with-compiler: ghc-9.4.8
 optimization: 2
 
 packages:

cabal.project.freeze

@@ -8,7 +8,7 @@ constraints: any.Cabal ==3.8.1.0,
              any.JuicyPixels ==3.3.9,
              JuicyPixels -mmap,
              any.KMP ==0.2.0.0,
-             any.MissingH ==1.4.3.1,
+             any.MissingH ==1.6.0.1,
              MissingH +network--ge-3_0_0,
              any.MonadRandom ==0.6,
              any.OneTuple ==0.4.2,
@@ -57,7 +57,7 @@ constraints: any.Cabal ==3.8.1.0,
              any.authenticate-oauth ==1.7,
              any.auto-update ==0.1.6,
              any.barbies ==2.1.1.0,
-             any.base ==4.17.2.0,
+             any.base ==4.17.2.1,
              any.base-compat ==0.13.1,
              any.base-compat-batteries ==0.13.1,
              any.base-orphans ==0.9.2,
@@ -84,7 +84,7 @@ constraints: any.Cabal ==3.8.1.0,
              any.bsb-http-chunked ==0.0.0.4,
              any.byteable ==0.1.1,
              any.byteorder ==1.0.4,
-             any.bytestring ==0.11.5.2,
+             any.bytestring ==0.11.5.3,
              any.bytestring-builder ==0.10.8.2.0,
              bytestring-builder +bytestring_has_builder,
              any.bzlib-conduit ==0.3.0.3,
@@ -203,13 +203,13 @@ constraints: any.Cabal ==3.8.1.0,
              any.generic-monoid ==0.1.0.1,
              any.generically ==0.1.1,
              any.generics-sop ==0.5.1.3,
-             any.ghc ==9.4.7,
+             any.ghc ==9.4.8,
              any.ghc-bignum ==1.3,
-             any.ghc-boot ==9.4.7,
-             any.ghc-boot-th ==9.4.7,
-             any.ghc-heap ==9.4.7,
+             any.ghc-boot ==9.4.8,
+             any.ghc-boot-th ==9.4.8,
+             any.ghc-heap ==9.4.8,
              any.ghc-prim ==0.9.1,
-             any.ghci ==9.4.7,
+             any.ghci ==9.4.8,
              any.githash ==0.1.7.0,
              any.graphviz ==2999.20.2.0,
              graphviz -test-parsing,
@@ -395,7 +395,7 @@ constraints: any.Cabal ==3.8.1.0,
              any.primitive ==0.7.4.0,
              any.primitive-extras ==0.10.2,
              any.primitive-unlifted ==2.1.0.0,
-             any.process ==1.6.17.0,
+             any.process ==1.6.18.0,
              any.product-profunctors ==0.11.1.1,
              any.profunctors ==5.6.2,
              any.promises ==0.3,

devops/docker/Dockerfile

@@ -3,7 +3,7 @@ FROM ubuntu:noble
 ## NOTA BENE: In order for this to be built successfully, you have to run ./devops/coreNLP/build.sh first.
 
 ARG DEBIAN_FRONTEND=noninteractive
-ARG GHC=9.4.7
+ARG GHC=9.4.8
 ARG CORENLP=4.5.4
 ARG CORE
 COPY ./shell.nix                                       /builds/gargantext/shell.nix

devops/postgres/schema.sql

@@ -404,35 +404,3 @@ FOR EACH ROW
 EXECUTE PROCEDURE check_node_stories_json();
 
 
-   CREATE OR REPLACE FUNCTION check_ngrams_json()
-    RETURNS TRIGGER AS $$
-    DECLARE
-      missing_ngrams_exist boolean;
-    BEGIN
-        WITH child_ngrams as
-          (SELECT jsonb_array_elements_text(ngrams_repo_element->'children') AS term
-           FROM node_stories
-           WHERE term = OLD.terms),
-          parent_ngrams AS
-          (SELECT ngrams_repo_element->>'root' AS term
-           FROM node_stories
-           WHERE term = OLD.terms),
-          child_parent_ngrams AS
-          (SELECT * FROM child_ngrams
-           UNION SELECT * FROM parent_ngrams)
-
-       SELECT EXISTS(SELECT * FROM child_parent_ngrams) INTO missing_ngrams_exist;
-
-       IF missing_ngrams_exist THEN
-          RAISE EXCEPTION 'ngrams are missing: %', row_to_json(OLD);
-       END IF;
-
-       RETURN OLD;
-    END;
-    $$ LANGUAGE plpgsql;
-
-  CREATE OR REPLACE TRIGGER check_ngrams_json_trg
-  AFTER DELETE
-  ON ngrams
-  FOR EACH ROW
-  EXECUTE PROCEDURE check_ngrams_json();

devops/postgres/upgrade/0.0.7.3.sql

+-- This removes the trigger prevening ngrams deletion
+-- because the function was not working.
+
+DROP TRIGGER check_ngrams_json_trg ON ngrams;
+DROP FUNCTION check_ngrams_json;

devops/stack/lts-21.17.yaml

+# https://github.com/commercialhaskell/stackage-snapshots/blob/master/lts/21/17.yaml
 flags:
   HsOpenSSL:
     fast-bignum: false

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 3.4
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.7.2.7
+version: 0.0.7.3.1
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data
@@ -34,6 +34,7 @@ data-files:
     ekg-assets/cross.png
     test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json
     test-data/ngrams/GarganText_DocsList-nodeId-177.json
+    test-data/ngrams/GarganText_NgramsTerms-nodeId-177.json
     test-data/ngrams/simple.json
     test-data/ngrams/simple.tsv
     test-data/phylo/bpa_phylo_test.json
@@ -249,6 +250,7 @@ library
       Gargantext.Database.Admin.Types.Hyperdata
       Gargantext.Database.Admin.Types.Hyperdata.Corpus
       Gargantext.Database.Admin.Types.Hyperdata.Document
+      Gargantext.Database.Admin.Types.Hyperdata.Folder
       Gargantext.Database.Admin.Types.Node
       Gargantext.Database.Prelude
       Gargantext.Database.Query.Facet
@@ -419,7 +421,6 @@ library
       Gargantext.Database.Admin.Types.Hyperdata.Dashboard
       Gargantext.Database.Admin.Types.Hyperdata.Default
       Gargantext.Database.Admin.Types.Hyperdata.File
-      Gargantext.Database.Admin.Types.Hyperdata.Folder
       Gargantext.Database.Admin.Types.Hyperdata.Frame
       Gargantext.Database.Admin.Types.Hyperdata.List
       Gargantext.Database.Admin.Types.Hyperdata.Model
@@ -472,7 +473,7 @@ library
     cpp-options: -DNO_PHYLO_DEBUG_LOGS
   build-depends:
       KMP ^>= 0.2.0.0
-    , MissingH ^>= 1.4.3.0
+    , MissingH ^>= 1.6.0.1
     , MonadRandom ^>= 0.6
     , QuickCheck ^>= 2.14.2
     , accelerate ^>= 1.3.0.0
@@ -485,14 +486,14 @@ library
     , base64-bytestring ^>= 1.2.1.0
     , bimap >= 0.5.0
     , boolexpr ^>= 0.3
-    , bytestring ^>= 0.11.5.2
+    , bytestring ^>= 0.11.5.3
     , cache >= 0.1.3.0
     , case-insensitive ^>= 1.2.1.0
     , cassava ^>= 0.5.2.0
     , cereal ^>= 0.5.8.2
     , clock >= 0.8
     , conduit ^>= 1.3.4.2
-    , containers ^>= 0.6.5.1
+    , containers ^>= 0.6.7
     , crawlerArxiv
     , crawlerHAL
     , crawlerISTEX
@@ -501,16 +502,16 @@ library
     , cron ^>= 0.7.0
     , data-time-segment ^>= 0.1.0.0
     , deferred-folds >= 0.9.18 && < 0.10
-    , directory ^>= 1.3.6.0
+    , directory ^>= 1.3.7.1
     , discrimination >= 0.5
     , ekg-core ^>= 0.1.1.7
     , ekg-json ^>= 0.1.0.7
     , epo-api-client
-    , exceptions ^>= 0.10.4
+    , exceptions ^>= 0.10.5
     , extra ^>= 1.7.9
     , fast-logger ^>= 3.2.2
     , fgl ^>= 5.8.0.0
-    , filepath ^>= 1.4.2.1
+    , filepath ^>= 1.4.2.2
     , fmt
     , formatting ^>= 7.2.0
     , fullstop ^>= 0.1.4
@@ -552,11 +553,11 @@ library
     , opaleye-textsearch >= 0.2.0.0
     , openalex
     , parallel ^>= 3.2.2.0
-    , parsec ^>= 3.1.14.0
+    , parsec ^>= 3.1.16.1
     , patches-class ^>= 0.1.0.1
     , patches-map ^>= 0.1.0.1
     , postgresql-simple ^>= 0.6.4
-    , process ^>= 1.6.13.2
+    , process ^>= 1.6.18.0
     , product-profunctors ^>= 0.11.0.3
     , protolude ^>= 0.3.3
     , quickcheck-instances ^>= 0.3.25.2
@@ -649,11 +650,11 @@ executable gargantext-cli
       aeson ^>= 2.1.2.1
     , aeson-pretty
     , async ^>= 2.2.4
-    , bytestring ^>= 0.11.5.2
+    , bytestring ^>= 0.11.5.3
     , cassava ^>= 0.5.2.0
-    , containers ^>= 0.6.5.1
+    , containers ^>= 0.6.7
     , cryptohash ^>= 0.11.9
-    , directory ^>= 1.3.6.0
+    , directory ^>= 1.3.7.1
     , extra ^>= 1.7.9
     , gargantext
     , gargantext-prelude
@@ -691,7 +692,7 @@ executable gargantext-server
       bin/gargantext-server
   build-depends:
       cassava ^>= 0.5.2.0
-    , containers ^>= 0.6.5.1
+    , containers ^>= 0.6.7
     , extra ^>= 1.7.9
     , gargantext
     , gargantext-prelude
@@ -711,14 +712,14 @@ common testDependencies
     , aeson-qq
     , async ^>= 2.2.4
     , boolexpr ^>= 0.3
-    , bytestring ^>= 0.11.5.2
+    , bytestring ^>= 0.11.5.3
     , cache >= 0.1.3.0
     , case-insensitive
     , conduit ^>= 1.3.4.2
-    , containers ^>= 0.6.5.1
+    , containers ^>= 0.6.7
     , crawlerArxiv
     , cryptohash
-    , directory
+    , directory ^>= 1.3.7.1
     , epo-api-client
     , extra ^>= 1.7.9
     , fast-logger ^>= 3.2.2
@@ -740,13 +741,13 @@ common testDependencies
     , monad-control >= 1.0.3 && < 1.1
     , mtl ^>= 2.2.2
     , network-uri
-    , parsec ^>= 3.1.14.0
+    , parsec ^>= 3.1.16.1
     , patches-class ^>= 0.1.0.1
     , patches-map ^>= 0.1.0.1
     , postgres-options >= 0.2 && < 0.3
     , postgresql-simple >= 0.6.4 && < 0.7
-    , pretty
-    , process ^>= 1.6.13.2
+    , pretty ^>= 1.1.3.6
+    , process ^>= 1.6.18.0
     , protolude ^>= 0.3.3
     , quickcheck-instances ^>= 0.3.25.2
     , raw-strings-qq
@@ -879,7 +880,7 @@ benchmark garg-bench
   other-modules:
       Paths_gargantext
   build-depends: base
-               , bytestring ^>= 0.11.5.2
+               , bytestring ^>= 0.11.5.3
                , gargantext
                , gargantext-prelude
                , tasty-bench

hie.yaml

+cradle:
+  cabal:
+    - path: "./src"
+      component: "lib:gargantext"
+
+    - path: "./bin/gargantext-cli/Main.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Admin.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/FileDiff.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/FilterTermsAndCooc.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Import.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Ini.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Init.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Invitations.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/ObfuscateDB.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Parsers.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Phylo.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Phylo/Common.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Phylo/Profile.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Server/Routes.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Types.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Upgrade.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/Paths_gargantext.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-server/Main.hs"
+      component: "gargantext:exe:gargantext-server"
+
+    - path: "./bin/gargantext-server/Paths_gargantext.hs"
+      component: "gargantext:exe:gargantext-server"
+
+    - path: "./test"
+      component: "gargantext:test:garg-test-tasty"
+
+    - path: "./bin/gargantext-cli"
+      component: "gargantext:test:garg-test-tasty"
+
+    - path: "./test"
+      component: "gargantext:test:garg-test-hspec"
+
+    - path: "./bench/Main.hs"
+      component: "gargantext:bench:garg-bench"
+
+    - path: "./bench/Paths_gargantext.hs"
+      component: "gargantext:bench:garg-bench"

nix/pkgs.nix

@@ -2,8 +2,8 @@
 
 rec {
   inherit pkgs;
-  ghc947 = if pkgs.stdenv.isDarwin
-           then pkgs.haskell.compiler.ghc947.overrideAttrs (finalAttrs: previousAttrs: {
+  ghc948 = if pkgs.stdenv.isDarwin
+           then pkgs.haskell.compiler.ghc948.overrideAttrs (finalAttrs: previousAttrs: {
                 patches = previousAttrs.patches ++ [
                             # Reverts the linking behavior of GHC to not resolve `-libc++` to `c++`.
                             (pkgs.fetchpatch {
@@ -12,8 +12,8 @@ rec {
                             })
                           ];
                 })
-           else pkgs.haskell.compiler.ghc947;
-  cabal_install_3_10_1_0 = pkgs.haskell.lib.compose.justStaticExecutables pkgs.haskell.packages.ghc947.cabal-install;
+           else pkgs.haskell.compiler.ghc948;
+  cabal_install_3_10_2_1 = pkgs.haskell.lib.compose.justStaticExecutables pkgs.haskell.packages.ghc948.cabal-install;
   graphviz_dev = pkgs.graphviz.overrideAttrs (finalAttrs: previousAttrs: {
     version = "11.0.0~dev";
     src = pkgs.fetchFromGitLab {
@@ -95,8 +95,8 @@ rec {
 
   });
   hsBuildInputs = [
-    ghc947
-    cabal_install_3_10_1_0
+    ghc948
+    cabal_install_3_10_2_1
     pkgs.haskellPackages.alex
     pkgs.haskellPackages.happy
     pkgs.haskellPackages.pretty-show

src/Gargantext/API.hs

@@ -92,12 +92,13 @@ startGargantext mode port sf@(SettingsFile settingsFile) = withLoggerHoisted mod
 
   where runDbCheck env = do
           r <- runExceptT (runReaderT DB.dbCheck env) `catch`
-            (\(_ :: SomeException) -> pure $ Right False)
+            (\(err :: SomeException) -> pure $ Left err)
           case r of
-            Right True -> pure ()
-            _ -> panicTrace $
-              "You must run 'gargantext-init " <> pack settingsFile <>
+            Right True  -> pure ()
+            Right False -> panicTrace $
+              "You must run 'gargantext-cli init " <> pack settingsFile <>
               "' before running gargantext-server (only the first time)."
+            Left err -> panicTrace $ "Unexpected exception:" <> show err
         oneHour = Clock.fromNanoSecs 3600_000_000_000
 
 portRouteInfo :: NotificationsConfig -> PortNumber -> MicroServicesProxyStatus -> IO ()

src/Gargantext/Core/Methods/Similarities/Accelerate/Distributional.hs

@@ -205,8 +205,8 @@ logDistributional' n m' = trace ("logDistributional'") result
     -- m_{i,j} = 0 if n_{i,j} = 0 or i = j, 
     -- m_{i,j} = log(to * n_{i,j} / s_{i,j}) otherwise.
     mi = (.*) (matrixEye n)
-              (map (lift1 (\x -> let x' = x * to in cond (x' < 0.5) 0 (log x'))) ((./) m ss))
-              -- (map (lift1 (\x -> let x' = x * to in cond (x' < 1) 0 (log x'))) ((./) m ss))
+              -- (map (lift1 (\x -> let x' = x * to in cond (x' < 0.5) 0 (log x'))) ((./) m ss))
+              (map (lift1 (\x -> let x' = x * to in cond (x' < 1) 0 (log x'))) ((./) m ss))
     -- mi_nnz :: Int
     -- mi_nnz = flip indexArray Z . run $
     --   foldAll (+) 0 $ map (\a -> ifThenElse (abs a < 10^(-6 :: Exp Int)) 0 1) mi

src/Gargantext/Core/Viz/Graph/Types.hs

@@ -14,9 +14,10 @@ Portability : POSIX
 module Gargantext.Core.Viz.Graph.Types
   where
 
+import Data.Aeson (defaultOptions)
 import Data.HashSet (HashSet)
 import Data.HashSet qualified as HashSet
-import Data.Swagger (ToSchema(..), genericDeclareNamedSchema)
+import Data.Swagger (ToSchema(..), genericDeclareNamedSchema, defaultSchemaOptions)
 import Data.Text (pack)
 import Database.PostgreSQL.Simple.FromField (FromField(..))
 import Gargantext.API.Ngrams.Types (NgramsTerm)
@@ -245,9 +246,9 @@ instance FromField HyperdataGraphAPI
 
 data GraphLegendAPI = GraphLegendAPI [LegendField]
   deriving (Show, Generic)
-$(deriveJSON (unPrefix "_graphAPI") ''GraphLegendAPI)
+$(deriveJSON defaultOptions ''GraphLegendAPI)
 instance ToSchema GraphLegendAPI where
-  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_graphAPI")
+  declareNamedSchema = genericDeclareNamedSchema defaultSchemaOptions
 
 makeLenses ''GraphLegendAPI
 

stack.yaml

@@ -2,13 +2,11 @@
 "extra-deps":
 - "JuicyPixels-3.3.9"
 - "KMP-0.2.0.0"
-- "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"
@@ -23,7 +21,6 @@
 - "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"
@@ -32,7 +29,6 @@
 - "crypton-x509-1.7.7"
 - "data-fix-0.3.4"
 - "dec-0.0.6"
-- "deferred-folds-0.9.18.6"
 - "digest-0.0.2.1"
 - "double-conversion-2.0.5.0"
 - "extra-1.7.16"
@@ -43,7 +39,6 @@
 - "foldl-1.4.17"
 - "free-5.2"
 - "fullstop-0.1.4"
-- "graphviz-2999.20.2.0"
 - "hashable-1.4.4.0"
 - "haskell-src-meta-0.8.14"
 - "hedgehog-1.5"
@@ -56,23 +51,20 @@
 - "hspec-expectations-0.8.4"
 - "http-accept-0.2"
 - "http-api-data-0.5.1"
+- "http-client-0.7.14"
 - "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"
@@ -87,7 +79,6 @@
 - "morpheus-graphql-subscriptions-0.24.3"
 - "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"
@@ -96,14 +87,12 @@
 - "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-1.2.1.2"
 - "recover-rtti-0.4.3"
 - "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"
@@ -147,7 +136,6 @@
 - "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"
@@ -703,5 +691,5 @@ flags:
     standalone: true
 packages:
 - .
-resolver: "lts-21.17"
+resolver: "lts-21.25"
 "system-ghc": true

test-data/ngrams/GarganText_DocsList-nodeId-177.json

@@ -58,5 +58,6 @@
       },
       "hash": ""
     }
-  ]
+  ],
+  "garg_version": "0.0.7.1.16"
 }

test-data/ngrams/GarganText_NgramsTerms-nodeId-177.json

+{ "NgramsTerms":{ "version":1 ,"data":{ "fortran":{"size":2,"list":"MapTerm","children":[]} } }
+}

test/Test/API/Routes.hs

@@ -8,24 +8,31 @@ module Test.API.Routes where
 import Data.Text.Encoding qualified as TE
 import Fmt (Builder, (+|), (|+))
 import Gargantext.API.Admin.Auth.Types (AuthRequest, AuthResponse, Token)
+import Gargantext.API.Admin.Orchestrator.Types (JobLog, asyncJobsAPI')
 import Gargantext.API.Errors
+import Gargantext.API.HashedResponse (HashedResponse)
 import Gargantext.API.Ngrams.Types ( NgramsTable, NgramsTablePatch, OrderBy, TabType, Versioned, VersionedWithCount )
 import Gargantext.API.Routes.Named
 import Gargantext.API.Routes.Named.Node
 import Gargantext.API.Routes.Named.Private hiding (tableNgramsAPI)
 import Gargantext.API.Routes.Named.Table
 import Gargantext.API.Types () -- MimeUnrender instances
-import Gargantext.Core.Types (ListId, NodeId)
+import Gargantext.Core.Text.Corpus.Query (RawQuery)
+import Gargantext.Core.Types (ListId, NodeId, NodeType, NodeTableResult)
 import Gargantext.Core.Types.Main (ListType)
 import Gargantext.Core.Types.Query (Limit, MaxSize, MinSize, Offset)
+import Gargantext.Database.Admin.Types.Hyperdata
+import Gargantext.Database.Query.Facet qualified as Facet
 import Gargantext.Prelude
 import Network.HTTP.Types qualified as H
 import Network.Wai.Handler.Warp (Port)
+import Servant ((:<|>)(..))
 import Servant.API.WebSocket qualified as WS
 import Servant.Auth.Client qualified as S
 import Servant.Client (ClientM)
 import Servant.Client.Core (RunClient, HasClient(..), Request)
 import Servant.Client.Generic ( genericClient, AsClientT )
+import Servant.Job.Async
 
 
 instance RunClient m => HasClient m WS.WebSocketPending where
@@ -47,6 +54,9 @@ mkUrl :: Port -> Builder -> ByteString
 mkUrl _port urlPiece =
   "/api/" +| curApi |+ urlPiece
 
+gqlUrl :: ByteString
+gqlUrl = "/gql"
+
 
 -- | The client for the full API. It also serves as a \"proof\" that our
 -- whole API has all the required instances to be used in a client.
@@ -64,19 +74,44 @@ auth_api = clientRoutes & apiWithCustomErrorScheme
                         & gargAuthAPI
                         & authEp
 
-table_ngrams_get_api :: Token
-                     -> NodeId
-                     -> TabType
-                     -> ListId
-                     -> Limit
-                     -> Maybe Offset
-                     -> Maybe ListType
-                     -> Maybe MinSize
-                     -> Maybe MaxSize
-                     -> Maybe OrderBy
-                     -> Maybe Text
-                     -> ClientM (VersionedWithCount NgramsTable)
-table_ngrams_get_api (toServantToken -> token) nodeId =
+toServantToken :: Token -> S.Token
+toServantToken = S.Token . TE.encodeUtf8
+
+update_node :: Token
+            -> NodeId
+            -> UpdateNodeParams
+            -> ClientM (JobStatus 'Safe JobLog)
+update_node (toServantToken -> token) nodeId params =
+  clientRoutes & apiWithCustomErrorScheme
+               & ($ GES_new)
+               & backendAPI
+               & backendAPI'
+               & mkBackEndAPI
+               & gargAPIVersion
+               & gargPrivateAPI
+               & mkPrivateAPI
+               & ($ token)
+               & nodeEp
+               & nodeEndpointAPI
+               & ($ nodeId)
+               & updateAPI
+               & updateNodeEp
+               & asyncJobsAPI'
+               & (\(_ :<|> submitForm :<|> _) -> submitForm (JobInput params Nothing))
+
+get_table_ngrams :: Token
+                 -> NodeId
+                 -> TabType
+                 -> ListId
+                 -> Limit
+                 -> Maybe Offset
+                 -> Maybe ListType
+                 -> Maybe MinSize
+                 -> Maybe MaxSize
+                 -> Maybe OrderBy
+                 -> Maybe Text
+                 -> ClientM (VersionedWithCount NgramsTable)
+get_table_ngrams (toServantToken -> token) nodeId =
   clientRoutes & apiWithCustomErrorScheme
                & ($ GES_new)
                & backendAPI
@@ -93,16 +128,13 @@ table_ngrams_get_api (toServantToken -> token) nodeId =
                & tableNgramsGetAPI
                & getNgramsTableEp
 
-toServantToken :: Token -> S.Token
-toServantToken = S.Token . TE.encodeUtf8
-
-table_ngrams_put_api :: Token
-                     -> NodeId
-                     -> TabType
-                     -> ListId
-                     -> Versioned NgramsTablePatch
-                     -> ClientM (Versioned NgramsTablePatch)
-table_ngrams_put_api (toServantToken -> token) nodeId =
+put_table_ngrams :: Token
+                 -> NodeId
+                 -> TabType
+                 -> ListId
+                 -> Versioned NgramsTablePatch
+                 -> ClientM (Versioned NgramsTablePatch)
+put_table_ngrams (toServantToken -> token) nodeId =
   clientRoutes & apiWithCustomErrorScheme
                & ($ GES_new)
                & backendAPI
@@ -118,3 +150,51 @@ table_ngrams_put_api (toServantToken -> token) nodeId =
                & tableNgramsAPI
                & tableNgramsPutAPI
                & putNgramsTableEp
+
+get_table :: Token
+          -> NodeId
+          -> Maybe TabType
+          -> Maybe Limit
+          -> Maybe Offset
+          -> Maybe Facet.OrderBy
+          -> Maybe RawQuery
+          -> Maybe Text
+          -> ClientM (HashedResponse FacetTableResult)
+get_table (toServantToken -> token) nodeId =
+  clientRoutes & apiWithCustomErrorScheme
+               & ($ GES_new)
+               & backendAPI
+               & backendAPI'
+               & mkBackEndAPI
+               & gargAPIVersion
+               & gargPrivateAPI
+               & mkPrivateAPI
+               & ($ token)
+               & nodeEp
+               & nodeEndpointAPI
+               & ($ nodeId)
+               & tableAPI
+               & getTableEp
+
+get_children :: Token
+             -> NodeId
+             -> Maybe NodeType
+             -> Maybe Offset
+             -> Maybe Limit
+             -> ClientM (NodeTableResult HyperdataAny)
+get_children (toServantToken -> token) nodeId =
+  clientRoutes & apiWithCustomErrorScheme
+               & ($ GES_new)
+               & backendAPI
+               & backendAPI'
+               & mkBackEndAPI
+               & gargAPIVersion
+               & gargPrivateAPI
+               & mkPrivateAPI
+               & ($ token)
+               & nodeEp
+               & nodeEndpointAPI
+               & ($ nodeId)
+               & childrenAPI
+               & summaryChildrenEp
+

test/Test/Utils.hs

@@ -7,33 +7,38 @@ module Test.Utils where
 
 import Control.Exception.Safe ()
 import Control.Monad ()
-import Data.Aeson qualified as JSON
 import Data.Aeson.KeyMap qualified as KM
+import Data.Aeson qualified as JSON
 import Data.ByteString.Char8 qualified as B
 import Data.ByteString.Lazy qualified as L
 import Data.Map.Strict qualified as Map
-import Data.Text qualified as T
 import Data.Text.Encoding qualified as TE
-import Data.Text.Lazy qualified as TL
 import Data.Text.Lazy.Encoding qualified as TLE
+import Data.Text.Lazy qualified as TL
+import Data.Text qualified as T
 import Data.TreeDiff
 import Fmt (Builder)
-import Gargantext.API.Routes.Types (xGargErrorScheme)
 import Gargantext.API.Admin.Auth.Types (AuthRequest(..), Token, authRes_token)
+import Gargantext.API.Admin.Orchestrator.Types
+import Gargantext.API.Routes.Types (xGargErrorScheme)
 import Gargantext.Core.Types.Individu (Username, GargPassword)
 import Gargantext.Prelude
 import Network.HTTP.Client (defaultManagerSettings, newManager)
-import Network.HTTP.Types (Header, Method, status200)
+import Network.HTTP.Client qualified as HTTP
 import Network.HTTP.Types.Header (hAccept, hAuthorization, hContentType)
+import Network.HTTP.Types (Header, Method, status200)
 import Network.Wai.Handler.Warp (Port)
 import Network.Wai.Test (SResponse(..))
 import Prelude qualified
-import Servant.Client (ClientEnv, baseUrlPort, mkClientEnv, parseBaseUrl, runClientM)
+import Servant.Client (ClientEnv, baseUrlPort, mkClientEnv, parseBaseUrl, runClientM, makeClientRequest, defaultMakeClientRequest)
+import Servant.Client.Core (BaseUrl)
+import Servant.Client.Core.Request qualified as Client
+import System.Environment (lookupEnv)
 import System.Timeout qualified as Timeout
 import Test.API.Routes (auth_api, mkUrl)
 import Test.Hspec.Expectations
-import Test.Hspec.Wai (MatchBody(..), WaiExpectation, WaiSession, request)
 import Test.Hspec.Wai.JSON (FromValue(..))
+import Test.Hspec.Wai (MatchBody(..), WaiExpectation, WaiSession, request)
 import Test.Hspec.Wai.Matcher (MatchHeader(..), ResponseMatcher(..), bodyEquals, formatHeader, match)
 import Test.Tasty.HUnit (Assertion, assertBool)
 import Test.Types
@@ -183,12 +188,27 @@ withValidLogin port ur pwd act = do
   case result of
     Left err  -> liftIO $ throwIO $ Prelude.userError (show err)
     Right res -> do
+      traceEnabled <- isJust <$> liftIO (lookupEnv "GARG_DEBUG_LOGS")
       let token = res ^. authRes_token
-      act clientEnv0 token
+      act (clientEnv0 { makeClientRequest = gargMkRequest traceEnabled }) token
+
+-- | Allows to enable/disable logging of the input 'Request' to check what the
+-- client is actually sending to the server.
+-- FIXME(adn) We cannot upgrade to servant-client 0.20 due to OpenAlex:
+-- https://gitlab.iscpif.fr/gargantext/crawlers/openalex/blob/main/src/OpenAlex/ServantClientLogging.hs#L24
+gargMkRequest :: Bool -> BaseUrl -> Client.Request -> HTTP.Request
+gargMkRequest traceEnabled bu clientRq =
+  let httpReq = defaultMakeClientRequest bu clientRq
+  in case traceEnabled of
+       True ->
+         traceShowId httpReq
+       False -> httpReq
 
 
 -- | Poll the given job URL every second until it finishes.
 -- Retries up to 60 times (i.e. for 1 minute, before giving up)
+-- /NOTE(adn)/: Check the content of the \"events\" logs as a stopgap
+-- measure for #390.
 pollUntilFinished :: HasCallStack
                   => Token
                   -> Port
@@ -208,7 +228,15 @@ pollUntilFinished tkn port mkUrlPiece = go 60
      | _jph_status h == "IsFailure"
      -> panicTrace $ "JobPollHandle contains a failure: " <> TE.decodeUtf8 (L.toStrict $ JSON.encode h)
      | otherwise
-     -> pure h
+     -> case any hasError (_jph_log h) of
+          True  -> panicTrace $ "JobPollHandle contains a failure: " <> TE.decodeUtf8 (L.toStrict $ JSON.encode h)
+          False -> pure h
+
+   -- FIXME(adn) This is wrong, errs should be >= 1.
+   hasError :: JobLog -> Bool
+   hasError JobLog{..} = case _scst_failed of
+     Nothing   -> False
+     Just errs -> errs > 1
 
 -- | Like HUnit's '@?=', but With a nicer error message in case the two entities are not equal.
 (@??=) :: (HasCallStack, ToExpr a, Eq a) => a -> a -> Assertion

test/Test/Utils/Jobs.hs

@@ -363,23 +363,30 @@ testMarkProgress = do
   myEnv <- newTestEnv
   -- evts  <- newTBQueueIO 7
   evts <- newTVarIO []
+  let expectedEvents = 7
   let getStatus hdl = do
         liftIO $ threadDelay 100_000
         st <- getLatestJobStatus hdl
         -- liftIO $ atomically $ writeTBQueue evts st
         liftIO $ atomically $ modifyTVar evts (\xs -> xs ++ [st])
-      readAllEvents = do  
+      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 1_000_000 $ atomically $ do
+        mRet <- timeout 5_000_000 $ atomically $ do
           -- allEventsArrived <- isFullTBQueue evts
           evts' <- readTVar evts
           -- STM retry if things failed
           -- check allEventsArrived
-          check (length evts' == 7)
+          check (length evts' == expectedEvents)
           -- flushTBQueue evts
-          return evts'
-        return $ fromMaybe [] mRet
+          pure evts'
+        case mRet of
+          Nothing -> Prelude.fail $ "testMarkProgress: timeout exceeded, but didn't receive all 7 required events."
+          Just xs
+            | length xs == expectedEvents
+            -> pure xs
+            | otherwise
+            -> Prelude.fail $ "testMarkProgress: received some events, but they were not of the expected number (" <> show expectedEvents <> "): " <> show xs
 
   withJob_ myEnv $ \hdl _input -> do
     markStarted 10 hdl
@@ -406,6 +413,8 @@ testMarkProgress = do
     getStatus hdl
 
   evts' <- readAllEvents
+  -- This pattern match should never fail, because the precondition is
+  -- checked in 'readAllEvents'.
   let [jl0, jl1, jl2, jl3, jl4, jl5, jl6] = evts'
 
   -- Check the events are what we expect
@@ -468,7 +477,7 @@ test = do
       testExceptions
     it "fairly picks equal-priority-but-different-kind jobs" $
       testFairness
-  describe "job status update and tracking" $ do
+  describe "job status update and tracking" $ sequential $ do
     it "can fetch the latest job status" $
       testFetchJobStatus
     it "can spin two separate jobs and track their status separately" $