Merge branch 'dev' into dev-openalex

bin/install

@@ -13,6 +13,7 @@ if [[ $1 == "dev" ]] ;
     echo "DEV install"
     env LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 stack --nix install --no-install-ghc --skip-ghc-check --no-haddock-deps
   else
-    echo "PROD install (with documentation)" 
-    env LANG=C.UTF-8 stack install --haddock --nix --test --no-install-ghc --skip-ghc-check --no-haddock-deps
+    echo "PROD install (with documentation)"
+    nix-shell --run "cabal install"
+    #env LANG=C.UTF-8 stack install --haddock --nix --test --no-install-ghc --skip-ghc-check --no-haddock-deps
 fi

bin/update-cabal-project

 #!/usr/bin/env bash
 
-hpack
 cabal v2-update 'hackage.haskell.org,2023-06-25T00:00:00Z'
+cabal v2-install hpack-0.35.0 --overwrite-policy=always
 cabal v2-install stack2cabal-1.0.14 --overwrite-policy=always
 stack2cabal --no-run-hpack -p '2023-06-25'

devops/postgres/schema.sql

@@ -357,3 +357,87 @@ ON context_node_ngrams(context_id, ngrams_id);
 
 CREATE INDEX IF NOT EXISTS node_stories_ngrams_id_idx
   ON node_stories(ngrams_id);
+----
+
+
+
+-- Version 0.0.6.9.9.6.4.sql
+-- ADD triggers
+ CREATE OR REPLACE FUNCTION check_node_stories_json()
+  RETURNS TRIGGER AS $$
+  DECLARE
+    missing_ngrams_exist boolean;
+  BEGIN
+      WITH child_ngrams as
+        (SELECT jsonb_array_elements_text(NEW.ngrams_repo_element->'children') AS term),
+        parent_ngrams AS
+        (SELECT NEW.ngrams_repo_element->>'root' AS term),
+
+        ngrams_child_parent AS
+            (SELECT child_ngrams.term, ngrams.terms
+         FROM child_ngrams
+         LEFT JOIN ngrams ON child_ngrams.term = ngrams.terms
+         WHERE ngrams.terms IS NULL
+
+        UNION
+
+        SELECT parent_ngrams.term, ngrams.terms
+        FROM parent_ngrams
+        LEFT JOIN ngrams ON parent_ngrams.term = ngrams.terms
+        WHERE ngrams.terms IS NULL
+        AND parent_ngrams.term IS NOT NULL)
+
+            SELECT EXISTS(SELECT * FROM ngrams_child_parent) INTO missing_ngrams_exist;
+
+            IF missing_ngrams_exist THEN
+              RAISE EXCEPTION 'node_stories: ngrams are missing: %', row_to_json(NEW);
+        END IF;
+
+            RETURN NEW;
+  END;
+  $$ LANGUAGE plpgsql;
+
+CREATE OR REPLACE TRIGGER check_node_stories_json_trg
+AFTER INSERT OR UPDATE
+ON node_stories
+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();
+
+
+
+
+

gargantext.cabal

@@ -28,7 +28,7 @@ data-files:
     test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json
     test-data/phylo/bpa_phylo_test.json
     test-data/phylo/open_science.json
-
+    .clippy.dhall
 library
   exposed-modules:
       Gargantext

nix/overlays/Cabal-3.10.1.0.nix

+{ mkDerivation, array, base, bytestring, Cabal-syntax, containers
+, deepseq, directory, filepath, lib, mtl, parsec, pretty, process
+, text, time, transformers, unix
+}:
+mkDerivation {
+  pname = "Cabal";
+  version = "3.10.1.0";
+  sha256 = "0bdbab8e4c3178016fb0f070d8b62bc3067f93afabfbd3aa17c8065d0ecc98ee";
+  setupHaskellDepends = [ mtl parsec ];
+  libraryHaskellDepends = [
+    array base bytestring Cabal-syntax containers deepseq directory
+    filepath mtl parsec pretty process text time transformers unix
+  ];
+  doCheck = false;
+  doHaddock = false;
+  homepage = "http://www.haskell.org/cabal/";
+  description = "A framework for packaging Haskell software";
+  license = lib.licenses.bsd3;
+}

nix/overlays/Cabal-syntax-3.10.1.0.nix

+{ mkDerivation, array, base, binary, bytestring, containers
+, deepseq, directory, filepath, lib, mtl, parsec, pretty, text
+, time, transformers, unix
+}:
+mkDerivation {
+  pname = "Cabal-syntax";
+  version = "3.10.1.0";
+  sha256 = "3b80092355327768a0de8298ac50ee906b7e82462e2ba14542730573b453f522";
+  libraryHaskellDepends = [
+    array base binary bytestring containers deepseq directory filepath
+    mtl parsec pretty text time transformers unix
+  ];
+  homepage = "http://www.haskell.org/cabal/";
+  description = "A library for working with .cabal files";
+  license = lib.licenses.bsd3;
+  doCheck = false;
+  doHaddock = false;
+}

nix/overlays/cabal-install-3.10.1.0.nix

+{ mkDerivation, array, async, base, base16-bytestring, binary
+, bytestring, Cabal, Cabal-described ? null, cabal-install-solver
+, Cabal-QuickCheck ? null, Cabal-syntax, Cabal-tree-diff ? null, containers
+, cryptohash-sha256, directory, echo, edit-distance, exceptions
+, filepath, hackage-security, hashable, HTTP, lib, lukko, mtl
+, network-uri, parsec, pretty, pretty-show, process, QuickCheck
+, random, regex-base, regex-posix, resolv, safe-exceptions, stm
+, tagged, tar, tasty, tasty-expected-failure, tasty-golden
+, tasty-hunit, tasty-quickcheck, text, time, tree-diff, unix, zlib
+}:
+mkDerivation {
+  pname = "cabal-install";
+  version = "3.10.1.0";
+  sha256 = "995de368555449230e0762b259377ed720798717f4dd26a4fa711e8e41c7838d";
+  revision = "1";
+  editedCabalFile = "0h1ra9kw7mk70202whiphbdyvknm7jbhqhkgw4h8abb1sgffhs3n";
+  isLibrary = true;
+  isExecutable = true;
+  libraryHaskellDepends = [
+    array async base base16-bytestring binary bytestring Cabal
+    cabal-install-solver Cabal-syntax containers cryptohash-sha256
+    directory echo edit-distance exceptions filepath hackage-security
+    hashable HTTP lukko mtl network-uri parsec pretty process random
+    regex-base regex-posix resolv safe-exceptions stm tar text time
+    unix zlib
+  ];
+  executableHaskellDepends = [
+    base Cabal Cabal-syntax directory filepath
+  ];
+  testHaskellDepends = [
+    array base bytestring Cabal Cabal-described cabal-install-solver
+    Cabal-QuickCheck Cabal-syntax Cabal-tree-diff containers directory
+    filepath hashable mtl network-uri pretty-show QuickCheck random
+    tagged tar tasty tasty-expected-failure tasty-golden tasty-hunit
+    tasty-quickcheck time tree-diff zlib
+  ];
+  doCheck = false;
+  doHaddock = false;
+  enableExecutableProfiling = false;
+  postInstall = ''
+    mkdir -p $out/share/bash-completion
+    mv bash-completion $out/share/bash-completion/completions
+  '';
+  homepage = "http://www.haskell.org/cabal/";
+  description = "The command-line interface for Cabal and Hackage";
+  license = lib.licenses.bsd3;
+  mainProgram = "cabal";
+}

nix/overlays/cabal-install-solver-3.10.1.0.nix

+{ mkDerivation, array, base, bytestring, Cabal, Cabal-syntax
+, containers, edit-distance, filepath, lib, mtl, pretty, tasty
+, tasty-hunit, tasty-quickcheck, transformers
+}:
+mkDerivation {
+  pname = "cabal-install-solver";
+  version = "3.10.1.0";
+  sha256 = "2c0d9edd4ccd746e9bf8ab4f92b1ecffe2f56eae29395c67ef5ca091a6f49f37";
+  revision = "1";
+  editedCabalFile = "1l3qhaiv0m2xc5vscggd2drinam1k4x0l3vfvvz15xrpvxypdv4d";
+  libraryHaskellDepends = [
+    array base bytestring Cabal Cabal-syntax containers edit-distance
+    filepath mtl pretty transformers
+  ];
+  testHaskellDepends = [
+    base Cabal Cabal-syntax tasty tasty-hunit tasty-quickcheck
+  ];
+  homepage = "http://www.haskell.org/cabal/";
+  description = "The command-line interface for Cabal and Hackage";
+  license = lib.licenses.bsd3;
+  doCheck = false;
+  doHaddock = false;
+}

nix/overlays/directory-1.3.7.0.nix

+{ mkDerivation, base, filepath, lib, time, unix }:
+mkDerivation {
+  pname = "directory";
+  version = "1.3.7.0";
+  sha256 = "9f86bd60a4909eef66907c15fc108883439b8fba3b428fb56aaa056631b62d10";
+  revision = "2";
+  editedCabalFile = "13krvs6zfswr3xndysq1bg7mz9n8mm1w7p4zcx8xjs0jqkm8hiyl";
+  libraryHaskellDepends = [ base filepath time unix ];
+  testHaskellDepends = [ base filepath time unix ];
+  description = "Platform-agnostic library for filesystem operations";
+  license = lib.licenses.bsd3;
+  doCheck = false;
+  doHaddock = false;
+}

nix/overlays/hackage-security-0.6.2.3.nix

+{ mkDerivation, aeson, base, base16-bytestring, base64-bytestring
+, bytestring, Cabal, Cabal-syntax, containers, cryptohash-sha256
+, directory, ed25519, filepath, ghc-prim, lib, lukko, mtl, network
+, network-uri, parsec, pretty, QuickCheck, tar, tasty, tasty-hunit
+, tasty-quickcheck, template-haskell, temporary, text, time
+, transformers, unordered-containers, vector, zlib
+}:
+mkDerivation {
+  pname = "hackage-security";
+  version = "0.6.2.3";
+  sha256 = "52ee0576971955571d846b8e6c09638f89f4f7881f4a95173e44ccc0d856a066";
+  revision = "3";
+  editedCabalFile = "1vdmpklil8a6r03ixzch5d36ngimmq5q8931i8bg9f7hh8nmq8jv";
+  libraryHaskellDepends = [
+    base base16-bytestring base64-bytestring bytestring Cabal
+    Cabal-syntax containers cryptohash-sha256 directory ed25519
+    filepath ghc-prim lukko mtl network network-uri parsec pretty tar
+    template-haskell time transformers zlib
+  ];
+  testHaskellDepends = [
+    aeson base bytestring Cabal Cabal-syntax containers network-uri
+    QuickCheck tar tasty tasty-hunit tasty-quickcheck temporary text
+    time unordered-containers vector zlib
+  ];
+  homepage = "https://github.com/haskell/hackage-security";
+  description = "Hackage security library";
+  license = lib.licenses.bsd3;
+  doCheck = false;
+  doHaddock = false;
+}

nix/overlays/process-1.6.15.0.nix

+{ mkDerivation, base, bytestring, deepseq, directory, filepath, lib
+, unix
+}:
+mkDerivation {
+  pname = "process";
+  version = "1.6.15.0";
+  sha256 = "44b31b6cd3129893ac1a007573dedb69dde667fa06ee108526d58f08b1a1f7ab";
+  libraryHaskellDepends = [ base deepseq directory filepath unix ];
+  testHaskellDepends = [ base bytestring directory ];
+  description = "Process libraries";
+  license = lib.licenses.bsd3;
+  doCheck = false;
+  doHaddock = false;
+}

nix/pkgs.nix

@@ -3,6 +3,23 @@
 rec {
   inherit pkgs;
   ghc = pkgs.haskell.compiler.ghc8107;
+  haskell1 = pkgs.haskell // {
+      packages = pkgs.haskell.packages // {
+        ghc8107 = pkgs.haskell.packages.ghc8107.override {
+          overrides = self: super: {
+            directory            = self.callPackage ./overlays/directory-1.3.7.0.nix {};
+            process              = self.callPackage ./overlays/process-1.6.15.0.nix {};
+            hackage-security     = self.callPackage ./overlays/hackage-security-0.6.2.3.nix {};
+            Cabal                = self.callPackage ./overlays/Cabal-3.10.1.0.nix {};
+            Cabal-syntax         = self.callPackage ./overlays/Cabal-syntax-3.10.1.0.nix {};
+            cabal-install-solver = self.callPackage ./overlays/cabal-install-solver-3.10.1.0.nix {};
+            cabal-install        = self.callPackage ./overlays/cabal-install-3.10.1.0.nix {};
+          };
+        };
+      };
+  };
+  cabal_install_3_10_1_0 = pkgs.haskell.lib.compose.justStaticExecutables haskell1.packages.ghc8107.cabal-install;
+
   igraph_0_10_4 = pkgs.igraph.overrideAttrs (finalAttrs: previousAttrs: {
     version = "0.10.4";
 
@@ -60,7 +77,7 @@ rec {
   });
   hsBuildInputs = [
     ghc
-    pkgs.cabal-install
+    cabal_install_3_10_1_0
   ];
   nonhsBuildInputs = with pkgs; [
     bzip2

package.yaml

@@ -47,6 +47,7 @@ data-files:
   - test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json
   - test-data/phylo/bpa_phylo_test.json
   - test-data/phylo/open_science.json
+  - .clippy.dhall
 library:
   source-dirs: src
   ghc-options: