Merge remote-tracking branch 'origin/dev-456-istex-tls-fix' into dev-merge

.gitlab-ci.yml

 # Optimising CI speed by using tips from https://blog.nimbleways.com/let-s-make-faster-gitlab-ci-cd-pipelines/
-#image: cgenie/gargantext:9.4.8
-image: adinapoli/gargantext:v3.5
+image: cgenie/gargantext:9.6.6
 
 variables:
   STACK_ROOT: "${CI_PROJECT_DIR}/.stack-root"
   STACK_OPTS: "--system-ghc"
   STORE_DIR: "${CI_PROJECT_DIR}/.cabal"
   CABAL_DIR: "${CI_PROJECT_DIR}/.cabal"
-  CORENLP: "4.5.4"
   FF_USE_FASTZIP: "true"
   ARTIFACT_COMPRESSION_LEVEL: "fast"
   CACHE_COMPRESSION_LEVEL: "fast"
@@ -95,17 +93,11 @@ test:
       nix-shell --run "./bin/update-project-dependencies $STORE_DIR"
       mkdir -p /root/.cache/cabal/logs
       chown -R test:test /root/.cache/cabal/logs/
-      chown -R test:test /root/.cache/cabal/packages/hackage.haskell.org/
       chown -R test:test "$TEST_TMPDIR"
 
-      mkdir -p /builds/gargantext/haskell-gargantext/devops/coreNLP/stanford-corenlp-current
-      cp -R /root/devops/coreNLP/stanford-corenlp-${CORENLP}/* /builds/gargantext/haskell-gargantext/devops/coreNLP/stanford-corenlp-current/
-
       nix-shell --run "chown -R test:test /root/.config/ && su -m test -c \"export PATH=$PATH:$TEST_NIX_PATH && export TMPDIR=$TEST_TMPDIR && cd /builds/gargantext/haskell-gargantext; $CABAL --store-dir=$STORE_DIR v2-test --test-show-details=streaming --flags 'test-crypto no-phylo-debug-logs' --ghc-options='-O0 -fclear-plugins'\""
 
       chown -R root:root dist-newstyle/
       chown -R root:root /root/
       chown -R root:root $STORE_DIR
       chown -R root:root /root/.cache/cabal/logs/
-      chown -R root:root /root/.cache/cabal/packages/hackage.haskell.org/
-      chown -Rh root:root /builds/gargantext/haskell-gargantext/devops/coreNLP/stanford-corenlp-current

README.md

@@ -103,6 +103,17 @@ Then initialize the database using the dedicated command: from inside the
 
 And provide a name and a password for the master user as requested.
 
+### Launching CoreNLP
+
+CoreNLP can be started with nix:
+```shell
+nix-shell --run startCoreNLPServer.sh
+```
+By default, this starts on port `9000`. If you want a different port, then do:
+```shell
+nix-shell --run 'startCoreNLPServer.sh -p 9001'
+```
+
 ### Running Gargantext
 
 From inside the `haskell-gargantext/` directory, run
@@ -237,11 +248,11 @@ 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 .
+podman build -t cgenie/gargantext:9.6.6 --pull -f ./devops/docker/Dockerfile --format=docker .
 ```
 or
 ```shell
-docker build -t cgenie/gargantext:9.4.8 -f ./devops/docker/Dockerfile .
+docker build -t cgenie/gargantext:9.6.6 --pull -f ./devops/docker/Dockerfile .
 ```
 
 NOTE: if podman/docker complains about not enough space, it's probably
@@ -263,9 +274,9 @@ When a development is needed on libraries (for instance, the HAL crawler in http
    2. When changes work and tests are OK, commit in repo `hal`
 2. When changes are commited / merged:
    1. Get the hash id, and edit `cabal.project` with the **new commit id**
-   2. run `./bin/update-project-dependencies`
+   2. run `nix-shell --run ./bin/update-project-dependencies`
       - get an error that sha256 don't match, so update the `./bin/update-project-dependencies` with new sha256 hash
-      - run again `./bin/update-project-dependencies` (to make sure it's a fixed point now)
+      - run again `nix-shell --run ./bin/update-project-dependencies` (to make sure it's a fixed point now)
 
 > Note: without `stack.yaml` we would have to only fix `cabal.project` -> `source-repository-package` commit id. Sha256 is there to make sure CI reruns the tests.
 

bin/install-cabal2stack

-#!/usr/bin/env bash
-
-set -euxo pipefail
-
-current_dir=$(basename "$PWD")
-
-if [ "$current_dir" == "bin" ]; then
-    source ./setup-ci-environment
-else
-    source ./bin/setup-ci-environment
-fi
-
-cabal --store-dir=$STORE_DIR v2-update "hackage.haskell.org,${INDEX_STATE}"
-
-# Install cabal2stack if it can't be found.
-if ! cabal2stack --help &> /dev/null
-then
-    echo "cabal2stack could not be found"
-    CURDIR=$PWD
-    git clone https://github.com/iconnect/cabal2stack.git cabal2stack-installer
-    cd cabal2stack-installer
-    cabal --store-dir=$STORE_DIR v2-install --allow-newer --index-state="${INDEX_STATE}" --overwrite-policy=always
-    cd $CURDIR
-    rm -rf cabal2stack-installer
-fi

bin/update-project-dependencies

@@ -6,10 +6,8 @@ current_dir=$(basename "$PWD")
 
 if [ "$current_dir" == "bin" ]; then
     source ./setup-ci-environment
-    ./install-cabal2stack
 else
     source ./bin/setup-ci-environment
-    ./bin/install-cabal2stack
 fi
 
 # README!
@@ -18,7 +16,7 @@ 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="37352ca36ca5e69d9945da11439be4c3909297b338242855fa588dffdf1ba02b" 
+expected_cabal_project_hash="0ce011cd483078936fe3385b3e0c90231774fd2ac05bfb9f4c646345a0208d66"
 expected_cabal_project_freeze_hash="cd52143d3a9d285360b59c6371d3e258552c1bc115bd612024db3de1f7593ff7" 
 
 

cabal.project

@@ -72,7 +72,7 @@ source-repository-package
 source-repository-package
     type: git
     location: https://gitlab.iscpif.fr/gargantext/crawlers/istex.git
-    tag: 521ca54f1502b13f629eff2223aaf5007e6d52ec
+    tag: 894482ef97eadce6b1c13ebced1edfe394b5be5e
 
 source-repository-package
     type: git

devops/coreNLP/.gitignore

-stanford-corenlp-*

devops/coreNLP/Dockerfile

-FROM openjdk
-
-#ADD home/debian/CoreNLP /CoreNLP
-ADD stanford-corenlp-current /CoreNLP
-WORKDIR /CoreNLP
-
-CMD ./startServer.sh

devops/coreNLP/build.sh

-#!/bin/bash
-
-# releases are here:
-# https://stanfordnlp.github.io/CoreNLP/history.html
-
-VERSION=4.5.4
-FILE="stanford-corenlp-${VERSION}.zip"
-DIR_V="stanford-corenlp-${VERSION}"
-DIR="stanford-corenlp-current"
-URL="http://nlp.stanford.edu/software/${FILE}"
-
-[ ! -f ${FILE} ] && echo 'Fetching file' && wget ${URL} -O ${FILE}
-
-[ ! -d ${DIR_V} ] && echo 'Unzipping file' && unzip ./${FILE}
-
-[ ! -L ${DIR} ] && echo "Symlinking ${DIR_V} -> ${DIR}" && ln -s ${DIR_V} ${DIR}
-
-[ ! -f ${DIR}/startServer.sh ] && echo "Copying startServer.sh" && cp ./startServer.sh ${DIR}/
-
-echo "You can now build with: docker build -t cgenie/corenlp-garg:${VERSION}" --pull .

devops/coreNLP/startServer.sh

-#!/bin/sh
-
-java -mx4g -cp "*" edu.stanford.nlp.pipeline.StanfordCoreNLPServer -port 9000 -timeout 15000

devops/docker/Dockerfile

@@ -3,16 +3,6 @@ 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=9.6.6
-ARG CORENLP=4.5.4
-ARG CORE
-COPY ./shell.nix                                       /builds/gargantext/shell.nix
-COPY ./nix/pkgs.nix                                    /builds/gargantext/nix/pkgs.nix
-COPY ./nix/pinned-25.05.nix                            /builds/gargantext/nix/pinned-25.05.nix
-COPY ./devops/coreNLP/build.sh                         /root/devops/coreNLP/build.sh
-COPY ./devops/coreNLP/startServer.sh                   /root/devops/coreNLP/startServer.sh
-COPY ./bin/setup-ci-environment                        /builds/gargantext/bin/setup-ci-environment
-COPY ./bin/install-cabal2stack                         /builds/gargantext/bin/install-cabal2stack
 
 ENV TZ=Europe/Rome
 ENV LANG='en_US.UTF-8' LANGUAGE='en_US:en' LC_ALL='en_US.UTF-8'
@@ -25,32 +15,15 @@ ENV PATH=/root/.local/bin:$PATH
 RUN apt-get update && \
     apt-get install --no-install-recommends -y \
       apt-transport-https \
-      autoconf \
-      automake \
-      build-essential \
       ca-certificates \
       curl \
-      gcc \
       git \
       gnupg2 \
-      libffi-dev \
-      libffi8 \
-      libgmp-dev \
-      libgmp10 \
-      libncurses-dev \
-      libncurses6 \
-      libnuma-dev \
-      libtinfo6 \
       locales \
-      lsb-release \
       software-properties-common \
-      strace \
       sudo \
-      wget \
-      vim \
       xz-utils \
-      zlib1g-dev \
-      openjdk-21-jdk \
+      #zlib1g-dev \
       unzip && \
     apt-get clean && rm -rf /var/lib/apt/lists/* && \
     mkdir -m 0755 /nix && groupadd -r nixbld && chown root /nix && \
@@ -60,16 +33,21 @@ RUN apt-get update && \
 
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
-RUN cd /root/devops/coreNLP; ./build.sh && \
-    set -o pipefail && \
+RUN set -o pipefail && \
+    locale-gen en_US.UTF-8 && \
     bash <(curl -L https://releases.nixos.org/nix/nix-2.26.2/install) --no-daemon && \
-    locale-gen en_US.UTF-8 && chown root -R /nix && \
+    chown root -R /nix && \
     . "$HOME/.nix-profile/etc/profile.d/nix.sh" && \
     mkdir -p "/builds/gargantext/" && chmod 777 -R "/builds/gargantext" && \
     echo "source $HOME/.nix-profile/etc/profile.d/nix.sh" >> "$HOME/.bashrc" && \
     echo `which nix-env` && \
-    . $HOME/.bashrc && nix-env --version && \
-    cd /builds/gargantext && nix-shell --run "./bin/install-cabal2stack"
+    . $HOME/.bashrc && nix-env --version
+
+# We want to cache nix artifacts in the Dockerfile to improve CI speed
+COPY ./shell.nix /nix-ci-build/
+COPY ./nix       /nix-ci-build/
+RUN set -o pipefail && \
+    pushd /nix-ci-build/ && nix-build shell.nix && popd
 
 WORKDIR "/builds/gargantext/"
 

devops/docker/docker-compose.yaml

 version: '3'
 
 services:
-  caddy:
-    image: caddy:alpine
-    ports:
-      - 8108:8108
-    volumes:
-      - ./Caddyfile:/etc/caddy/Caddyfile:ro
-      - ../../purescript-gargantext:/srv/purescript-gargantext:ro
+  # caddy:
+  #   image: caddy:alpine
+  #   ports:
+  #     - 8108:8108
+  #   volumes:
+  #     - ./Caddyfile:/etc/caddy/Caddyfile:ro
+  #     - ../../purescript-gargantext:/srv/purescript-gargantext:ro
 
   #postgres11:
   #  #image: 'postgres:latest'
@@ -61,12 +61,6 @@ services:
   #   volumes:
   #     - pgadmin:/var/lib/pgadmin
 
-  corenlp:
-    #image: 'cgenie/corenlp-garg:latest'
-    image: 'cgenie/corenlp-garg:4.5.4'
-    ports:
-      - 9000:9000
-
   # johnsnownlp:
   #   image: 'johnsnowlabs/nlp-server:latest'
   #   volumes:

devops/install-corenlp

-#!/bin/bash
-
-if [ ! -d coreNLP ]; then
-    mkdir -v coreNLP
-fi
-
-pushd coreNLP
-
-wget https://dl.gargantext.org/coreNLP.tar.bz2
-tar xvjf coreNLP.tar.bz2
-pushd home/debian/CoreNLP
-./startServer.sh

nix/cabal2stack.nix

+{ lib,
+  ghc,
+  haskellPackages,
+  fetchFromGitHub }:
+
+let
+  src = fetchFromGitHub {
+    repo = "cabal2stack";
+    owner = "iconnect";
+    rev = "e4960683f518ab4c964e7646706fe2a7e1bf751a";
+    hash = "sha256-KE9VUXFy9QfRmu/+DFcgxV/E6oPBAR7hRaFrSt93eeY=";
+  };
+in
+with haskellPackages;
+mkDerivation {
+  inherit src;
+  pname = "cabal2stack";
+  version = "0";
+  isExecutable = true;
+  executableHaskellDepends = [ base
+                               aeson
+                               cabal-plan
+                               HsYAML
+                               HsYAML-aeson
+                               optics-core
+                               optics-extra
+                               optparse-applicative
+                               transformers ];
+  patches = [
+    ./patches/cabal2stack.patch
+  ];
+  license = lib.licenses.bsd3;
+  mainProgram = "cabal2stack"; 
+}

nix/corenlp.nix

+# https://nixos.wiki/wiki/Java
+
+{ fetchzip,
+  makeWrapper,
+  stdenv,
+  writeShellScript,
+  jre,
+
+  version ? "4.5.8",
+  hash ? "sha256-HZHNyw+LrxAN4OLueAhyxRG2onPWNMm5MwJDLLzsE2M="
+}:
+
+stdenv.mkDerivation (finalAttrs:
+  let
+    startServer = writeShellScript "startCoreNLPServer.sh" ''
+      set -x
+      PORT=9000
+  
+      while getopts ':p:h' opt; do
+        case $opt in
+          (p) PORT=$OPTARG;;
+          (h) echo "$(basename $0) [-p 9000]"
+              exit 0
+              ;;
+        esac
+      done
+  
+      shift "$((OPTIND - 1))"
+
+      ${jre}/bin/java -mx4g -cp "$CORENLP_PATH/*" edu.stanford.nlp.pipeline.StanfordCoreNLPServer -port $PORT -timeout 15000 "$@"
+    '';
+  in
+
+  {
+    name = "corenlp";
+    inherit version;
+    src = fetchzip {
+      inherit hash;
+      url = "http://nlp.stanford.edu/software/stanford-corenlp-${finalAttrs.version}.zip";
+    };
+    buildInputs = [
+      jre
+    ];
+    nativeBuildInputs = [
+      makeWrapper
+    ];
+    phases = [ "unpackPhase" "installPhase" ];
+    installPhase = ''
+      runHook preInstall
+      mkdir -p $out/bin
+      mkdir -p $out/share/corenlp
+      cp -r . $out/share/corenlp
+      makeWrapper ${startServer} $out/bin/startCoreNLPServer.sh \
+        --set CORENLP_PATH "$out/share/corenlp"
+      runHook postInstall
+    '';
+  }
+)

nix/graphviz.nix

+{ fetchFromGitLab,
+  fetchpatch,
+  graphviz }:
+let
+  graphviz_dev = graphviz.overrideAttrs (finalAttrs: previousAttrs: {
+    version = "11.0.0~dev";
+    src = fetchFromGitLab {
+      owner = "graphviz";
+      repo = "graphviz";
+      rev = "f3ec849249ef9cb824feb7f97449d7159e1dcb4e"; # head as of 2024-03-25, see gargantext#329
+      hash = "sha256-s86IqWz6zeKbcRqpV3cVQBVviHbhUSX1U8GVuJBfjC4=";
+    };
+  });
+in
+graphviz_dev.overrideAttrs
+  (finalAttrs: previousAttrs: {
+    # Increase the YY_BUF_SIZE, see https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/290#note_9015
+    patches = [
+      (fetchpatch {
+        url = "https://gist.githubusercontent.com/adinapoli/e93ca7b1d714d27f4af537716b03e3bb/raw/b9cc297c3465878da2d18ee92a3f9b8273923493/graphviz-yy-buf-size.patch";
+        sha256 = "sha256-8Q3tf37iYaPV50P+Vf/n263ordECiu5eKwONCy3ynV8=";
+      })
+    ];
+  })

nix/igraph.nix

+{ fetchFromGitHub,
+
+  igraph,
+
+  arpack,
+  blas,
+  glpk,
+  gmp,
+  lapack,
+  libxml2,
+  nanomsg,
+  plfit,
+  llvmPackages,
+  
+  version ? "0.10.4",
+  hash ? "sha256-LsTOxUktGZcp46Ec9QH3+9C+VADMYTZZCjKF1gp36xk=" }:
+
+igraph.overrideAttrs (finalAttrs: previousAttrs: {
+  inherit version;
+
+  nativeBuildInputs = previousAttrs.nativeBuildInputs;
+
+  src = fetchFromGitHub {
+    inherit hash;
+    owner = "igraph";
+    repo = "igraph";
+    rev = version;
+  };
+
+  postPatch = ''
+    echo "${version}" > IGRAPH_VERSION
+  '';
+
+  outputs = [ "dev" "out" "doc" ];
+
+  buildInputs = [
+    arpack
+    blas
+    glpk
+    gmp
+    lapack
+    libxml2
+    nanomsg
+    plfit
+    llvmPackages.openmp
+  ];
+
+  cmakeFlags = [
+    "-DIGRAPH_USE_INTERNAL_BLAS=OFF"
+    "-DIGRAPH_USE_INTERNAL_LAPACK=OFF"
+    "-DIGRAPH_USE_INTERNAL_ARPACK=OFF"
+    "-DIGRAPH_USE_INTERNAL_GLPK=OFF"
+    "-DIGRAPH_USE_INTERNAL_GMP=OFF"
+    "-DIGRAPH_USE_INTERNAL_PLFIT=OFF"
+    "-DIGRAPH_GLPK_SUPPORT=ON"
+    "-DIGRAPH_GRAPHML_SUPPORT=OFF"
+    "-DIGRAPH_OPENMP_SUPPORT=ON"
+    "-DIGRAPH_ENABLE_LTO=AUTO"
+    "-DIGRAPH_ENABLE_TLS=ON"
+    "-DBUILD_SHARED_LIBS=ON"
+    "-DCMAKE_INSTALL_PREFIX=${placeholder "out"}"
+    "-DCMAKE_INSTALL_LIBDIR=${placeholder "out"}/lib"
+    "-DCMAKE_INSTALL_DATADIR=${placeholder "out"}/share"
+  ];
+
+  doCheck = false;
+
+  postInstall = ''
+    mkdir -p "$out/share"
+    cp -r doc "$out/share"
+  '';
+
+  postFixup = previousAttrs.postFixup + ''
+    echo "Copying files where they belong .."
+    CUR_DIR=$PWD
+    cd "$dev/include/igraph" && cp *.h ../
+    cd $CUR_DIR
+  '';
+
+})

nix/patches/cabal2stack.patch

+diff --git i/cabal2stack.cabal w/cabal2stack.cabal
+index 69767a2..92c4895 100644
+--- i/cabal2stack.cabal
++++ w/cabal2stack.cabal
+@@ -26,14 +26,14 @@ executable cabal2stack
+ 
+   -- boot dependencies
+   build-depends:
+-    , base          >=4.12     && <4.18
++    , base          >=4.12     && <5
+     , bytestring    ^>=0.10.8.2 || ^>=0.11.3.0
+     , containers    ^>=0.6.0.1
+     , directory     ^>=1.3.3.0
+     , filepath      ^>=1.4.2.1
+     , process       ^>=1.6.5.0
+     , text          >=1.2.3.0 && <2.1
+-    , transformers  ^>=0.5.6.2
++    , transformers  >=0.5.6.2 && < 0.7
+ 
+   -- other dependencies
+   build-depends:
+@@ -43,4 +43,4 @@ executable cabal2stack
+     , HsYAML-aeson          ^>=0.2.0.1
+     , optics-core           ^>=0.4
+     , optics-extra          ^>=0.4
+-    , optparse-applicative  ^>=0.17.0.0
++    , optparse-applicative  >=0.17.0.0 && < 0.20

nix/pkgs.nix

@@ -6,88 +6,12 @@ rec {
   inherit pkgs;
   ghc966 = pkgs.haskell.compiler.ghc966;
   cabal_install = pkgs.haskell.lib.compose.justStaticExecutables pkgs.haskell.packages.ghc966.cabal-install;
-  graphviz_dev = pkgs.graphviz.overrideAttrs (finalAttrs: previousAttrs: {
-    version = "11.0.0~dev";
-    src = pkgs.fetchFromGitLab {
-      owner = "graphviz";
-      repo = "graphviz";
-      rev = "f3ec849249ef9cb824feb7f97449d7159e1dcb4e"; # head as of 2024-03-25, see gargantext#329
-      hash = "sha256-s86IqWz6zeKbcRqpV3cVQBVviHbhUSX1U8GVuJBfjC4=";
-    };
-  });
-  graphviz = graphviz_dev.overrideAttrs (finalAttrs: previousAttrs: {
-                # Increase the YY_BUF_SIZE, see https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/290#note_9015
-                patches = [
-                            (pkgs.fetchpatch {
-                              url = "https://gist.githubusercontent.com/adinapoli/e93ca7b1d714d27f4af537716b03e3bb/raw/b9cc297c3465878da2d18ee92a3f9b8273923493/graphviz-yy-buf-size.patch";
-                              sha256 = "sha256-8Q3tf37iYaPV50P+Vf/n263ordECiu5eKwONCy3ynV8=";
-                            })
-                          ];
-                });
-
-  igraph_0_10_4 = pkgs.igraph.overrideAttrs (finalAttrs: previousAttrs: {
-    version = "0.10.4";
   
-    nativeBuildInputs = previousAttrs.nativeBuildInputs;
+  graphviz = pkgs.callPackage ./graphviz.nix {};
+  igraph_0_10_4 = pkgs.callPackage ./igraph.nix {};
+  corenlp = pkgs.callPackage ./corenlp.nix { };  # 4.5.8
+  cabal2stack = pkgs.callPackage ./cabal2stack.nix { ghc = ghc966; };
   
-    src = pkgs.fetchFromGitHub {
-      owner = "igraph";
-      repo = "igraph";
-      rev = "0.10.4";
-      hash = "sha256-LsTOxUktGZcp46Ec9QH3+9C+VADMYTZZCjKF1gp36xk=";
-    };
-
-    postPatch = ''
-      echo "0.10.4" > IGRAPH_VERSION
-    '';
-
-    outputs = [ "dev" "out" "doc" ];
-
-    buildInputs = [
-      pkgs.arpack
-      pkgs.blas
-      pkgs.glpk
-      pkgs.gmp
-      pkgs.lapack
-      pkgs.libxml2
-      pkgs.nanomsg
-      pkgs.plfit
-      pkgs.llvmPackages.openmp
-    ];
-
-    cmakeFlags = [
-      "-DIGRAPH_USE_INTERNAL_BLAS=OFF"
-      "-DIGRAPH_USE_INTERNAL_LAPACK=OFF"
-      "-DIGRAPH_USE_INTERNAL_ARPACK=OFF"
-      "-DIGRAPH_USE_INTERNAL_GLPK=OFF"
-      "-DIGRAPH_USE_INTERNAL_GMP=OFF"
-      "-DIGRAPH_USE_INTERNAL_PLFIT=OFF"
-      "-DIGRAPH_GLPK_SUPPORT=ON"
-      "-DIGRAPH_GRAPHML_SUPPORT=OFF"
-      "-DIGRAPH_OPENMP_SUPPORT=ON"
-      "-DIGRAPH_ENABLE_LTO=AUTO"
-      "-DIGRAPH_ENABLE_TLS=ON"
-      "-DBUILD_SHARED_LIBS=ON"
-      "-DCMAKE_INSTALL_PREFIX=${placeholder "out"}"
-      "-DCMAKE_INSTALL_LIBDIR=${placeholder "out"}/lib"
-      "-DCMAKE_INSTALL_DATADIR=${placeholder "out"}/share"
-    ];
-
-    doCheck = false;
-
-    postInstall = ''
-      mkdir -p "$out/share"
-      cp -r doc "$out/share"
-    '';
-
-    postFixup = previousAttrs.postFixup + ''
-      echo "Copying files where they belong .."
-      CUR_DIR=$PWD
-      cd "$dev/include/igraph" && cp *.h ../
-      cd $CUR_DIR
-    '';
-
-  });
   hsBuildInputs = [
     ghc966
     cabal_install
@@ -96,34 +20,36 @@ rec {
     pkgs.haskellPackages.pretty-show
   ];
   nonhsBuildInputs = with pkgs; [
+    #haskell-language-server
+    blas
     bzip2
+    cabal2stack
+    corenlp
+    curl
     czmq
     docker-compose
+    expat
+    gfortran
     git
     gmp
+    graphviz
     gsl
-    #haskell-language-server
     hlint
-    libffi
+    icu
+    igraph_0_10_4
+    jre
     lapack
-    xz
+    libffi
+    libpqxx
+    libsodium
+    nanomsg
+    nil  # nix language server
     pcre
     pkg-config
     postgresql
+    stdenv.cc.cc
     xz
     zlib
-    blas
-    gfortran
-    expat
-    icu
-    graphviz
-    gcc13
-    igraph_0_10_4
-    libpqxx
-    libsodium
-    nanomsg
-    zeromq
-    curl
   ] ++ ( lib.optionals stdenv.isDarwin [
        darwin.apple_sdk.frameworks.Accelerate
        ]);

stack.yaml

@@ -158,7 +158,7 @@
   git: "https://gitlab.iscpif.fr/gargantext/crawlers/isidore.git"
   subdirs:
   - .
-- commit: 521ca54f1502b13f629eff2223aaf5007e6d52ec
+- commit: 894482ef97eadce6b1c13ebced1edfe394b5be5e
   git: "https://gitlab.iscpif.fr/gargantext/crawlers/istex.git"
   subdirs:
   - .

test/drivers/hspec/Main.hs

@@ -20,8 +20,8 @@ startCoreNLPServer :: IO ProcessHandle
 startCoreNLPServer = do
   putText "calling start core nlp"
   devNull <- openFile "/dev/null" WriteMode
-  let p = proc "./startServer.sh" []
-  (_, _, _, hdl) <- (createProcess $ p { cwd = Just "devops/coreNLP/stanford-corenlp-current"
+  let p = proc "startCoreNLPServer.sh" []
+  (_, _, _, hdl) <- (createProcess $ p { cwd = Nothing
                     -- NOTE(adn) Issue #451, this one has to stay disabled, because if we
                     -- turn it on, despite the confusing documentation on the `process` library
                     -- it will cause the Haskell RTS to completely ignore the Ctrl^c and instead
@@ -34,10 +34,7 @@ startCoreNLPServer = do
                     , std_err = UseHandle devNull
                     }) `catch` \e -> case e of
                                            _ | True <- "does not exist" `isInfixOf` (T.pack . show @SomeException $ e)
-                                             -> fail $ "Cannot execute the 'startServer.sh' script. If this is the " <>
-                                                       "first time you are running the tests, you have to run " <>
-                                                       "cd devops/coreNLP && ./build.sh first. You have to run it only once, " <>
-                                                       "and then you are good to go for the time being."
+                                             -> fail $ "Cannot execute the 'startCoreNLPServer.sh' script. Make sure you are in a nix environment."
                                              | otherwise -> throwIO e
   pure hdl