Merge branch 'devel'

.github/workflows/unit-tests.yml

@@ -4,99 +4,55 @@ on: [push, pull_request]
 
 jobs:
   build:
-    runs-on: ubuntu-18.04
-    continue-on-error: ${{ matrix.experimental }} # Experimental builds may fail
-
-    defaults:
-      run:
-        shell: bash -l -e -o pipefail {0}
+    runs-on: ubuntu-latest
 
-    env:
-      WSI_CONDA_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic"
-      CONDA_TEST_ENVIRONMENT: "testenv"
-      CK_DEFAULT_TIMEOUT: 20
+    continue-on-error: ${{ matrix.experimental }} # Experimental builds may fail
 
     strategy:
       matrix:
         include:
-          - irods: "4.2.7"
-            server_image: "wsinpg/ub-16.04-irods-4.2.7:latest"
-            experimental: false
-          - irods: "4.2.7"
-            server_image: "wsinpg/ub-18.04-irods-4.2.10:latest"
-            experimental: true
-          - irods: "4.2.7"
-            server_image: "wsinpg/ub-18.04-irods-4.2.11:latest"
-            experimental: true
-
-          - irods: "4.2.10"
-            server_image: "wsinpg/ub-16.04-irods-4.2.7:latest"
-            experimental: true
-          - irods: "4.2.10"
-            server_image: "wsinpg/ub-18.04-irods-4.2.10:latest"
+          # iRODS 4.2.11 clients on bionic
+          - irods: "4.2.11"
+            build_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-dev-4.2.11:latest"
+            server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.11:latest"
             experimental: false
-          - irods: "4.2.10"
-            server_image: "wsinpg/ub-18.04-irods-4.2.11:latest"
+          # iRODS 4.3.0 clients on bionic
+          - irods: "4.3.0"
+            build_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-dev-4.3.0:latest"
+            server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.3.0:latest"
             experimental: true
-
-          - irods: "4.2.11"
-            server_image: "wsinpg/ub-16.04-irods-4.2.7:latest"
+          # iRODS 4.3.0 clients on focal
+          - irods: "4.3.0"
+            build_image: "ghcr.io/wtsi-npg/ub-20.04-irods-clients-dev-4.3.0:latest"
+            server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.3.0:latest"
             experimental: true
-          - irods: "4.2.11"
-            server_image: "wsinpg/ub-18.04-irods-4.2.10:latest"
-            experimental: true
-          - irods: "4.2.11"
-            server_image: "wsinpg/ub-18.04-irods-4.2.11:latest"
-            experimental: false
 
+    container:
+      image: ${{ matrix.build_image }}
 
     services:
-      irods:
+      irods-server:
         image: ${{ matrix.server_image }}
-        options: --name irods-server # A consistent container name is necessary
-                                     # to allow creation of bad replicas.
-                                     # 'irods-server' is the default container
-                                     # name in the bad replica script
         ports:
-          - 1247:1247
-          - 20000-20199:20000-20199
+          - "1247:1247"
+          - "20000-20199:20000-20199"
+        options: >-
+          --health-cmd "nc -z -v localhost 1247"
+          --health-start-period 30s
+          --health-interval 10s
+          --health-timeout 20s
+          --health-retries 6
 
     steps:
-      - uses: actions/checkout@v2
-
-      - name: "Initialize Miniconda"
-        run: |
-          echo 'source $CONDA/etc/profile.d/conda.sh' >> "$HOME/.bash_profile"
-
-      - name: "Configure Miniconda"
-        run: |
-          conda config --prepend pkgs_dirs "$HOME/conda/pkgs"
-          conda config --prepend envs_dirs "$HOME/conda/envs"
-
-          conda config --set auto_update_conda False
-          conda config --prepend channels "$WSI_CONDA_CHANNEL"
-          conda info
-
-      - name: "Install iRODS clients"
-        run: |
-          conda create -y -n "$CONDA_TEST_ENVIRONMENT"
-          conda install -y -n "$CONDA_TEST_ENVIRONMENT" python=3.9
-          conda install -y -n "$CONDA_TEST_ENVIRONMENT" sphinx=2.4
-
-          conda install -y -n "$CONDA_TEST_ENVIRONMENT" check
-          conda install -y -n "$CONDA_TEST_ENVIRONMENT" libjansson-dev
-          conda install -y -n "$CONDA_TEST_ENVIRONMENT" "irods-dev ==${{ matrix.irods }}"
-
-          conda install -y -n "$CONDA_TEST_ENVIRONMENT" "irods-icommands ==${{ matrix.irods }}"
+      - name: Checkout
+        uses: actions/checkout@v3
 
       - name: "Configure iRODS clients"
         run: |
-          conda activate "$CONDA_TEST_ENVIRONMENT"
-
           mkdir -p "$HOME/.irods"
           cat <<'EOF' > "$HOME/.irods/irods_environment.json"
           {
-              "irods_host": "localhost",
+              "irods_host": "irods-server",
               "irods_port": 1247,
               "irods_user_name": "irods",
               "irods_zone_name": "testZone",
@@ -105,29 +61,24 @@ jobs:
           }
           EOF
 
+          # Without this, Actions refuses the connection between the containers:
+          nc -z -v irods-server 1247
+
           echo "irods" | script -q -c "iinit" /dev/null
           ienv
           ils
           ilsresc
 
       - name: "Build and test baton"
+        env:
+          CK_DEFAULT_TIMEOUT: 20 
         run: |
-          conda activate "$CONDA_TEST_ENVIRONMENT"
-
-          # Is there an environment variable for this?
-          CONDA_ENV="/home/runner/conda/envs/$CONDA_TEST_ENVIRONMENT"
-
-          CPPFLAGS="-I$CONDA_ENV/include -I$CONDA_ENV/include/irods"
-          LDFLAGS="-L$CONDA_ENV/lib -L$CONDA_ENV/lib/irods/externals"
-          PKG_CONFIG_PATH="$CONDA_ENV/lib/pkgconfig"
-
-          autoreconf -i
-          ./configure CPPFLAGS="$CPPFLAGS" LDFLAGS="$LDFLAGS" PKG_CONFIG_PATH="$PKG_CONFIG_PATH"
-
-          export LD_LIBRARY_PATH="$CONDA_ENV/lib"
+          # Avoid git exiting when Actions runs this:
+          git config --global --add safe.directory "$PWD"
 
-          make check
-          make distcheck DISTCHECK_CONFIGURE_FLAGS="CPPFLAGS=\"$CPPFLAGS\" LDFLAGS=\"$LDFLAGS\""
+          autoreconf -fi
+          ./configure
+          make distcheck
 
       - name: "Show test log"
         if: ${{ failure() }}

ChangeLog

@@ -1,5 +1,10 @@
 	[Upcoming]
 
+	[4.0.1]
+
+	Fix missing format string in logging which caused a segfault when
+	log message arugments contained a printf placeholder.
+
 	[4.0.0]
 
 	Improve connection management by closing the connection while

Dockerfile

@@ -0,0 +1,62 @@
+FROM ubuntu:bionic
+
+RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections && \
+    apt-get update && \
+    apt-get install -q -y --no-install-recommends \
+    apt-utils \
+    ca-certificates \
+    curl \
+    gpg \
+    gpg-agent \
+    lsb-release \
+    locales && \
+    locale-gen en_GB en_GB.UTF-8 && \
+    localedef -i en_GB -c -f UTF-8 -A /usr/share/locale/locale.alias en_GB.UTF-8
+
+ENV LANG=en_GB.UTF-8 \
+    LANGUAGE=en_GB \
+    LC_ALL=en_GB.UTF-8
+
+ENV IRODS_VERSION=4.2.11-1~bionic
+
+RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
+    echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" |\
+    tee /etc/apt/sources.list.d/renci-irods.list && \
+    apt-get update && \
+    apt-get install -q -y --no-install-recommends \
+    irods-dev="$IRODS_VERSION" \
+    irods-runtime="$IRODS_VERSION" \
+    irods-icommands="$IRODS_VERSION"
+
+RUN apt-get update && \
+    apt-get install -q -y --no-install-recommends \
+    autoconf \
+    automake \
+    build-essential \
+    check \
+    gdb \
+    git \
+    jq \
+    lcov \
+    less \
+    libjansson-dev \
+    libtool \
+    pkg-config \
+    ssh \
+    valgrind \
+    unattended-upgrades && \
+    unattended-upgrade -d -v
+
+ARG USER=baton
+ARG UID=1000
+ARG GID=$UID
+
+RUN groupadd --gid $GID $USER && \
+    useradd --uid $UID --gid $GID --shell /bin/bash --create-home $USER
+
+USER $USER
+
+ENV CPPFLAGS="-I/usr/include/irods" \
+    CK_DEFAULT_TIMEOUT=20
+
+CMD ["/bin/bash"]

README

@@ -96,6 +96,17 @@ Installation:
    make clean install
 
 
+Development:
+
+To set up a development environment in Docker, use the provided
+docker-compose.yml and corresponding Dockerfile. These create a Linux
+C development and testing environment with an accompanying iRODS server.
+The recommended way to use this is by remote development in the container
+using VSCode. VSCode's manual explains how to do this, see:
+
+    https://code.visualstudio.com/docs/remote/containers
+
+
 Synopsis:
 
 For full details of the JSON accepted and returned by the programs in

docker-compose.yml

@@ -0,0 +1,21 @@
+services:
+  irods-server:
+    container_name: irods-server
+    image: "ghcr.io/wtsi-npg/ub-18.04-irods-${IRODS_VERSION:-4.2.11}:${DOCKER_TAG:-latest}"
+    restart: always
+    ports:
+      - "1247:1247"
+      - "20000-20199:20000-20199"
+
+  baton:  
+    image: baton
+    platform: linux/amd64
+    build:
+      context: .
+      dockerfile: ./Dockerfile
+    volumes:
+      - "${PWD}:/code"
+    environment:
+      IRODS_ENVIRONMENT_FILE: "/code/tests/.irods/irods_environment.json"
+    depends_on:
+      - irods-server

src/baton.c

@@ -1,5 +1,5 @@
 /**
- * Copyright (C) 2013, 2014, 2015, 2016, 2017, 2020 Genome Research
+ * Copyright (C) 2013, 2014, 2015, 2016, 2017, 2020, 2023 Genome Research
  * Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
@@ -560,7 +560,7 @@ json_t *search_metadata(rcComm_t *conn, json_t *query, char *zone_name,
     return results;
 
 error:
-    logmsg(ERROR, error->message);
+    logmsg(ERROR, "%s", error->message);
 
     if (results)      json_decref(results);
     if (collections)  json_decref(collections);
@@ -589,7 +589,7 @@ json_t *search_specific(rcComm_t *conn, json_t *query, char *zone_name,
     return results;
 
 error:
-    logmsg(ERROR, error->message);
+    logmsg(ERROR, "%s", error->message);
 
     if (results) json_decref(results);
 
@@ -658,11 +658,11 @@ int modify_permissions(rcComm_t *conn, rodsPath_t *rods_path,
 
 error:
     if (conn->rError) {
-        logmsg(ERROR, error->message);
+        logmsg(ERROR, "%s", error->message);
         log_rods_errstack(ERROR, conn->rError);
     }
     else {
-        logmsg(ERROR, error->message);
+        logmsg(ERROR, "%s", error->message);
     }
 
     return error->code;
@@ -775,11 +775,11 @@ int modify_metadata(rcComm_t *conn, rodsPath_t *rods_path,
 
 error:
     if (conn->rError) {
-        logmsg(ERROR, error->message);
+        logmsg(ERROR, "%s", error->message);
         log_rods_errstack(ERROR, conn->rError);
     }
     else {
-        logmsg(ERROR, error->message);
+        logmsg(ERROR, "%s", error->message);
     }
 
     return error->code;

src/json_query.c

@@ -1,5 +1,5 @@
 /**
- * Copyright (C) 2013, 2014, 2015, 2016, 2019, 2021 Genome Research
+ * Copyright (C) 2013, 2014, 2015, 2016, 2019, 2021, 2023 Genome Research
  * Ltd. All rights reserved.
  *
  * This program is free software: you can redistribute it and/or modify
@@ -473,11 +473,11 @@ json_t *do_query(rcComm_t *conn, genQueryInp_t *query_in,
 
 error:
     if (conn->rError) {
-        logmsg(ERROR, error->message);
+        logmsg(ERROR, "%s", error->message);
         log_rods_errstack(ERROR, conn->rError);
     }
     else {
-        logmsg(ERROR, error->message);
+        logmsg(ERROR, "%s", error->message);
     }
 
     if (query_out) free_query_output(query_out);
@@ -572,11 +572,11 @@ json_t *do_squery(rcComm_t *conn, specificQueryInp_t *squery_in,
 
 error:
     if (conn->rError) {
-        logmsg(ERROR, error->message);
+        logmsg(ERROR, "%s", error->message);
         log_rods_errstack(ERROR, conn->rError);
     }
     else {
-        logmsg(ERROR, error->message);
+        logmsg(ERROR, "%s", error->message);
     }
 
     if (query_out) free_query_output(query_out);
@@ -1369,4 +1369,3 @@ json_t *revmap_replicate_results(rcComm_t *conn, json_t *results,
 
     return NULL;
 }
-