Update file path, try out z-trick

.github/workflows/build_debug_image.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        image: ["java-no-dl", "java-no-dl-lz4", "rust-no-dl-lz4"]
+        image: ["java-no-dl", "java-no-dl-lz4", "rust-no-dl-lz4", "rust-no-dl-lz4-z-truc"]
     steps:
       - name: Checkout
         uses: actions/checkout@v2

unipept-database/rust-no-dl-lz4-z-truc.Dockerfile

@@ -0,0 +1,119 @@
+FROM mariadb:jammy
+
+###
+# Name: unipept-database
+#
+# This Dockerfile can be used to build an image that contains everything required to spin up a container with a
+# functioning Unipept database (the database will be filled with all of the required data).
+#
+# Parameters (are being referenced as environment variables in the Dockerfile)
+#   * DB_TYPES: names of the database sources that are to be parsed by this script (comma-delimited, one name per
+#   source).
+#   * DB_SOURCES: list of URLs that point to the database sources that should be used as a basis to construct the
+#   database.
+#   * FILTER_TAXA: a list of NCBI taxon ID's (comma-delimited) by which the resulting Unipept database should be
+#   filtered. Only UniProt-entries that are associated with these ID's (or their children in the NCBI taxonomy
+#   tree) are being kept during the build process.
+#   * VERBOSE: Should all debugging information be printed during the Docker build? Is false by default.
+#
+# Mount-points:
+#   * /index: Directory that will hold the Unipept database index. If this index is present from previous database
+#   builds, and it is valid, it can help to speed up the construction process of future containers.
+#   * /tmp: Directory that will be used by this container to store temporary files. Note that this directory can
+#   become very large and that it will benefit from very fast storage.
+#   * /tables: Directory that contains the generated database table files (that are used to fill up the constructed
+#   database). These files will typically only be available during the construction process of the container.
+#   * /var/lib/mysql: Directory that will contain the persistent MySQL datafiles. This directory should always be
+#   mounted at the same location in order to start the database.
+###
+
+LABEL maintainer="Stijn De Clercq <[email protected]>"
+
+RUN mkdir -p /usr/share/man/man1
+RUN apt update && \
+    apt install -y \
+    default-jdk \
+    git \
+    dos2unix \
+    maven \
+    make \
+    wget \
+    unzip \
+    expect \
+    gawk \
+    binutils \
+    gcc \
+    libssl-dev \
+    uuid-runtime \
+    pv \
+    nodejs \
+    pigz \
+    parallel \
+    curl \
+    sudo \
+    lz4
+
+# Now, build curl from source to upgrade it to version 7.68.0 (instead of the default 7.52.0 in this image)
+# This fixes https://github.com/curl/curl/issues/3750 which is present in older versions of curl
+#RUN wget https://curl.haxx.se/download/curl-7.68.0.zip && \
+#    unzip curl-7.68.0.zip && \
+#    cd curl-7.68.0 && \
+#    ./configure --disable-dependency-tracking --with-ssl && \
+#    make && \
+#    make install && \
+#    cd "/"
+
+# Configure curl to use the newly builded libcurl
+#RUN ldconfig
+
+RUN git clone https://github.com/stijndcl/unipept-database make-database && cd make-database && git checkout feature/z-truc && git pull
+COPY "db_entrypoint.sh" "/docker-entrypoint-initdb.d/db_entrypoint.sh"
+COPY "uniprot_sprot.xml.gz" "/uniprot_sprot.xml.gz"
+
+# Sometimes, these files are copied over from Windows systems and need to be converted into Unix line endings to make
+# sure that these can be properly executed by the container.
+RUN dos2unix /make-database/scripts/**/*.sh /make-database/scripts/**/*.js && chmod u+x /make-database/scripts/*.sh
+
+COPY "config/custom_mysql_config.cnf" "/etc/mysql/conf.d/custom_mysql_config.cnf"
+RUN chmod a-w "/etc/mysql/conf.d/custom_mysql_config.cnf"
+
+RUN echo 'root:unipept' | chpasswd
+
+# To keep the next commands short, use
+WORKDIR /make-database/scripts/helper_scripts/unipept-database-rs
+
+# Install Rust toolchain (https://rustup.rs/)
+RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | bash -s -- -y
+RUN echo 'source $HOME/.cargo/env' >> $HOME/.bashrc
+ENV PATH="/root/.cargo/bin:${PATH}"
+
+# Compile Rust binaries
+RUN cargo build --release
+
+# Copy binaries to helper_scripts folder
+RUN mv target/release/functional-analysis ../functional-analysis
+RUN mv target/release/taxons-uniprots-tables ../taxons-uniprots-tables
+RUN mv target/release/xml-parser ../xml-parser
+
+# Clean up build artifacts so they don't end up in the image
+RUN rm -rf target/
+
+# Uninstall Rust again to keep the image size down
+RUN rustup self uninstall -y
+
+WORKDIR /
+
+# Database types that should be processed by this image. Delimited by comma's.
+ENV DB_TYPES swissprot
+# Database URLs that should be downloaded and processed by this container. Delimited by comma's, n'th item in this list
+# should correspond to n'th db type given in DB_TYPES arg.
+ENV DB_SOURCES https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz
+# List of taxa (separated by comma's) for which all children (and the nodes themselves) should be present in the final
+# database.
+ENV FILTER_TAXA 1
+
+ENV VERBOSE false
+
+ENV SORT_MEMORY 2G
+
+EXPOSE 3306

unipept-database/rust-no-dl-lz4.Dockerfile

@@ -80,7 +80,7 @@ RUN chmod a-w "/etc/mysql/conf.d/custom_mysql_config.cnf"
 RUN echo 'root:unipept' | chpasswd
 
 # To keep the next commands short, use
-WORKDIR /make-database/scripts/helper_scripts/new-parsers
+WORKDIR /make-database/scripts/helper_scripts/unipept-database-rs
 
 # Install Rust toolchain (https://rustup.rs/)
 RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | bash -s -- -y