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Migrate to Postgres, use parallel db scripts #7

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Migrate to Postgres, use parallel db scripts #7

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fd4f68e
Migrate image to psql
stijndcl May 6, 2024
eca5fe6
Remove mariadb config file
stijndcl May 6, 2024
a645b3c
Change web db ports
stijndcl May 6, 2024
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14 changes: 4 additions & 10 deletions unipept-database/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM mariadb:jammy
FROM postgres:16.2-bullseye

###
# Name: unipept-database
Expand Down Expand Up @@ -49,20 +49,14 @@ RUN apt update && \
sudo \
lz4


# Configure curl to use the newly builded libcurl
#RUN ldconfig

RUN git clone --depth 1 https://github.com/unipept/unipept-database
# TODO change to unipept repo once changes are merged to master!
RUN git clone --depth 1 -b feature/postgres https://github.com/stijndcl/unipept-database
COPY "db_entrypoint.sh" "/docker-entrypoint-initdb.d/db_entrypoint.sh"

# 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 /unipept-database/scripts/**/*.sh && chmod u+x /unipept-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

# Install Rust toolchain (https://rustup.rs/)
Expand Down Expand Up @@ -92,4 +86,4 @@ ENV VERBOSE false

ENV SORT_MEMORY 2G

EXPOSE 3306
EXPOSE 5432
7 changes: 0 additions & 7 deletions unipept-database/config/custom_mysql_config.cnf
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11 changes: 7 additions & 4 deletions unipept-database/db_entrypoint.sh
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Expand Up @@ -21,11 +21,14 @@ echo "unipept" | su -c "./scripts/build_database.sh $VERBOSE-f $FILTER_TAXA -i '

echo "***** START LOADING TABLES *****"

# Data has been generated by this point. Now, we can load it into the MySQL-database for use later on.
mariadb -uunipept -punipept < schemas/structure_no_index.sql
echo "unipept" | su -c "./scripts/load.sh '/tmp/tables'" root
# Data has been generated by this point. Now, we can load it into the PSQL-database for use later on.
PGPASSWORD=unipept psql -U unipept < schemas/structure_no_index_no_constraints.sql
echo "unipept" | su -c "./scripts/parallel_load.sh '/tmp/tables'" root
rm -f '/tables/**/*.tsv.lz4'

echo "***** START APPLYING CONSTRAINTS *****"
PGPASSWORD=unipept psql -U unipept < schemas/structure_constraints_only.sql

echo "***** START INDEXING TABLES *****"

echo "unipept" | su -c "./scripts/index.sh" root
echo "unipept" | su -c "./scripts/parallel_index.sh" root
4 changes: 2 additions & 2 deletions unipept-web/Dockerfile
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Expand Up @@ -33,10 +33,10 @@ RUN apt-get autoremove -y \

RUN git clone https://github.com/unipept/unipept-api.git
RUN cd unipept-api && git checkout main && gem install bundler
RUN cd unipept-api/config && printf " host: host.docker.internal\n port: 3306\n" >> database.yml
RUN cd unipept-api/config && printf " host: host.docker.internal\n port: 5432\n" >> database.yml
RUN cd unipept-api && bundle install

ENV RAILS_ENV=production
ENV DB_PORT=3300

CMD cd unipept-api && sed -i "s/port: 3306/port: $DB_PORT/g" config/database.yml && bundle exec rails server -b 0.0.0.0 -e production
CMD cd unipept-api && sed -i "s/port: 5432/port: $DB_PORT/g" config/database.yml && bundle exec rails server -b 0.0.0.0 -e production