build.sh

#!/usr/bin/env bash

# Script to create the database from the schema .sql files and identify any
# update .sql files that haven't been run. Also generate documentation from
# inline comments in the schema.

# Some code borrowed from Stefan Buck's gist file at:
# https://gist.github.com/stefanbuck/ce788fee19ab6eb0b4447a85fc99f447

# Author: Karl Levik

set -e
source bin/functions.sh

function drop_db {
  echo "Dropping + creating build database"
  mariadb --defaults-file=.my.cnf -e "DROP DATABASE IF EXISTS $1; CREATE DATABASE $1; SET GLOBAL log_bin_trust_function_creators=ON;"
}

function exec_schema {
  mariadb --defaults-file=.my.cnf -D $1 < schemas/ispyb/tables.sql
  mariadb --defaults-file=.my.cnf -D $1 < schemas/ispyb/lookups.sql
  mariadb --defaults-file=.my.cnf -D $1 < schemas/ispyb/data.sql
  mariadb --defaults-file=.my.cnf -D $1 < schemas/ispyb/routines.sql
}

function exec_grants {
  mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_acquisition.sql
  mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_import.sql
  mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_processing.sql
  mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_ro_nopii.sql
  mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_scripts_processing.sql
  mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_touchscreen.sql
  mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_web.sql
  mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_web_verify_tests.sql
  mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_ssx_writer.sql
}

function exec_missed_updates {
  arr=$(bin/missed_updates.sh)

  if [ -n "$arr" ]; then
    echo "Running schemas/ispyb/updates/*.sql files that haven't yet been run:"
    for sql_file in ${arr[@]}; do
      echo "$sql_file"
      mariadb --defaults-file=.my.cnf -D ${1} < "schemas/ispyb/updates/${sql_file}"
    done
  else
    echo "No new schemas/ispyb/updates/*.sql files."
  fi
}

function generate_docs {
  # Generate table and sproc documentation
  cd bin
  ./db_procs_to_rst.sh ${1} > /tmp/list_of_procs.rst
  html_tmp=$(mktemp /tmp/procs.XXXXXX.tmp.html)
  pandoc --self-contained --metadata title:"List of procedures" -c ../docs/list.css -o ${html_tmp} /tmp/list_of_procs.rst
  awk -v RS='</tr>' -v FS='</td>' -v ORS='</tr>' -v OFS='</td>' '{gsub(", ", "<br>\n", $0); gsub(", ", "<br>\n", $1); printf("%s", $0)}' ${html_tmp} > /tmp/list_of_procs.html
  rm ${html_tmp}
  ./db_tables_to_rst.sh ${1} > /tmp/list_of_tables_and_columns.rst
  pandoc --self-contained --metadata title:"List of tables and columns" -c ../docs/list.css -o /tmp/list_of_tables_and_columns.html /tmp/list_of_tables_and_columns.rst
  echo "HTML documentation written to files in /tmp/"
  cd ..
}

function usage_help {
  echo "usage: build.sh [COMMANDS]"
  echo
  echo "List of commands"
  echo "nodrop      don't drop and recreate the build database"
  echo "noschema    don't create the schema from the schema SQL files"
  echo "nogrants    don't execute the grant SQL files"
  echo "noupdates   don't execute any outstanding SQL update files"
  echo "nodocs      don't build the documentation"
  echo "updatesonly only execute outstanding SQL update files (mutually exclusive with other commands)"
  echo "docsonly    only build the documentation (mutually exclusive with other commands)"
  echo
  echo "By default without any commands specified the script will:"
  echo "- drop and re-create the build database"
  echo "- execute the schema create SQL files"
  echo "- execute the grant statements and any non-recorded SQL update files"
  echo "- generate the documentation"
}


# Set default database name
if [ -z "${DB}" ]; then
  DB="ispyb_build"
fi

# Handle command-line arguments
DROP=true; SCHEMA=true; GRANTS=true; UPDATES=true; DOCS=true;
for arg in $@
do
   case $arg in
        nodrop) DROP=false;;
        noschema) SCHEMA=false;;
        nogrants) GRANTS=false;;
        noupdates) UPDATES=false;;
        nodocs) DOCS=false;;
        updatesonly)
          exec_missed_updates "$DB"
          exit 0;;
        docsonly)
          generate_docs "$DB"
          exit 0;;
        help)
          usage_help
          exit 0;;
        *)
          echo "Unrecognised command '$arg'"
          usage_help
          exit 1;;
    esac
done

if [ $DROP = true ]; then
  drop_db "$DB"
fi
if [ $SCHEMA = true ]; then
  exec_schema "$DB"
fi
if [ $UPDATES = true ]; then
  exec_missed_updates "$DB"
fi
if [ $GRANTS = true ]; then
  exec_grants "$DB"
fi

if [ $DOCS = true ]; then
  # Attempt generating docs only if pandoc is installed, otherwise output warning
  if ! hash pandoc 2>/dev/null; then
    echo "'pandoc' was not found in PATH: skipping documentation generation"
  elif [ -d "bin" ]; then
    generate_docs "$DB"
  fi
fi