From a4177ba3b1b4f94737e7e4fa4c8bebbca70a4b38 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Thu, 14 Mar 2024 09:43:11 +0100
Subject: [PATCH] Update static database action according to migration to Rust
 and LZ4

---
 .github/workflows/static_database.yml | 25 ++++++++++++++-----------
 scripts/build_database.sh             |  3 +++
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/static_database.yml b/.github/workflows/static_database.yml
index 7d76be0..5218896 100644
--- a/.github/workflows/static_database.yml
+++ b/.github/workflows/static_database.yml
@@ -10,19 +10,22 @@ jobs:
   generate_static_database:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-java@v1
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+      - uses: Swatinem/rust-cache@v2
+        id: cache
         with:
-          java-version: '11'
-          java-package: jdk
-          architecture: x64
+          shared-key: ${{ env.CACHE_KEY }}
+      - run: cd scripts/helper_scripts/unipept-database-rs && cargo fetch
+        if: ${{ !steps.cache.outputs.cache-hit }}
+      - run: ./scripts/build_binaries.sh
       - name: Get current date
         id: date
         run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
       - name: Install required utilities
         run: |
           sudo apt-get update
-          sudo apt-get -y install git maven curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget
+          sudo apt-get -y install git curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget uuid-runtime pigz lz4 parallel
       - name: Download Taxdmp file
         shell: bash
         run: wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
@@ -36,11 +39,11 @@ jobs:
           sqlite3 output.db < workflows/static_database/structure.sql
 
           # Read all generated data into this database
-          zcat output/ec_numbers.tsv.gz | sqlite3 -csv -separator '	' output.db '.import /dev/stdin ec_numbers'
-          zcat output/go_terms.tsv.gz | sqlite3 -csv -separator '	' output.db '.import /dev/stdin go_terms'
-          zcat output/interpro_entries.tsv.gz | sqlite3 -csv -separator '	' output.db '.import /dev/stdin interpro_entries'
-          zcat output/taxons.tsv.gz | sqlite3 -csv -separator '	' output.db '.import /dev/stdin taxons'
-          zcat output/lineages.tsv.gz | sqlite3 -csv -separator '	' output.db '.import /dev/stdin lineages'
+          lz4cat output/ec_numbers.tsv.lz4 | sqlite3 -csv -separator '	' output.db '.import /dev/stdin ec_numbers'
+          lz4cat output/go_terms.tsv.lz4 | sqlite3 -csv -separator '	' output.db '.import /dev/stdin go_terms'
+          lz4cat output/interpro_entries.tsv.lz4 | sqlite3 -csv -separator '	' output.db '.import /dev/stdin interpro_entries'
+          lz4cat output/taxons.tsv.lz4 | sqlite3 -csv -separator '	' output.db '.import /dev/stdin taxons'
+          lz4cat output/lineages.tsv.lz4 | sqlite3 -csv -separator '	' output.db '.import /dev/stdin lineages'
 
           # Create virtual tables
           sqlite3 output.db < workflows/static_database/init_virtual_tables.sql
diff --git a/scripts/build_database.sh b/scripts/build_database.sh
index 08f4015..3cf903e 100755
--- a/scripts/build_database.sh
+++ b/scripts/build_database.sh
@@ -332,7 +332,10 @@ download_taxdmp() {
   # Check if our self-hosted version is available or not using the GitHub API
   LATEST_RELEASE_URL="https://api.github.com/repos/unipept/unipept-database/releases/latest"
   TAXDMP_RELEASE_ASSET_RE="unipept/unipept-database/releases/download/[^/]+/ncbi-taxdmp.zip"
+  # Temporary disable the pipefail check (cause egrep can exit with code 1 if nothing is found).
+  set +eo pipefail
   SELF_HOSTED_URL=$(curl -s "$LATEST_RELEASE_URL" | egrep -o "$TAXDMP_RELEASE_ASSET_RE")
+  set -eo pipefail
 
   if [ "$SELF_HOSTED_URL" ]
   then