inline build database script

unipept · Feb 17, 2021 · dd047aa · dd047aa
1 parent dab72b8
commit dd047aa
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Showing 2 changed files with 13 additions and 13 deletions.
diff --git a/.github/workflows/static_database.yml b/.github/workflows/static_database.yml
@@ -30,7 +30,19 @@ jobs:
         run: ./run.sh static-database
       - name: Build SQLite database from generated files
         shell: bash
-        run: ./workflows/static_database/build_database.sh
+        run: |
+          # Initialize the database
+          sqlite3 output.db < workflows/static_database/structure.sql 
+          
+          # Read all generated data into this database
+          zcat data/tables/ec_numbers.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin ec_numbers'
+          zcat data/tables/go_terms.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin go_terms'
+          zcat data/tables/interpro_entries.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin interpro_entries'
+          zcat data/tables/taxons.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin taxons'
+          zcat data/tables/lineages.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin lineages'
+          
+          # Compress the database before uploading it to a Github release
+          zip output.zip output.db
       - name: Update database versioning
         shell: bash
         run: |

diff --git a/workflows/static_database/build_database.sh b/workflows/static_database/build_database.sh