fixing docker

Author: madhavajay

.github/workflows/ci.yml

@@ -82,9 +82,19 @@ jobs:
           mkdir -p out
           docker run --rm --read-only \
             --tmpfs /tmp:rw,exec,mode=1777 \
-            -v "${{ github.workspace }}/test_data:/data:ro" \
+            -e BVS_READ_ONLY_DB=1 \
+            -v "${{ github.workspace }}/out:/out" \
+            biosynth:ci \
+            synthetic \
+            --output /out/genotypes/{index}.txt \
+            --count 1 \
+            --seed 42
+
+          docker run --rm --read-only \
+            --tmpfs /tmp:rw,exec,mode=1777 \
+            -e BVS_READ_ONLY_DB=1 \
             -v "${{ github.workspace }}/out:/out" \
             biosynth:ci \
             genotype-to-vcf \
-            --input /data/274939/274939_X_X_GSAv3-DTC_GRCh38-12-06-2025.txt \
+            --input /out/genotypes/0001.txt \
             --output /out/out.vcf

cli/src/commands/synthetic.rs

@@ -71,8 +71,12 @@ pub fn run_synthetic(args: SyntheticArgs) -> Result<()> {
         bail!("Day range must be between 1 and 31");
     }
 
-    let sqlite_path = ensure_reference_db(Some(&args.sqlite), args.force_download)?;
-    let store = StatsStore::connect(&sqlite_path)?;
+    let sqlite_path = resolve_sqlite_path(&args)?;
+    let store = if read_only_db_requested() {
+        StatsStore::connect_read_only(&sqlite_path)?
+    } else {
+        StatsStore::connect(&sqlite_path)?
+    };
     let references = store.all_references(args.limit)?;
     if references.is_empty() {
         bail!(
@@ -123,6 +127,26 @@ pub fn run_synthetic(args: SyntheticArgs) -> Result<()> {
     Ok(())
 }
 
+fn read_only_db_requested() -> bool {
+    match std::env::var("BVS_READ_ONLY_DB") {
+        Ok(value) => matches!(
+            value.to_ascii_lowercase().as_str(),
+            "1" | "true" | "yes" | "on"
+        ),
+        Err(_) => false,
+    }
+}
+
+fn resolve_sqlite_path(args: &SyntheticArgs) -> Result<PathBuf> {
+    if read_only_db_requested() {
+        let baked_in = PathBuf::from("/app/data/genostats.sqlite");
+        if baked_in.exists() {
+            return Ok(baked_in);
+        }
+    }
+    ensure_reference_db(Some(&args.sqlite), args.force_download)
+}
+
 fn write_single_file(
     path: &PathBuf,
     references: &[ReferenceVariant],

test-docker.sh

@@ -2,7 +2,6 @@
 set -eu
 
 IMAGE_TAG="${IMAGE_TAG:-biosynth:ci}"
-INPUT_FILE="${INPUT_FILE:-/data/274939/274939_X_X_GSAv3-DTC_GRCh38-12-06-2025.txt}"
 OUTPUT_FILE="${OUTPUT_FILE:-/out/out.vcf}"
 
 docker build -f docker/Dockerfile -t "${IMAGE_TAG}" .
@@ -11,9 +10,19 @@ mkdir -p out
 
 docker run --rm --read-only \
   --tmpfs /tmp:rw,exec,mode=1777 \
-  -v "$PWD/test_data:/data:ro" \
+  -e BVS_READ_ONLY_DB=1 \
+  -v "$PWD/out:/out" \
+  "${IMAGE_TAG}" \
+  synthetic \
+  --output /out/genotypes/{index}.txt \
+  --count 1 \
+  --seed 42
+
+docker run --rm --read-only \
+  --tmpfs /tmp:rw,exec,mode=1777 \
+  -e BVS_READ_ONLY_DB=1 \
   -v "$PWD/out:/out" \
   "${IMAGE_TAG}" \
   genotype-to-vcf \
-  --input "${INPUT_FILE}" \
+  --input /out/genotypes/0001.txt \
   --output "${OUTPUT_FILE}"