fix parsing empty config JSON & regression test

Author: mlin

src/genomicsqlite.cc

@@ -84,21 +84,24 @@ class ConfigParser {
             throw SQLite::Exception("GenomicSQLite::ConfigParser()::sqlite3_open_v2()", rc);
         }
 
-        // merge config_json into defaults
-        if ((rc = sqlite3_prepare_v2(db_, "SELECT json_patch(?,?)", -1, &patch_, nullptr)) !=
-            SQLITE_OK)
-            throw SQLite::Exception(db_, rc);
-        if ((rc = sqlite3_bind_text(patch_, 1, GenomicSQLiteDefaultConfigJSON().c_str(), -1,
-                                    SQLITE_TRANSIENT)) != SQLITE_OK)
-            throw SQLite::Exception(db_, rc);
-        if ((rc = sqlite3_bind_text(patch_, 2, config_json.c_str(), -1, SQLITE_TRANSIENT)) !=
-            SQLITE_OK)
-            throw SQLite::Exception(db_, rc);
-        const char *merged_config_json = nullptr;
-        if ((rc = sqlite3_step(patch_)) != SQLITE_ROW ||
-            !(merged_config_json = (const char *)sqlite3_column_text(patch_, 0)) ||
-            merged_config_json[0] != '{') {
-            throw SQLite::Exception("error parsing config JSON", rc);
+        string default_json = GenomicSQLiteDefaultConfigJSON();
+        const char *merged_config_json = default_json.c_str();
+        if (config_json.size() > 2) { // "{}"
+            // merge config_json into defaults
+            if ((rc = sqlite3_prepare_v2(db_, "SELECT json_patch(?,?)", -1, &patch_, nullptr)) !=
+                SQLITE_OK)
+                throw SQLite::Exception(db_, rc);
+            if ((rc = sqlite3_bind_text(patch_, 1, default_json.c_str(), -1, SQLITE_TRANSIENT)) !=
+                SQLITE_OK)
+                throw SQLite::Exception(db_, rc);
+            if ((rc = sqlite3_bind_text(patch_, 2, config_json.c_str(), -1, SQLITE_TRANSIENT)) !=
+                SQLITE_OK)
+                throw SQLite::Exception(db_, rc);
+            if ((rc = sqlite3_step(patch_)) != SQLITE_ROW ||
+                !(merged_config_json = (const char *)sqlite3_column_text(patch_, 0)) ||
+                merged_config_json[0] != '{') {
+                throw SQLite::Exception("error parsing config JSON", rc);
+            }
         }
 
         if ((rc = sqlite3_prepare_v2(db_, "SELECT json_extract(?,?)", -1, &extract_, nullptr)) !=

test/genomicsqlite_big_tests.wdl

@@ -42,7 +42,7 @@ task build {
 
         apt-get -qq update
         DEBIAN_FRONTEND=noninteractive apt-get -qq install -y \
-            zip pigz wget build-essential git-core \
+            zip pigz wget build-essential git-core sqlite3 \
             cmake libsqlite3-dev libzstd-dev \
             python3-pip maven cargo \
             libhts-dev samtools tabix

test/test_bam.py

@@ -16,6 +16,19 @@ def sam_into_sqlite(infilename, outfilename, *options):
         check=True,
     )
     print(outfilename)
+    # test CLI
+    cmd = (
+        "python3",
+        os.path.join(HERE, "../bindings/python/genomicsqlite/__init__.py"),
+        outfilename,
+        "-readonly",
+        "SELECT * from sqlite_master",
+    )
+    print(" ".join(cmd))
+    subprocess.run(
+        cmd,
+        check=True,
+    )
 
 
 def test_bam(tmp_path):