strike unnecessary gri_refseq_ddl

Author: mlin

.github/workflows/build.yml

@@ -43,7 +43,9 @@ jobs:
     - uses: actions/upload-artifact@v2
       with:
         name: GenomicSQLite-Linux-x86_64-so-${{ env.GIT_REVISION }}
-        path: build/libgenomicsqlite.so
+        path: |
+          build/libgenomicsqlite.so
+          include/genomicsqlite.h
 
   lint:
     runs-on: ubuntu-20.04

bindings/python/genomicsqlite.py

@@ -23,6 +23,7 @@ def _execute1(conn, sql, params=None):
     """
     conn.execute(sql,params) and return row 1 column 1
     """
+    assert isinstance(conn, sqlite3.Connection)
     return next(conn.execute(sql, params) if params else conn.execute(sql))[0]
 
 
@@ -182,7 +183,14 @@ def _cli():
             file=sys.stderr,
         )
         sys.exit(1)
-    uri = _execute1(_MEMCONN, "SELECT genomicsqlite_uri(?)", (sys.argv[1],))
+
+    dbfilename = sys.argv[1]
+    if os.path.islink(dbfilename):
+        target = os.path.realpath(dbfilename)
+        print(f"[warning] following symlink {dbfilename} -> {target}")
+        dbfilename = target
+
+    uri = _execute1(_MEMCONN, "SELECT genomicsqlite_uri(?)", (dbfilename,))
     tuning_sql = _execute1(_MEMCONN, "SELECT genomicsqlite_tuning_sql()")
 
     if "-readonly" in sys.argv:

src/genomicsqlite.cc

@@ -485,8 +485,7 @@ string CreateGenomicRangeIndexSQL(const string &schema_table, const string &rid,
     }
     size_t p;
     ostringstream out;
-    out << gri_refseq_ddl(schema);
-    out << ";\nALTER TABLE " << schema_table << " ADD COLUMN _gri_rid INTEGER AS (" << rid
+    out << "ALTER TABLE " << schema_table << " ADD COLUMN _gri_rid INTEGER AS (" << rid
         << ") VIRTUAL";
     out << ";\nALTER TABLE " << schema_table << " ADD COLUMN _gri_beg INTEGER AS (" << beg
         << ") VIRTUAL";