fix C genomicsqlite_open and add smoke test

mlin · mlin · commit cac2de9f11b1 · 2020-08-06T01:05:42.000-10:00
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -83,7 +83,9 @@ jobs:
         /usr/local/bin/pip3 install $PIP_DEPS
     - name: build
       run: |
-        CFLAGS="-I$(brew --prefix)/include -I$(brew --prefix)/opt/sqlite/include" CXXFLAGS=-I$(brew --prefix)/include LDFLAGS=-L$(brew --prefix)/lib \
+        CFLAGS="-I$(brew --prefix)/include -I$(brew --prefix)/opt/sqlite/include -march=sandybridge" \
+        CXXFLAGS="-I$(brew --prefix)/include -march=sandybridge" \
+        LDFLAGS="-L$(brew --prefix)/lib -L$(brew --prefix)/opt/sqlite/lib" \
           cmake -DCMAKE_BUILD_TYPE=Release \
                 -DCMAKE_PREFIX_PATH=$(brew --prefix)/opt/sqlite \
                 -B build .
@@ -95,6 +97,7 @@ jobs:
         export PREFIX=$(brew --prefix)
         export PATH=${PREFIX}/opt/python@3.8/bin:${PREFIX}/opt/sqlite/bin:$PATH
         cd build
+        otool -L test/capi_smoke_test
         ctest -V
     - name: prepare artifacts
       run: cp build/libgenomicsqlite.dylib include/genomicsqlite.h .
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -48,13 +48,13 @@ else()
     target_link_libraries(genomicsqlite PRIVATE libsqlite3.so.0 SQLiteCpp zstd)
 endif()
 
-
-add_subdirectory(loaders)
-
 if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
+    add_subdirectory(loaders)
+    add_subdirectory(test)
     include(CTest)
     enable_testing()
     set(GENOMICSQLITE_TEST_ENV env PYTHONPATH=${CMAKE_CURRENT_SOURCE_DIR}/bindings/python:${PYTHONPATH} LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}:${LD_LIBRARY_PATH} GENOMICSQLITE_SYSTEM_LIBRARY=1)
-    add_test(NAME smoketest COMMAND ${GENOMICSQLITE_TEST_ENV} python3 ${CMAKE_CURRENT_SOURCE_DIR}/test/genomicsqlite_smoke_test.py)
+    add_test(NAME smoke_test COMMAND ${GENOMICSQLITE_TEST_ENV} python3 ${CMAKE_CURRENT_SOURCE_DIR}/test/genomicsqlite_smoke_test.py)
+    add_test(NAME capi_smoke_test COMMAND ${GENOMICSQLITE_TEST_ENV} ${CMAKE_BINARY_DIR}/test/capi_smoke_test)
     add_test(NAME pytest COMMAND ${GENOMICSQLITE_TEST_ENV} python3 -m pytest -xv -n 4 --tb=short ${CMAKE_CURRENT_SOURCE_DIR}/test)
 endif()
diff --git a/bindings/python/release.sh b/bindings/python/release.sh
@@ -9,13 +9,13 @@ if grep dirty <(git describe --always --dirty); then
     >&2 echo "Cannot release dirty working tree"
     exit 1
 fi
-if [[ ! -f genomicsqlite/libgenomicsqlite.so ]]; then
-    >&2 echo "Download the portable libgenomicsqlite.so to ${HERE}/genomicsqlite/"
+if [[ ! -f genomicsqlite/libgenomicsqlite.so ]] || [[ ! -f genomicsqlite/libgenomicsqlite.dylib ]]; then
+    >&2 echo "Download the portable libgenomicsqlite.{so,dylib} to ${HERE}/genomicsqlite/"
     exit 1
 fi
 function cleanup {
-    # force us to put it there each time; ensures a stale version can't be left behind
-    rm -f genomicsqlite/libgenomicsqlite.so
+    # force us to put libs on each attempt; ensures a stale version can't be left behind
+    rm -f genomicsqlite/libgenomicsqlite.*
 }
 trap cleanup EXIT
 
diff --git a/include/genomicsqlite.h b/include/genomicsqlite.h
@@ -1,4 +1,6 @@
+#ifndef SQLITE3EXT_H
 #include <sqlite3.h>
+#endif
 
 /*
  * C bindings
diff --git a/src/genomicsqlite.cc b/src/genomicsqlite.cc
@@ -23,18 +23,7 @@ using namespace std;
  * connection & tuning helpers
  **************************************************************************************************/
 
-std::string GenomicSQLiteVersion() {
-    // The newest SQLite feature currently required is "Generated Columns"
-    const int MIN_SQLITE_VERSION_NUMBER = 3031000;
-    const string MIN_SQLITE_VERSION = "3.31.0";
-    if (sqlite3_libversion_number() < MIN_SQLITE_VERSION_NUMBER) {
-        string version_msg = "SQLite library version (" + string(sqlite3_libversion()) +
-                             ") is older than required by the GenomicSQLite extension (" +
-                             MIN_SQLITE_VERSION + ")";
-        throw std::runtime_error(version_msg);
-    }
-    return string(GIT_REVISION);
-}
+std::string GenomicSQLiteVersion() { return string(GIT_REVISION); }
 
 // boilerplate for C bindings to C++ functions
 #define C_WRAPPER(call)                                                                            \
@@ -268,50 +257,37 @@ static void sqlfn_genomicsqlite_tuning_sql(sqlite3_context *ctx, int argc, sqlit
     SQL_WRAPPER(GenomicSQLiteTuningSQL(config_json, schema))
 }
 
-bool _ext_loaded = false;
+static void ensure_ext_loaded() {
+    // for C/C++ GenomicSQLiteOpen
+    static bool ext_loaded = false;
+    if (!ext_loaded) {
+        SQLite::Database db(":memory:", SQLite::OPEN_READWRITE | SQLite::OPEN_CREATE);
+        db.loadExtension("libgenomicsqlite", nullptr);
+        ext_loaded = true;
+    }
+}
+
 int GenomicSQLiteOpen(const string &dbfile, sqlite3 **ppDb, string &errmsg_out, int flags,
                       const string &config_json) noexcept {
-    // ensure extension is registered
-    int ret;
-    char *zErrmsg = nullptr;
-    *ppDb = nullptr;
-    if (!_ext_loaded) {
-        ret =
-            sqlite3_open_v2(":memory:", ppDb, SQLITE_OPEN_READWRITE | SQLITE_OPEN_CREATE, nullptr);
-        if (ret != SQLITE_OK) {
-            errmsg_out = sqlite3_errstr(ret);
-            return ret;
-        }
-        ret = sqlite3_load_extension(*ppDb, "libgenomicsqlite", nullptr, &zErrmsg);
-        if (ret != SQLITE_OK) {
-            errmsg_out = "failed loading libgenomicsqlite shared library: ";
-            if (zErrmsg) {
-                errmsg_out += zErrmsg;
-                sqlite3_free(zErrmsg);
-            } else {
-                errmsg_out += sqlite3_errmsg(*ppDb);
-            }
-            sqlite3_close_v2(*ppDb);
-            *ppDb = nullptr;
-            return ret;
-        }
-        ret = sqlite3_close_v2(*ppDb);
-        *ppDb = nullptr;
-        if (ret != SQLITE_OK) {
-            errmsg_out = sqlite3_errstr(ret);
-            return ret;
-        }
-        _ext_loaded = true;
+    try {
+        ensure_ext_loaded();
+    } catch (SQLite::Exception &exn) {
+        errmsg_out = "failed loading libgenomicsqlite shared library: " + string(exn.what());
+        return exn.getErrorCode();
+    } catch (std::exception &exn) {
+        errmsg_out = "failed loading libgenomicsqlite shared library: " + string(exn.what());
+        return SQLITE_ERROR;
     }
 
     // open as requested
     try {
-        ret = sqlite3_open_v2(GenomicSQLiteURI(dbfile, config_json).c_str(), ppDb,
-                              SQLITE_OPEN_URI | flags, nullptr);
+        int ret = sqlite3_open_v2(GenomicSQLiteURI(dbfile, config_json).c_str(), ppDb,
+                                  SQLITE_OPEN_URI | flags, nullptr);
         if (ret != SQLITE_OK) {
             errmsg_out = sqlite3_errstr(ret);
             return ret;
         }
+        char *zErrmsg = nullptr;
         ret = sqlite3_exec(*ppDb, GenomicSQLiteTuningSQL(config_json).c_str(), nullptr, nullptr,
                            &zErrmsg);
         if (ret != SQLITE_OK) {
@@ -327,8 +303,10 @@ int GenomicSQLiteOpen(const string &dbfile, sqlite3 **ppDb, string &errmsg_out,
         }
         return SQLITE_OK;
     } catch (SQLite::Exception &exn) {
+        errmsg_out = exn.what();
         return exn.getErrorCode();
     } catch (std::exception &exn) {
+        errmsg_out = exn.what();
         return SQLITE_ERROR;
     }
 }
@@ -347,18 +325,9 @@ extern "C" int genomicsqlite_open(const char *filename, sqlite3 **ppDb, char **p
 
 unique_ptr<SQLite::Database> GenomicSQLiteOpen(const string &dbfile, int flags,
                                                const string &config_json) {
-    unique_ptr<SQLite::Database> db;
-    if (!_ext_loaded) {
-        db.reset(new SQLite::Database(":memory:", SQLite::OPEN_READWRITE | SQLite::OPEN_CREATE));
-        try {
-            db->loadExtension("libgenomicsqlite", nullptr);
-        } catch (std::exception &exn) {
-            throw std::runtime_error("failed loading libgenomicsqlite shared library: " +
-                                     string(exn.what()));
-        }
-        _ext_loaded = true;
-    }
-    db.reset(new SQLite::Database(GenomicSQLiteURI(dbfile, config_json), SQLITE_OPEN_URI | flags));
+    ensure_ext_loaded();
+    unique_ptr<SQLite::Database> db(
+        new SQLite::Database(GenomicSQLiteURI(dbfile, config_json), SQLITE_OPEN_URI | flags));
     db->exec(GenomicSQLiteTuningSQL(config_json));
     return db;
 }
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_executable(capi_smoke_test capi_smoke_test.c)
+target_link_libraries(capi_smoke_test PRIVATE sqlite3 genomicsqlite)
diff --git a/test/capi_smoke_test.c b/test/capi_smoke_test.c
@@ -0,0 +1,73 @@
+#include "genomicsqlite.h"
+#include <errno.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+int sql_callback(void *ctx, int nCol, char **values, char **names) {
+    fprintf(stderr, "sql_callback(%d,\"%s\")\n", nCol, values[0] ? values[0] : "");
+    char *ans = (char *)ctx;
+    if (!ans || !nCol || !values[0]) {
+        return -1;
+    }
+    strcpy(ans, values[0]);
+    return 0;
+}
+
+int main(int argc, char **argv) {
+    fprintf(stderr, "tempnam()\n");
+    char *dbfilename = tempnam("/tmp", "gsqlt");
+    if (!dbfilename) {
+        fprintf(stderr, "tempnam -> %d\n", errno);
+        return 1;
+    }
+    sqlite3 *pDb = 0;
+    char *zErrMsg = 0;
+    fprintf(stderr, "genomicsqlite_open()\n");
+    int rc = genomicsqlite_open(dbfilename, &pDb, &zErrMsg,
+                                SQLITE_OPEN_CREATE | SQLITE_OPEN_READWRITE, "{}");
+    if (rc != SQLITE_OK) {
+        fprintf(stderr, "genomicsqlite_open -> %d // %s\n", rc,
+                zErrMsg ? zErrMsg : sqlite3_errstr(rc));
+        return 1;
+    }
+
+    fprintf(stderr, "genomicsqlite_version()\n");
+    char *version1 = genomicsqlite_version();
+    printf("%s\n", version1);
+    fprintf(stderr, "sqlite3_free()\n");
+    sqlite3_free(version1);
+
+    char version[1024];
+    version[0] = 0;
+    fprintf(stderr, "sqlite3_exec()\n");
+    rc = sqlite3_exec(pDb, "SELECT genomicsqlite_version()", &sql_callback, version, &zErrMsg);
+    if (rc != SQLITE_OK) {
+        fprintf(stderr, "sqlite3_exec(\"SELECT genomicsqlite_version()\") -> %d // %s\n", rc,
+                zErrMsg ? zErrMsg : sqlite3_errstr(rc));
+        return 1;
+    }
+    if (!version[0]) {
+        fprintf(stderr, "no result from sqlite3_exec(\"SELECT genomicsqlite_version()\")\n");
+        return 1;
+    }
+    printf("%s\n", version);
+
+    fprintf(stderr, "create_genomic_range_index_sql()\n");
+    char *sql = create_genomic_range_index_sql("test", "rid", "beg", "end", -1);
+    if (!sql) {
+        fprintf(stderr, "create_genomic_range_index_sql -> null\n");
+        return 1;
+    }
+    printf("%s\n", sql);
+    fprintf(stderr, "sqlite3_free()\n");
+    sqlite3_free(sql);
+
+    fprintf(stderr, "sqlite3_close()\n");
+    rc = sqlite3_close(pDb);
+    if (rc != SQLITE_OK) {
+        fprintf(stderr, "sqlite3_close -> %d %s\n", rc, sqlite3_errstr(rc));
+        return 1;
+    }
+    return 0;
+}

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+add_executable(capi_smoke_test capi_smoke_test.c)`
	`2`	`+target_link_libraries(capi_smoke_test PRIVATE sqlite3 genomicsqlite)`