[TEST] do not allow shared mem metagenome search

eaasna · Oct 6, 2023 · fa3e939 · fa3e939
1 parent 55caac7
commit fa3e939
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Showing 3 changed files with 29 additions and 4 deletions.
diff --git a/include/valik/search/search_local.hpp b/include/valik/search/search_local.hpp
@@ -78,18 +78,16 @@ bool search_local(search_arguments const & arguments, search_time_statistics & t
         }
     }
 
-    std::cout << "Launching stellar search on a shared memory machine...\n";
-    stellar::stellar_runtime input_databases_time{};
-
     auto bin_paths = index.bin_path();
     if (bin_paths.size() > 1 || bin_paths[0].size() > 1)
         throw std::runtime_error("Multiple reference files can not be searched in shared memory mode. "
                                  "Add --distribute argument to launch multiple distributed instances of DREAM-Stellar search.");
 
+    stellar::stellar_runtime input_databases_time{};
     bool const databasesSuccess = input_databases_time.measure_time([&]()
     {
         std::cout << "Launching stellar search on a shared memory machine...\n";
-        return stellar::_importAllSequences(bin_paths[0].c_str(), "database", databases, databaseIDs, refLen, std::cout, std::cerr);
+        return stellar::_importAllSequences(bin_paths[0][0].c_str(), "database", databases, databaseIDs, refLen, std::cout, std::cerr);
     });
     if (!databasesSuccess)
         return false;

diff --git a/test/cli/CMakeLists.txt b/test/cli/CMakeLists.txt
@@ -16,6 +16,7 @@ target_use_datasources (valik_options_test FILES bin_2.fasta)
 target_use_datasources (valik_options_test FILES bin_3.fasta)
 target_use_datasources (valik_options_test FILES query.fq)
 target_use_datasources (valik_options_test FILES various_chromosome_lengths.fasta)
+target_use_datasources (valik_options_test FILES 150overlap4bins.txt)
 
 add_cli_test (valik_test.cpp)
 target_use_datasources (valik_test FILES bin_0.fasta)

diff --git a/test/cli/valik_options_test.cpp b/test/cli/valik_options_test.cpp
@@ -291,3 +291,29 @@ TEST_F(argparse_search, pattern_window)
     EXPECT_EQ(result.out, std::string{});
     EXPECT_EQ(result.err, std::string{"[Error] The minimiser window cannot be bigger than the pattern.\n"});
 }
+
+TEST_F(argparse_search, not_dist_no_meta)
+{
+    cli_test_result const result = execute_app("valik", "search",
+                                                         "--query ", data("query.fq"),
+                                                         "--index ", data("8bins19window.ibf"),
+                                                         "--output search.gff",
+                                                         "--pattern 100");
+    EXPECT_NE(result.exit_code, 0);
+    EXPECT_EQ(result.out, std::string{});
+    EXPECT_EQ(result.err, std::string{"[Error] Provide --ref-meta to search a single genome or launch a --distribute run to search multiple reference files instead.\n"});
+}
+
+TEST_F(argparse_search, shared_mem_metagenome)
+{
+    cli_test_result const result = execute_app("valik", "search",
+                                                         "--query ", data("query.fq"),
+                                                         "--index ", data("8bins19window.ibf"),
+                                                         "--output search.gff",
+                                                         "--ref-meta ", data("150overlap4bins.txt"),
+                                                         "--pattern 100");
+    EXPECT_NE(result.exit_code, 0);
+    EXPECT_EQ(result.out, std::string{});
+    EXPECT_EQ(result.err, std::string{"[Error] Multiple reference files can not be searched in shared memory mode. "
+                                      "Add --distribute argument to launch multiple distributed instances of DREAM-Stellar search.\n"});
+}