support test only;

add test for fileutility;
build docker on ubuntu1804 with binary.

ArchiveSearch/CMakeLists.txt

@@ -9,8 +9,6 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/Release)
 
 link_directories(${CMAKE_BINARY_DIR}/Release ${fcgi_install_dir}/lib)
 
-# set(CMAKE_INSTALL_RPATH "${ORIGIN}/lib")
-
 # code can be moved to other places: might rely libraries in dependentlibs
 add_subdirectory(dependentlibs)
 include_directories(External)
@@ -52,18 +50,12 @@ msbasic_small_static mstoolkit spectrastlib_static
 
 file(READ "${CMAKE_SOURCE_DIR}/version.txt" MY_SPECTROSCAPE_VERSION)
 
-# target_compile_definitions(spectroscape PRIVATE SPECTROSCAPE_VERSION=${MY_SPECTROSCAPE_VERSION})
-add_compile_definitions(SPECTROSCAPE_VERSION="${MY_SPECTROSCAPE_VERSION}")
+target_compile_definitions(spectroscape PRIVATE SPECTROSCAPE_VERSION="${MY_SPECTROSCAPE_VERSION}")
 
 add_dependencies(spectroscape boost ${DPGPU})
 
-#The commandline tool for library search
-#add_executable(LibraryRetrieval	LibSearchEngine.cpp	)
-#target_link_libraries(LibraryRetrieval specarchive)
-
 install(TARGETS spectroscape DESTINATION bin )
-# install(TARGETS    linear  DESTINATION lib OPTIONAL)
-# install(TARGETS  msfileramp msbasic_small linear  DESTINATION lib OPTIONAL)
+
 
 set(CPACK_DEBIAN_PACKAGE_DEPENDS "libopenblas-dev,libgomp1,sqlite")
 set(CPACK_PACKAGE_NAME Spectroscape_CPU)
@@ -79,7 +71,7 @@ set(CPACK_PACKAGE_FILE_NAME ${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION})
 
 set(CPACK_DEBIAN_PACKAGE_MAINTAINER Long WU)
 set(CPACK_OUTPUT_FILE_PREFIX ${CMAKE_SOURCE_DIR}/package)
-set(CPACK_THREADS 0)
+set(CPACK_THREADS 0) # USING MULTICORE.
 SET(CPACK_GENERATOR "ZIP")  #.ZIP
 SET(CPACK_GENERATOR "STGZ" "DEB") #.sh #deb
 SET(CPACK_SOURCE_GENERATOR "TBZ2")

ArchiveSearch/FileUtility.cpp

@@ -1,15 +1,8 @@
-#include "dependentlibs/msbasic/commonfun.h"
-#include "dependentlibs/msbasic/CDebugMode.h"
-#include "../librarymsms/CMzFileReader.h"
-#include "FastCgiInterface.h"
-#include "dependentlibs/spectralIndex/CKMeans.h"
-#include "CSpectralArchive.h"
-#include <thread>
-#include "CTimerSummary.h"
-#include "Util.h"
-// #include <filesystem>
-// namespace fs = std::filesystem;
+#include <algorithm>
+#include <iostream>
+#include <string>
 #include <boost/filesystem.hpp>
+using namespace std;
 namespace fs = boost::filesystem;
 
 std::vector<fs::path> get_mz_file_list(const fs::path& dir_path) {

ArchiveSearch/spectroscapeMain.cpp

@@ -16,6 +16,7 @@
 // namespace fs = std::filesystem;
 #include <csignal>
 #include <atomic>
+#include <unistd.h>
 
 
 #include <boost/filesystem.hpp>
@@ -208,7 +209,7 @@ boost::program_options::variables_map getParam(int argc, char *argv[]) {
             ("maxconnection", po::value<int>()->default_value(10),
              "The port which socket to listen to. Default: port=10; "
              "check /proc/sys/net/core/somaxconn for maximal number of connections allowed on local computer")
-             ("wwwroot", po::value<string>()->default_value("./"),
+             ("wwwroot", po::value<string>()->default_value(""),
              "path of root folder of spectroscape web UI, config this to the SpectralArchiveWeb/arxiv folder. ")
             ("indexstring", po::value<string>()->default_value("IVF100,PQ8"),
              "the string for index_factory() to build index")
@@ -233,6 +234,8 @@ boost::program_options::variables_map getParam(int argc, char *argv[]) {
     po::positional_options_description p;
     p.add("inputfile", -1);
     po::store(po::command_line_parser(argc, argv).options(cmdline_options).positional(p).run(), vm);
+    // const int PATH_MAX = 4096;
+
 
     // po::store(po::command_line_parser(argc, argv).options(visible).run(), visiable_vm);
     bool run = vm["run"].as<bool>();
@@ -505,6 +508,20 @@ int main(int argc, char *argv[]) {
             int initcenoption = vm.at("centroidinit").as<int>();
             string indexstrs = vm.at("indexstrs").as<string>();
             string wwwroot = vm.at("wwwroot").as<string>();
+            char buffer[PATH_MAX + 1];
+            ssize_t len = readlink("/proc/self/exe",buffer,PATH_MAX);
+
+            if(len!=-1){
+                buffer[len] = '\0';
+                // set_env_var("SPECTROSCAPE_PATH", path);
+            }
+            string path = fs::path(buffer).parent_path().string();
+            cout << "------------------------------------The path is " << path << endl;
+            if(wwwroot == ""){
+                wwwroot = (fs::path(buffer).parent_path().parent_path() / "www").string();
+                // set the path back to vm
+                cout << "The wwwroot is " << wwwroot << endl;
+            }
             string indexshuffleseeds = vm.at("indexshuffleseeds").as<string>();
             string gpuidx = vm.at("gpuidx").as<string>();
             int tolerance = vm["tolerance"].as<int>();

CMakeLists.txt

@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.20)
 project(mytool LANGUAGES CXX)
 
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -std=c++11 -fpermissive -fopenmp  -fPIC -Wreturn-type  -Werror=return-type ")
+# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -std=c++11 -fpermissive -fopenmp  -fPIC -Wreturn-type  -Werror=return-type ")
 
 
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/Release)

compile.bash

@@ -9,6 +9,7 @@ show_help() {
     echo "  -g, --gpu           compile GPU version, otherwise, CPU version; Default to CPU."
     echo "  -b, --build-type    compile release version, otherwise, debug version, Default to release. "
     echo "  -c, --cores         number of cores to use for compilation. Default to nproc / 16 + 1"
+    echo "  -t, --test-only     only compile and run tests" 
     echo "  -h, --help          display this help and exit"
     echo ""
     echo "Examples:"
@@ -66,6 +67,11 @@ while [[ $# -gt 0 ]]; do
       shift # past argument
       shift # past value
       ;;
+    -t|--test-only)
+      test_only="TRUE"
+      echo "test only"
+      shift # past argument
+      ;;
     -c|--cores)
       cores="$2"
       # limit core number to 1 to 128
@@ -136,6 +142,14 @@ cmake ${cmake_build_options} ..
 # cmake  --graphviz=foo.dot ..
 # cmake ..
 
+# if TEST_ONLY is set, only compile msmstest
+if [ ${test_only} = "TRUE" ]; then
+    cmake  --build ../${releasePath}  --target msmstest -- -j $cores
+    ctest --verbose
+    echo "TEST ONLY RUN FINISHED."
+    exit 0
+fi
+
 cmake  --build ../${releasePath}  --target spectroscape msmstest using_all_cpu_cores -- -j $cores
 
 # run tests added into CMakeLists.txt file with add_test(Name XXX Command YYY)

docker/ubuntu1804bin/Dockerfile

@@ -0,0 +1,9 @@
+# syntax=docker/dockerfile:1
+FROM ubuntu:18.04
+
+# install app dependencies
+RUN apt update && apt install -y wget 
+RUN wget https://github.com/wulongict/SpectralArchive/releases/download/v1.2.0/Spectroscape_CPU-1.2.0.deb
+RUN apt install -y ./Spectroscape_CPU-1.2.0.deb
+
+

docker/ubuntu1804bin/create_docker_and_run.bash

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# create the docker
+docker build --no-cache -t spectroscape-ubuntu1804bin .
+
+# docker run -it spectroscape-ubuntu2004:latest  gcc --version 
+# run spectroscape
+docker run -it   spectroscape-ubuntu1804bin:latest spectroscape 
+output=$?
+status="compiled successfully;"
+if [ $output -eq 0 ]; then
+    echo "spectroscape run successfully"
+    # run the docker with bash
+    echo docker run -it --rm spectroscape-ubuntu1804bin:latest bash
+else
+    status="compiled failed;"
+    echo "spectroscape run failed"
+    echo `date` `pwd` $status tested by Long > ../log.txt
+fi
+
+
+
+

scripts/start_service.bash

@@ -2,6 +2,6 @@
 
 
 archive_path="$HOME/data/spectroscape/spectral_archives_latest"
-bin_path="$HOME/code/SpectralArchive/build/bin/spectroscape"
+bin_path=`which spectroscape`
 wwwroot_path="`dirname $bin_path`/../www"
-cd $archive_path && spawn-fcgi -p 8710 -n -- $bin_path --run --wwwroot $wwwroot_path
+cd $archive_path && spawn-fcgi -p 8710 -n -- $bin_path --run 

tests/CMakeLists.txt

@@ -3,7 +3,7 @@ project(tests)
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -fpermissive -fopenmp  -fPIC -Wreturn-type  -Werror=return-type ")
 
 include_directories(../External/gtest-1.7.0/include ../librarymsms)
-add_executable(msmstest msmstest.cpp)
+add_executable(msmstest msmstest.cpp  ../ArchiveSearch/FileUtility.cpp)
 target_link_libraries(msmstest gtest_main gtest msbasic_small  msfileramp_static)
 
 add_executable(using_all_cpu_cores multiple-threads-usage.cpp

tests/msmstest.cpp

@@ -112,10 +112,25 @@ TEST(FILE_SEARCH, SPEED_TEST){
         cin >> filename;
     }
 
+}
 
-
-
+#include <boost/filesystem.hpp>
+namespace fs = boost::filesystem;
+#include "../ArchiveSearch/FileUtility.h"
+
+TEST(FILE_SEARCH, FILE_SEARCH){
+    // fs::path dir = "../tests/data";
+    fs::path dir = "../tests/data/fileutility";
+    vector<string> ext_list = {".mzxml", ".mzml", ".tsv"};
+    vector<fs::path> file_list = get_file_list(dir, ext_list);
+    cout << "file list size " << file_list.size() << endl;
+    for(auto file: file_list){
+        cout << file.string() << endl;
+    }
+    ASSERT_EQ(2, file_list.size());
 }
 
+// create test for function in FileUtility.cpp
+