From f251a889dd9458f15e88d80dfdf9736dbec332fd Mon Sep 17 00:00:00 2001
From: Long <lwuai@connect.ust.hk>
Date: Fri, 31 May 2024 13:34:30 -0500
Subject: [PATCH] www root set. atomic stage number added.

---
 ArchiveSearch/CSpectralArchive.cpp | 5 ++++-
 ArchiveSearch/CSpectralArchive.h   | 3 +++
 ArchiveSearch/spectroscapeMain.cpp | 6 ++++--
 scripts/start_service.bash         | 7 +++++++
 4 files changed, 18 insertions(+), 3 deletions(-)
 create mode 100755 scripts/start_service.bash

diff --git a/ArchiveSearch/CSpectralArchive.cpp b/ArchiveSearch/CSpectralArchive.cpp
index ed0325e..d6931e9 100644
--- a/ArchiveSearch/CSpectralArchive.cpp
+++ b/ArchiveSearch/CSpectralArchive.cpp
@@ -188,7 +188,8 @@ CSpectralArchive::CSpectralArchive(string mzXMLList, string pepxml, string index
                                    bool usegpu, bool rebuildsqldb, int seedpvalue, const int topPeakNum,
                                    bool createfilenameBlackList, bool saveBackgroundScore, bool verbose,
                                    string archivename, string indexshuffleseeds, string gpuidx) : PeakNumPerSpec(
-        topPeakNum) {
+        topPeakNum), m_stage(STAGE_INIT) {
+            
             m_savebackgroundscore = saveBackgroundScore;
     // checking the parameters.
     if(mzXMLList.empty()){
@@ -311,6 +312,7 @@ void CSpectralArchive::createMzFileObject() {
 // get number of indices to be created, using indexstr, split by ';'
 // create multiIndices object. each corresponding to a file in multiIndices folder. 
 void CSpectralArchive::createIndices(bool myOwnIndex, shared_ptr<CPQParam> option, string &indexstrings, string indexshuffleseeds) {
+    m_stage = STAGE_TRAIN;
     int cnts = count(indexstrings.begin(), indexstrings.end(), ';') + 1;
     if (cnts > 6 and cnts < 1) {
         cout << "Error: invalid cnts " << cnts << endl;
@@ -332,6 +334,7 @@ CSpectralArchive::~CSpectralArchive() {}
 
 void CSpectralArchive::update(string new_experimental_data, string new_search_result, string new_search_result_list,
                               string new_experimental_datalist) {
+    m_stage = STAGE_UPDATE;
     updateIndex(m_verbose);
     bool newFilesAdded = false;
     addRawData(new_experimental_data, newFilesAdded);
diff --git a/ArchiveSearch/CSpectralArchive.h b/ArchiveSearch/CSpectralArchive.h
index 442107e..8b0c923 100644
--- a/ArchiveSearch/CSpectralArchive.h
+++ b/ArchiveSearch/CSpectralArchive.h
@@ -8,6 +8,7 @@
 #include <string>
 #include <fstream>
 #include <map>
+#include <atomic>
 using namespace std;
 class CAnnotationDB;
 class ICQuery;
@@ -217,6 +218,8 @@ class CSpectralArchive {
 	int m_tol;
 	int m_minPeakNum;
 	bool m_usegpu;
+    std::atomic_int m_stage; 
+    enum Archive_Stage {STAGE_ANNOTATION, STAGE_TRAIN, STAGE_ADD, STAGE_INIT, STAGE_INDEX, STAGE_SEARCH, STAGE_UPDATE};
 public:
     CSpectralArchive(string mzXMLList, string pepxml, string indexfile, bool removeprecursor, bool useflankingbins,
                      int tol, int minPeakNum, bool myOwnIndex, CPQParam option, string indexstrings, bool usegpu,
diff --git a/ArchiveSearch/spectroscapeMain.cpp b/ArchiveSearch/spectroscapeMain.cpp
index a03d03c..40b7446 100644
--- a/ArchiveSearch/spectroscapeMain.cpp
+++ b/ArchiveSearch/spectroscapeMain.cpp
@@ -35,8 +35,10 @@ void sigint_handler(int signal) {
         std::cout << "Force to exit Spectroscape." << std::endl;
         exit(0);
     }
-    std::cout << "Please wait for a few seconds for Spectroscape save data and exit safely.\n" << std::endl;
-    std::cout << "To stop Spectroscape immediately, press ctrl-c again .\n" << std::endl;
+    std::cout << "If spectroscape is adding new raw data files, please wait for a few seconds for Spectroscape save data and exit safely.\n" << std::endl;
+    std::cout << "Otherwise, to stop Spectroscape immediately, press ctrl-c again .\n" << std::endl;
+    std::cout << "Attention:" << std::endl;
+    std::cout << "Forced interruption when adding new data files to archive can results in corrupted files. A fresh building is required. " << std::endl;
 }
 
 boost::program_options::variables_map getParam(int argc, char *argv[]) {
diff --git a/scripts/start_service.bash b/scripts/start_service.bash
new file mode 100755
index 0000000..99d7cb0
--- /dev/null
+++ b/scripts/start_service.bash
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+
+archive_path="$HOME/data/spectroscape/spectral_archives_latest"
+bin_path="$HOME/code/SpectralArchive/build/bin/spectroscape"
+wwwroot_path="`dirname $bin_path`/../www"
+cd $archive_path && spawn-fcgi -p 8710 -n -- $bin_path --run --wwwroot $wwwroot_path
\ No newline at end of file