Server

Makefile

@@ -26,7 +26,7 @@ LOC_INCLUDE=include
 LOC_SRC=src
 OBJDIR=obj
 
-CXXFLAGS += -Wall $(DEBUG) $(PROFILE) $(OPT) $(ARCH) -m64 -I. -I$(LOC_INCLUDE) \
+CXXFLAGS += -Wall $(DEBUG) $(PROFILE) $(OPT) $(ARCH) -m64 -I. -I$(LOC_INCLUDE) -I$(MYINCL) \
 -Wno-unused-result -Wno-strict-aliasing -Wno-unused-function -Wno-sign-compare
 
 CFLAGS += -Wall $(DEBUG) $(PROFILE) $(OPT) $(ARCH) -m64 -I. -I$(LOC_INCLUDE)\
@@ -59,6 +59,7 @@ $(OBJDIR)/hashutil.o: 			$(LOC_INCLUDE)/hashutil.h
 # dependencies between .o files and .cc (or .c) files
 
 $(OBJDIR)/gqf.o: $(LOC_SRC)/cqf/gqf.c $(LOC_INCLUDE)/cqf/gqf.h
+$(OBJDIR)/query.o: $(LOC_SRC)/sockets.h
 
 #
 # generic build rules

README.md

@@ -86,18 +86,59 @@ OPTIONS
         <query>     Prefix of input files.
 ```
 
- The command takes the following options :
+ The command takes the following options:
  - `--input-prefix,-p`: the directory where the output of coloreddbg command is present.
  - `--output,-o`: the file where the query results should be written (default : `samples.output`).
 
  additionally the command takes the following mandatory _positional_ argument :
  - query transcripts: input transcripts to be queried.
 
  Finally, rather than writing the results in the "simple" output format, they can be written in JSON if you
- provide the `--json,-j` flag to the `query` comamnd.
+ provide the `--json,-j` flag to the `query` command.
 
 The output file in contains the list of experiments (i.e., hits) corresponding to each queried transcript.
 
+Server
+-------
+
+`mantis server` lets you run mantis as a server which loads a mantis index and waits for queries. 
+
+```bash
+ $ make mantis
+ $ ./mantis server -p raw/ 
+```
+
+The options and arguments are as follows:
+
+```bash
+SYNOPSIS
+        mantis server [-j] -p <query_prefix>
+
+OPTIONS
+        -j, --json  Write the output in JSON format
+
+        <query_prefix>
+                    Prefix of input files.
+```
+
+ The command takes the following options:
+ - `--input-prefix,-p`: the directory where the output of coloreddbg command is present.
+
+  Rather than writing the results in the "simple" output format, they can be written in JSON if you
+ provide the `--json,-j` flag to the `query` command.
+
+ The server loads mantis index to memory and starts to accept queries (port 23901 is used by default) in the following format:
+
+```
+<query_filepath> <output_filepath>
+```
+
+ The query has the following arguments: 
+ - query filepath: input transcripts to be queried.
+ - output filepath: the file where the query results should be written. The output file in contains the list of experiments (i.e., hits) corresponding to each queried transcript.
+
+ There is a client example written in python `src/client.py` which demonstrates how one can communicate with the server. 
+
 Contributing
 ------------
 Contributions via GitHub pull requests are welcome.

scripts/install_mantis_server.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+. load_deps_spack.sh  # load mantis dependencies with spack and save environment variables
+
+TOOLS=~/tools
+mkdir -p $TOOLS/src
+git clone https://github.com/simongog/sdsl-lite.git $TOOLS/src/sdsl-lite
+$TOOLS/src/sdsl-lite/install.sh $TOOLS
+
+git clone https://github.com/effect/mantis.git $TOOLS/mantis
+
+LIBRARY_PATH=$TOOLS/lib:$LIBRARY_PATH
+./patch_makefile.sh $TOOLS/mantis/Makefile
+cd $TOOLS/mantis
+MYINCL=$TOOLS/include make NH=1

scripts/libpaths.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+IFS=":"
+for line in $LIBRARY_PATH; do
+  echo -L$line '\\'
+done
+

scripts/load_deps_spack.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+spack load gcc
+spack load cmake
+spack load boost
+spack load zlib
+spack load bzip2
+spack load binutils

scripts/patch_makefile.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+MAKEFILE=$1
+LIBPATHS="$(./libpaths.sh)"
+LIBPATHS="$(echo "$LIBPATHS" | sed '$ ! s/$/\\/')"    # escape new lines
+sed -i "/TARGETS=/aMYLIBS=$LIBPATHS" $MAKEFILE        # add MYLIBS var with all libraries path
+sed -i "s/LDFLAGS += /LDFLAGS += \$\(MYLIBS\) /g" $MAKEFILE  # add MYLIBS to LDFLAGS

src/client.py

@@ -0,0 +1,17 @@
+import socket
+import sys
+
+HOST, PORT = "localhost", 23901
+
+s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+
+s.connect((HOST, PORT))
+
+query_filepath = "/home/paf2023/run_mantis/queries/query{0}.fa"
+output_filepath = "/home/paf2023/run_mantis/out/out{0}.res"
+
+for x in range(0, 5):
+    print("Send request {0}".format(query_filepath.format(x)))
+    s.send(query_filepath.format(x) + " " + output_filepath.format(x))
+    result = str(s.recv(4096))
+    print("Got result {0}".format(result))

src/mantis.cc

@@ -46,6 +46,7 @@ void explore_options_verbose(T& res) {
 }
 
 int query_main (QueryOpts& opt);
+int server_main (QueryOpts& opt);
 int build_main (BuildOpts& opt);
 int validate_main (ValidateOpts& opt);
 
@@ -57,16 +58,18 @@ int validate_main (ValidateOpts& opt);
  */
 int main ( int argc, char *argv[] ) {
   using namespace clipp;
-  enum class mode {build, query, validate, help};
+  enum class mode {build, query, server, validate, help};
   mode selected = mode::help;
 
   auto console = spdlog::stdout_color_mt("mantis_console");
 
   BuildOpts bopt;
-  QueryOpts qopt;
+  QueryOpts qopt, sopt;
   ValidateOpts vopt;
+
   bopt.console = console;
   qopt.console = console;
+  sopt.console = console;
   vopt.console = console;
 
 	start_time = time(NULL);
@@ -145,6 +148,11 @@ int main ( int argc, char *argv[] ) {
                      option("-o", "--output") & value("output_file", qopt.output) % "Where to write query output.",
                      value(ensure_file_exists, "query", qopt.query_file) % "Prefix of input files."
                      );
+  auto server_mode = (
+                     command("server").set(selected, mode::server),
+                     option("-j", "--json").set(sopt.use_json) % "Write the output in JSON format",
+                     required("-p", "--input-prefix") & value(ensure_dir_exists, "query_prefix", sopt.prefix) % "Prefix of input files." // ,
+                     );
 
   auto validate_mode = (
                      command("validate").set(selected, mode::validate),
@@ -155,11 +163,12 @@ int main ( int argc, char *argv[] ) {
                      );
 
   auto cli = (
-              (build_mode | query_mode | validate_mode | command("help").set(selected,mode::help) ),
+              (build_mode | query_mode | server_mode | validate_mode | command("help").set(selected,mode::help) ),
               option("-v", "--version").call([]{std::cout << "version 1.0\n\n";}).doc("show version")  );
 
   assert(build_mode.flags_are_prefix_free());
   assert(query_mode.flags_are_prefix_free());
+  assert(server_mode.flags_are_prefix_free());
   assert(validate_mode.flags_are_prefix_free());
 
   decltype(parse(argc, argv, cli)) res;
@@ -178,6 +187,7 @@ int main ( int argc, char *argv[] ) {
     switch(selected) {
     case mode::build: build_main(bopt);  break;
     case mode::query: query_main(qopt);  break;
+    case mode::server: server_main(sopt);  break;
     case mode::validate: validate_main(vopt);  break;
     case mode::help: std::cout << make_man_page(cli, "mantis"); break;
     }