Add Rservice

README.md

@@ -1,12 +1,16 @@
-# bedboss
+<h1 align="center">bedboss</h1>
 
+<div align="center">
+
 [![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pep.databio.org/)
 ![Run pytests](https://github.com/bedbase/bedboss/workflows/Run%20instalation%20test/badge.svg)
 [![pypi-badge](https://img.shields.io/pypi/v/bedboss?color=%2334D058)](https://pypi.org/project/bedboss)
 [![pypi-version](https://img.shields.io/pypi/pyversions/bedboss.svg?color=%2334D058)](https://pypi.org/project/bedboss)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Github badge](https://img.shields.io/badge/source-github-354a75?logo=github)](https://github.com/databio/bedboss)
 
+</div>
+
 ---
 
 **Documentation**: <a href="https://docs.bedbase.org/bedboss" target="_blank">https://docs.bedbase.org/bedboss</a>

bedboss/bedstat/r_demo.py

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+import subprocess
+import socket
+import signal
+import os
+
+
+class RServiceManager:
+    """
+    A class to manage the lifecycle of an R service, allowing files to be processed through the service.
+
+    Attributes:
+        r_script_path (str): Path to the R script that starts the service.
+        host (str): Host address for the socket connection.
+        port (int): Port number for the socket connection.
+        process (subprocess.Popen): The process running the R service.
+    """
+
+    def __init__(self, r_script_path="tools/r-service.R", host="127.0.0.1", port=8888):
+        """
+        Initializes the RServiceManager with the given R script path, host, and port.
+
+        Args:
+            r_script_path (str): Path to the R script that starts the service.
+            host (str): Host address for the socket connection. Default is "127.0.0.1".
+            port (int): Port number for the socket connection. Default is 8888.
+        """
+        self.r_script_path = r_script_path
+        self.host = host
+        self.port = port
+        self.process = None
+
+    def start_service(self):
+        """
+        Starts the R service by running the R script in a subprocess.
+        """
+        cmd = ["Rscript", self.r_script_path]
+        self.process = subprocess.Popen(cmd, shell=False, preexec_fn=os.setsid)
+        print(f"Running R process with PID: {self.process.pid}")
+
+    def run_file(self, file_path):
+        """
+        Sends a file path to the R service for processing.
+
+        Args:
+            file_path (str): The path to the file to be processed by the R service.
+        """
+        try:
+            s = socket.socket()
+            s.connect((self.host, self.port))
+            s.send(file_path.encode())
+            s.close()
+        except ConnectionRefusedError:
+            print("Connection refused. Make sure the R service is running.")
+
+    def terminate_service(self):
+        """
+        Terminates the R service by sending a termination signal and ensuring the process is stopped.
+        """
+        self.run_file("done")  # send secrete "terminate" code
+        if self.process:
+            self.process.terminate()
+            try:
+                self.process.wait(timeout=5)
+            except subprocess.TimeoutExpired:
+                os.killpg(os.getpgid(self.process.pid), signal.SIGTERM)
+            print("R process terminated.")
+
+
+# TODO: "tools/r-service.R" needs to be embedded in the package
+
+
+# Start the R service at the beginning of the pipeline
+rsm = RServiceManager("tools/r-service.R")
+rsm.start_service()
+
+
+# Run any BED files through bedstat
+rsm.run_file("bedstat/data/beds/bed1.bed")
+rsm.run_file("../../test/data/bed/simpleexamples/bed1.bed")
+
+# After the pipeline finishes, terminate the R service
+rsm.terminate_service()

bedboss/bedstat/tools/r-service.R

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+# This function should run the process
+processBED = function(path, client, port) {
+	message("Processing BED file: ", path)
+	if (path == "done") {  # Secret shutdown signal
+		message("Received done signal")
+		assign("done", TRUE, envir=.GlobalEnv)
+		return(0)
+	}	
+	if (!file.exists(path)) {
+		message("File not found: ", path)
+		return(1)
+	}
+	return(1)
+}
+
+message("Starting R server")
+svSocket::start_socket_server(procfun=processBED)
+message ("R server started")
+while (!exists("done")) Sys.sleep(1)
+
+message("Shutting down R service")