service.py

import http.server
import socketserver
import subprocess
import threading
import queue
import io
import select
import re
import os
import urllib.request
import urllib.parse
import urllib.error

PORT = 8080
command_executed = False
command_output = queue.Queue()
command_queue = queue.Queue()


def sanitize_output(output):
    # Remove any non-printable characters except for carriage return
    return re.sub(r'[^\x20-\x7E\r]+', '', output)


def run_command(command):
    print("Running command ", command)
    process = subprocess.Popen(
        command,
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE,
        text=True,
        bufsize=1  # Line-buffered
    )
    while True:
        reads = [process.stdout.fileno(), process.stderr.fileno()]
        ret = select.select(reads, [], [], 0.1)  # Timeout to periodically flush
        for fd in ret[0]:
            if fd == process.stdout.fileno():
                output = process.stdout.readline()
                if output:
                    command_output.put(sanitize_output(output) + "\n")
            if fd == process.stderr.fileno():
                error = process.stderr.readline()
                if error:
                    command_output.put(sanitize_output(error) + "\n")
        if process.poll() is not None:
            break
        process.stdout.flush()
        process.stderr.flush()
    process.stdout.close()
    process.stderr.close()
    process.wait()
    command_output.put("Leaving")


def command_worker():
    print("Starting worker command")
    while True:
        command = command_queue.get()
        if command is None:
            break
        run_command(command)
        command_queue.task_done()


def start_commands():
    commands = [
        ["echo", "## standard process"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/PMC_sample_1943', '-Prun=1', '-PfileRatio=1'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-pmc_sample_1943.md"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/PLOS_1000', '-Prun=1', '-PfileRatio=1'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-plos_1000.md"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/biorxiv-10k-test-2000', '-Prun=1', '-PfileRatio=1'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-biorxiv-10k-test-2000.md"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/eLife_984', '-Prun=1', '-PfileRatio=1'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-elife_984.md"],
        ["echo", "## article/light"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/PMC_sample_1943', '-Prun=1', '-PfileRatio=1', '-Pflavor=article/light'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-pmc_sample_1943-article_light.md"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/PLOS_1000', '-Prun=1', '-PfileRatio=1', '-Pflavor=article/light'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-plos_1000-article_light.md"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/biorxiv-10k-test-2000', '-Prun=1', '-PfileRatio=1', '-Pflavor=article/light'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-biorxiv-10k-test-2000-article_light.md"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/eLife_984', '-Prun=1', '-PfileRatio=1', '-Pflavor=article/light'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-eLife_984-article_light.md"],
        ["echo", "## article/light-ref"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/PMC_sample_1943', '-Prun=1', '-PfileRatio=1', '-Pflavor=article/light-ref'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-pmc_sample_1943-article_light_ref.md"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/PLOS_1000', '-Prun=1', '-PfileRatio=1', '-Pflavor=article/light-ref'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-plos_1000-article_light_ref.md"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/biorxiv-10k-test-2000', '-Prun=1', '-PfileRatio=1', '-Pflavor=article/light-ref'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-biorxiv-10k-test-2000-article_light_ref.md"],
        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/eLife_984', '-Prun=1', '-PfileRatio=1', '-Pflavor=article/light-ref'],
        ["cp", "/opt/grobid/grobid-home/tmp/report.md", "/opt/grobid/grobid-home/tmp/report-eLife_984-article_light_ref.md"],
    ]
    for command in commands:
        command_queue.put(command)
    threading.Thread(target=command_worker).start()


class Handler(http.server.SimpleHTTPRequestHandler):
    def do_GET(self):
        global command_executed

        # Check if the request is for downloading a file from URL
        if self.path.startswith('/fetch?filename='):
            try:
                # Parse the URL from the query string
                filename = urllib.parse.unquote(self.path.split('=', 1)[1])

                # Construct the full file path
                file_path = os.path.join('/opt/grobid/grobid-home/tmp/', filename)

                # Check if the file exists
                if not os.path.isfile(file_path):
                    self.send_error(404, f"File '{filename}' not found.")
                    return

                # Read the file content
                with open(file_path, 'r') as file:
                    content = file.read()

                response = content

            except urllib.error.URLError as e:
                self.send_error(500, f"Failed to download file: {str(e)}")
            except Exception as e:
                self.send_error(500, f"An error occurred: {str(e)}")

        elif not command_executed:
            command_executed = True
            threading.Thread(target=start_commands).start()
            response = "Starting evaluation."

        else:
            response = io.StringIO()
            response.write("Command output:\n")
            for item in list(command_output.queue):
                response.write(item)

            response = response.getvalue()

        self.send_response(200)
        self.send_header("Content-type", "text/plain")
        self.end_headers()
        self.wfile.write(response.encode())


with socketserver.TCPServer(("", PORT), Handler) as httpd:
    print(f"Serving on port {PORT}")
    httpd.serve_forever()