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| 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() | |