Update Dockerfile

Dockerfile

@@ -1,151 +1,24 @@
-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
+FROM lfoppiano/grobid-evaluation:latest
+USER root
+RUN mkdir -m 777 -p /opt/grobid/grobid-home/tmp
+RUN mkdir -m 777 -p /opt/grobid/logs
+RUN chmod -R 777 /opt/grobid
+RUN chmod -R uog+rw /data/db
 
-PORT = 8080
-command_executed = False
-command_output = queue.Queue()
-command_queue = queue.Queue()
+# CRF 
+COPY --chown=lfoppiano grobid.yaml /opt/grobid/grobid-home/config/grobid.yaml
 
+# official evaluation configuration 
+COPY --chown=lfoppiano grobid-full.yml /opt/grobid/grobid-home/config/grobid.yaml
+RUN ls -R /opt/grobid/evaluation/
 
-def sanitize_output(output):
-    # Remove any non-printable characters except for carriage return
-    return re.sub(r'[^\x20-\x7E\r]+', '', output)
+WORKDIR /opt/grobid
+RUN git lfs install && git clone --depth 1 https://huggingface.co/datasets/sciencialab/grobid-evaluation evaluation
+RUN chmod -R uog+rw /opt/grobid/evaluation
 
+COPY --chown=lfoppiano service.py /opt/grobid/service.py
 
-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")
+WORKDIR /opt/grobid 
 
 
-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()
+CMD ["/bin/bash", "-c", "python service.py"]