Update service.py

service.py

@@ -1,43 +1,53 @@
 import http.server
-import select
 import socketserver
 import subprocess
 import threading
 import queue
 import io
+import select
+import re
 
 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
+        text=True,
+        bufsize=1  # Line-buffered
     )
     while True:
         reads = [process.stdout.fileno(), process.stderr.fileno()]
-        ret = select.select(reads, [], [])
+        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(output)
+                    command_output.put(sanitize_output(output) + "\n")
+            if fd == process.stderr.fileno():
                 error = process.stderr.readline()
                 if error:
-                    command_output.put(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:
@@ -48,15 +58,10 @@ def command_worker():
 
 def start_commands():
     commands = [
-        ['/Users/lfoppiano/development/projects/grobid/./gradlew', '-p', '/Users/lfoppiano/development/projects/grobid',
-         'jatsEval', '-Pp2t=/Volumes/ExtremePro/sciencialab/science-miner/grobid/grobid-evaluation/PMC_sample_1943',
-         '-Prun=1', '-PfileRatio=1'],
-        ['/Users/lfoppiano/development/projects/grobid/./gradlew', '-p', '/Users/lfoppiano/development/projects/grobid',
-         'jatsEval', '-Pp2t=/Volumes/ExtremePro/sciencialab/science-miner/grobid/grobid-evaluation/PLOS_1000',
-         '-Prun=1', '-PfileRatio=1'],
-        # ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/PLOS_1000', '-Prun=1', '-PfileRatio=1'],
-        # ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/biorxiv-10k-test-2000', '-Prun=1', '-PfileRatio=1'],
-        # ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/eLife_984', '-Prun=1', '-PfileRatio=1']
+        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/PMC_sample_1943', '-Prun=1', '-PfileRatio=1'],
+        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/PLOS_1000', '-Prun=1', '-PfileRatio=1'],
+        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/biorxiv-10k-test-2000', '-Prun=1', '-PfileRatio=1'],
+        ['./gradlew', 'jatsEval', '-Pp2t=/opt/grobid/evaluation/eLife_984', '-Prun=1', '-PfileRatio=1']
     ]
     for command in commands:
         command_queue.put(command)
@@ -69,7 +74,7 @@ class Handler(http.server.SimpleHTTPRequestHandler):
         if not command_executed:
             command_executed = True
             threading.Thread(target=start_commands).start()
-            response = "Command is being executed."
+            response = "Starting evaluation."
         else:
             response = io.StringIO()
             response.write("Command output:\n")