Guard more extractor file operations to avoid race conditions caused by multi-file extractors

biostools/extractors.py

@@ -293,7 +293,11 @@ class ASTExtractor(Extractor):
 
 	def extract(self, file_path, file_header, dest_dir, dest_dir_0):
 		# Stop if this file is too small.
-		if os.path.getsize(file_path) <= 0x9083:
+		try:
+			file_size = os.path.getsize(file_path)
+		except:
+			return False
+		if file_size <= 0x9083:
 			return False
 
 		# Look for the AST signatures.
@@ -305,48 +309,51 @@ class ASTExtractor(Extractor):
 			return True
 
 		# Open AST image.
-		with open(file_path, 'rb') as in_f:
-			# Skip the initial 72 sectors.
-			in_f.seek(0x9000)
+		try:
+			with open(file_path, 'rb') as in_f:
+				# Skip the initial 72 sectors.
+				in_f.seek(0x9000)
 
-			# Copy payload.
-			header = b''
-			dest_file_path = os.path.join(dest_dir, 'ast.bin')
-			try:
-				with open(dest_file_path, 'wb') as out_f:
-					data = remaining = True
-					while data and remaining > 0:
-						payload_size = 15 * 512
-						if data == True:
-							# Check the header on the first payload sector.
-							header += in_f.read(0x83)
-							if not self._ast_payload_pattern.match(header[:0x10]):
-								raise Exception('missing header')
-
-							# Subtract header from payload.
-							remaining, = struct.unpack('<I', header[-5:-1])
-							payload_size -= 0x83
-
-						# Copy the next 15 sectors of payload.
-						data = in_f.read(min(payload_size, remaining))
-						out_f.write(data)
-						remaining -= len(data)
-
-						# Skip the next 3 blank sectors.
-						in_f.seek(3 * 512, 1)
-			except:
+				# Copy payload.
+				header = b''
+				dest_file_path = os.path.join(dest_dir, 'ast.bin')
 				try:
-					os.remove(dest_file_path)
+					with open(dest_file_path, 'wb') as out_f:
+						data = remaining = True
+						while data and remaining > 0:
+							payload_size = 15 * 512
+							if data == True:
+								# Check the header on the first payload sector.
+								header += in_f.read(0x83)
+								if not self._ast_payload_pattern.match(header[:0x10]):
+									raise Exception('missing header')
+
+								# Subtract header from payload.
+								remaining, = struct.unpack('<I', header[-5:-1])
+								payload_size -= 0x83
+
+							# Copy the next 15 sectors of payload.
+							data = in_f.read(min(payload_size, remaining))
+							out_f.write(data)
+							remaining -= len(data)
+
+							# Skip the next 3 blank sectors.
+							in_f.seek(3 * 512, 1)
+				except:
+					try:
+						os.remove(dest_file_path)
+					except:
+						pass
+					return True
+
+				# Write header.
+				try:
+					with open(os.path.join(dest_dir, ':header:'), 'wb') as out_f:
+						out_f.write(header)
 				except:
 					pass
-				return True
-
-			# Write header.
-			try:
-				with open(os.path.join(dest_dir, ':header:'), 'wb') as out_f:
-					out_f.write(header)
-			except:
-				pass
+		except:
+			pass
 
 		# Remove AST image.
 		os.remove(file_path)
@@ -924,7 +931,11 @@ class ImageExtractor(Extractor):
 			width, height = struct.unpack('<HH', file_header[4:8])
 
 			# Determine if this file is a 4-bit or 8-bit EPA according to the file size.
-			if os.path.getsize(file_path) >= 8 + (width * height):
+			try:
+				file_size = os.path.getsize(file_path)
+			except:
+				file_size = len(file_header)
+			if file_size >= 8 + (width * height):
 				func = self._convert_epav2_8b
 			else:
 				func = self._convert_epav2_4b
@@ -941,7 +952,10 @@ class ImageExtractor(Extractor):
 			paletted = file_header[3] != 0
 			payload_size = math.ceil((width * height) / 2)
 			if paletted:
-				file_size = os.path.getsize(file_path)
+				try:
+					file_size = os.path.getsize(file_path)
+				except:
+					file_size = len(file_header)
 				if file_size > 18 + payload_size:
 					palette_size, = struct.unpack('<H', file_header[10:12])
 					file_header += util.read_complement(file_path, file_header, max_size=len(file_header) + (4 * palette_size))
@@ -957,9 +971,9 @@ class ImageExtractor(Extractor):
 			if width != 0 and height != 0:
 				func = self._convert_pgx
 		if not func:
-			# Determine if this file is the right size for a v1 EPA.
+			# Determine if this file has valid dimensions and is the right size for a v1 EPA.
 			width, height = struct.unpack('BB', file_header[:2])
-			if os.path.getsize(file_path) == 72 + (15 * width * height):
+			if width < 80 and height < 25 and len(file_header) == 72 + (15 * width * height):
 				func = self._convert_epav1
 			else:
 				# Determine if this is a common image format.
@@ -1468,9 +1482,12 @@ class ISOExtractor(ArchiveExtractor):
 			# Does the size match known bad extractions?
 			if elt_size == 512:
 				# Read file.
-				f = open(elt_path, 'rb')
-				data = f.read(512)
-				f.close()
+				try:
+					f = open(elt_path, 'rb')
+					data = f.read(512)
+					f.close()
+				except:
+					data = b''
 
 				# Check for MBR boot signature.
 				if data[-2:] == b'\x55\xAA':
@@ -2185,7 +2202,10 @@ class OMFExtractor(Extractor):
 			return False
 
 		# Stop if the OMF size is invalid. Should catch other files that match the quick check.
-		file_size = os.path.getsize(file_path)
+		try:
+			file_size = os.path.getsize(file_path)
+		except:
+			return False
 		omf_size, = struct.unpack('<I', match.group(1))
 		if omf_size > file_size:
 			return False