Rerun tests using shared constants.

src/main/python/org/broadinstitute/hellbender/gatktool/tool.py

@@ -16,6 +16,7 @@
 import os
 import cProfile, pstats, io
 import traceback
+from gatktool import toolconstants
 
 _ackFIFO = None
 _dataFIFO = None
@@ -152,9 +153,6 @@ class AckFIFO:
     Manage the FIFO used to notify GATK (via an ack) that a command has
     completed, or failed due to an unhandled exception (via a nck).
     """
-    _ackString = "ack"
-    _nackString = "nck"
-    _nkmString = "nkm"
 
     def __init__(self, ackFIFOName: str) -> None:
         """Open the ack fifo stream for writing only"""
@@ -168,7 +166,7 @@ def writeAck(self):
         """
         if self.fileWriter is None:
             raise RuntimeError("ack FIFO has not been initialized")
-        self.fileWriter.write(AckFIFO._ackString)
+        self.fileWriter.write(toolconstants._ackString)
         self.fileWriter.flush()
 
     def writeNack(self):
@@ -180,7 +178,7 @@ def writeNack(self):
         """
         if self.fileWriter is None:
             raise RuntimeError("ack FIFO has not been initialized")
-        self.fileWriter.write(AckFIFO._nackString)
+        self.fileWriter.write(toolconstants._nackString)
         self.fileWriter.flush()
 
     def writeNackWithMessage(self, message: str) -> None:
@@ -197,21 +195,18 @@ def writeNackWithMessage(self, message: str) -> None:
         Calling this method will result in an exception being thrown
         in the GATK tool on whose behalf this module is running.
         """
-        """The length of the message to be written must be 4 bytes long when serialized as a string"""
-        nckMaxMessageLength = 9999
-        nckMessageLengthSerializedSize = 4
         if self.fileWriter is None:
             raise RuntimeError("ack FIFO has not been initialized")
-        self.fileWriter.write(AckFIFO._nkmString)
+        self.fileWriter.write(toolconstants._nkmString)
         actualMessageLength = len(message)
         """The message length must be exactly 4 bytes"""
-        if len(str(actualMessageLength)) <= nckMessageLengthSerializedSize:
-            self.fileWriter.write(str(actualMessageLength).zfill(nckMessageLengthSerializedSize))
+        if len(str(actualMessageLength)) <= toolconstants.nckMessageLengthSerializedSize:
+            self.fileWriter.write(str(actualMessageLength).zfill(toolconstants.nckMessageLengthSerializedSize))
             self.fileWriter.write(message)
         else:
             """Message is too long, trim to 9999 bytes"""
-            self.fileWriter.write(str(nckMaxMessageLength))
-            self.fileWriter.write(message[:nckMaxMessageLength])
+            self.fileWriter.write(str(toolconstants.nckMaxMessageLength))
+            self.fileWriter.write(message[:toolconstants.nckMaxMessageLength])
         self.fileWriter.flush()
 
 

src/main/python/org/broadinstitute/hellbender/gatktool/toolconstants.py

@@ -0,0 +1,21 @@
+"""
+Constants that must remain in sync with the companion Java code in GATK.
+
+"""
+
+"""
+Command acknowledgement messages used to signal positive acknowledgement ('ack',
+negative acknowledgement ('nck'), and negative acknowledgement with an accompanying
+message ('nkm').
+"""
+_ackString = "ack"
+_nackString = "nck"
+_nkmString = "nkm"
+
+
+"""
+The length of a message written with a negative ack (nkm) must be 4 bytes long when
+serialized as a string, and cannot have a value > 9999.
+"""
+_nckMessageLengthSerializedSize = 4
+_nckMaxMessageLength = 9999