From 4adafc8417d1aa75345e5e52b3ae594c3b099bec Mon Sep 17 00:00:00 2001
From: David Hammer <dhammer@mailbox.org>
Date: Thu, 31 Aug 2023 14:58:27 +0200
Subject: [PATCH] Improve temporary file handling
---
src/calng/CrystfelRunner.py | 40 ++++++++++++++++---------------------
1 file changed, 17 insertions(+), 23 deletions(-)
diff --git a/src/calng/CrystfelRunner.py b/src/calng/CrystfelRunner.py
index 48401f7d..086db51c 100644
--- a/src/calng/CrystfelRunner.py
+++ b/src/calng/CrystfelRunner.py
@@ -1,7 +1,9 @@
import itertools
+import os
import queue
import re
import subprocess
+import tempfile
import threading
import time
@@ -386,6 +388,12 @@ class CrystfelRunner(PythonDevice):
self.startCrystfel()
def startCrystfel(self):
+ if hasattr(self, "_temporary_stream_fd"):
+ # if we made up a temporary file already and stopped CrystFEL
+ if self.get("crystfelArgs.streamOutputPath") == self._temporary_stream_fd.name:
+ # then forget about it so we can make a new one
+ self.set("crystfelArgs.streamOutputPath", "")
+ delattr(self, "_temporary_stream_fd")
self._run_crystfel()
self.updateState(State.STARTED)
@@ -407,7 +415,6 @@ class CrystfelRunner(PythonDevice):
fashion). The argument should be a hash (via WebProxy, a JSON-encoded dict)
with a list of strings (with newline characters already there) under
'fileContents'."""
- import tempfile
fd = tempfile.NamedTemporaryFile(mode="w")
fd.writelines(data["fileContents"])
fd.flush()
@@ -516,7 +523,6 @@ class CrystfelRunner(PythonDevice):
threading.Thread(target=server, daemon=True).start()
def _run_crystfel(self):
- import os
env = os.environ.copy()
env["PATH"] = (
self.get("crystfelArgs.crystfelBinPath") +
@@ -524,21 +530,18 @@ class CrystfelRunner(PythonDevice):
)
# we must have a stream output!
# if empty, set it to something and delete after we are done reading it
- streamOutputPath = self.get("crystfelArgs.streamOutputPath")
- deleteOutput = False
- if len(streamOutputPath) == 0:
- # TODO: Is /tmp ok?
- # the goal is only to prevent
- name = self.get("deviceId").replace("/", "_")
- streamOutputPath = f"/tmp/out_{name}.stream"
- deleteOutput = True
+ if not self.get("crystfelArgs.streamOutputPath"):
+ stream_fd = tempfile.NamedTemporaryFile()
+ self._temporary_stream_fd = stream_fd
+ self.set("crystfelArgs.streamOutputPath", stream_fd.name)
+ stream_fn = self.get("crystfelArgs.streamOutputPath")
args = [
"indexamajig",
f"--zmq-input=tcp://localhost:{self.get('crystfelArgs.zmqPort')}",
"--zmq-request=next",
"--data-format=msgpack",
"-o",
- streamOutputPath,
+ stream_fn,
"-g",
self.get("crystfelArgs.geometryPath"),
]
@@ -552,8 +555,7 @@ class CrystfelRunner(PythonDevice):
# Somehow Karabo substitutes ["--int-radius=3,4,5"] with ["--int-radius=3", "4", "5"] for Danilo
# and it adds \\ escape sequences for David H.
# both of those "effects" are handled in the hack function below
- fixed_misc = reparse_fix_comma_mess(self.get("crystfelArgs.misc"))
- args += fixed_misc
+ args.extend(reparse_fix_comma_mess(self.get("crystfelArgs.misc")))
# this should override the --peaks option set by the user, if they
# want to use an external peakfinder
@@ -586,7 +588,7 @@ class CrystfelRunner(PythonDevice):
## do something with stream file
#self._tail_proc = subprocess.Popen(
- # ["tail", "-F", "-n", "+0", streamOutputPath],
+ # ["tail", "-F", "-n", "+0", stream_fn],
# stdout=subprocess.PIPE,
# stderr=subprocess.PIPE,
# shell=False,
@@ -619,7 +621,7 @@ class CrystfelRunner(PythonDevice):
n_reflections = list()
cell = list()
det_centre = list()
- with open(streamOutputPath, "r") as outFile:
+ with open(stream_fn, "r") as outFile:
#for line in self._tail_proc.stdout:
for line in outFile:
if reading_chunk:
@@ -669,14 +671,6 @@ class CrystfelRunner(PythonDevice):
f"crystfelStats", Hash(*itertools.chain.from_iterable(results.items()))
)
- # ... and delete output stream file if requested:
- if deleteOutput:
- try:
- os.remove(streamOutputPath)
- except:
- pass
-
threading.Thread(target=collect_details, daemon=True).start()
utils.add_unsafe_get(CrystfelRunner)
-
--
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