Speed and reliability fixes in services

src/relion/zocalo/class2d_wrapper.py

@@ -190,6 +190,7 @@ def run(self):
  )
 
  # Run Class2D and confirm it ran successfully
+ self.log.info(" ".join(class2d_command))
  result = subprocess.run(
  class2d_command, cwd=str(project_dir), capture_output=True
  )

src/relion/zocalo/class3d_wrapper.py

@@ -53,7 +53,7 @@ class Class3DParameters(BaseModel):
  skip_align: bool = False
  healpix_order: float = 2
  offset_range: float = 5
- offset_step: float = 2
+ offset_step: float = 4
  allow_coarser: bool = False
  symmetry: str = "C1"
  do_norm: bool = True
@@ -393,6 +393,7 @@ def run(self):
  )
 
  # Run Class3D and confirm it ran successfully
+ self.log.info(" ".join(class3d_command))
  result = subprocess.run(
  class3d_command, cwd=str(project_dir), capture_output=True
  )

src/relion/zocalo/images_service_plugin.py

@@ -97,10 +97,6 @@ def picked_particles(plugin_params):
  logger.info(f"Replacing jpeg extension with mrc extension for {basefilename}")
  basefilename = basefilename.replace(".jpeg", ".mrc")
  coords = plugin_params.parameters("coordinates")
- if not coords:
- logger.warning(f"No coordinates provided for {basefilename}")
- # If there were no coordinates don't bother nacking the message
- return True
  angpix = plugin_params.parameters("angpix")
  diam = plugin_params.parameters("diameter")
  contrast_factor = plugin_params.parameters("contrast_factor", default=6)
@@ -139,15 +135,18 @@ def picked_particles(plugin_params):
  enhanced = enhancer.enhance(contrast_factor)
  fim = enhanced.filter(ImageFilter.BLUR)
  dim = ImageDraw.Draw(fim)
- for x, y in coords:
- dim.ellipse(
- [
- (float(x) - radius, float(y) - radius),
- (float(x) + radius, float(y) + radius),
- ],
- width=8,
- outline="#f58a07",
- )
+ if coords and coords[0]:
+ for x, y in coords:
+ dim.ellipse(
+ [
+ (float(x) - radius, float(y) - radius),
+ (float(x) + radius, float(y) + radius),
+ ],
+ width=8,
+ outline="#f58a07",
+ )
+ else:
+ logger.warning(f"No coordinates provided for {basefilename}")
  try:
  fim.save(outfile)
  except FileNotFoundError:

src/relion/zocalo/motioncorr_wilson.py

@@ -208,6 +208,22 @@ def motioncor2(self, command: list, mrc_out: Path):
  stderr=slurm_status_json.stderr,
  )
 
+ if loop_counter >= 60:
+ slurm_cancel_command = (
+ f'curl -H "X-SLURM-USER-NAME:{user}" '
+ f'-H "X-SLURM-USER-TOKEN:{slurm_token}" '
+ '-H "Content-Type: application/json" -X DELETE '
+ f'{slurm_rest["url"]}/slurm/{slurm_rest["api_version"]}/job/{job_id}'
+ )
+ subprocess.run(slurm_cancel_command, capture_output=True, shell=True)
+ self.log.error("Timeout running motion correction")
+ return subprocess.CompletedProcess(
+ args="",
+ returncode=1,
+ stdout="".encode("utf8"),
+ stderr="Timeout running motion correction".encode("utf8"),
+ )
+
  # Read in the MotionCor output then clean up the files
  self.log.info(f"Job {job_id} has finished!")
  try: