Merge pull request #515 from DiamondLightSource/487_log_no_diffraction

Improve logging to ispyb when there is no diffraction

fake_zocalo/__main__.py

@@ -2,6 +2,7 @@
 import os
 import time
 from pathlib import Path
+from typing import Tuple
 
 import ispyb.sqlalchemy
 import pika
@@ -12,7 +13,7 @@
 from sqlalchemy import create_engine
 from sqlalchemy.orm import sessionmaker
 
-NO_DIFFRACTION_ID = 1
+NO_DIFFRACTION_PREFIX = "NO_DIFF"
 
 DEV_ISPYB_CONFIG = "/dls_sw/dasc/mariadb/credentials/ispyb-dev.cfg"
 
@@ -22,20 +23,22 @@ def load_configuration_file(filename):
  return conf
 
 
-def get_dcgid(dcid: int, Session) -> int:
- if dcid == NO_DIFFRACTION_ID:
- return NO_DIFFRACTION_ID
+def get_dcgid_and_prefix(dcid: int, Session) -> Tuple[int, str]:
  try:
  with Session() as session:
- query = session.query(DataCollection).filter(
- DataCollection.dataCollectionId == dcid
+ query = (
+ session.query(DataCollection)
+ .filter(DataCollection.dataCollectionId == dcid)
+ .first()
  )
- dcgid: int = query.first().dataCollectionGroupId
+ dcgid: int = query.dataCollectionGroupId
+ prefix: str = query.imagePrefix
  except Exception as e:
  print("Exception occured when reading from ISPyB database:\n")
  print(e)
  dcgid = 4
- return dcgid
+ prefix = ""
+ return dcgid, prefix
 
 
 def main():
@@ -81,8 +84,7 @@ def main():
  "queue": "xrc.i03",
  "exchange": "results",
  "parameters": {
- "dcid": str(NO_DIFFRACTION_ID),
- "dcgid": str(NO_DIFFRACTION_ID),
+ "parameters": {"dcid": "2", "dcgid": "4"},
  },
  },
  },
@@ -103,18 +105,18 @@ def on_request(ch: BlockingChannel, method, props, body):
  print('Doing "processing"...')
 
  dcid = message.get("parameters").get("ispyb_dcid")
- print(f"getting dcgid for dcid {dcid} from ispyb:")
- dcgid = get_dcgid(dcid, Session)
- print(dcgid)
+ print(f"Getting info for dcid {dcid} from ispyb:")
+ dcgid, prefix = get_dcgid_and_prefix(dcid, Session)
+ print(f"Dcgid {dcgid} and prefix {prefix}")
 
- time.sleep(3)
+ time.sleep(1)
  print('Sending "results"...')
  resultprops = BasicProperties(
  delivery_mode=2,
  headers={"workflows-recipe": True, "x-delivery-count": 1},
  )
 
- if message.get("parameters").get("ispyb_dcid") == NO_DIFFRACTION_ID:
+ if prefix == NO_DIFFRACTION_PREFIX:
  result = no_diffraction_result
  else:
  result = single_crystal_result

src/artemis/external_interaction/callbacks/fgs/zocalo_callback.py

@@ -100,6 +100,7 @@ def wait_for_results(self, fallback_xyz: Point3D) -> Point3D:
  log_msg = (
  f"Zocalo: No diffraction found, using fallback centre {fallback_xyz}"
  )
+ self.ispyb.append_to_comment("Found no diffraction.")
  xray_centre = fallback_xyz
  LOGGER.warn(log_msg)
 

src/artemis/external_interaction/system_tests/test_zocalo_system.py

@@ -1,5 +1,4 @@
 import os
-from unittest.mock import MagicMock
 
 import pytest
 
@@ -28,56 +27,50 @@ def test_when_running_start_stop_then_get_expected_returned_results(zocalo_env):
  assert zc.zocalo_interactor.wait_for_result(4) == Point3D(x=1.2, y=2.3, z=1.4)
 
 
-@pytest.mark.s03
-def test_zocalo_callback_calls_append_comment(zocalo_env):
- params = FullParameters()
- zc: FGSZocaloCallback = FGSCallbackCollection.from_params(params).zocalo_handler
- zc.ispyb.append_to_comment = MagicMock()
- dcids = [1, 2]
- zc.ispyb.ispyb_ids = (dcids, 0, 4)
- for dcid in dcids:
- zc.zocalo_interactor.run_start(dcid)
- for dcid in dcids:
- zc.zocalo_interactor.run_end(dcid)
- zc.wait_for_results(fallback_xyz=Point3D(0, 0, 0))
- assert zc.ispyb.append_to_comment.call_count == 1
+@pytest.fixture
+def run_zocalo_with_dev_ispyb(dummy_params, dummy_ispyb_3d):
+ def inner(sample_name="", fallback=Point3D(0, 0, 0)):
+ dummy_params.detector_params.prefix = sample_name
+ zc: FGSZocaloCallback = FGSCallbackCollection.from_params(
+ dummy_params
+ ).zocalo_handler
+ zc.ispyb.ispyb.ISPYB_CONFIG_PATH = dummy_ispyb_3d.ISPYB_CONFIG_PATH
+ zc.ispyb.ispyb_ids = zc.ispyb.ispyb.begin_deposition()
+ for dcid in zc.ispyb.ispyb_ids[0]:
+ zc.zocalo_interactor.run_start(dcid)
+ zc.stop({})
+ centre = zc.wait_for_results(fallback_xyz=fallback)
+ return zc, centre
+
+ return inner
 
 
 @pytest.mark.s03
 def test_given_a_result_with_no_diffraction_when_zocalo_called_then_move_to_fallback(
- zocalo_env,
+ run_zocalo_with_dev_ispyb, zocalo_env
 ):
- params = FullParameters()
- NO_DIFFFRACTION_ID = 1
- zc: FGSZocaloCallback = FGSCallbackCollection.from_params(params).zocalo_handler
- zc.ispyb.append_to_comment = MagicMock()
- dcids = [NO_DIFFFRACTION_ID, NO_DIFFFRACTION_ID]
- zc.ispyb.ispyb_ids = (dcids, 0, NO_DIFFFRACTION_ID)
- for dcid in dcids:
- zc.zocalo_interactor.run_start(dcid)
- for dcid in dcids:
- zc.zocalo_interactor.run_end(dcid)
  fallback = Point3D(1, 2, 3)
- centre = zc.wait_for_results(fallback_xyz=fallback)
+ zc, centre = run_zocalo_with_dev_ispyb("NO_DIFF", fallback)
  assert centre == fallback
 
 
 @pytest.mark.s03
-def test_zocalo_adds_nonzero_comment_time(zocalo_env, dummy_ispyb_3d, fetch_comment):
- params = FullParameters()
- zc: FGSZocaloCallback = FGSCallbackCollection.from_params(params).zocalo_handler
- zc.ispyb.ispyb = dummy_ispyb_3d
- zc.ispyb.ispyb_ids = zc.ispyb.ispyb.begin_deposition()
- ispyb_numbers = zc.ispyb.ispyb_ids
- assert ispyb_numbers[0] is not None
- dcids = ispyb_numbers[0]
- for dcid in dcids:
- zc.zocalo_interactor.run_start(dcid)
- zc.stop({})
- zc.wait_for_results(fallback_xyz=Point3D(0, 0, 0))
- zc.ispyb.ispyb.end_deposition("success", "")
+def test_given_a_result_with_no_diffraction_ispyb_comment_updated(
+ run_zocalo_with_dev_ispyb, zocalo_env, fetch_comment
+):
+ zc, centre = run_zocalo_with_dev_ispyb("NO_DIFF")
+
+ comment = fetch_comment(zc.ispyb.ispyb_ids[0][0])
+ assert "Found no diffraction." in comment
+
+
+@pytest.mark.s03
+def test_zocalo_adds_nonzero_comment_time(
+ run_zocalo_with_dev_ispyb, zocalo_env, fetch_comment
+):
+ zc, centre = run_zocalo_with_dev_ispyb()
 
- comment = fetch_comment(ispyb_numbers[0][0])
+ comment = fetch_comment(zc.ispyb.ispyb_ids[0][0])
  assert comment[-29:-6] == "Zocalo processing took "
  assert float(comment[-6:-2]) > 0
  assert float(comment[-6:-2]) < 90

src/artemis/external_interaction/unit_tests/test_write_nexus.py

@@ -290,7 +290,7 @@ def test_nexus_file_validity_for_zocalo_with_three_linked_datasets(
  check_validity_through_zocalo(dummy_nexus_writers_with_more_images)
 
 
-@pytest.mark.skip("Needs fixing in Nexgen")
+@pytest.mark.skip(reason="Needs fixing in Nexgen")
 def test_GIVEN_some_datafiles_outside_of_VDS_range_THEN_they_are_not_in_nexus_file(
  dummy_nexus_writers_with_more_images: tuple[NexusWriter, NexusWriter]
 ):

src/artemis/system_tests/test_fgs_plan.py

@@ -85,7 +85,7 @@ def fgs_composite():
  return fast_grid_scan_composite
 
 
-@pytest.mark.skip("Broken due to eiger issues in s03")
+@pytest.mark.skip(reason="Broken due to eiger issues in s03")
 @pytest.mark.s03
 @patch("artemis.fast_grid_scan_plan.wait_for_fgs_valid")
 @patch("bluesky.plan_stubs.wait")