Service to run imod batchruntomo

pyproject.toml

@@ -87,6 +87,8 @@ torch = [
 [project.entry-points."ccpem_pipeliner.jobs"]
     "combine_star_files_job" = "cryoemservices.pipeliner_plugins.combine_star_job:ProcessStarFiles"
 [project.entry-points."cryoemservices.services"]
+    AreTomoAlign = "cryoemservices.services.tomo_align_aretomo:AreTomoAlign"
+    AreTomoAlignSlurm = "cryoemservices.services.tomo_align_aretomo_slurm:AreTomoAlignSlurm"
     BFactor = "cryoemservices.services.bfactor_setup:BFactor"
     CLEMAlignAndMerge = "cryoemservices.services.clem_align_and_merge:AlignAndMergeService"
     CLEMProcessRawLIFs = "cryoemservices.services.clem_process_raw_lifs:ProcessRawLIFsService"
@@ -104,6 +106,7 @@ torch = [
     ExtractClass = "cryoemservices.services.extract_class:ExtractClass"
     IceBreaker = "cryoemservices.services.icebreaker:IceBreaker"
     Images = "cryoemservices.services.images:Images"
+    ImodTomoAlign = "cryoemservices.services.tomo_align_imod:ImodTomoAlign"
     MembrainSeg = "cryoemservices.services.membrain_seg:MembrainSeg"
     MotionCorr = "cryoemservices.services.motioncorr:MotionCorr"
     MurfeyDBConnector = "cryoemservices.services.murfey_db_connector:MurfeyDBConnector"
@@ -113,8 +116,6 @@ torch = [
     Refine3D = "cryoemservices.services.refine3d:Refine3D"
     SelectClasses = "cryoemservices.services.select_classes:SelectClasses"
     SelectParticles = "cryoemservices.services.select_particles:SelectParticles"
-    TomoAlign = "cryoemservices.services.tomo_align:TomoAlign"
-    TomoAlignSlurm = "cryoemservices.services.tomo_align_slurm:TomoAlignSlurm"
     TopazPick = "cryoemservices.services.topaz_pick:TopazPick"
 [project.entry-points."cryoemservices.services.images.plugins"]
     "mrc_central_slice" = "cryoemservices.services.images_plugins:mrc_central_slice"

src/cryoemservices/services/tomo_align.py → src/cryoemservices/services/tomo_align_aretomo.py

@@ -101,7 +101,7 @@ def create_tilt_stack(input_file_list_of_lists: List[Any], stack_file: Path):
         mrc.header.cella.z *= len(input_file_list_of_lists)
 
 
-class TomoParameters(BaseModel):
+class AreTomoParameters(BaseModel):
     aretomo_version: Literal[2, 3] = 3
     stack_file: str = Field(..., min_length=1)
     pixel_size: float
@@ -175,14 +175,13 @@ def check_list_of_lists_is_not_empty(cls, v):
             raise ValueError("input_file_list is not a list of lists")
 
 
-class TomoAlign(CommonService):
+class AreTomoAlign(CommonService):
     """
-    A service for grouping and aligning tomography tilt-series
-    with Newstack and AreTomo2 or AreTomo3
+    A service for grouping and aligning tomography tilt-series with AreTomo2 or AreTomo3
     """
 
     # Logger name
-    _logger_name = "cryoemservices.services.tomo_align"
+    _logger_name = "cryoemservices.services.tomo_align_aretomo"
 
     # Job name
     job_type = "relion.reconstructtomograms"
@@ -218,7 +217,7 @@ def initializing(self):
         )
 
     @staticmethod
-    def check_visit(tomo_params: TomoParameters):
+    def check_visit(tomo_params: AreTomoParameters):
         return True
 
     def parse_tomo_output(self, tomo_stdout: str):
@@ -289,11 +288,13 @@ def tomo_align(self, rw, header: dict, message: dict):
 
         try:
             if isinstance(message, dict):
-                tomo_params = TomoParameters(
+                tomo_params = AreTomoParameters(
                     **{**rw.recipe_step.get("parameters", {}), **message}
                 )
             else:
-                tomo_params = TomoParameters(**{**rw.recipe_step.get("parameters", {})})
+                tomo_params = AreTomoParameters(
+                    **{**rw.recipe_step.get("parameters", {})}
+                )
         except (ValidationError, TypeError) as e:
             self.log.warning(
                 f"TomoAlign parameter validation failed for message: {message} "
@@ -891,7 +892,7 @@ def assemble_aretomo3_command(
         self,
         aretomo_executable: str,
         input_file: str,
-        tomo_parameters: TomoParameters,
+        tomo_parameters: AreTomoParameters,
     ):
         """
         Assemble the command to run AreTomo3, using a base command with
@@ -977,7 +978,7 @@ def assemble_aretomo2_command(
         self,
         aretomo_executable: str,
         input_file: str,
-        tomo_parameters: TomoParameters,
+        tomo_parameters: AreTomoParameters,
         aretomo_output_path: Path,
         angle_file: Path,
     ):
@@ -1046,7 +1047,7 @@ def assemble_aretomo2_command(
 
     def aretomo(
         self,
-        tomo_parameters: TomoParameters,
+        tomo_parameters: AreTomoParameters,
         aretomo_output_path: Path,
         angle_file: Path,
     ):

src/cryoemservices/services/tomo_align_slurm.py → src/cryoemservices/services/tomo_align_aretomo_slurm.py

@@ -10,7 +10,7 @@
 
 import requests
 
-from cryoemservices.services.tomo_align import TomoAlign, TomoParameters
+from cryoemservices.services.tomo_align_aretomo import AreTomoAlign, AreTomoParameters
 from cryoemservices.util.slurm_submission import slurm_submission_for_services
 
 
@@ -85,21 +85,21 @@ def get_iris_state(logger, wait=True) -> str:
     return "unknown"
 
 
-class TomoAlignSlurm(TomoAlign):
+class AreTomoAlignSlurm(AreTomoAlign):
     """
     A service for submitting AreTomo2 jobs to a slurm cluster via RestAPI
     """
 
     # Logger name
-    _logger_name = "cryoemservices.services.tomo_align_slurm"
+    _logger_name = "cryoemservices.services.tomo_align_aretomo_slurm"
 
     def initializing(self):
         if not get_iris_state(self.log):
             exit()
         super().initializing()
 
     @staticmethod
-    def check_visit(tomo_params: TomoParameters):
+    def check_visit(tomo_params: AreTomoParameters):
         # Requeue visits that should not be sent via slurm
         visit_search = re.search(
             "/[a-z]{2}[0-9]{5}-[0-9]{1,3}/", tomo_params.stack_file
@@ -128,7 +128,7 @@ def parse_tomo_output_file(self, tomo_output_file: Path):
 
     def aretomo(
         self,
-        tomo_parameters: TomoParameters,
+        tomo_parameters: AreTomoParameters,
         aretomo_output_path: Path,
         angle_file: Path,
     ):