add -i flag to rerun EPP

cg_lims/EPPs/move/rerun_samples.py

@@ -9,28 +9,30 @@
 from cg_lims.exceptions import DuplicateSampleError, LimsError, MissingArtifactError
 from cg_lims.get.artifacts import filter_artifacts, get_artifacts, get_latest_analyte
 from cg_lims.put.queue import queue_artifacts
-from genologics.entities import Artifact
+from genologics.entities import Artifact, Process, Sample
 from genologics.lims import Lims
 
 LOG = logging.getLogger(__name__)
 
 
 def get_artifacts_to_requeue(
-    lims: Lims, rerun_arts: List[Artifact], process_type: List[str]
+    lims: Lims, rerun_artifacts: List[Artifact], process_types: List[str]
 ) -> List[Artifact]:
     """Get input artifacts to define step (output artifacts of sort step)
     Args:
         lims: Lims
-        rerun_arts: List # Artifacts with Rerun flag
-        process_type: List[str] # Name of step(s) before the requeue step
+        rerun_artifacts: List # Artifacts with Rerun flag
+        process_types: List[str] # Name of step(s) before the requeue step
     """
 
-    artifacts_to_requeue = []
-    break_rerun = False
-    for art in rerun_arts:
-        representative_sample_id = art.samples[0].id  ## hantera med if samples..
+    artifacts_to_requeue: List[Artifact] = []
+    break_rerun: bool = False
+    for artifact in rerun_artifacts:
+        representative_sample_id: str = artifact.samples[0].id
         try:
-            requeue_art = get_latest_analyte(lims, representative_sample_id, process_type)
+            requeue_art: Artifact = get_latest_analyte(
+                lims=lims, sample_id=representative_sample_id, process_types=process_types
+            )
         except MissingArtifactError as e:
             LOG.warning(e.message)
             break_rerun = True
@@ -44,13 +46,13 @@ def get_artifacts_to_requeue(
 def check_same_sample_in_many_rerun_pools(rerun_arts: List[Artifact]) -> None:
     """Check that the same sample does not occure in more than one of the pools to rerun."""
 
-    all_samples = []
+    all_samples: List[Sample] = []
 
     for art in rerun_arts:
         all_samples += art.samples
     for s in set(all_samples):
         all_samples.remove(s)
-    duplicate_samples = list(set(all_samples))
+    duplicate_samples: List[Sample] = list(set(all_samples))
     if duplicate_samples:
         raise DuplicateSampleError(
             f"Waring same sample in many pools: {' ,'.join([sample.id for sample in duplicate_samples])}"
@@ -64,16 +66,24 @@ def check_same_sample_in_many_rerun_pools(rerun_arts: List[Artifact]) -> None:
     help="The name(s) of the process type(s) before the requeue step. Fetching artifact to requeue from here."
 )
 @options.udf(help="UDF that will tell wich artifacts to move.")
+@options.input(
+    help="Use this flag if you want to queue the input artifacts of the current process. Default is to queue the "
+    "output artifacts (analytes) of the process. "
+)
 @click.pass_context
-def rerun_samples(ctx, workflow_id, stage_id, udf, process_types):
+def rerun_samples(
+    ctx, workflow_id: str, stage_id: str, process_types: List[str], udf: str, input: bool
+):
     """Script to requeue samples for sequencing."""
-    process = ctx.obj["process"]
-    lims = ctx.obj["lims"]
-    artifacts = get_artifacts(process, False)
-    rerun_arts = filter_artifacts(artifacts, udf, True)
-    if rerun_arts:
+    process: Process = ctx.obj["process"]
+    lims: Lims = ctx.obj["lims"]
+    artifacts: List[Artifact] = get_artifacts(process=process, input=input)
+    rerun_artifacts: List[Artifact] = filter_artifacts(artifacts=artifacts, udf=udf, value=True)
+    if rerun_artifacts:
         try:
-            artifacts_to_requeue = get_artifacts_to_requeue(lims, rerun_arts, process_types)
+            artifacts_to_requeue: List[Artifact] = get_artifacts_to_requeue(
+                lims=lims, rerun_artifacts=rerun_artifacts, process_types=process_types
+            )
             check_same_sample_in_many_rerun_pools(artifacts_to_requeue)
             queue_artifacts(lims, artifacts_to_requeue, workflow_id, stage_id)
             click.echo("Artifacts have been queued.")