Fix metrics path (#2909)(patch)

cg/exc.py

@@ -138,7 +138,7 @@ class MicrosaltError(CgError):
     """
 
 
-class MissingAnalysisDir(CgError):
+class MissingAnalysisRunDirectory(CgError):
     """
     Error related to missing analysis.
     """

cg/meta/workflow/microsalt/microsalt.py

@@ -1,5 +1,4 @@
 import logging
-import os
 import re
 import shutil
 from datetime import datetime
@@ -16,6 +15,7 @@
 from cg.meta.workflow.fastq import MicrosaltFastqHandler
 from cg.meta.workflow.microsalt.quality_controller import QualityController
 from cg.meta.workflow.microsalt.quality_controller.models import QualityResult
+from cg.meta.workflow.microsalt.utils import get_most_recent_project_directory
 from cg.models.cg_config import CGConfig
 from cg.store.models import Case, Sample
 from cg.utils import Process
@@ -301,16 +301,7 @@ def get_project_id(self, case_id: str) -> str:
     def get_results_dir(self) -> Path:
         return Path(self.root_dir, "results")
 
-    def get_analyses_result_dirs(self, case_id: str) -> list[str]:
-        project_id: str = self.get_project_id(case_id)
-        results_dir: Path = self.get_results_dir()
-        matches: list[str] = [d for d in os.listdir(results_dir) if d.startswith(project_id)]
-        if not matches:
-            LOG.error(f"No result directory found for {case_id} with project id {project_id}")
-        return matches
-
     def get_case_path(self, case_id: str) -> Path:
+        project_id: str = self.get_project_id(case_id)
         results_dir: Path = self.get_results_dir()
-        matching_cases: list[str] = self.get_analyses_result_dirs(case_id)
-        case_dir: str = max(matching_cases, default="")
-        return Path(results_dir, case_dir)
+        return get_most_recent_project_directory(project_id=project_id, directory=results_dir)

cg/meta/workflow/microsalt/utils.py

@@ -0,0 +1,32 @@
+from datetime import datetime
+import os
+from pathlib import Path
+
+from cg.exc import MissingAnalysisRunDirectory
+
+
+def get_project_directory_date(dir_name: str) -> datetime:
+    # Assumes format like <project_id>_year.month.day_hour.minute.second
+    _, date, time = dir_name.split("_")
+    date_time = f"{date}_{time}"
+    return datetime.strptime(date_time, "%Y.%m.%d_%H.%M.%S")
+
+
+def get_project_directories(project_id: str, directory: Path) -> list[str]:
+    return [sub_dir for sub_dir in os.listdir(directory) if sub_dir.startswith(project_id)]
+
+
+def sort_project_directories_by_date(project_directories: list[str]) -> list[str]:
+    return sorted(project_directories, key=get_project_directory_date, reverse=True)
+
+
+def get_most_recent_project_directory(project_id: str, directory: Path) -> Path:
+    project_directories: list[str] = get_project_directories(
+        project_id=project_id, directory=directory
+    )
+    sorted_project_directories: list[str] = sort_project_directories_by_date(project_directories)
+
+    if not sorted_project_directories:
+        raise MissingAnalysisRunDirectory(f"No analysis directory found for project {project_id}.")
+
+    return Path(directory, sorted_project_directories[0])

tests/meta/workflow/test_microsalt.py

@@ -1,11 +1,13 @@
 """Tests for MicroSALT analysis."""
 
+from datetime import datetime
 from pathlib import Path
 
 from mock import MagicMock
 
 from cg.apps.lims.api import LimsAPI
 from cg.meta.workflow.microsalt import MicrosaltAnalysisAPI
+from cg.meta.workflow.microsalt.utils import get_project_directory_date
 from cg.models.cg_config import CGConfig
 from cg.store.models import Case
 
@@ -32,3 +34,14 @@ def test_get_cases_to_store_pass(
 
     # THEN cases should returned
     assert cases_to_store
+
+
+def test_get_date_from_project_directory():
+    # GIVEN a microsalt analysis run directory name
+    run_dir_name = "ACC13796_2024.2.5_15.58.22"
+
+    # WHEN parsing the project directory date
+    run_date: datetime = get_project_directory_date(run_dir_name)
+
+    # THEN the date should be parsed correctly
+    assert run_date == datetime(2024, 2, 5, 15, 58, 22)