Merge branch 'master' into fix_missing_samplesheet

VERSIONLOG.md

@@ -1,9 +1,21 @@
 # TACA Version Log
 
-## 20241211.1
+## 20241216.1
 
 Email user instead of craching if unable to create Illumina runobject
 
+## 20241212.2
+
+Fix for ONT demultiplexing status in bioinfo deliveries script
+
+## 20241212.1
+
+Add ONT instrument data to bioinfo_tab
+
+## 20241211.1
+
+No longer reserve PromethION column 3 for Clinical Genomics.
+
 ## 20241210.4
 
 Change server_status nas to update statusdb by default

taca/nanopore/instrument_transfer.py

@@ -12,10 +12,9 @@
 from glob import glob
 
 RUN_PATTERN = re.compile(
-    # Run folder name expected as yyyymmdd_HHMM_1A-3H/MN19414_flowCellId_randomHash
+    # Run folder name expected as yyyymmdd_HHMM_positionOrInstrument_flowCellId_randomHash
     # Flow cell names starting with "CTC" are configuration test cells and should not be included
-    # As of december 2023, the third column (3A-3H) is excluded, because it will be used by Clinical Genomics
-    r"^\d{8}_\d{4}_(([1-2][A-H])|(MN19414))_(?!CTC)[A-Za-z0-9]+_[A-Za-z0-9]+$"
+    r"^\d{8}_\d{4}_(([1-3][A-H])|(MN19414))_(?!CTC)[A-Za-z0-9]+_[A-Za-z0-9]+$"
 )
 
 

taca/utils/bioinfo_tab.py

@@ -8,6 +8,7 @@
 from flowcell_parser.classes import RunParametersParser, SampleSheetParser
 
 from taca.element.Aviti_Runs import Aviti_Run
+from taca.nanopore.ONT_run_classes import ONT_RUN_PATTERN, ONT_run
 from taca.utils import statusdb
 from taca.utils.config import CONFIG
 from taca.utils.misc import send_mail
@@ -47,6 +48,14 @@ def collect_runs():
                                 continue
                             logger.info(f"Working on {run_dir}")
                             update_statusdb(run_dir, inst_brand)
+                        elif inst_brand == "ont":
+                            # Skip archived, no_backup, nosync and qc folders
+                            if re.match(
+                                ONT_RUN_PATTERN,
+                                os.path.basename(os.path.abspath(run_dir)),
+                            ):
+                                logger.info(f"Working on {run_dir}")
+                                update_statusdb(run_dir, inst_brand)
 
                 nosync_data_dir = os.path.join(data_dir, "nosync")
                 potential_nosync_run_dirs = glob.glob(
@@ -59,7 +68,7 @@ def collect_runs():
                             and illumina_rundir_re.match(
                                 os.path.basename(os.path.abspath(run_dir))
                             )
-                        ) or inst_brand == "element":
+                        ) or (inst_brand == "element" or inst_brand == "ont"):
                             # Skip archived dirs
                             if run_dir == os.path.join(nosync_data_dir, "archived"):
                                 continue
@@ -79,6 +88,15 @@ def update_statusdb(run_dir, inst_brand):
             # Logger in Aviti_Run.parse_run_parameters() will print the warning
             # WARNING - Run parameters file not found for ElementRun(<run_dir>), might not be ready yet
             return
+    elif inst_brand == "ont":
+        run_dir = os.path.abspath(run_dir)
+        try:
+            ont_run = ONT_run(run_dir)
+        except AssertionError as e:
+            logger.error(f"ONT Run folder error: {e}")
+            return
+
+        run_id = ont_run.run_name
 
     statusdb_conf = CONFIG.get("statusdb")
     couch_connection = statusdb.StatusdbSession(statusdb_conf).connection
@@ -91,6 +109,8 @@ def update_statusdb(run_dir, inst_brand):
         project_info = get_ss_projects_illumina(run_dir)
     elif inst_brand == "element":
         project_info = get_ss_projects_element(aviti_run)
+    elif inst_brand == "ont":
+        project_info = get_ss_projects_ont(ont_run, couch_connection)
     # Construction and sending of individual records, if samplesheet is incorrectly formatted the loop is skipped
     if project_info:
         for flowcell in project_info:
@@ -103,6 +123,8 @@ def update_statusdb(run_dir, inst_brand):
                             sample_status = get_status(run_dir)
                         elif inst_brand == "element":
                             sample_status = get_status_element(aviti_run)
+                        elif inst_brand == "ont":
+                            sample_status = get_status_ont(ont_run)
                         project_info[flowcell][lane][sample].value = sample_status
                         obj = {
                             "run_id": run_id,
@@ -234,6 +256,46 @@ def get_status_element(aviti_run):
     return status
 
 
+def get_status_ont(ont_run):
+    """Gets status of a ONT sample run, based on flowcell info."""
+    # Default state, should never occur
+    status = "ERROR"
+    run_status = ont_run.db.check_run_status(ont_run)
+
+    if run_status in ["finished"]:
+        status = "New"
+    elif run_status in ["ongoing"]:
+        status = "Sequencing"
+
+    return status
+
+
+def get_ss_projects_ont(ont_run, couch_connection):
+    """Fetches project, FC, lane & sample (sample-run) status for a given folder for ONT runs"""
+    proj_tree = Tree()
+    flowcell_id = ont_run.run_name
+    flowcell_info = (
+        couch_connection["nanopore_runs"].view("info/lims")[flowcell_id].rows[0]
+    )
+    if (
+        flowcell_info.value
+        and flowcell_info.value.get("loading", [])
+        and "sample_data" in flowcell_info.value["loading"][-1]
+    ):
+        samples = flowcell_info.value["loading"][-1]["sample_data"]
+        for sample_dict in samples:
+            sample_id = sample_dict["sample_name"]
+            project = sample_id.split("_")[0]
+            # Use default lane of 0 for ONT
+            proj_tree[flowcell_id]["0"][sample_id][project]
+
+    if list(proj_tree.keys()) == []:
+        logger.info(
+            f"There was no data in StatusDB for the ONT run, CHECK {flowcell_id}"
+        )
+    return proj_tree
+
+
 def get_ss_projects_element(aviti_run):
     """Fetches project, FC, lane & sample (sample-run) status for a given folder for element runs"""
     proj_tree = Tree()

taca/utils/cli.py

@@ -14,9 +14,15 @@ def bioinfo_deliveries():
 # bioinfo subcommands
 @bioinfo_deliveries.command()
 @click.argument("rundir")
-def updaterun(rundir):
+@click.option(
+    "-i",
+    "--inst_type",
+    type=click.Choice(["illumina", "element", "ont"]),
+    required=True,
+)
+def updaterun(rundir, inst_type):
     """Saves the bioinfo data to statusdb."""
-    bt.update_statusdb(rundir)
+    bt.update_statusdb(rundir, inst_brand=inst_type)
 
 
 @bioinfo_deliveries.command()

tests/nanopore/test_instrument_transfer.py

@@ -135,28 +135,6 @@ def test_main_ignore_CTC(setup_test_fixture):
         mock_dump_path.assert_not_called()
 
 
-def test_main_ignore_col3(setup_test_fixture):
-    """Check so that runs on column 3 (set aside for Clinical Genomics as of december 2023)
-    are not picked up.
-    """
-
-    # Run fixture
-    args, tmp, file_paths = setup_test_fixture
-
-    # Setup run
-    run_path = (
-        f"{args.source_dir}/experiment/sample/{DUMMY_RUN_NAME.replace('MN19414', '3A')}"
-    )
-    os.makedirs(run_path)
-
-    with patch("taca.nanopore.instrument_transfer.dump_path") as mock_dump_path:
-        # Start testing
-        instrument_transfer.main(args)
-
-        # Check dump_path was not called
-        mock_dump_path.assert_not_called()
-
-
 @pytest.mark.parametrize(
     "finished, qc", [(True, True), (True, False), (False, True), (False, False)]
 )