Merge pull request #12 from ssjunnebo/miseqi100

Miseqi100 integration

Author: ssjunnebo

dataflow_transfer/run_classes/__init__.py

@@ -5,6 +5,7 @@
     MiSeqRun,  # noqa: F401
     NextSeqRun,  # noqa: F401
     NovaSeqXPlusRun,  # noqa: F401
+    MiSeqi100Run,  # noqa: F401
 )
 from dataflow_transfer.run_classes.ont_runs import MinIONRun, PromethIONRun  # noqa: F401
 

dataflow_transfer/run_classes/element_runs.py

@@ -22,6 +22,6 @@ class AVITIRun(ElementRun):
 
     def __init__(self, run_dir, configuration):
         self.run_id_format = (
-            "^\d{8}_AV\d{6}_(A|BP)\d{10}$"  # 20251007_AV242106_A2507535225
+            r"^\d{8}_AV\d{6}_(A|BP)\d{10}$"  # 20251007_AV242106_A2507535225
         )
         super().__init__(run_dir, configuration)

dataflow_transfer/run_classes/illumina_runs.py

@@ -20,7 +20,7 @@ class NovaSeqXPlusRun(IlluminaRun):
 
     def __init__(self, run_dir, configuration):
         self.run_id_format = (
-            "^\d{8}_[A-Z0-9]+_\d{4}_[A-Z0-9]+$"  # 20251010_LH00202_0284_B22CVHTLT1
+            r"^\d{8}_[A-Z0-9]+_\d{4}_[A-Z0-9]+$"  # 20251010_LH00202_0284_B22CVHTLT1
         )
         super().__init__(run_dir, configuration)
 
@@ -33,7 +33,7 @@ class NextSeqRun(IlluminaRun):
 
     def __init__(self, run_dir, configuration):
         self.run_id_format = (
-            "^\d{6}_[A-Z0-9]+_\d{3}_[A-Z0-9]+$"  # 251015_VH00203_572_AAHFHCCM5
+            r"^\d{6}_[A-Z0-9]+_\d{3}_[A-Z0-9]+$"  # 251015_VH00203_572_AAHFHCCM5
         )
         super().__init__(run_dir, configuration)
 
@@ -46,6 +46,17 @@ class MiSeqRun(IlluminaRun):
 
     def __init__(self, run_dir, configuration):
         self.run_id_format = (
-            "^\d{6}_[A-Z0-9]+_\d{4}_[A-Z0-9\-]+$"  # 251015_M01548_0646_000000000-M6D7K
+            r"^\d{6}_[A-Z0-9]+_\d{4}_[A-Z0-9\-]+$"  # 251015_M01548_0646_000000000-M6D7K
         )
         super().__init__(run_dir, configuration)
+
+
+@register_run_class
+class MiSeqi100Run(IlluminaRun):
+    """Defines a MiSeqi100 sequencing run"""
+
+    run_type = "MiSeqi100"
+
+    def __init__(self, run_dir, configuration):
+        self.run_id_format = r"^\d{8}_[A-Z0-9]+_\d{4}_[A-Z0-9]{10}-SC3$"  # 20260128_SH01140_0002_ASC2150561-SC3
+        super().__init__(run_dir, configuration)

dataflow_transfer/run_classes/ont_runs.py

@@ -19,7 +19,7 @@ class PromethIONRun(ONTRun):
     run_type = "PromethION"
 
     def __init__(self, run_dir, configuration):
-        self.run_id_format = "^\d{8}_\d{4}_[A-Z0-9]{2}_P[A-Z0-9]+_[a-f0-9]{8}$"  # 20251015_1051_3B_PBG60686_0af3a2e0
+        self.run_id_format = r"^\d{8}_\d{4}_[A-Z0-9]{2}_P[A-Z0-9]+_[a-f0-9]{8}$"  # 20251015_1051_3B_PBG60686_0af3a2e0
         super().__init__(run_dir, configuration)
 
 
@@ -30,5 +30,5 @@ class MinIONRun(ONTRun):
     run_type = "MinION"
 
     def __init__(self, run_dir, configuration):
-        self.run_id_format = "^\d{8}_\d{4}_MN[A-Z0-9]+_[A-Z0-9]+_[a-f0-9]{8}$"  # 20240229_1404_MN19414_ASH657_7a74bf8f
+        self.run_id_format = r"^\d{8}_\d{4}_MN[A-Z0-9]+_[A-Z0-9]+_[a-f0-9]{8}$"  # 20240229_1404_MN19414_ASH657_7a74bf8f
         super().__init__(run_dir, configuration)

dataflow_transfer/tests/test_run_classes.py

@@ -85,6 +85,32 @@ def miseqseq_testobj(tmp_path):
     return illumina_runs.MiSeqRun(str(run_dir), config)
 
 
+@pytest.fixture
+def miseqseqi100_testobj(tmp_path):
+    config = {
+        "log": {"file": "test.log"},
+        "transfer_details": {"user": "testuser", "host": "testhost"},
+        "statusdb": {
+            "username": "dbuser",
+            "password": "dbpass",
+            "url:": "dburl",
+            "database": "dbname",
+        },
+        "sequencers": {
+            "MiSeqi100": {
+                "miarka_destination": "/data/MiSeqi100",
+                "metadata_for_statusdb": ["RunInfo.xml", "RunParameters.xml"],
+                "ignore_folders": ["nosync"],
+                "rsync_options": ["--chmod=Dg+s,g+rw"],
+            }
+        },
+    }
+    run_id = "20260128_SH01140_0002_ASC2150561-SC3"
+    run_dir = tmp_path / run_id
+    run_dir.mkdir()
+    return illumina_runs.MiSeqi100Run(str(run_dir), config)
+
+
 @pytest.fixture(autouse=True)
 def mock_statusdbsession(monkeypatch):
     class MockStatusdbSession:
@@ -106,6 +132,7 @@ def update_db_doc(self, doc):
         ("novaseqxplus_testobj", "NovaSeqXPlus"),
         ("nextseq_testobj", "NextSeq"),
         ("miseqseq_testobj", "MiSeq"),
+        ("miseqseqi100_testobj", "MiSeqi100"),
     ],
 )
 def test_confirm_run_type(run_fixture, expected_run_type, request):
@@ -124,6 +151,7 @@ def test_confirm_run_type(run_fixture, expected_run_type, request):
         "novaseqxplus_testobj",
         "nextseq_testobj",
         "miseqseq_testobj",
+        "miseqseqi100_testobj",
     ],
 )
 def test_sequencing_ongoing(run_fixture, request):
@@ -146,6 +174,8 @@ def test_sequencing_ongoing(run_fixture, request):
         ("nextseq_testobj", True),
         ("miseqseq_testobj", False),
         ("miseqseq_testobj", True),
+        ("miseqseqi100_testobj", False),
+        ("miseqseqi100_testobj", True),
     ],
 )
 def test_generate_rsync_command(run_fixture, final_sync, request):
@@ -174,6 +204,10 @@ def test_generate_rsync_command(run_fixture, final_sync, request):
         ("miseqseq_testobj", True, False),
         ("miseqseq_testobj", False, True),
         ("miseqseq_testobj", True, True),
+        ("miseqseqi100_testobj", False, False),
+        ("miseqseqi100_testobj", True, False),
+        ("miseqseqi100_testobj", False, True),
+        ("miseqseqi100_testobj", True, True),
     ],
 )
 def test_start_transfer(run_fixture, rsync_running, final, request, monkeypatch):
@@ -219,6 +253,8 @@ def mock_update_statusdb(status, additional_info=None):
         ("nextseq_testobj", False),
         ("miseqseq_testobj", True),
         ("miseqseq_testobj", False),
+        ("miseqseqi100_testobj", True),
+        ("miseqseqi100_testobj", False),
     ],
 )
 def test_final_sync_successful(run_fixture, sync_successful, request):
@@ -249,6 +285,10 @@ def test_final_sync_successful(run_fixture, sync_successful, request):
         ("miseqseq_testobj", "sequencing_started", True),
         ("miseqseq_testobj", "sequencing_finished", False),
         ("miseqseq_testobj", "sequencing_finished", True),
+        ("miseqseqi100_testobj", "sequencing_started", False),
+        ("miseqseqi100_testobj", "sequencing_started", True),
+        ("miseqseqi100_testobj", "sequencing_finished", False),
+        ("miseqseqi100_testobj", "sequencing_finished", True),
     ],
 )
 def test_has_status(run_fixture, status_to_check, expected_result, request):
@@ -268,6 +308,12 @@ def get_events(self, run_id):
 @pytest.mark.parametrize(
     "run_fixture, existing_statuses, status_to_update",
     [
+        ("novaseqxplus_testobj", [], "sequencing_started"),
+        (
+            "novaseqxplus_testobj",
+            [{"event_type": "sequencing_started"}],
+            "transfer_started",
+        ),
         (
             "nextseq_testobj",
             [],
@@ -288,6 +334,16 @@ def get_events(self, run_id):
             [{"event_type": "sequencing_started"}],
             "transfer_started",
         ),
+        (
+            "miseqseqi100_testobj",
+            [],
+            "sequencing_started",
+        ),
+        (
+            "miseqseqi100_testobj",
+            [{"event_type": "sequencing_started"}],
+            "transfer_started",
+        ),
     ],
 )
 def test_update_statusdb(

pyproject.toml

@@ -20,7 +20,7 @@ ignore = [
 
 [project]
 name = "dataflow_transfer"
-version = "1.0.4"
+version = "1.0.5"
 description = "Script for transferring sequencing data from sequencers to storage"
 authors = [
     { name = "Sara Sjunnebo", email = "sara.sjunnebo@scilifelab.se" },