Merge from devel to master to create release 1.2.0

CHANGELOG

@@ -5,6 +5,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Unreleased]
 
+## [1.2.0] 2026-09-16
+
+### Added
+
+* `validate_studies` and `get_sample_id_for_name` functions are added to
+  `npgmlwarehouse.db.product`. Both are needed for extending phase2 Ultimagen
+  pipeline to walkup runs.
+
 ## [1.1.1] - 2026-05-20
 
 ### Fixed

src/npgmlwarehouse/db/product.py

@@ -15,11 +15,16 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-from sqlalchemy import select
+from sqlalchemy import or_, select
 from sqlalchemy.dialects.mysql import insert
 from sqlalchemy.orm import Session
 
-from npgmlwarehouse.db.schema import SeqProductIrodsLocations, UseqProductMetrics
+from npgmlwarehouse.db.schema import (
+    Sample,
+    SeqProductIrodsLocations,
+    Study,
+    UseqProductMetrics,
+)
 
 
 def get_ultimagen_target_product_records(session: Session, id_run: int):
@@ -47,6 +52,85 @@ def get_ultimagen_target_product_records(session: Session, id_run: int):
     return records.all()
 
 
+def validate_studies(session: Session, study_ids: list[str]):
+    """
+    Validates a list of string study IDs.
+
+    Validates a list of study IDs by checking whether the `study` table
+    record is available for each of the IDs. The input least can contain
+    duplicate values. An empty input list will cause an error.
+
+    Errors if any of the given study IDs
+      * is not a string,
+      * is invalid, the error message lists all invalid IDs,
+      * maps to multiple database rows.
+
+    Args:
+        session (Session):
+            Database session.
+        study_ids (str):
+            Study IDs to validate.
+    Returns:
+        True if all sudies have been validated.
+    """
+
+    if len(study_ids) == 0:
+        raise ValueError("A non-empty list of string study IDs is required")
+    if len([id for id in study_ids if isinstance(id, str)]) < len(study_ids):
+        raise TypeError("All study IDs should be strings")
+
+    unique_ids = set(study_ids)
+
+    q = select(Study.id_study_lims).where(Study.id_study_lims.in_(unique_ids))
+    available = session.scalars(q).all()
+    missing = [study_id for study_id in unique_ids if study_id not in available]
+    if len(missing):
+        raise ValueError(
+            "Invalid stud{end}: {list_of}".format(
+                end="y" if len(missing) == 1 else "ies",
+                list_of=", ".join(sorted(missing)),
+            )
+        )
+    if len(available) > len(unique_ids):
+        raise Exception(
+            (
+                "Duplicate MLWH rows for some IDs in "
+                f"{', '.join(sorted(list(unique_ids)))}"
+            )
+        )
+
+    return True
+
+
+def get_sample_id_for_name(session: Session, sample_name: str) -> str | None:
+    """
+    Retrieves sample ID for the sample name given as the argument.
+
+    Searches the `sample` table for a record with the given name. Examines
+    values in two columns - `name` and `supplier_name`.
+
+    Errors if multiple records are found. Returns sample's ID if a single
+    record is found or `None` if no record is found.
+
+    Args:
+        session (Session):
+            Database session.
+        name (name):
+            Sample name.
+    Returns:
+        String sample ID if found or None
+    """
+    if not isinstance(sample_name, str):
+        raise TypeError("sample_name argument should be a string")
+    if not sample_name:
+        raise ValueError("sample_name argument should be a non-empty string")
+
+    q = select(Sample.id_sample_lims).where(
+        or_(Sample.name == sample_name, Sample.supplier_name == sample_name)
+    )
+    return session.scalars(q).one_or_none()
+
+
 def create_upload_irods_location_records(
     session: Session,
     product_data: dict[str, dict],

tests/data/db_fixtures/000-Sample.yml

@@ -9,6 +9,7 @@
   id_sample_lims: 10000
   id_sample_tmp: 1
   last_updated: 2012-08-03 10:07:02
+  name: 'Burkholderia 1'
   organism: Burkholderia pseudomallei
   recorded_at: 2014-11-18 13:06:19
   reference_genome: ' '
@@ -27,6 +28,8 @@
   id_sample_lims: 10001
   id_sample_tmp: 2
   last_updated: 2012-08-03 10:07:02
+  name: 'Burkholderia 22'
+  supplier_name: 'Burkholderia 2'
   organism: Burkholderia pseudomallei
   recorded_at: 2014-11-18 13:06:19
   reference_genome: ' '

tests/data/db_fixtures/000-Study.yml

@@ -1,7 +1,7 @@
 ---
 - abbreviation: 619STDY
   abstract: For further information on this study please see
-  accession_number: ERP000251
+  accession_number: 251
   aligned: 1
   array_express_accession_number: ~
   contains_human_dna: 0
@@ -33,3 +33,105 @@
   study_type: Whole Genome Sequencing
   study_visibility: Hold
   uuid_study_lims: 1231de50-6ffb-11e4-b9db-68b59977951c
+- abbreviation: 622STDY
+  abstract: For further information on this study please see
+  accession_number: 34
+  aligned: 1
+  array_express_accession_number: ~
+  contains_human_dna: 0
+  contaminated_human_dna: 0
+  created: 2010-06-25 11:19:52
+  data_access_group: ~
+  data_release_delay_period: ~
+  data_release_delay_reason: ~
+  data_release_sort_of_study: genomic sequencing
+  data_release_strategy: open
+  data_release_timing: standard
+  deleted_at: ~
+  description: 'For further information on this study please'
+  ega_dac_accession_number: ~
+  ega_policy_accession_number: ~
+  ena_project_id: 0
+  ethically_approved: ~
+  id_lims: SQSCP
+  id_study_lims: 622
+  id_study_tmp: 197
+  last_updated: 2012-11-26 14:15:32
+  name: Burkholderia pseudomallei
+  recorded_at: 2014-11-19 14:48:06
+  reference_genome: ' '
+  remove_x_and_autosomes: 0
+  separate_y_chromosome_data: 0
+  state: active
+  study_title: Burkholderia pseudomallei
+  study_type: Whole Genome Sequencing
+  study_visibility: Hold
+  uuid_study_lims: 1231de50-6ffb-11e4-b9db-68b59977951b
+- abbreviation: 623STDY
+  abstract: For further information on this study please see
+  accession_number: 34
+  aligned: 1
+  array_express_accession_number: ~
+  contains_human_dna: 0
+  contaminated_human_dna: 0
+  created: 2010-06-25 11:19:52
+  data_access_group: ~
+  data_release_delay_period: ~
+  data_release_delay_reason: ~
+  data_release_sort_of_study: genomic sequencing
+  data_release_strategy: open
+  data_release_timing: standard
+  deleted_at: ~
+  description: 'For further information on this study please'
+  ega_dac_accession_number: ~
+  ega_policy_accession_number: ~
+  ena_project_id: 0
+  ethically_approved: ~
+  id_lims: SQSCP
+  id_study_lims: 623
+  id_study_tmp: 198
+  last_updated: 2012-11-26 14:15:32
+  name: Burkholderia pseudomallei
+  recorded_at: 2014-11-19 14:48:06
+  reference_genome: ' '
+  remove_x_and_autosomes: 0
+  separate_y_chromosome_data: 0
+  state: active
+  study_title: Burkholderia pseudomallei
+  study_type: Whole Genome Sequencing
+  study_visibility: Hold
+  uuid_study_lims: 1231de50-6ffb-11e4-b9db-68b59977951d
+- abbreviation: 623STDY
+  abstract: For further information on this study please see
+  accession_number: 34
+  aligned: 1
+  array_express_accession_number: ~
+  contains_human_dna: 0
+  contaminated_human_dna: 0
+  created: 2010-06-25 11:19:52
+  data_access_group: ~
+  data_release_delay_period: ~
+  data_release_delay_reason: ~
+  data_release_sort_of_study: genomic sequencing
+  data_release_strategy: open
+  data_release_timing: standard
+  deleted_at: ~
+  description: 'For further information on this study please'
+  ega_dac_accession_number: ~
+  ega_policy_accession_number: ~
+  ena_project_id: 0
+  ethically_approved: ~
+  id_lims: Sapio
+  id_study_lims: 623
+  id_study_tmp: 199
+  last_updated: 2012-11-26 14:15:32
+  name: Burkholderia pseudomallei
+  recorded_at: 2014-11-19 14:48:06
+  reference_genome: ' '
+  remove_x_and_autosomes: 0
+  separate_y_chromosome_data: 0
+  state: active
+  study_title: Burkholderia pseudomallei
+  study_type: Whole Genome Sequencing
+  study_visibility: Hold
+  uuid_study_lims: 1231de50-6ffb-11e4-b9db-68b59977951k

tests/test_product.py

@@ -1,11 +1,14 @@
 from time import sleep
 
 from pytest import mark as m
+from pytest import raises
 from sqlalchemy import select
 
 from npgmlwarehouse.db.product import (
     create_upload_irods_location_records,
+    get_sample_id_for_name,
     get_ultimagen_target_product_records,
+    validate_studies,
 )
 from npgmlwarehouse.db.schema import SeqProductIrodsLocations
 
@@ -385,3 +388,49 @@ def test_create_upload_irods_location_records_duplicate_unique_key_part_input_up
         record = records.pop()
         assert record.irods_data_relative_path == None
         assert record.irods_secondary_data_relative_path == None
+
+
+@m.describe("Test Sample Retrieval")
+class TestSampleRetrieval(object):
+    def test_get_sample_id(self, testdb):
+
+        with raises(TypeError):
+            get_sample_id_for_name(testdb)
+        with raises(TypeError, match=r"sample_name argument should be a string"):
+            get_sample_id_for_name(testdb, 45)
+        with raises(TypeError, match=r"sample_name argument should be a string"):
+            get_sample_id_for_name(testdb, None)
+        with raises(
+            ValueError, match=r"sample_name argument should be a non-empty string"
+        ):
+            get_sample_id_for_name(testdb, "")
+
+        assert get_sample_id_for_name(testdb, "Burkholderia 1") == "10000"
+        assert get_sample_id_for_name(testdb, "Burkholderia 2") == "10001"
+        assert get_sample_id_for_name(testdb, "Burkholderia 25") is None
+
+
+@m.describe("Test Study Validation")
+class TestStudyValidation(object):
+    def test_validate_studies(self, testdb):
+
+        with raises(TypeError):
+            assert validate_studies(testdb)
+        with raises(
+            ValueError, match=r"A non-empty list of string study IDs is required"
+        ):
+            assert validate_studies(testdb, [])
+        with raises(TypeError, match=r"All study IDs should be strings"):
+            assert validate_studies(testdb, ["1234", 34])
+        with raises(Exception, match=r"Duplicate MLWH rows for some IDs in 619, 623"):
+            assert validate_studies(testdb, ["623", "619", "623"])
+
+        assert validate_studies(testdb, ["619"]) is True
+        assert validate_studies(testdb, ["619", "622"]) is True
+
+        with raises(ValueError, match=r"Invalid study: 620"):
+            assert validate_studies(testdb, ["620"])
+        with raises(ValueError, match=r"Invalid studies: 620, 621"):
+            assert validate_studies(testdb, ["621", "620"])
+        with raises(ValueError, match=r"Invalid study: 620"):
+            assert validate_studies(testdb, ["619", "620"])