Add support for updating Sequenom metadata in iRODS

src/npg_irods/cli/locate_data_objects.py

@@ -28,7 +28,7 @@
 from partisan.irods import AVU, DataObject, query_metadata
 from sqlalchemy.orm import Session
 
-from npg_irods import illumina, ont, pacbio
+from npg_irods import illumina, ont, pacbio, sequenom
 from npg_irods.cli.util import (
     add_date_range_arguments,
     add_db_config_arguments,
@@ -73,14 +73,14 @@
 
 Examples:
 
-    locate-data-objects --verbose --colour --database-config db.ini --zone seq \\
+    locate-data-objects --verbose --colour --db-config db.ini --zone seq \\
         consent-withdrawn
 
-    locate-data-objects --verbose --json  --database-config db.ini --zone seq \\
+    locate-data-objects --verbose --json  --db-config db.ini --zone seq \\
         illumina-updates --begin-date `date --iso --date=-7day` \\
         --skip-absent-runs 5
 
-    locate-data-objects --verbose --colour --database-config db.ini --zone seq \\
+    locate-data-objects --verbose --colour --db-config db.ini --zone seq \\
         ont-updates --begin-date `date --iso --date=-7day`
 
 The --skip-absent-runs option is used to skip runs that cannot be found in iRODS after
@@ -109,7 +109,7 @@
 
 
 def consent_withdrawn(cli_args: argparse.ArgumentParser):
-    dbconfig = DBConfig.from_file(cli_args.database_config.name, "mlwh_ro")
+    dbconfig = DBConfig.from_file(cli_args.db_config.name, "mlwh_ro")
     engine = sqlalchemy.create_engine(dbconfig.url)
     with Session(engine) as session:
         num_processed = num_errors = 0
@@ -150,7 +150,7 @@ def consent_withdrawn(cli_args: argparse.ArgumentParser):
 def illumina_updates_cli(cli_args: argparse.ArgumentParser):
     """Process the command line arguments for finding Illumina data objects and execute
     the command."""
-    dbconf = DBConfig.from_file(cli_args.database_config.name, "mlwh_ro")
+    dbconf = DBConfig.from_file(cli_args.db_config.name, "mlwh_ro")
     eng = sqlalchemy.create_engine(dbconf.url)
     since = cli_args.begin_date
     until = cli_args.end_date
@@ -262,7 +262,7 @@ def illumina_updates(
 def ont_updates_cli(cli_args: argparse.ArgumentParser):
     """Process the command line arguments for finding ONT data objects and execute the
     command."""
-    dbconf = DBConfig.from_file(cli_args.database_config.name, "mlwh_ro")
+    dbconf = DBConfig.from_file(cli_args.db_config.name, "mlwh_ro")
     eng = sqlalchemy.create_engine(dbconf.url)
     since = cli_args.begin_date
     until = cli_args.end_date
@@ -328,7 +328,7 @@ def ont_updates(
 def pacbio_updates_cli(cli_args: argparse.ArgumentParser):
     """Process the command line arguments for finding PacBio data objects and execute
     the command."""
-    dbconf = DBConfig.from_file(cli_args.database_config.name, "mlwh_ro")
+    dbconf = DBConfig.from_file(cli_args.db_config.name, "mlwh_ro")
     eng = sqlalchemy.create_engine(dbconf.url)
     since = cli_args.begin_date
     until = cli_args.end_date
@@ -415,7 +415,7 @@ def pacbio_updates(
 def infinium_updates_cli(cli_args: argparse.ArgumentParser):
     """Process the command line arguments for finding Infinium microarray data objects
     and execute the command."""
-    dbconf = DBConfig.from_file(cli_args.database_config.name, "mlwh_ro")
+    dbconf = DBConfig.from_file(cli_args.db_config.name, "mlwh_ro")
     eng = sqlalchemy.create_engine(dbconf.url)
     since = cli_args.begin_date
     until = cli_args.end_date
@@ -433,9 +433,49 @@ def infinium_updates_cli(cli_args: argparse.ArgumentParser):
 def infinium_microarray_updates(
     sess: Session, since: datetime, until: datetime, zone: str = None
 ) -> (int, int):
-    num_processed = num_errors = 0
-
     query = [AVU(infinium.Instrument.BEADCHIP, "%", operator="like")]
+    num_processed, num_errors = _print_data_objects_updated_in_mlwh(
+        sess, query, since=since, until=until, zone=zone
+    )
+
+    log.info(f"Processed {num_processed} with {num_errors} errors")
+
+    return num_processed, num_errors
+
+
+def sequenom_updates_cli(cli_args: argparse.ArgumentParser):
+    """Process the command line arguments for finding Sequenom genotype data objects
+    and execute the command."""
+    dbconf = DBConfig.from_file(cli_args.db_config.name, "mlwh_ro")
+    eng = sqlalchemy.create_engine(dbconf.url)
+    since = cli_args.begin_date
+    until = cli_args.end_date
+    zone = cli_args.zone
+
+    with Session(eng) as sess:
+        num_proc, num_errors = sequenom_genotype_updates(sess, since, until, zone=zone)
+
+        if num_errors:
+            sys.exit(1)
+
+
+def sequenom_genotype_updates(
+    sess: Session, since: datetime, until: datetime, zone: str = None
+) -> (int, int):
+    query = [AVU(sequenom.Instrument.SEQUENOM_PLATE, "%", operator="like")]
+    num_processed, num_errors = _print_data_objects_updated_in_mlwh(
+        sess, query, since=since, until=until, zone=zone
+    )
+
+    log.info(f"Processed {num_processed} with {num_errors} errors")
+
+    return num_processed, num_errors
+
+
+def _print_data_objects_updated_in_mlwh(
+    sess: Session, query: list[AVU], since: datetime, until: datetime, zone: str = None
+) -> (int, int):
+    num_processed = num_errors = 0
 
     studies = find_updated_studies(sess, since=since, until=until)
     np, ne = _find_and_print_data_objects(
@@ -451,8 +491,6 @@ def infinium_microarray_updates(
     num_processed += np
     num_errors += ne
 
-    log.info(f"Processed {num_processed} with {num_errors} errors")
-
     return num_processed, num_errors
 
 

src/npg_irods/sequenom.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright © 2024 Genome Research Ltd. All rights reserved.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+# @author Keith James <kdj@sanger.ac.uk>
+
+from partisan.metadata import AsValueEnum
+
+
+class Instrument(AsValueEnum):
+    """Sequenom genotyping platform metadata"""
+
+    SEQUENOM_PLATE = "sequenom_plate"
+    SEQUENOM_WELL = "sequenom_well"
+    SEQUENOM_PLEX = "sequenom_plex"