register missing combiner analysis script (#984)

* register missing combiner analysis script

* docstring

* moar docstring

* turn on hail and fix spelling mistake

scripts/register_missing_combiner_analysis.py

@@ -0,0 +1,54 @@
+"""Register a missing combiner analysis in Metamist
+
+Ad-hoc script to register a missing combiner analysis in Metamist.
+Is supremely inflexible since there is a short timeframe for combining previous
+VDS' for the OurDNA browser release.
+"""
+
+from argparse import ArgumentParser
+
+from hail.vds import read_vds
+
+from cpg_utils import to_path
+from cpg_utils.hail_batch import init_batch
+from metamist.apis import AnalysisApi
+from metamist.models import Analysis, AnalysisStatus
+
+
+def get_sg_ids(vds: str) -> list[str]:
+    """Gets all sequencing group IDs from a VDS
+
+    Args:
+        vds (str): The VDS to extract the sequencing group IDs from
+
+    Returns:
+        list[str]: A list of sequencing group IDs.
+    """
+    return read_vds(to_path(vds)).variant_data.s.collect()
+
+
+def main(vds: str, dataset: str):
+    """Create and register a missing combiner analysis
+
+    Args:
+        vds (str): The existing VDS that needs to be registered
+        dataset (str): The project / dataset to register the analysis in
+    """
+    init_batch()
+    aapi = AnalysisApi()
+    am = Analysis(
+        type='combiner',
+        output=vds,
+        status=AnalysisStatus('completed'),
+        sequencing_group_ids=get_sg_ids(vds),
+        meta=None,
+    )
+    aapi.create_analysis(project=dataset, analysis=am)
+
+
+if __name__ == '__main__':
+    parser = ArgumentParser()
+    parser.add_argument('--vds', help='VDS to register analysis for.')
+    parser.add_argument('--dataset', help='Dataset to register analysis in.')
+    args = parser.parse_args()
+    main(args.vds, args.dataset)