Populate tob-wgs-test metamist with nagim gvcf files

scripts/add_nagim_gvcfs_to_tob_wgs_test_metamist.py

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+from metamist.graphql import gql, query
+from metamist.apis import ParticipantApi, AnalysisApi
+from metamist.models import (
+    ParticipantUpsert,
+    SampleUpsert,
+    SequencingGroupUpsert,
+    AssayUpsert,
+    AnalysisStatus,
+    Analysis,
+)
+from cpg_utils import to_path
+import csv
+
+import click
+
+PARTICIPANT_QUERY = gql(
+    """
+    query ($project: String!) {
+        project(name: $project) {
+            id
+            participants {
+            externalId
+            id
+            samples {
+                id
+                externalId
+                sequencingGroups {
+                externalIds
+                id
+                meta
+                platform
+                technology
+                type
+                assays {
+                    meta
+                    id
+                    }
+                }
+            }
+        }
+    }
+}
+"""
+)
+
+
+@click.command()
+@click.option(
+    '--project',
+    required=True,
+    help='The name of the project to add samples to.',
+)
+@click.option(
+    '--project_id',
+    required=True,
+    type=int,
+    help='The ID of the project to add samples to.',
+)
+@click.option(
+    '--new_samples_path',
+    required=True,
+    help='The path to the file containing the newly created samples.',
+)
+def main(project: str, projectID: int, new_samples_path: str):
+    # Read the CSV file into a dictionary
+    extID_to_row = {}
+    with to_path(new_samples_path).open() as f:
+        reader = csv.reader(f)
+        next(reader)  # skip the header
+        for row in reader:
+            sgid, extID, gvcf, gvcf_idx = row[0], row[1], row[2], row[3]
+            extID_to_row[extID] = (sgid, gvcf, gvcf_idx)
+
+    query_response = query(PARTICIPANT_QUERY, {"project": project})
+    p_upserts = []
+    for participant in query_response['project']['participants']:
+        if participant['externalId'] not in extID_to_row:
+            continue
+        extID = f"{participant['externalId']}-test"
+        p = ParticipantUpsert(
+            external_id=extID,
+            active=None,
+            samples=[],
+        )
+        for sample in participant['samples']:
+            s = SampleUpsert(
+                external_id=extID,
+                project=projectID,
+                sequencing_groups=[],
+            )
+            for sg in sample['sequencingGroups']:
+                s.sequencing_groups.append(
+                    sg=SequencingGroupUpsert(
+                        type=sg['type'],
+                        technology=sg['technology'],
+                        platform=sg['platform'],
+                        meta=None,
+                        sample_id=None,
+                        external_ids=None,
+                        assays=[
+                            AssayUpsert(
+                                type=sg['assays'][0]['type'],
+                                meta={
+                                    'sequencing_type': sg['assays'][0]['meta'][
+                                        'sequencing_type'
+                                    ],
+                                    'sequencing_platform': sg['assays'][0]['meta'][
+                                        'sequencing_platform'
+                                    ],
+                                    'sequencing_technology': sg['assays'][0]['meta'][
+                                        'sequencing_technology'
+                                    ],
+                                },
+                            ),
+                        ],
+                    )
+                )
+            p.samples.append(s)
+        p_upserts.append(p)
+
+    upserted_participants = ParticipantApi().upsert_participants(project, p_upserts)
+
+    for participant in upserted_participants:
+        for sample in participant['samples']:
+            old_extID = sample['externalId'][:-5]  # remove '-test' from the end
+            gvcf_path = extID_to_row[old_extID][1]  # get gvcf path from dictionary
+            AnalysisApi().create_analysis(
+                project,
+                Analysis(
+                    type='gvcf',
+                    status=AnalysisStatus('completed'),
+                    output=gvcf_path,
+                    sequencing_group_id=sample['sequencingGroups '][0]['id'],
+                    project=projectID,
+                    active=True,
+                    external_id=sample['externalId'],
+                    sample=sample['id'],
+                ),
+            )
+
+
+if __name__ == '__main__':
+    main()