Populate tob-wgs-test metamist with nagim gvcf files

scripts/add_nagim_gvcfs_to_tob_wgs_test_metamist.py

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+import csv
+from dataclasses import dataclass
+from pprint import pprint
+
+import click
+from cpg_utils import to_path
+
+from metamist.apis import ParticipantApi, AnalysisApi
+from metamist.graphql import gql, query
+from metamist.models import (
+    ParticipantUpsert,
+    SampleUpsert,
+    SequencingGroupUpsert,
+    AssayUpsert,
+    AnalysisStatus,
+    Analysis,
+)
+
+
+@dataclass
+class RowData:
+    """
+    A class used to represent a row of data.
+
+    Attributes
+    ----------
+    sgid : str
+        an identifier for the sequencing group
+    ext_id : str
+        an external identifier for the row
+    gvcf : str
+        the path to the gvcf file
+    gvcf_idx : str
+        the path to the gvcf index file
+    """
+
+    sgid: str
+    ext_id: str
+    gvcf: str
+    gvcf_idx: str
+
+
+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(
+    '--sample-path-mappings',
+    required=True,
+    help="""The path to a CSV file containing mappings of `main` CPG ID's,
+            the `external_id` and `gvcf` paths.
+            The file should have at least four columns: sgid, ext_id, gvcf, and gvcf_idx.
+            Here's an example of what the first couple of lines might look like:
+
+            sgid,ext_id,gvcf,gvcf_idx
+            sg1,ext1,gvcf1,gvcf_idx1
+            sg2,ext2,gvcf2,gvcf_idx2
+        """,
+)
+@click.option(
+    '--project-id',
+    required=True,
+    type=int,
+    help="""The ID of the project to add samples to.
+            For example: iterate over `main` project (identified by the --project flag) to get data for each sample, then create a new participant
+            with the same data, but with a new external ID that has the suffix (--suffix) specified by the user.
+            Then upsert these into the `test` project.
+        """,
+)
+@click.option(
+    '--suffix',
+    required=True,
+    help="""The suffix to add to the external ID's of the participants.
+            For example, if the suffix is `test`, then the external ID's of the participants
+            will be `ext_id1-test`, `ext_id2-test`, etc.
+        """,
+)
+def main(project: str, project_id: int, sample_path_mappings: str, suffix: str):
+    """
+    Iterate over `main` project to get data for each sample, then create a new participant
+    with the same data, but with a new external ID that has the suffix specified by the user.
+    Then upsert these into the `test` project.
+    """
+    # Read the CSV file into a dictionary
+    ext_id_to_row = {}
+    with to_path(sample_path_mappings).open() as f:
+        reader = csv.reader(f)
+        next(reader)  # skip the header
+        for row in reader:
+            data = RowData(*row[:4])
+            ext_id_to_row[data.ext_id] = data
+
+    query_response = query(PARTICIPANT_QUERY, {'project': project})
+    p_upserts = []
+    # pylint: disable=unsubscriptable-object
+    for participant in query_response['project']['participants']:
+        if participant['externalId'] not in ext_id_to_row:
+            continue
+        ext_id = f"{participant['externalId']}-{suffix}"
+        p = ParticipantUpsert(
+            external_id=ext_id,
+            active=None,
+            samples=[],
+        )
+        for sample in participant['samples']:
+            s = SampleUpsert(
+                external_id=ext_id,
+                project=project_id,
+                sequencing_groups=[],
+            )
+            for sg in sample['sequencingGroups']:
+                pprint(sg)
+                s.sequencing_groups.append(
+                    SequencingGroupUpsert(
+                        type=sg['type'],
+                        technology=sg['technology'],
+                        platform=sg['platform'],
+                        meta=None,
+                        sample_id=None,
+                        external_ids=None,
+                        assays=[
+                            AssayUpsert(
+                                type=sg['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)
+    # pylint: enable=unsubscriptable-object
+
+    upserted_participants = ParticipantApi().upsert_participants(project, p_upserts)
+
+    for participant in upserted_participants:
+        for sample in participant['samples']:
+            old_ext_id = sample['externalId'].removesuffix(f'-{suffix}')
+            row_data = ext_id_to_row[old_ext_id]
+            gvcf_path = row_data.gvcf  # 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'],
+                    active=True,
+                ),
+            )
+
+
+if __name__ == '__main__':
+    # pylint: disable=no-value-for-parameter
+    main()
+    # pylint: enable=no-value-for-parameter