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Merge pull request #85 from CSCfi/feature/matename
Adding support for mateName
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,8 @@ | ||
| """Extension Module.""" | ||
| """Extensions Module. | ||
| This module contains optional extensions to the Beacon Python Server. | ||
| Currently we have two extensions: | ||
| * handover - used to convey extra information regarding the Beacon service, or the dataset response; | ||
| * mate fusion - used for finding breakend records. | ||
| """ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| """Prepare mate.""" | ||
| from functools import partial | ||
| from ..utils.logging import LOG | ||
| from ..api.exceptions import BeaconServerError | ||
| from ..conf.config import DB_SCHEMA | ||
| from .handover import add_handover | ||
| from ..utils.data_query import handle_wildcard, transform_misses, transform_record | ||
| from .. import __handover_drs__ | ||
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| async def fetch_fusion_dataset(db_pool, assembly_id, position, chromosome, reference, mate, | ||
| datasets=None, access_type=None, misses=False): | ||
| """Execute filter datasets. | ||
| There is an Uber query that aims to retrieve specific for data for mate fusion table. | ||
| """ | ||
| # Take one connection from the database pool | ||
| async with db_pool.acquire(timeout=180) as connection: | ||
| # Start a new session with the connection | ||
| async with connection.transaction(): | ||
| # Fetch dataset metadata according to user request | ||
| datasets_query = None if not datasets else datasets | ||
| access_query = None if not access_type else access_type | ||
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| start_pos = None if position[0] is None or (position[2] and position[3]) else position[0] | ||
| end_pos = None if position[1] is None or (position[4] and position[5]) else position[1] | ||
| startMax_pos = position[3] | ||
| startMin_pos = position[2] | ||
| endMin_pos = position[4] | ||
| endMax_pos = position[5] | ||
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| refbase = None if not reference else handle_wildcard(reference) | ||
| try: | ||
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| # UBER QUERY - TBD if it is what we need | ||
| # referenceBases, alternateBases and variantType fields are NOT part of beacon's specification response | ||
| query = f"""SELECT {"DISTINCT ON (a.datasetId)" if misses else ''} | ||
| a.datasetId as "datasetId", b.accessType as "accessType", a.chromosome as "referenceName", | ||
| a.reference as "referenceBases", a.alternate as "alternateBases", a.chromosomeStart as "start", | ||
| a.mate as "mateName", | ||
| a.chromosomePos as "referenceID", a.matePos as "mateID", a.mateStart as "start", a.end as "end", | ||
| b.externalUrl as "externalUrl", b.description as "note", | ||
| a.alleleCount as "variantCount", CAST('BND' as text) as "variantType", | ||
| a.callCount as "callCount", b.sampleCount as "sampleCount", | ||
| a.frequency, {"FALSE" if misses else "TRUE"} as "exists" | ||
| FROM {DB_SCHEMA}beacon_dataset_table b, {DB_SCHEMA}beacon_mate_table a | ||
| WHERE a.datasetId=b.datasetId | ||
| AND b.assemblyId=$3 | ||
| AND coalesce(a.mate=$4, true) | ||
| AND coalesce(a.reference LIKE any($5::varchar[]), true) | ||
| AND {"NOT" if misses else ''} (coalesce(a.mateStart=$7, true) | ||
| AND coalesce(a.end=$6, true) | ||
| AND coalesce(a.end<=$8, true) AND coalesce(a.end>=$9, true) | ||
| AND coalesce(a.mateStart>=$10, true) AND coalesce(a.mateStart<=$11, true)) | ||
| AND coalesce(b.accessType = any($2::varchar[]), true) | ||
| {"<>" if misses and datasets else "AND"} coalesce(a.datasetId = any($1::varchar[]), true) | ||
| UNION | ||
| SELECT {"DISTINCT ON (a.datasetId)" if misses else ''} | ||
| a.datasetId as "datasetId", b.accessType as "accessType", a.chromosome as "referenceName", | ||
| a.reference as "referenceBases", a.alternate as "alternateBases", a.chromosomeStart as "start", | ||
| a.mate as "mateName", | ||
| a.chromosomePos as "referenceID", a.matePos as "mateID", a.mateStart as "mateStart", a.end as "end", | ||
| b.externalUrl as "externalUrl", b.description as "note", | ||
| a.alleleCount as "variantCount", CAST('BND' as text) as "variantType", | ||
| a.callCount as "callCount", b.sampleCount as "sampleCount", | ||
| a.frequency, {"FALSE" if misses else "TRUE"} as "exists" | ||
| FROM {DB_SCHEMA}beacon_dataset_table b, {DB_SCHEMA}beacon_mate_table a | ||
| WHERE a.datasetId=b.datasetId | ||
| AND b.assemblyId=$3 | ||
| AND coalesce(a.mate=$12, true) | ||
| AND coalesce(a.reference LIKE any($5::varchar[]), true) | ||
| AND {"NOT" if misses else ''} (coalesce(a.mateStart=$6, true) | ||
| AND coalesce(a.end=$7, true) | ||
| AND coalesce(a.mateStart<=$8, true) AND coalesce(a.mateStart>=$9, true) | ||
| AND coalesce(a.end>=$10, true) AND coalesce(a.end<=$11, true)) | ||
| AND coalesce(b.accessType = any($2::varchar[]), true) | ||
| {"<>" if misses and datasets else "AND"} coalesce(a.datasetId = any($1::varchar[]), true);""" | ||
| datasets = [] | ||
| statement = await connection.prepare(query) | ||
| db_response = await statement.fetch(datasets_query, access_query, assembly_id, | ||
| mate, refbase, | ||
| start_pos, end_pos, | ||
| startMax_pos, startMin_pos, | ||
| endMin_pos, endMax_pos, chromosome) | ||
| LOG.info(f"Query for dataset(s): {datasets} that are {access_type} matching conditions.") | ||
| for record in list(db_response): | ||
| processed = transform_misses(record) if misses else transform_record(record) | ||
| if __handover_drs__: | ||
| # If handover feature is enabled, add handover object to response | ||
| processed = add_handover(processed) | ||
| datasets.append(processed) | ||
| return datasets | ||
| except Exception as e: | ||
| raise BeaconServerError(f'Query dataset DB error: {e}') | ||
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| async def find_fusion(db_pool, assembly_id, position, chromosome, reference, mate, dataset_ids, access_type, include_dataset): | ||
| """Find datasets based on filter parameters. | ||
| This also takes into consideration the token value as to establish permissions. | ||
| """ | ||
| hit_datasets = [] | ||
| miss_datasets = [] | ||
| response = [] | ||
| fetch_call = partial(fetch_fusion_dataset, db_pool, assembly_id, position, chromosome, reference, mate) | ||
| hit_datasets = await fetch_call(dataset_ids, access_type) | ||
| if include_dataset in ['ALL', 'MISS']: | ||
| miss_datasets = await fetch_call([item["datasetId"] for item in hit_datasets], access_type, misses=True) | ||
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| response = hit_datasets + miss_datasets | ||
| return response |
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