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__version__ = "0.7.0dev2" | ||
__version__ = "0.7.0" |
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from fastapi import APIRouter, HTTPException | ||
from fastapi import APIRouter, HTTPException, Request, Response | ||
import logging | ||
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from bbconf.models.bedset_models import ( | ||
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@@ -108,65 +108,62 @@ async def get_bedfiles_in_bedset( | |
return bbagent.bedset.get_bedset_bedfiles(bedset_id) | ||
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# TODO: how are we using it? | ||
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# @router.get("/{bedset_id}/track_hub") | ||
# async def get_track_hub_bedset(request: Request, bedset_id: str): | ||
# """ | ||
# Generate track hub files for the BED set | ||
# """ | ||
# | ||
# hit = bbc.bedset.retrieve_one(bedset_id) | ||
# name = hit.get("name", "") | ||
# | ||
# hub_txt = ( | ||
# f"hub \t BEDBASE_{name}\n" | ||
# f"shortLabel \t BEDBASE_{name}\n" | ||
# f"longLabel\t BEDBASE {name} signal tracks\n" | ||
# f"genomesFile\t {request.url_for('get_genomes_file_bedset', bedset_id=bedset_id)}\n" | ||
# "email\t [email protected]\n" | ||
# "descriptionUrl\t http://www.bedbase.org/" | ||
# ) | ||
# | ||
# return Response(hub_txt, media_type="text/plain") | ||
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# @router.get("/{bedset_id}/track_hub_genome_file", include_in_schema=False) | ||
# async def get_genomes_file_bedset(request: Request, bedset_id: str): | ||
# """ | ||
# Generate genomes file for the BED set track hub | ||
# """ | ||
# | ||
# genome = bbc.bedset.retrieve_one(bedset_id, "genome") | ||
# | ||
# genome_txt = ( | ||
# f"genome\t {genome['alias']}\n" | ||
# f"trackDb\t {request.url_for('get_trackDb_file_bedset', bedset_id=bedset_id)}" | ||
# ) | ||
# | ||
# return Response(genome_txt, media_type="text/plain") | ||
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# @router.get("/{md5sum}/track_hub_trackDb_file", include_in_schema=False) | ||
# async def get_trackDb_file_bedset(request: Request, bedset_id: str): | ||
# """ | ||
# Generate trackDb file for the BED set track hub | ||
# """ | ||
# | ||
# hit = bbc.select_bedfiles_for_bedset( | ||
# bedset_id, | ||
# metadata=True, | ||
# ) | ||
# | ||
# trackDb_txt = "" | ||
# for bed in hit: | ||
# trackDb_txt = ( | ||
# trackDb_txt + f"track\t {bed.get('name', '')}\n" | ||
# "type\t bigBed\n" | ||
# f"bigDataUrl\t http://data.bedbase.org/bigbed_files/{bed.get('name', '')}.bigBed\n" | ||
# f"shortLabel\t {bed.get('name', '')}\n" | ||
# f"longLabel\t {bed.get('description', '')}\n" | ||
# "visibility\t full\n\n" | ||
# ) | ||
# | ||
# return Response(trackDb_txt, media_type="text/plain") | ||
@router.get("/{bedset_id}/track_hub") | ||
async def get_track_hub_bedset(request: Request, bedset_id: str): | ||
""" | ||
Generate track hub files for the BED set | ||
""" | ||
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bbagent.bedset.get(bedset_id) | ||
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hub_txt = ( | ||
f"hub \t BEDBASE_{bedset_id}\n" | ||
f"shortLabel \t BEDBASE_{bedset_id}\n" | ||
f"longLabel\t BEDBASE {bedset_id} signal tracks\n" | ||
f"genomesFile\t {request.url_for('get_genomes_file_bedset', bedset_id=bedset_id)}\n" | ||
"email\t [email protected]\n" | ||
"descriptionUrl\t https://bedbase.org/" | ||
) | ||
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return Response(hub_txt, media_type="text/plain") | ||
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@router.get("/{bedset_id}/track_hub_genome_file", include_in_schema=False) | ||
async def get_genomes_file_bedset(request: Request, bedset_id: str): | ||
""" | ||
Generate genomes file for the BED set track hub | ||
""" | ||
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genome = "hg38" | ||
genome_txt = ( | ||
f"genome\t {genome}\n" | ||
f"trackDb\t {request.url_for('get_trackDb_file_bedset', bedset_id=bedset_id)}" | ||
) | ||
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return Response(genome_txt, media_type="text/plain") | ||
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@router.get("/{bedset_id}/track_hub_trackDb_file", include_in_schema=False) | ||
async def get_trackDb_file_bedset(bedset_id: str): | ||
""" | ||
Generate trackDb file for the BED set track hub | ||
""" | ||
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hit = bbagent.bedset.get_bedset_bedfiles(bedset_id) | ||
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trackDb_txt = "" | ||
for bed in hit.results: | ||
metadata = bbagent.bed.get(bed.id, full=True) | ||
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if metadata.files.bigbed_file: | ||
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trackDb_txt = ( | ||
trackDb_txt + f"track\t {metadata.name}\n" | ||
"type\t bigBed\n" | ||
f"bigDataUrl\t {metadata.files.bigbed_file.access_methods[0].access_url.url} \n" | ||
f"shortLabel\t {metadata.name}\n" | ||
f"longLabel\t {metadata.description}\n" | ||
"visibility\t full\n\n" | ||
) | ||
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return Response(trackDb_txt, media_type="text/plain") |