def test_tileset_info(self):
filename_matched = op.join("data", "SRR1770413.sorted.short.bam")
filename_mismatched = op.join("data", "SRR1770413.mismatched_bai.bam")
tsinfo = ctb.tileset_info(filename_matched)
assert "max_zoom" in tsinfo
tsinfo = ctb.tileset_info(filename_mismatched)
assert "max_zoom" in tsinfo
def test_tileset_info(self):
filename_matched = op.join('data', 'SRR1770413.sorted.short.bam')
filename_mismatched = op.join('data', 'SRR1770413.mismatched_bai.bam')
tsinfo = ctb.tileset_info(filename_matched)
assert 'max_zoom' in tsinfo
tsinfo = ctb.tileset_info(filename_mismatched)
assert 'max_zoom' in tsinfo
def test_tileset_info(self):
filename_matched = op.join("data", "SRR1770413.sorted.short.bam")
filename_mismatched = op.join("data", "SRR1770413.mismatched_bai.bam")
tsinfo = ctb.tileset_info(filename_matched)
assert "max_zoom" in tsinfo
tsinfo = ctb.tileset_info(filename_mismatched)
assert "max_zoom" in tsinfo
assert "chromsizes" in tsinfo
# the following is in here to make sure no error
# gets thrown when dumping to JSON (e.g. from int64)
json_str = json.dumps(tsinfo)
assert len(json_str)
def tileset_info(cls, tileset_dict):
filetype = tileset_dict.get("filetype", "")
if filetype == "bam":
info = bam_tiles.tileset_info(tileset_dict['datafile'])
info['max_tile_width'] = int(1e5)
elif filetype == "cooler":
info = cooler_tiles.tileset_info(tileset_dict['datafile'])
elif filetype == "bigwig":
info = bigwig_tiles.tileset_info(tileset_dict['datafile'])
else:
info = {'error': f"Unknown tileset filetype: {filetype}"}
for column in cls.info_colums:
info[column] = tileset_dict.get(column)
return info
def tileset_info(request):
"""Get information about a tileset
Tilesets have information critical to their display
such as the maximum number of dimensions and well as
their width. This needs to be relayed to the client
in order for it to know which tiles to request.
Args:
request (django.http.HTTPRequest): The request object
containing tileset_ids in the 'd' parameter.
Return:
django.http.JsonResponse: A JSON object containing
the tileset meta-information
"""
queryset = tm.Tileset.objects.all()
tileset_uuids = request.GET.getlist("d")
tileset_infos = {}
chromsizes_error = None
if "cs" in request.GET:
# we need to call a different server to get the tiles
if not "ci" in request.GET.getlist:
chromsizes_error = "cs param present without ci"
# call the request server and get the chromsizes
pass
else:
if "ci" in request.GET:
try:
chromsizes = tm.Tileset.objects.get(uuid=request.GET["ci"])
data = tcs.chromsizes_array_to_series(
tcs.get_tsv_chromsizes(chromsizes.datafile.path)
)
except Exception as ex:
pass
for tileset_uuid in tileset_uuids:
tileset_object = queryset.filter(uuid=tileset_uuid).first()
if tileset_uuid == "osm-image":
tileset_infos[tileset_uuid] = {
"min_x": 0,
"max_height": 134217728,
"min_y": 0,
"max_y": 134217728,
"max_zoom": 19,
"tile_size": 256,
}
continue
if tileset_object is None:
tileset_infos[tileset_uuid] = {
"error": "No such tileset with uid: {}".format(tileset_uuid)
}
continue
if tileset_object.private and request.user != tileset_object.owner:
# dataset is not public
tileset_infos[tileset_uuid] = {"error": "Forbidden"}
continue
if tileset_object.requiresAuthentication and not request.user.is_authenticated:
# dataset is not public
tileset_infos[tileset_uuid] = {
"error": "This request required authentication"
}
continue
#print(tileset_uuid,"accessibleTilesets" in request.session)
if tileset_object.requiresAuthentication and (
("accessibleTilesets" not in request.session)
or (tileset_uuid not in request.session["accessibleTilesets"])
):
# dataset is not accessible for this user
tileset_infos[tileset_uuid] = {
"error": "You don't have access to this tileset"
}
continue
if tileset_object.filetype == "hitile" or tileset_object.filetype == "hibed":
tileset_info = hdft.get_tileset_info(
h5py.File(tileset_object.datafile.path, "r")
)
tileset_infos[tileset_uuid] = {
"min_pos": [int(tileset_info["min_pos"])],
"max_pos": [int(tileset_info["max_pos"])],
"max_width": 2
** math.ceil(
math.log(tileset_info["max_pos"] - tileset_info["min_pos"])
/ math.log(2)
),
"tile_size": int(tileset_info["tile_size"]),
"max_zoom": int(tileset_info["max_zoom"]),
}
elif tileset_object.filetype == "bigwig":
chromsizes = tgt.get_chromsizes(tileset_object)
tsinfo = hgbi.tileset_info(tileset_object.datafile.path, chromsizes)
# print('tsinfo:', tsinfo)
if "chromsizes" in tsinfo:
tsinfo["chromsizes"] = [(c, int(s)) for c, s in tsinfo["chromsizes"]]
tileset_infos[tileset_uuid] = tsinfo
elif tileset_object.filetype == "bigbed":
chromsizes = tgt.get_chromsizes(tileset_object)
tsinfo = hgbi.tileset_info(tileset_object.datafile.path, chromsizes)
# print('tsinfo:', tsinfo)
if "chromsizes" in tsinfo:
tsinfo["chromsizes"] = [(c, int(s)) for c, s in tsinfo["chromsizes"]]
tileset_infos[tileset_uuid] = tsinfo
elif tileset_object.filetype == "multivec":
tileset_infos[tileset_uuid] = hgmu.tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == "elastic_search":
response = urllib.urlopen(tileset_object.datafile + "/tileset_info")
tileset_infos[tileset_uuid] = json.loads(response.read())
elif tileset_object.filetype == "beddb":
tileset_infos[tileset_uuid] = cdt.get_tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == "bed2ddb":
tileset_infos[tileset_uuid] = cdt.get_2d_tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == "cooler":
tileset_infos[tileset_uuid] = hgco.tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == "time-interval-json":
tileset_infos[tileset_uuid] = hgti.tileset_info(
tileset_object.datafile.path
)
elif (
tileset_object.filetype == "2dannodb"
or tileset_object.filetype == "imtiles"
):
tileset_infos[tileset_uuid] = hgim.get_tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == "geodb":
tileset_infos[tileset_uuid] = hggo.tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == "bam":
tileset_infos[tileset_uuid] = ctb.tileset_info(tileset_object.datafile.path)
tileset_infos[tileset_uuid]["max_tile_width"] = hss.MAX_BAM_TILE_WIDTH
else:
# Unknown filetype
tileset_infos[tileset_uuid] = {
"error": "Unknown filetype " + tileset_object.filetype
}
tileset_infos[tileset_uuid]["name"] = tileset_object.name
tileset_infos[tileset_uuid]["datatype"] = tileset_object.datatype
tileset_infos[tileset_uuid]["coordSystem"] = tileset_object.coordSystem
tileset_infos[tileset_uuid]["coordSystem2"] = tileset_object.coordSystem2
return JsonResponse(tileset_infos)
def tileset_info(request):
''' Get information about a tileset
Tilesets have information critical to their display
such as the maximum number of dimensions and well as
their width. This needs to be relayed to the client
in order for it to know which tiles to request.
Args:
request (django.http.HTTPRequest): The request object
containing tileset_ids in the 'd' parameter.
Return:
django.http.JsonResponse: A JSON object containing
the tileset meta-information
'''
queryset = tm.Tileset.objects.all()
tileset_uuids = request.GET.getlist("d")
tileset_infos = {}
chromsizes_error = None
if 'cs' in request.GET:
# we need to call a different server to get the tiles
if not 'ci' in request.GET.getlist:
chromsizes_error = 'cs param present without ci'
# call the request server and get the chromsizes
pass
else:
if 'ci' in request.GET:
try:
chromsizes = tm.Tileset.objects.get(uuid=request.GET['ci'])
data = tcs.chromsizes_array_to_series(
tcs.get_tsv_chromsizes(chromsizes.datafile.path))
except Exception as ex:
pass
for tileset_uuid in tileset_uuids:
tileset_object = queryset.filter(uuid=tileset_uuid).first()
if tileset_uuid == 'osm-image':
tileset_infos[tileset_uuid] = {
'min_x': 0,
'max_height': 134217728,
'min_y': 0,
'max_y': 134217728,
'max_zoom': 19,
'tile_size': 256
}
continue
if tileset_object is None:
tileset_infos[tileset_uuid] = {
'error': 'No such tileset with uid: {}'.format(tileset_uuid)
}
continue
if tileset_object.private and request.user != tileset_object.owner:
# dataset is not public
tileset_infos[tileset_uuid] = {'error': "Forbidden"}
continue
if (
tileset_object.filetype == 'hitile' or
tileset_object.filetype == 'hibed'
):
tileset_info = hdft.get_tileset_info(
h5py.File(tileset_object.datafile.path, 'r'))
tileset_infos[tileset_uuid] = {
"min_pos": [int(tileset_info['min_pos'])],
"max_pos": [int(tileset_info['max_pos'])],
"max_width": 2 ** math.ceil(
math.log(
tileset_info['max_pos'] - tileset_info['min_pos']
) / math.log(2)
),
"tile_size": int(tileset_info['tile_size']),
"max_zoom": int(tileset_info['max_zoom'])
}
elif tileset_object.filetype == 'bigwig':
chromsizes = tgt.get_chromsizes(tileset_object)
tsinfo = hgbi.tileset_info(
tileset_object.datafile.path,
chromsizes
)
#print('tsinfo:', tsinfo)
if 'chromsizes' in tsinfo:
tsinfo['chromsizes'] = [(c, int(s)) for c,s in tsinfo['chromsizes']]
tileset_infos[tileset_uuid] = tsinfo
elif tileset_object.filetype == 'bigbed':
chromsizes = tgt.get_chromsizes(tileset_object)
tsinfo = hgbi.tileset_info(
tileset_object.datafile.path,
chromsizes
)
#print('tsinfo:', tsinfo)
if 'chromsizes' in tsinfo:
tsinfo['chromsizes'] = [(c, int(s)) for c,s in tsinfo['chromsizes']]
tileset_infos[tileset_uuid] = tsinfo
elif tileset_object.filetype == 'multivec':
tileset_infos[tileset_uuid] = hgmu.tileset_info(
tileset_object.datafile.path)
elif tileset_object.filetype == "elastic_search":
response = urllib.urlopen(
tileset_object.datafile + "/tileset_info")
tileset_infos[tileset_uuid] = json.loads(response.read())
elif tileset_object.filetype == 'beddb':
tileset_infos[tileset_uuid] = cdt.get_tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == 'bed2ddb':
tileset_infos[tileset_uuid] = cdt.get_2d_tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == 'cooler':
tileset_infos[tileset_uuid] = hgco.tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == 'time-interval-json':
tileset_infos[tileset_uuid] = hgti.tileset_info(
tileset_object.datafile.path
)
elif (
tileset_object.filetype == '2dannodb' or
tileset_object.filetype == 'imtiles'
):
tileset_infos[tileset_uuid] = hgim.get_tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == 'geodb':
tileset_infos[tileset_uuid] = hggo.tileset_info(
tileset_object.datafile.path
)
elif tileset_object.filetype == 'bam':
tileset_infos[tileset_uuid] = ctb.tileset_info(
tileset_object.datafile.path
)
tileset_infos[tileset_uuid]['max_tile_width'] = hss.MAX_BAM_TILE_WIDTH
else:
# Unknown filetype
tileset_infos[tileset_uuid] = {
'error': 'Unknown filetype ' + tileset_object.filetype
}
tileset_infos[tileset_uuid]['name'] = tileset_object.name
tileset_infos[tileset_uuid]['datatype'] = tileset_object.datatype
tileset_infos[tileset_uuid]['coordSystem'] = tileset_object.coordSystem
tileset_infos[tileset_uuid]['coordSystem2'] =\
tileset_object.coordSystem2
return JsonResponse(tileset_infos)
