def test_cooler_info(): filename = op.join("data", "Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool") hgco.tileset_info(filename) # TODO: Make assertion about info returned. tiles = hgco.generate_tiles(filename, ["a.0.0.0"]) r = base64.decodestring(tiles[0][1]["dense"].encode("utf-8")) q = np.frombuffer(r, dtype=np.float32) q = q.reshape((256, 256)) filename = op.join("data", "hic-resolutions.cool")
def beddb(filepath, uuid=None, **kwargs): from clodius.tiles.beddb import tileset_info, tiles return Tileset(uuid=uuid, tileset_info=lambda: tileset_info(filepath), tiles=lambda tids: tiles(filepath, tids), **kwargs)
def dfpoints(df, x_col, y_col, uuid=None, **kwargs): """ Generate a tileset that serves 2d labelled points from a pandas dataframe. Parameters ---------- df: :class:`pandas.DataFrame` The dataframe containining the data x_col: str The name of the column containing the x-coordinates y_col: str The name of the column containing the y-coordinates uuid: str The uuid of this tileset Returns ------- A tileset capapble of serving tiles from this dataframe. """ from clodius.tiles.points import tileset_info, tiles, format_data tsinfo = tileset_info(df, x_col, y_col) tiles_fn = lambda z, x, y, width=1, height=1: tiles( df, x_col, y_col, tsinfo, z, x, y, width, height) return Tileset(uuid=uuid, tileset_info=lambda: tsinfo, tiles=lambda tile_ids: format_data( bundled_tiles_wrapper_2d(tile_ids, tiles_fn)), datatype="scatter-point", **kwargs)
def cooler(filepath, uuid=None, **kwargs): from clodius.tiles.cooler import tileset_info, tiles return Tileset(uuid=uuid, tileset_info=lambda: tileset_info(filepath), tiles=lambda tids: tiles(filepath, tids), datatype="matrix", **kwargs)
def bigbed(filepath, uuid=None, chromsizes=None, **kwargs): from clodius.tiles.bigbed import tileset_info, tiles return Tileset( uuid=uuid, tileset_info=lambda: tileset_info(filepath, chromsizes), tiles=lambda tids: tiles(filepath, tids, chromsizes=chromsizes), **kwargs)
def cooler(filepath, uuid=None): return Tileset( tileset_info=lambda: hgco.tileset_info(filepath), tiles=lambda tids: hgco.tiles(filepath, tids), uuid=uuid, track_type="heatmap", track_position="center", )
def bigwig(filepath, uuid=None, chromsizes=None, **kwargs): from clodius.tiles.bigwig import tileset_info, tiles return Tileset( uuid=uuid, tileset_info=lambda: tileset_info(filepath, chromsizes), tiles=lambda tids: tiles(filepath, tids, chromsizes=chromsizes), datatype="vector", **kwargs)
def multivec(filepath, uuid=None, **kwargs): from clodius.tiles.multivec import tileset_info, tiles return Tileset( uuid=uuid, tileset_info=lambda: tileset_info(filepath), tiles=lambda tile_ids: tiles(filepath, tile_ids), **kwargs )
def mrmatrix(filepath, uuid=None, **kwargs): from clodius.tiles.mrmatrix import tileset_info, tiles f = h5py.File(filepath, "r") return Tileset( uuid=uuid, tileset_info=lambda: tileset_info(f), tiles=lambda tile_ids: tiles_wrapper_2d( tile_ids, lambda z, x, y: format_dense_tile(tiles(f, z, x, y))), datatype="matrix", **kwargs)
def test_cooler_info(): filename = op.join('data', 'Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool') info = hgco.tileset_info(filename) tiles = hgco.generate_tiles(filename, ['a.0.0.0']) import base64 r = base64.decodestring(tiles[0][1]['dense'].encode('utf-8')) q = np.frombuffer(r, dtype=np.float32) q = q.reshape((256,256)) filename = op.join('data', 'hic-resolutions.cool')
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)