from flask import (
Blueprint, render_template, request, url_for
)
from flask_restful_swagger_2 import Api, swagger, Resource
from ..util.utils import make_payload
from ..util.filter import parse_filter, QueryStringError
class InitializeAPI(Resource):
@swagger.doc({
'summary': 'get metadata schema, ranges for values, and cell count to initialize cellxgene app',
'tags': ['initialize'],
'parameters': [],
'responses': {
'200': {
'description': 'initialization data for UI',
'examples': {
'application/json': {
"data": {
"cellcount": 3589,
"options": {
"Sample.type": {
"options": {
"Glioblastoma": 3589
}
},
"Selection": {
"options": {
"Astrocytes(HEPACAM)": 714,
"Endothelial(BSC)": 123,
"Microglia(CD45)": 1108,
"Neurons(Thy1)": 685,
"Oligodendrocytes(GC)": 294,
"Unpanned": 665
}
},
"Splice_sites_AT.AC": {
"range": {
"max": 1025,
"min": 152
}
},
"Splice_sites_Annotated": {
"range": {
"max": 1075869,
"min": 26
}
}
},
"schema": {
"CellName": {
"displayname": "Name",
"type": "string",
"variabletype": "categorical"
},
"Class": {
"displayname": "Class",
"type": "string",
"variabletype": "categorical"
},
"ERCC_reads": {
"displayname": "ERCC Reads",
"type": "int",
"variabletype": "continuous"
},
"ERCC_to_non_ERCC": {
"displayname": "ERCC:Non-ERCC",
"type": "float",
"variabletype": "continuous"
},
"Genes_detected": {
"displayname": "Genes Detected",
"type": "int",
"variabletype": "continuous"
}
},
"genes": ["1/2-SBSRNA4", "A1BG", "A1BG-AS1"]
},
"status": {
"error": False,
"errormessage": ""
}
}
}
}
}
})
def get(self):
from cxg import data, REACTIVE_LIMIT
return make_payload({
"schema": data.schema,
"ranges": data.metadata_ranges(data.ADATA, data.schema),
"cellcount": data.cell_count(),
"reactivelimit": REACTIVE_LIMIT,
"genes": data.all_genes(),
})
class CellsAPI(Resource):
@swagger.doc({
'summary': 'filter based on metadata fields to get a subset cells, expression data, and metadata',
'tags': ['cells'],
'description': "Cells takes query parameters defined in the schema retrieved from the /initialize enpoint. "
"
For categorical metadata keys filter based on `key=value`
"
" For continuous metadata keys filter by `key=min,max`
Either value "
"can be replaced by a \*. To have only a minimum value `key=min,\*` To have only a maximum "
"value `key=\*,max`
Graph data (if retrieved) is normalized"
" To only retrieve cells that don't have a value for the key filter by `key`",
'parameters': [],
'responses': {
'200': {
'description': 'initialization data for UI',
'examples': {
'application/json': {
"data": {
"badmetadatacount": 0,
"cellcount": 0,
"cellids": ["..."],
"metadata": [
{
"CellName": "1001000173.G8",
"Class": "Neoplastic",
"Cluster_2d": "11",
"Cluster_2d_color": "#8C564B",
"Cluster_CNV": "1",
"Cluster_CNV_color": "#1F77B4",
"ERCC_reads": "152104",
"ERCC_to_non_ERCC": "0.562454470489481",
"Genes_detected": "1962",
"Location": "Tumor",
"Location.color": "#FF7F0E",
"Multimapping_reads_percent": "2.67",
"Neoplastic": "Neoplastic",
"Non_ERCC_reads": "270429",
"Sample.name": "BT_S2",
"Sample.name.color": "#AEC7E8",
"Sample.type": "Glioblastoma",
"Sample.type.color": "#1F77B4",
"Selection": "Unpanned",
"Selection.color": "#98DF8A",
"Splice_sites_AT.AC": "102",
"Splice_sites_Annotated": "122397",
"Splice_sites_GC.AG": "761",
"Splice_sites_GT.AG": "125741",
"Splice_sites_non_canonical": "56",
"Splice_sites_total": "126660",
"Total_reads": "1741039",
"Unique_reads": "1400382",
"Unique_reads_percent": "80.43",
"Unmapped_mismatch": "2.15",
"Unmapped_other": "0.18",
"Unmapped_short": "14.56",
"housekeeping_cluster": "2",
"housekeeping_cluster_color": "#AEC7E8",
"recluster_myeloid": "NA",
"recluster_myeloid_color": "NA"
},
],
"reactive": True,
"graph": [
[
"1001000173.G8",
0.93836,
0.28623
],
[
"1001000173.D4",
0.1662,
0.79438
]
],
"status": {
"error": False,
"errormessage": ""
}
},
}
},
},
'400': {
'description': 'bad query params',
}
}
})
def get(self):
from cxg import data
payload = {
"cellids": [],
"metadata": [],
"cellcount": 0,
"graph": [],
"ranges": {},
}
# get query params
filter = parse_filter(request.args, data.schema)
filtered_data = data.filter_cells(filter)
payload["metadata"], payload["cellids"] = data.metadata(filtered_data)
payload["ranges"] = data.metadata_ranges(filtered_data, data.schema)
payload["cellcount"] = len(payload["cellids"])
payload["graph"] = data.create_graph(filtered_data)
return make_payload(payload)
def get_api_resources():
bp = Blueprint('api', __name__, url_prefix='/api/v2.0')
api = Api(bp, add_api_spec_resource=False)
api.add_resource(InitializeAPI, "/initialize")
api.add_resource(CellsAPI, "/cells")
return api