def getcategories(gene_type):
"""
Endpoint for returning categories of genes.
"""
results = (sparql.get_categories(gene_type))
return Response.format_categories(results)
def getcategories(gene_type):
"""
Endpoint for returning categories of genes.
"""
results = sparql.get_categories(gene_type)
return Response.format_categories(results)
def meta():
"""
General query that returns all genomes and metadata.
"""
return Response.bulk_download(
sparql.get_all_genome_metadata(),
{"date": (datetime.datetime.now() + datetime.timedelta(minutes=30)).isoformat()},
)
def meta():
"""
General query that returns all genomes and metadata.
"""
return Response.bulk_download(
sparql.get_all_genome_metadata(), {
'date': (datetime.datetime.now() +
datetime.timedelta(minutes=30)).isoformat()
})
def genesearchresults():
"""
Endpoint for returning gene search results
"""
data_ = request.get_json()
print "data", data_
genomes_ = data_["genome"]
genes_ = data_["genes"]
## Prepping dictionary to be returned
genomeDict = {}
for genome in genomes_:
genomeDict[genome] = {}
for gene in genes_:
genomeDict[genome][gene] = 0
results = sparql.get_regions(genomes_, genes_)
return Response.format_gene_search(results, genomeDict)
def genesearchresults():
"""
Endpoint for returning gene search results
"""
data_ = request.get_json()
print "data", data_
genomes_ = data_["genome"]
genes_ = data_["genes"]
## Prepping dictionary to be returned
genomeDict = {}
for genome in genomes_:
genomeDict[genome] = {}
for gene in genes_:
genomeDict[genome][gene] = 0
results = sparql.get_regions(genomes_, genes_)
return Response.format_gene_search(results, genomeDict)
def region(geneid, genomeid):
"""
Queries for the instances of geneid in genomeid.
"""
results = sparql.find_regions(geneid, genomeid)
return Response.default(results)
def gene(geneid):
"""
Returns the metadata of a particular gene in json format.
"""
return Response.default(sparql.get_gene(geneid))
def regions(genomeid):
"""
Returns all the genes inside a particular genome
"""
return Response.default(sparql.find_alleles(genomeid))
def vfs():
"""
General query that returns all virulence factors.
"""
return Response.default(sparql.get_all_genes("vf"))
def amrs():
"""
General query that returns all antimicrobial resistance genes.
"""
return Response.default(sparql.get_all_genes("amr"))
def genes():
"""
General query that returns all genes and their metadata.
"""
return Response.default(sparql.get_all_genes())
def genes():
"""
General query that returns all genes and their metadata.
"""
return Response.default(sparql.get_all_genes())
def vfs():
"""
General query that returns all virulence factors.
"""
return Response.default(sparql.get_all_genes('vf'))
def region(geneid, genomeid):
"""
Queries for the instances of geneid in genomeid.
"""
results = (sparql.find_regions(geneid, genomeid))
return Response.default(results)
def regions(genomeid):
"""
Returns all the genes inside a particular genome
"""
return Response.default(sparql.find_alleles(genomeid))
def gene(geneid):
"""
Returns the metadata of a particular gene in json format.
"""
return Response.default(sparql.get_gene(geneid))
def amrs():
"""
General query that returns all antimicrobial resistance genes.
"""
return Response.default(sparql.get_all_genes('amr'))
