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Merge fb7a50a into 2d711c2
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@talavis
talavis committed Apr 17, 2019
2 parents 2d711c2 + fb7a50a commit 2bb2a06
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Showing 3 changed files with 158 additions and 91 deletions.
97 changes: 59 additions & 38 deletions backend/modules/browser/browser_handlers.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,4 @@
"""
Request handlers for the browser
"""
"""Request handlers for the variant browser."""

import logging

Expand All @@ -12,7 +10,17 @@


class Autocomplete(handlers.UnsafeHandler):
"""Provide autocompletion for protein names based on current query."""

def get(self, dataset:str, query:str, ds_version:str=None):
"""
Provide autocompletion for protein names based on current query.
Args:
dataset (str): dataset short name
query (str): query
ds_version (str): dataset version
"""
dataset, ds_version = utils.parse_dataset(dataset, ds_version)
ret = {}

Expand All @@ -23,9 +31,13 @@ def get(self, dataset:str, query:str, ds_version:str=None):


class Download(handlers.UnsafeHandler):
"""Download variants in CSV format."""

def get(self, dataset:str, datatype:str, item:str, ds_version:str=None, filter_type:str=None):
"""
Download variants as csv
Download variants in CSV format.
Will filter the variants if filter_type is provided.
Args:
dataset (str): dataset short name
Expand Down Expand Up @@ -62,10 +74,18 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None, filter_t


class GetCoverage(handlers.UnsafeHandler):
"""
Retrieve coverage
"""
"""Retrieve coverage."""

def get(self, dataset:str, datatype:str, item:str, ds_version:str=None):
"""
Retrieve coverage.
Args:
dataset (str): dataset short name
datatype (str): type of data
item (str): query item
ds_version (str): dataset version
"""
dataset, ds_version = utils.parse_dataset(dataset, ds_version)
ret = utils.get_coverage(dataset, datatype, item, ds_version)
if 'region_too_large' in ret:
Expand All @@ -78,26 +98,34 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None):


class GetCoveragePos(handlers.UnsafeHandler):
"""
Retrieve coverage range
"""
"""Retrieve coverage range."""

def get(self, dataset:str, datatype:str, item:str, ds_version:str=None):
"""
Retrieve coverage range.
Args:
dataset (str): dataset short name
datatype (str): type of data
item (str): query item
ds_version (str): dataset version
"""
dataset, ds_version = utils.parse_dataset(dataset, ds_version)
ret = utils.get_coverage_pos(dataset, datatype, item, ds_version)
self.finish(ret)


class GetGene(handlers.UnsafeHandler):
"""
Request information about a gene
"""
"""Request information about a gene."""

def get(self, dataset:str, gene:str, ds_version:str=None):
"""
Request information about a gene
Request information about a gene.
Args:
dataset (str): short name of the dataset
gene (str): the gene id
ds_version (str): dataset version
"""
dataset, ds_version = utils.parse_dataset(dataset, ds_version)
gene_id = gene
Expand All @@ -123,7 +151,6 @@ def get(self, dataset:str, gene:str, ds_version:str=None):
for transcript in transcripts_in_gene:
ret['transcripts'] += [{'transcript_id':transcript['transcript_id']}]


# temporary fix for names
gene['gene_name'] = gene['name']
gene['full_gene_name'] = gene['full_name']
Expand All @@ -132,19 +159,16 @@ def get(self, dataset:str, gene:str, ds_version:str=None):


class GetRegion(handlers.UnsafeHandler):
"""
Request information about genes in a region
"""
"""Request information about genes in a region."""

def get(self, dataset:str, region:str, ds_version:str=None):
"""
Request information about genes in a region
Request information about genes in a region.
Args:
dataset (str): short name of the dataset
region (str): the region in the format chr-startpos-endpos
Returns:
dict: information about the region and the genes found there
ds_version (str): dataset version
"""
dataset, ds_version = utils.parse_dataset(dataset, ds_version)
try:
Expand Down Expand Up @@ -178,19 +202,19 @@ def get(self, dataset:str, region:str, ds_version:str=None):


class GetTranscript(handlers.UnsafeHandler):
"""
Request information about a transcript
"""
"""Request information about a transcript."""

def get(self, dataset:str, transcript:str, ds_version:str=None):
"""
Request information about a transcript
Request information about a transcript.
Args:
dataset (str): short name of the dataset
transcript (str): the transcript id
Returns:
dict: transcript (transcript and exons), gene (gene information)
"""
dataset, ds_version = utils.parse_dataset(dataset, ds_version)
transcript_id = transcript
Expand Down Expand Up @@ -225,12 +249,11 @@ def get(self, dataset:str, transcript:str, ds_version:str=None):


class GetVariant(handlers.UnsafeHandler):
"""
Request information about a gene
"""
"""Request information about a gene."""

def get(self, dataset:str, variant:str, ds_version:str=None):
"""
Request information about a gene
Request information about a gene.
Args:
dataset (str): short name of the dataset
Expand Down Expand Up @@ -338,12 +361,11 @@ def get(self, dataset:str, variant:str, ds_version:str=None):


class GetVariants(handlers.UnsafeHandler):
"""
Retrieve variants
"""
"""Retrieve variants."""

def get(self, dataset:str, datatype:str, item:str, ds_version:str=None):
"""
Retrieve variants
Retrieve variants.
Args:
dataset (str): short name of the dataset
Expand All @@ -369,12 +391,11 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None):


class Search(handlers.UnsafeHandler):
"""
Perform a search for the wanted object
"""
"""Perform a search for the wanted object."""

def get(self, dataset:str, query:str, ds_version:str=None):
"""
Perform a search for the wanted object
Perform a search for the wanted object.
Args:
dataset (str): short name of the dataset
Expand Down

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