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hosted gene sets routes, plus a few bug fixes (#2155)

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* first cut at hosted gs routes

* lint

* update tests to match csv parser changes

* update tests to new API

* update gene set name validation rules to match requirements

* add path mapping from dataset to geneset

* add test cases for geneset GET route

* fix test assertion

* remove debugging code

* update gene set uri mapping function

* fix error message

* allow extra user-specified headers in gene set csv file

* clarify comment
This commit is contained in:
Bruce Martin
2021-04-27 13:58:58 -07:00
committed by GitHub
parent ebeb1c8818
commit f2e9aecebe
19 changed files with 702 additions and 267 deletions
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backend/server/common/annotations/annotations.py
+8 -33
View File
@@ -5,10 +5,11 @@ import fsspec
from backend.common.errors import OntologyLoadFailure, DisabledFeatureError
from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array
from backend.common.genesets import write_gene_sets_tidycsv
class Annotations(metaclass=ABCMeta):
""" baseclass for annotations, including ontologies and genesets"""
""" baseclass for annotations, including ontologies and gene sets"""
""" our default ontology is the PURL for the Cell Ontology.
See http://www.obofoundry.org/ontology/cl.html """
@@ -30,7 +31,7 @@ class Annotations(metaclass=ABCMeta):
def check_gene_sets_save_enabled(self):
if not self.gene_sets_save_enabled():
raise DisabledFeatureError("User genesets save is disabled.")
raise DisabledFeatureError("User gene sets save is disabled.")
def load_ontology(self, path):
"""Load and parse ontologies - currently support OBO files only."""
@@ -81,12 +82,12 @@ class Annotations(metaclass=ABCMeta):
@abstractmethod
def read_gene_sets(self, data_adaptor):
"""Return the genesets from persistent storage """
"""Return the gene sets from persistent storage """
pass
@abstractmethod
def write_gene_sets(self, gs, data_adaptor):
"""Write the genesets (gs) to a persistent storage such that it can later be read"""
"""Write the gene sets (gs) to a persistent storage such that it can later be read"""
pass
@abstractmethod
@@ -94,51 +95,25 @@ class Annotations(metaclass=ABCMeta):
"""Update configuration parameters that describe information about the annotations feature"""
pass
Genesets_Header = [
"gene_set_name",
"gene_set_description",
"gene_symbol",
"gene_description",
]
@staticmethod
def gene_sets_to_csv(genesets):
"""
Convert the internal genesets format (returned by read_gene_set) into
Convert the internal gene sets format (returned by read_gene_set) into
the simple Tidy CSV.
"""
from io import StringIO
import csv
if isinstance(genesets, dict):
genesets = genesets.values()
with StringIO() as sio:
writer = csv.writer(sio, dialect='excel')
writer.writerow(Annotations.Genesets_Header)
for geneset in genesets:
# genes may be empty, in which case we skip the geneset entirely
genes = geneset["genes"]
if not genes:
writer.writerow([geneset["geneset_name"], geneset.get("geneset_description", ""), "", ""])
else:
writer.writerows(
[
[
geneset["geneset_name"],
geneset.get("geneset_description", ""),
gene["gene_symbol"],
gene.get("gene_description", ""),
]
for gene in genes
]
)
write_gene_sets_tidycsv(sio, genesets)
return sio.getvalue()
@staticmethod
def gene_sets_to_response(genesets):
"""
Convert the internal genesets format (returned by read_gene_set) into
Convert the internal gene sets format (returned by read_gene_set) into
the dict expected by the JSON REST API
"""
return list(genesets.values())