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gene sets summary route (#2099)

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* gene sets summary route

* lint

* clarify return type

* style
This commit is contained in:
Bruce Martin
2021-03-10 16:02:05 -08:00
committed by GitHub
parent 1d3d9237e7
commit 31e0326ded
10 changed files with 228 additions and 38 deletions
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local_server/common/annotations/annotations.py
+1 -1
View File
@@ -110,7 +110,7 @@ class Annotations(metaclass=ABCMeta):
from io import StringIO
import csv
if type(genesets) == dict:
if isinstance(genesets, dict):
genesets = genesets.values()
with StringIO() as sio:
local_server/common/annotations/local_file_csv.py
+29 -7
View File
@@ -26,10 +26,14 @@ class AnnotationsLocalFile(Annotations):
self.label_lock = threading.RLock()
self.gene_sets_lock = threading.RLock()
# cache the most recent annotations.
self.last_fname = None
# cache the most recent cell labels/annotations.
self.last_label_fname = None
self.last_labels = None
# cache the most recent gene sets.
self.last_geneset_fname = None
self.last_geneset = None
# txn ID - used to de-dup geneset writes
self.last_geneset_tid = 0
@@ -63,14 +67,14 @@ class AnnotationsLocalFile(Annotations):
with self.label_lock:
if fname is not None and os.path.exists(fname) and os.path.getsize(fname) > 0:
# returned the cached labels if possible, otherwise read them from the file
if fname == self.last_fname:
if fname == self.last_label_fname:
return self.last_labels
else:
labels = pd.read_csv(
fname, dtype="category", index_col=0, header=0, comment="#", keep_default_na=False
)
# update the cache
self.last_fname = fname
self.last_label_fname = fname
self.last_labels = labels
return labels
else:
@@ -102,7 +106,7 @@ class AnnotationsLocalFile(Annotations):
open(fname, "w").close()
# update the cache
self.last_fname = fname
self.last_label_fname = fname
self.last_labels = df
def read_gene_sets(self, data_adaptor, context=None):
@@ -116,8 +120,19 @@ class AnnotationsLocalFile(Annotations):
with self.gene_sets_lock:
tid = self.last_geneset_tid # inside the critical section
if fname is not None and os.path.exists(fname) and os.path.getsize(fname) > 0:
with open(fname, newline="") as f:
gene_sets = read_gene_set_tidycsv(f, context)
# return the cached genesets if possible, otherwise read from file and validate them
if fname == self.last_geneset_fname:
gene_sets = self.last_geneset
else:
with open(fname, newline="") as f:
gene_sets = read_gene_set_tidycsv(f, context)
# validate
gene_sets = data_adaptor.check_new_gene_sets(gene_sets, context)
# update cache
self.last_geneset_fname = fname
self.last_geneset = gene_sets
return (gene_sets, tid)
@@ -127,6 +142,9 @@ class AnnotationsLocalFile(Annotations):
if type(tid) != int or tid < 0:
raise ValueError("tid must be a positive integer")
# may raise
gene_sets = data_adaptor.check_new_gene_sets(gene_sets)
with self.gene_sets_lock:
# skip if the request is stale
if tid is not None:
@@ -149,6 +167,10 @@ class AnnotationsLocalFile(Annotations):
f.write(header)
f.write(self.gene_sets_to_csv(gene_sets))
# update the cache
self.last_geneset_fname = fname
self.last_geneset = gene_sets if type(gene_sets) == dict else {g["geneset_name"]: g for g in gene_sets}
def _get_userdata_idhash(self, data_adaptor):
"""
Return a short hash that weakly identifies the user and dataset.