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rename "geneset" to "gene set" in CLI (#2088)

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* remove dead code

* rename geneset to gene_set
This commit is contained in:
Bruce Martin
2021-03-02 15:36:01 -08:00
committed by GitHub
parent b00496198d
commit c037f4eaa6
14 changed files with 101 additions and 102 deletions
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local_server/common/annotations/annotations.py
+11 -11
View File
@@ -21,15 +21,15 @@ class Annotations(metaclass=ABCMeta):
def user_annotations_enabled(self):
return self.config.get("user-annotations", False)
def genesets_save_enabled(self):
def gene_sets_save_enabled(self):
return self.config.get("genesets-save", False)
def check_user_annotations_enabled(self):
if not self.user_annotations_enabled():
raise DisabledFeatureError("User annotations are disabled.")
def check_genesets_save_enabled(self):
if not self.genesets_save_enabled():
def check_gene_sets_save_enabled(self):
if not self.gene_sets_save_enabled():
raise DisabledFeatureError("User genesets save is disabled.")
def load_ontology(self, path):
@@ -80,12 +80,12 @@ class Annotations(metaclass=ABCMeta):
pass
@abstractmethod
def read_genesets(self, data_adaptor):
def read_gene_sets(self, data_adaptor):
"""Return the genesets from persistent storage """
pass
@abstractmethod
def write_genesets(self, gs, data_adaptor):
def write_gene_sets(self, gs, data_adaptor):
"""Write the genesets (gs) to a persistent storage such that it can later be read"""
pass
@@ -95,16 +95,16 @@ class Annotations(metaclass=ABCMeta):
pass
Genesets_Header = [
"geneset_name",
"geneset_description",
"gene_set_name",
"gene_set_description",
"gene_symbol",
"gene_description",
]
@staticmethod
def genesets_to_csv(genesets):
def gene_sets_to_csv(genesets):
"""
Convert the internal genesets format (returned by read_geneset) into
Convert the internal genesets format (returned by read_gene_set) into
the simple Tidy CSV.
"""
from io import StringIO
@@ -136,9 +136,9 @@ class Annotations(metaclass=ABCMeta):
return sio.getvalue()
@staticmethod
def genesets_to_response(genesets):
def gene_sets_to_response(genesets):
"""
Convert the internal genesets format (returned by read_geneset) into
Convert the internal genesets format (returned by read_gene_set) into
the dict expected by the JSON REST API
"""
return list(genesets.values())
local_server/common/annotations/local_file_csv.py
+26 -26
View File
@@ -17,14 +17,14 @@ from local_server.common.errors import AnnotationsError, ObsoleteRequest
class AnnotationsLocalFile(Annotations):
CXG_ANNO_COLLECTION = "cxg_anno_collection"
def __init__(self, config, output_dir, label_output_file, genesets_output_file):
def __init__(self, config, output_dir, label_output_file, gene_sets_output_file):
super().__init__(config)
self.output_dir = output_dir
self.label_output_file = label_output_file
self.genesets_output_file = genesets_output_file
self.gene_sets_output_file = gene_sets_output_file
# lock used to protect label file write ops
self.label_lock = threading.RLock()
self.genesets_lock = threading.RLock()
self.gene_sets_lock = threading.RLock()
# cache the most recent annotations.
self.last_fname = None
@@ -105,29 +105,29 @@ class AnnotationsLocalFile(Annotations):
self.last_fname = fname
self.last_labels = df
def read_genesets(self, data_adaptor, context=None):
def read_gene_sets(self, data_adaptor, context=None):
if has_request_context():
if not current_app.auth.is_user_authenticated():
return ({}, self.last_geneset_tid)
fname = self._get_genesets_filename(data_adaptor)
genesets = {}
gene_sets = {}
tid = None
with self.genesets_lock:
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:
genesets = read_geneset_tidycsv(f, context)
gene_sets = read_gene_set_tidycsv(f, context)
return (genesets, tid)
return (gene_sets, tid)
def write_genesets(self, genesets, tid, data_adaptor):
self.check_genesets_save_enabled() # raises
def write_gene_sets(self, gene_sets, tid, data_adaptor):
self.check_gene_sets_save_enabled() # raises
if type(tid) != int or tid < 0:
raise ValueError("tid must be a positive integer")
with self.genesets_lock:
with self.gene_sets_lock:
# skip if the request is stale
if tid is not None:
if tid <= self.last_geneset_tid:
@@ -137,7 +137,7 @@ class AnnotationsLocalFile(Annotations):
lastmod = data_adaptor.get_last_mod_time()
lastmodstr = "'unknown'" if lastmod is None else lastmod.isoformat(timespec="seconds")
header = (
f"# Geneset generated on {datetime.now().isoformat(timespec='seconds')} "
f"# Gene set generated on {datetime.now().isoformat(timespec='seconds')} "
f"using cellxgene version {cellxgene_version}\n"
f"# Input data file was {data_adaptor.get_location()}, "
f"which was last modified on {lastmodstr}\n"
@@ -147,7 +147,7 @@ class AnnotationsLocalFile(Annotations):
self._backup(fname)
with open(fname, "w", newline="") as f:
f.write(header)
f.write(self.genesets_to_csv(genesets))
f.write(self.gene_sets_to_csv(gene_sets))
def _get_userdata_idhash(self, data_adaptor):
"""
@@ -163,7 +163,7 @@ class AnnotationsLocalFile(Annotations):
if self.output_dir:
return self.output_dir
output_file = self.label_output_file or self.genesets_output_file
output_file = self.label_output_file or self.gene_sets_output_file
if output_file:
return os.path.dirname(os.path.abspath(output_file))
@@ -177,9 +177,9 @@ class AnnotationsLocalFile(Annotations):
return self._get_filename(data_adaptor, "celllabels")
def _get_genesets_filename(self, data_adaptor):
""" return the current genesets file name """
if self.genesets_output_file:
return self.genesets_output_file
""" return the current gene sets file name """
if self.gene_sets_output_file:
return self.gene_sets_output_file
return self._get_filename(data_adaptor, "genesets")
@@ -236,7 +236,7 @@ class AnnotationsLocalFile(Annotations):
def update_parameters(self, parameters, data_adaptor):
params = {}
params["annotations"] = self.user_annotations_enabled()
params["annotations_genesets_readonly"] = not self.genesets_save_enabled()
params["annotations_genesets_readonly"] = not self.gene_sets_save_enabled()
params["user_annotation_collection_name_enabled"] = True
if self.ontology_data:
@@ -263,7 +263,7 @@ class AnnotationsLocalFile(Annotations):
parameters.update(params)
def read_geneset_tidycsv(f, context=None):
def read_gene_set_tidycsv(f, context=None):
"""
Read & parse the Tidy CSV format, applying validation checks for mandatory
values, and de-duping rules.
@@ -271,9 +271,9 @@ def read_geneset_tidycsv(f, context=None):
Format is a four-column CSV, with a mandatory header row, and optional "#" prefixed
comments. Format:
geneset_name, geneset_description, gene_symbol, gene_description
gene_set_name, gene_set_description, gene_symbol, gene_description
geneset_name and gene_symbol must be non-null; others are optional.
gene_set_name must be non-null; others are optional.
Returns: a dictionary of the shape (values in angle-brackets vary):
@@ -305,7 +305,7 @@ def read_geneset_tidycsv(f, context=None):
messagefn = context["messagefn"] if context else (lambda x: None)
reader = csv.reader(f, dialect=myDialect())
genesets = {}
gene_sets = {}
haveReadHeader = False
lineno = 0
for row in reader:
@@ -329,10 +329,10 @@ def read_geneset_tidycsv(f, context=None):
if (not gene_symbol) and gene_description:
messagefn(f"Warning: Missing gene name in geneset name {geneset_name} on line {lineno}.")
if geneset_name in genesets:
gs = genesets[geneset_name]
if geneset_name in gene_sets:
gs = gene_sets[geneset_name]
else:
gs = genesets[geneset_name] = {
gs = gene_sets[geneset_name] = {
"geneset_name": geneset_name,
"geneset_description": geneset_description,
"genes": [],
@@ -349,4 +349,4 @@ def read_geneset_tidycsv(f, context=None):
}
)
return genesets
return gene_sets