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-rw-r--r--wqflask/base/data_set.py110
1 files changed, 53 insertions, 57 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 44325d5b..3183363b 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -17,7 +17,10 @@
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-
+from dataclasses import dataclass
+from dataclasses import field
+from dataclasses import InitVar
+from typing import Optional, Dict
from db.call import fetchall, fetchone, fetch1
from utility.logger import getLogger
from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
@@ -59,7 +62,8 @@ logger = getLogger(__name__)
DS_NAME_MAP = {}
-def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_name=None):
+def create_dataset(dataset_name, dataset_type=None,
+ get_samplelist=True, group_name=None):
if dataset_name == "Temp":
dataset_type = "Temp"
@@ -74,11 +78,10 @@ def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_n
return dataset_class(dataset_name, get_samplelist)
+@dataclass
class DatasetType:
-
- def __init__(self, redis_instance):
- """Create a dictionary of samples where the value is set to Geno,
-Publish or ProbeSet. E.g.
+ """Create a dictionary of samples where the value is set to Geno,
+ Publish or ProbeSet. E.g.
{'AD-cases-controls-MyersGeno': 'Geno',
'AD-cases-controls-MyersPublish': 'Publish',
@@ -89,21 +92,28 @@ Publish or ProbeSet. E.g.
'All Phenotypes': 'Publish',
'B139_K_1206_M': 'ProbeSet',
'B139_K_1206_R': 'ProbeSet' ...
-
+ }
"""
+ redis_instance: InitVar[Redis]
+ datasets: Optional[Dict] = field(init=False, default_factory=dict)
+ data: Optional[Dict] = field(init=False)
+
+ def __post_init__(self, redis_instance):
self.redis_instance = redis_instance
- self.datasets = {}
- data = self.redis_instance.get("dataset_structure")
+ data = redis_instance.get("dataset_structure")
if data:
self.datasets = json.loads(data)
- else: # ZS: I don't think this should ever run unless Redis is emptied
+ else:
+ # ZS: I don't think this should ever run unless Redis is
+ # emptied
try:
data = json.loads(requests.get(
- GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content)
- for species in data['datasets']:
- for group in data['datasets'][species]:
- for dataset_type in data['datasets'][species][group]:
- for dataset in data['datasets'][species][group][dataset_type]:
+ GN2_BASE_URL + "/api/v_pre1/gen_dropdown",
+ timeout=5).content)
+ for _species in data['datasets']:
+ for group in data['datasets'][_species]:
+ for dataset_type in data['datasets'][_species][group]:
+ for dataset in data['datasets'][_species][group][dataset_type]:
short_dataset_name = dataset[1]
if dataset_type == "Phenotypes":
new_type = "Publish"
@@ -112,15 +122,15 @@ Publish or ProbeSet. E.g.
else:
new_type = "ProbeSet"
self.datasets[short_dataset_name] = new_type
- except:
+ except Exception: # Do nothing
pass
-
- self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
+ self.redis_instance.set("dataset_structure",
+ json.dumps(self.datasets))
+ self.data = data
def set_dataset_key(self, t, name):
- """If name is not in the object's dataset dictionary, set it, and update
- dataset_structure in Redis
-
+ """If name is not in the object's dataset dictionary, set it, and
+ update dataset_structure in Redis
args:
t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
'other_pheno', 'geno'
@@ -128,19 +138,20 @@ Publish or ProbeSet. E.g.
"""
sql_query_mapping = {
- 'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ +
- """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """),
- 'pheno': ("""SELECT InfoFiles.GN_AccesionId """ +
- """FROM InfoFiles, PublishFreeze, InbredSet """ +
- """WHERE InbredSet.Name = '{}' AND """ +
- """PublishFreeze.InbredSetId = InbredSet.Id AND """ +
- """InfoFiles.InfoPageName = PublishFreeze.Name"""),
- 'other_pheno': ("""SELECT PublishFreeze.Name """ +
- """FROM PublishFreeze, InbredSet """ +
- """WHERE InbredSet.Name = '{}' AND """ +
- """PublishFreeze.InbredSetId = InbredSet.Id"""),
- 'geno': ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ +
- """GenoFreeze.Name = "{}" """)
+ 'mrna_expr': ("SELECT ProbeSetFreeze.Id FROM "
+ "ProbeSetFreeze WHERE "
+ "ProbeSetFreeze.Name = \"%s\" "),
+ 'pheno': ("SELECT InfoFiles.GN_AccesionId "
+ "FROM InfoFiles, PublishFreeze, InbredSet "
+ "WHERE InbredSet.Name = '%s' AND "
+ "PublishFreeze.InbredSetId = InbredSet.Id AND "
+ "InfoFiles.InfoPageName = PublishFreeze.Name"),
+ 'other_pheno': ("SELECT PublishFreeze.Name "
+ "FROM PublishFreeze, InbredSet "
+ "WHERE InbredSet.Name = '%s' AND "
+ "PublishFreeze.InbredSetId = InbredSet.Id"),
+ 'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE "
+ "GenoFreeze.Name = \"%s\" ")
}
dataset_name_mapping = {
@@ -154,22 +165,22 @@ Publish or ProbeSet. E.g.
if t in ['pheno', 'other_pheno']:
group_name = name.replace("Publish", "")
- results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone()
+ results = g.db.execute(sql_query_mapping[t] % group_name).fetchone()
if results:
self.datasets[name] = dataset_name_mapping[t]
self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
return True
-
return None
def __call__(self, name):
-
if name not in self.datasets:
for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
- # This has side-effects, with the end result being a truth-y value
+ # This has side-effects, with the end result being a
+ # truth-y value
if(self.set_dataset_key(t, name)):
break
- return self.datasets.get(name, None) # Return None if name has not been set
+ # Return None if name has not been set
+ return self.datasets.get(name, None)
# Do the intensive work at startup one time only
@@ -209,7 +220,7 @@ def create_datasets_list():
return datasets
-class Markers(object):
+class Markers:
"""Todo: Build in cacheing so it saves us reading the same file more than once"""
def __init__(self, name):
@@ -262,8 +273,6 @@ class Markers(object):
elif isinstance(p_values, dict):
filtered_markers = []
for marker in self.markers:
- #logger.debug("marker[name]", marker['name'])
- #logger.debug("p_values:", p_values)
if marker['name'] in p_values:
#logger.debug("marker {} IS in p_values".format(i))
marker['p_value'] = p_values[marker['name']]
@@ -276,10 +285,6 @@ class Markers(object):
marker['lrs_value'] = - \
math.log10(marker['p_value']) * 4.61
filtered_markers.append(marker)
- # else:
- #logger.debug("marker {} NOT in p_values".format(i))
- # self.markers.remove(marker)
- #del self.markers[i]
self.markers = filtered_markers
@@ -306,13 +311,12 @@ class HumanMarkers(Markers):
marker['Mb'] = float(splat[3]) / 1000000
self.markers.append(marker)
- #logger.debug("markers is: ", pf(self.markers))
def add_pvalues(self, p_values):
super(HumanMarkers, self).add_pvalues(p_values)
-class DatasetGroup(object):
+class DatasetGroup:
"""
Each group has multiple datasets; each species has multiple groups.
@@ -520,7 +524,6 @@ def datasets(group_name, this_group=None):
break
if tissue_already_exists:
- #logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
dataset_menu[i]['datasets'].append((dataset, dataset_short))
else:
dataset_menu.append(dict(tissue=tissue_name,
@@ -537,7 +540,7 @@ def datasets(group_name, this_group=None):
return dataset_menu
-class DataSet(object):
+class DataSet:
"""
DataSet class defines a dataset in webqtl, can be either Microarray,
Published phenotype, genotype, or user input dataset(temp)
@@ -569,10 +572,6 @@ class DataSet(object):
self.group.get_samplelist()
self.species = species.TheSpecies(self)
- def get_desc(self):
- """Gets overridden later, at least for Temp...used by trait's get_given_name"""
- return None
-
def get_accession_id(self):
if self.type == "Publish":
results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
@@ -730,9 +729,6 @@ class PhenotypeDataSet(DataSet):
DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
def setup(self):
-
- #logger.debug("IS A PHENOTYPEDATASET")
-
# Fields in the database table
self.search_fields = ['Phenotype.Post_publication_description',
'Phenotype.Pre_publication_description',
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 22:38:43 +0000