From b0ccb12682fed83bf72d22ff42f1f442a8e6176e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 19 Apr 2021 14:43:16 +0300
Subject: Remove stale comments
---
wqflask/base/data_set.py | 11 -----------
1 file changed, 11 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 178234fe..cc5a428c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -262,8 +262,6 @@ 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 +274,6 @@ 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
@@ -306,7 +300,6 @@ 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)
@@ -520,7 +513,6 @@ 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,
@@ -735,9 +727,6 @@ 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',
--
cgit v1.2.3
From 10da4248b29b92e18c61323640acea59dd7244dc Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 20:31:26 +0300
Subject: base: data_set: Rewrite data_set using @dataclass
@dataclasses should be used to hold only data. Since dataset only
encapsulates data, re-writing it using a dataclass makes it more
readable and easier to follow.
---
wqflask/base/data_set.py | 86 +++++++++++++++++++++++++++---------------------
1 file changed, 48 insertions(+), 38 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index cc5a428c..e3a85ff6 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
@@ -74,11 +77,10 @@ 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 +91,28 @@ 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 +121,15 @@ 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 +137,20 @@ 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 +164,22 @@ 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
--
cgit v1.2.3
From 61972109b36c752264b89ae98bcb40cc3657fa1d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 20:52:11 +0300
Subject: base: data_set: Remove unused method
* wqflask/base/data_set.py (riset): Delete class method.
---
wqflask/base/data_set.py | 5 -----
1 file changed, 5 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index e3a85ff6..5bd3e40c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -575,11 +575,6 @@ class DataSet(object):
"""Gets overridden later, at least for Temp...used by trait's get_given_name"""
return None
- # Delete this eventually
- @property
- def riset():
- Weve_Renamed_This_As_Group
-
def get_accession_id(self):
if self.type == "Publish":
results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
--
cgit v1.2.3
From c10f4670c103f8d3d65aaedb7f297b539b08c2f8 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 20:52:45 +0300
Subject: base: data_set: Apply pep-8
---
wqflask/base/data_set.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5bd3e40c..2ab3204d 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -62,7 +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"
--
cgit v1.2.3
From dd0116f7cc3bed84777d625b6a22d716a3ba4fe2 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 20:53:56 +0300
Subject: base: data_set: Remove unused method
* wqflask/base/data_set.py (Dataset.get_accession_id): Delete it.
---
wqflask/base/data_set.py | 4 ----
1 file changed, 4 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 2ab3204d..1ae138d2 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -572,10 +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
--
cgit v1.2.3
From 67703a57db19c9a1ebcc6991087479979cbbca18 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 21:33:11 +0300
Subject: base: trait: Remove unused function
* wqflask/base/trait.py (jsonable_table_row): Delete it.
---
wqflask/base/trait.py | 68 ---------------------------------------------------
1 file changed, 68 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index df96d46e..a9223a32 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -341,74 +341,6 @@ def jsonable(trait):
return dict()
-def jsonable_table_row(trait, dataset_name, index):
- """Return a list suitable for json and intended to be displayed in a table
-
- Actual turning into json doesn't happen here though"""
-
- dataset = create_dataset(dataset_name)
-
- if dataset.type == "ProbeSet":
- if trait.mean == "":
- mean = "N/A"
- else:
- mean = "%.3f" % round(float(trait.mean), 2)
- if trait.additive == "":
- additive = "N/A"
- else:
- additive = "%.3f" % round(float(trait.additive), 2)
- return ['',
- index,
- ''+str(trait.name)+'',
- trait.symbol,
- trait.description_display,
- trait.location_repr,
- mean,
- trait.LRS_score_repr,
- trait.LRS_location_repr,
- additive]
- elif dataset.type == "Publish":
- if trait.additive == "":
- additive = "N/A"
- else:
- additive = "%.2f" % round(float(trait.additive), 2)
- if trait.pubmed_id:
- return ['',
- index,
- ''+str(trait.name)+'',
- trait.description_display,
- trait.authors,
- '' + trait.pubmed_text + '',
- trait.LRS_score_repr,
- trait.LRS_location_repr,
- additive]
- else:
- return ['',
- index,
- ''+str(trait.name)+'',
- trait.description_display,
- trait.authors,
- trait.pubmed_text,
- trait.LRS_score_repr,
- trait.LRS_location_repr,
- additive]
- elif dataset.type == "Geno":
- return ['',
- index,
- ''+str(trait.name)+'',
- trait.location_repr]
- else:
- return dict()
-
-
def retrieve_trait_info(trait, dataset, get_qtl_info=False):
assert dataset, "Dataset doesn't exist"
--
cgit v1.2.3
From 23e8e222e8016ea8335d4850070f884ab9b043fe Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 21:45:51 +0300
Subject: Run `sed -i 's/(object)//g'`
See: https://is.gd/pL7IJF
Ran:
find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g'
---
webtests/browser_run.py | 2 +-
wqflask/base/data_set.py | 6 +++---
wqflask/base/mrna_assay_tissue_data.py | 2 +-
wqflask/base/species.py | 6 +++---
wqflask/base/trait.py | 2 +-
wqflask/maintenance/convert_geno_to_bimbam.py | 4 ++--
.../maintenance/generate_kinship_from_bimbam.py | 2 +-
wqflask/maintenance/geno_to_json.py | 4 ++--
wqflask/maintenance/print_benchmark.py | 2 +-
wqflask/utility/__init__.py | 4 ++--
wqflask/utility/benchmark.py | 2 +-
wqflask/utility/gen_geno_ob.py | 6 +++---
wqflask/utility/genofile_parser.py | 4 ++--
wqflask/utility/temp_data.py | 2 +-
.../comparison_bar_chart/comparison_bar_chart.py | 2 +-
wqflask/wqflask/correlation/corr_scatter_plot.py | 2 +-
wqflask/wqflask/correlation/show_corr_results.py | 2 +-
.../wqflask/correlation_matrix/show_corr_matrix.py | 2 +-
wqflask/wqflask/ctl/ctl_analysis.py | 2 +-
wqflask/wqflask/db_info.py | 2 +-
wqflask/wqflask/do_search.py | 2 +-
wqflask/wqflask/docs.py | 2 +-
wqflask/wqflask/external_tools/send_to_bnw.py | 2 +-
.../wqflask/external_tools/send_to_geneweaver.py | 2 +-
.../wqflask/external_tools/send_to_webgestalt.py | 2 +-
wqflask/wqflask/gsearch.py | 2 +-
wqflask/wqflask/heatmap/heatmap.py | 2 +-
.../marker_regression/display_mapping_results.py | 2 +-
wqflask/wqflask/marker_regression/run_mapping.py | 2 +-
wqflask/wqflask/network_graph/network_graph.py | 2 +-
wqflask/wqflask/news.py | 2 +-
wqflask/wqflask/search_results.py | 2 +-
wqflask/wqflask/server_side.py | 2 +-
wqflask/wqflask/show_trait/SampleList.py | 2 +-
wqflask/wqflask/show_trait/show_trait.py | 6 +++---
wqflask/wqflask/snp_browser/snp_browser.py | 2 +-
wqflask/wqflask/update_search_results.py | 2 +-
wqflask/wqflask/user_manager.py | 22 +++++++++++-----------
wqflask/wqflask/user_session.py | 2 +-
wqflask/wqflask/wgcna/wgcna_analysis.py | 2 +-
40 files changed, 62 insertions(+), 62 deletions(-)
(limited to 'wqflask/base')
diff --git a/webtests/browser_run.py b/webtests/browser_run.py
index 7ee540b7..6cf46de5 100644
--- a/webtests/browser_run.py
+++ b/webtests/browser_run.py
@@ -9,7 +9,7 @@ from selenium import webdriver
from selenium.common.exceptions import NoSuchElementException, ElementNotVisibleException
from selenium.webdriver.common.keys import Keys
-class Test(object):
+class Test:
def __init__(self):
#self.browser = webdriver.Chrome('/home/gn2/gn2/webtests/chromedriver')
self.browser = webdriver.Firefox()
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1ae138d2..3183363b 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -220,7 +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):
@@ -316,7 +316,7 @@ class HumanMarkers(Markers):
super(HumanMarkers, self).add_pvalues(p_values)
-class DatasetGroup(object):
+class DatasetGroup:
"""
Each group has multiple datasets; each species has multiple groups.
@@ -540,7 +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)
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index f1929518..1f8224af 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -11,7 +11,7 @@ from utility.db_tools import escape
from utility.logger import getLogger
logger = getLogger(__name__ )
-class MrnaAssayTissueData(object):
+class MrnaAssayTissueData:
def __init__(self, gene_symbols=None):
self.gene_symbols = gene_symbols
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 2771d116..eae3325a 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -6,7 +6,7 @@ from flask import Flask, g
from utility.logger import getLogger
logger = getLogger(__name__ )
-class TheSpecies(object):
+class TheSpecies:
def __init__(self, dataset=None, species_name=None):
if species_name != None:
self.name = species_name
@@ -15,7 +15,7 @@ class TheSpecies(object):
self.dataset = dataset
self.chromosomes = Chromosomes(dataset=self.dataset)
-class IndChromosome(object):
+class IndChromosome:
def __init__(self, name, length):
self.name = name
self.length = length
@@ -25,7 +25,7 @@ class IndChromosome(object):
"""Chromosome length in megabases"""
return self.length / 1000000
-class Chromosomes(object):
+class Chromosomes:
def __init__(self, dataset=None, species=None):
self.chromosomes = collections.OrderedDict()
if species != None:
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index a9223a32..968b6d4b 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -51,7 +51,7 @@ def create_trait(**kw):
return None
-class GeneralTrait(object):
+class GeneralTrait:
"""
Trait class defines a trait in webqtl, can be either Microarray,
Published phenotype, genotype, or user input trait
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index d49742f2..0853b3ac 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -22,7 +22,7 @@ from pprint import pformat as pf
class EmptyConfigurations(Exception): pass
-class Marker(object):
+class Marker:
def __init__(self):
self.name = None
self.chr = None
@@ -30,7 +30,7 @@ class Marker(object):
self.Mb = None
self.genotypes = []
-class ConvertGenoFile(object):
+class ConvertGenoFile:
def __init__(self, input_file, output_files):
self.input_file = input_file
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 60257b28..3e4d1741 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -13,7 +13,7 @@ sys.path.append("..")
import os
import glob
-class GenerateKinshipMatrices(object):
+class GenerateKinshipMatrices:
def __init__(self, group_name, geno_file, pheno_file):
self.group_name = group_name
self.geno_file = geno_file
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 7e7fd241..f5f7e0e7 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -29,7 +29,7 @@ class EmptyConfigurations(Exception): pass
-class Marker(object):
+class Marker:
def __init__(self):
self.name = None
self.chr = None
@@ -37,7 +37,7 @@ class Marker(object):
self.Mb = None
self.genotypes = []
-class ConvertGenoFile(object):
+class ConvertGenoFile:
def __init__(self, input_file, output_file):
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
index b24ce4f1..a1046c86 100644
--- a/wqflask/maintenance/print_benchmark.py
+++ b/wqflask/maintenance/print_benchmark.py
@@ -5,7 +5,7 @@ import time
from pprint import pformat as pf
-class TheCounter(object):
+class TheCounter:
Counters = {}
def __init__(self):
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index 204ff59a..df926884 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -2,7 +2,7 @@ from pprint import pformat as pf
# Todo: Move these out of __init__
-class Bunch(object):
+class Bunch:
"""Like a dictionary but using object notation"""
def __init__(self, **kw):
self.__dict__ = kw
@@ -11,7 +11,7 @@ class Bunch(object):
return pf(self.__dict__)
-class Struct(object):
+class Struct:
'''The recursive class for building and representing objects with.
From http://stackoverflow.com/a/6573827/1175849
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index ea5a0ab6..91ea91e8 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -6,7 +6,7 @@ from utility.tools import LOG_BENCH
from utility.logger import getLogger
logger = getLogger(__name__ )
-class Bench(object):
+class Bench:
entries = collections.OrderedDict()
def __init__(self, name=None, write_output=LOG_BENCH):
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 81085ffe..0a381c9b 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,7 +1,7 @@
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class genotype(object):
+class genotype:
"""
Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
"""
@@ -119,7 +119,7 @@ class genotype(object):
self.chromosomes.append(chr_ob)
-class Chr(object):
+class Chr:
def __init__(self, name, geno_ob):
self.name = name
self.loci = []
@@ -140,7 +140,7 @@ class Chr(object):
def add_marker(self, marker_row):
self.loci.append(Locus(self.geno_ob, marker_row))
-class Locus(object):
+class Locus:
def __init__(self, geno_ob, marker_row = None):
self.chr = None
self.name = None
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 0b736176..f8e96d19 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -12,7 +12,7 @@ import simplejson as json
from pprint import pformat as pf
-class Marker(object):
+class Marker:
def __init__(self):
self.name = None
self.chr = None
@@ -21,7 +21,7 @@ class Marker(object):
self.genotypes = []
-class ConvertGenoFile(object):
+class ConvertGenoFile:
def __init__(self, input_file):
self.mb_exists = False
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 4144ae00..b2cbd458 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -2,7 +2,7 @@ from redis import Redis
import simplejson as json
-class TempData(object):
+class TempData:
def __init__(self, temp_uuid):
self.temp_uuid = temp_uuid
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 92de6073..5855ccf0 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -31,7 +31,7 @@ from MySQLdb import escape_string as escape
from flask import Flask, g
-class ComparisonBarChart(object):
+class ComparisonBarChart:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index c87776bb..d5dc26f5 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -11,7 +11,7 @@ import numpy as np
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class CorrScatterPlot(object):
+class CorrScatterPlot:
"""Page that displays a correlation scatterplot with a line fitted to it"""
def __init__(self, params):
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index fb4dc4f4..cb341e79 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -58,7 +58,7 @@ TISSUE_METHODS = [METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK]
TISSUE_MOUSE_DB = 1
-class CorrelationResults(object):
+class CorrelationResults:
def __init__(self, start_vars):
# get trait list from db (database name)
# calculate correlation with Base vector and targets
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index f77761d8..d0b4a156 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -41,7 +41,7 @@ Redis = get_redis_conn()
THIRTY_DAYS = 60 * 60 * 24 * 30
-class CorrelationMatrix(object):
+class CorrelationMatrix:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 72b4f3a3..1556e370 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -39,7 +39,7 @@ r_write_table = ro.r["write.table"] # Map the write.table function
r_data_frame = ro.r["data.frame"] # Map the write.table function
r_as_numeric = ro.r["as.numeric"] # Map the write.table function
-class CTL(object):
+class CTL:
def __init__(self):
logger.info("Initialization of CTL")
#log = r_file("/tmp/genenetwork_ctl.log", open = "wt")
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index f420b472..25e624ef 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -10,7 +10,7 @@ from utility.logger import getLogger
logger = getLogger(__name__)
-class InfoPage(object):
+class InfoPage:
def __init__(self, start_vars):
self.info = None
self.gn_accession_id = None
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 00636563..364a3eed 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -17,7 +17,7 @@ from utility.logger import getLogger
logger = getLogger(__name__)
-class DoSearch(object):
+class DoSearch:
"""Parent class containing parameters/functions used for all searches"""
# Used to translate search phrases into classes
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 23fc3cad..207767c4 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -5,7 +5,7 @@ from flask import g
from utility.logger import getLogger
logger = getLogger(__name__)
-class Docs(object):
+class Docs:
def __init__(self, entry, start_vars={}):
sql = """
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index efa17f05..c5c79e98 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -24,7 +24,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class SendToBNW(object):
+class SendToBNW:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 4c958a88..47e4c53a 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -29,7 +29,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class SendToGeneWeaver(object):
+class SendToGeneWeaver:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index 2f068792..e1e5e655 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -29,7 +29,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class SendToWebGestalt(object):
+class SendToWebGestalt:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 907f1180..9bf23d57 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -18,7 +18,7 @@ from utility.type_checking import is_float, is_int, is_str, get_float, get_int,
from utility.logger import getLogger
logger = getLogger(__name__)
-class GSearch(object):
+class GSearch:
def __init__(self, kw):
assert('type' in kw)
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index cca5a4fc..20e3559a 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -14,7 +14,7 @@ Redis = Redis()
logger = getLogger(__name__ )
-class Heatmap(object):
+class Heatmap:
def __init__(self, start_vars, temp_uuid):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 6a5fe2f6..4074f098 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -152,7 +152,7 @@ class HtmlGenWrapper:
return map_
-class DisplayMappingResults(object):
+class DisplayMappingResults:
"""Inteval Mapping Plot Page"""
cMGraphInterval = 5
GRAPH_MIN_WIDTH = 900
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 8f051c14..7dd0bcb6 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -45,7 +45,7 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class RunMapping(object):
+class RunMapping:
def __init__(self, start_vars, temp_uuid):
helper_functions.get_species_dataset_trait(self, start_vars)
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 1d5316a2..f5ee5303 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -28,7 +28,7 @@ from utility import corr_result_helpers
from utility.tools import GN2_BRANCH_URL
-class NetworkGraph(object):
+class NetworkGraph:
def __init__(self, start_vars):
trait_db_list = [trait.strip()
diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py
index 0675ec4b..861a93f2 100644
--- a/wqflask/wqflask/news.py
+++ b/wqflask/wqflask/news.py
@@ -1,6 +1,6 @@
from flask import g
-class News(object):
+class News:
def __init__(self):
sql = """
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index f23c0582..36500a8d 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -24,7 +24,7 @@ from utility.type_checking import is_str
from utility.logger import getLogger
logger = getLogger(__name__ )
-class SearchResultPage(object):
+class SearchResultPage:
#maxReturn = 3000
def __init__(self, kw):
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 5f764767..48761fa0 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -2,7 +2,7 @@
-class ServerSideTable(object):
+class ServerSideTable:
"""
This class is used to do server-side processing
on the DataTables table such as paginating, sorting,
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 857e4456..f955f632 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -8,7 +8,7 @@ from pprint import pformat as pf
from utility import Plot
from utility import Bunch
-class SampleList(object):
+class SampleList:
def __init__(self,
dataset,
sample_names,
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index e5e94c7e..f9c5fbe6 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -35,8 +35,7 @@ logger = getLogger(__name__)
##############################################
-class ShowTrait(object):
-
+class ShowTrait:
def __init__(self, kw):
if 'trait_id' in kw and kw['dataset'] != "Temp":
self.temp_trait = False
@@ -54,7 +53,8 @@ class ShowTrait(object):
self.dataset = data_set.create_dataset(
dataset_name="Temp", dataset_type="Temp", group_name=self.temp_group)
- # Put values in Redis so they can be looked up later if added to a collection
+ # Put values in Redis so they can be looked up later if
+ # added to a collection
Redis.set(self.trait_id, kw['trait_paste'], ex=ONE_YEAR)
self.trait_vals = kw['trait_paste'].split()
self.this_trait = create_trait(dataset=self.dataset,
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index a52399a2..8658abf8 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -9,7 +9,7 @@ logger = getLogger(__name__)
from base import species
from base import webqtlConfig
-class SnpBrowser(object):
+class SnpBrowser:
def __init__(self, start_vars):
self.strain_lists = get_browser_sample_lists()
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 672f95b1..22a46ef2 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -10,7 +10,7 @@ from utility.benchmark import Bench
from utility.logger import getLogger
logger = getLogger(__name__)
-class GSearch(object):
+class GSearch:
def __init__(self, kw):
self.type = kw['type']
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 7b25b68e..fcec3b67 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -58,7 +58,7 @@ def timestamp():
return datetime.datetime.utcnow().isoformat()
-class AnonUser(object):
+class AnonUser:
"""Anonymous user handling"""
cookie_name = 'anon_user_v1'
@@ -158,7 +158,7 @@ def create_signed_cookie():
logger.debug("uuid_signed:", uuid_signed)
return the_uuid, uuid_signed
-class UserSession(object):
+class UserSession:
"""Logged in user handling"""
cookie_name = 'session_id_v1'
@@ -353,12 +353,12 @@ def set_cookie(response):
response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie)
return response
-class UsersManager(object):
+class UsersManager:
def __init__(self):
self.users = model.User.query.all()
logger.debug("Users are:", self.users)
-class UserManager(object):
+class UserManager:
def __init__(self, kw):
self.user_id = kw['user_id']
logger.debug("In UserManager locals are:", pf(locals()))
@@ -377,7 +377,7 @@ class UserManager(object):
#logger.debug(" ---> self.datasets:", self.datasets)
-class RegisterUser(object):
+class RegisterUser:
def __init__(self, kw):
self.thank_you_mode = False
self.errors = []
@@ -454,7 +454,7 @@ def set_password(password, user):
)
-class VerificationEmail(object):
+class VerificationEmail:
template_name = "email/verification.txt"
key_prefix = "verification_code"
subject = "GeneNetwork email verification"
@@ -511,7 +511,7 @@ class ForgotPasswordEmail(VerificationEmail):
send_email(toaddr, msg.as_string())
-class Password(object):
+class Password:
def __init__(self, unencrypted_password, salt, iterations, keylength, hashfunc):
hashfunc = getattr(hashlib, hashfunc)
logger.debug("hashfunc is:", hashfunc)
@@ -589,7 +589,7 @@ def password_reset_step2():
return response
-class DecodeUser(object):
+class DecodeUser:
def __init__(self, code_prefix):
verify_url_hmac(request.url)
@@ -695,7 +695,7 @@ def get_github_user_details(access_token):
result = requests.get(GITHUB_API_URL, params={"access_token":access_token})
return result.json()
-class LoginUser(object):
+class LoginUser:
remember_time = 60 * 60 * 24 * 30 # One month in seconds
def __init__(self):
@@ -1039,12 +1039,12 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
server.quit()
logger.info("Successfully sent email to "+toaddr)
-class GroupsManager(object):
+class GroupsManager:
def __init__(self, kw):
self.datasets = create_datasets_list()
-class RolesManager(object):
+class RolesManager:
def __init__(self):
self.roles = model.Role.query.all()
logger.debug("Roles are:", self.roles)
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index c5a577df..cc0ac744 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -63,7 +63,7 @@ def manage_user():
return render_template("admin/manage_user.html", user_details = user_details)
-class UserSession(object):
+class UserSession:
"""Logged in user handling"""
user_cookie_name = 'session_id_v2'
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 6bf75216..21516b30 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -42,7 +42,7 @@ r_png = ro.r["png"] # Map the png function for plotting
r_dev_off = ro.r["dev.off"] # Map the dev.off function
-class WGCNA(object):
+class WGCNA:
def __init__(self):
# To log output from stdout/stderr to a file add `r_sink(log)`
print("Initialization of WGCNA")
--
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