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authorAlexander Kabui2021-10-13 08:28:16 +0300
committerAlexander Kabui2021-10-13 08:28:16 +0300
commit5f855ab3c605201175482591073a10692516fd5c (patch)
tree4ae1dc86a467ea3b7e3b23519b8875fa0da0548f /wqflask
parentdb9225caf0a78b13af1892d47c69463e00262d03 (diff)
parenta212ad123f902b6a9c74bcac1d98bc274cebbdda (diff)
downloadgenenetwork2-5f855ab3c605201175482591073a10692516fd5c.tar.gz
resolve merge conflict
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/.DS_Storebin6148 -> 0 bytes
-rw-r--r--wqflask/base/data_set.py21
-rw-r--r--wqflask/base/trait.py8
-rw-r--r--wqflask/runserver.py3
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py12
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py43
-rw-r--r--wqflask/utility/Plot.py4
-rw-r--r--wqflask/utility/redis_tools.py20
-rw-r--r--wqflask/utility/startup_config.py6
-rw-r--r--wqflask/wqflask/correlation/correlation_gn3_api.py9
-rw-r--r--wqflask/wqflask/decorators.py28
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py83
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py95
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py7
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py100
-rw-r--r--wqflask/wqflask/resource_manager.py2
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py51
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py60
-rw-r--r--wqflask/wqflask/static/new/css/show_trait.css30
-rw-r--r--wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js62
-rw-r--r--wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js8
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js95
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js10
-rw-r--r--wqflask/wqflask/templates/admin/group_manager.html2
-rw-r--r--wqflask/wqflask/templates/base.html1
-rw-r--r--wqflask/wqflask/templates/collections/add.html29
-rw-r--r--wqflask/wqflask/templates/collections/view.html2
-rw-r--r--wqflask/wqflask/templates/loading.html51
-rw-r--r--wqflask/wqflask/templates/mapping_results.html19
-rw-r--r--wqflask/wqflask/templates/new_security/_scripts.html1
-rw-r--r--wqflask/wqflask/templates/new_security/forgot_password.html1
-rw-r--r--wqflask/wqflask/templates/new_security/forgot_password_step2.html1
-rw-r--r--wqflask/wqflask/templates/new_security/login_user.html26
-rw-r--r--wqflask/wqflask/templates/new_security/password_reset.html1
-rw-r--r--wqflask/wqflask/templates/new_security/register_user.html1
-rw-r--r--wqflask/wqflask/templates/new_security/registered.html1
-rw-r--r--wqflask/wqflask/templates/new_security/thank_you.html1
-rw-r--r--wqflask/wqflask/templates/new_security/verification_still_needed.html1
-rw-r--r--wqflask/wqflask/templates/search_result_page.html8
-rw-r--r--wqflask/wqflask/templates/show_trait.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html5
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html55
-rw-r--r--wqflask/wqflask/templates/show_trait_transform_and_filter.html29
-rw-r--r--wqflask/wqflask/views.py83
44 files changed, 623 insertions, 454 deletions
diff --git a/wqflask/.DS_Store b/wqflask/.DS_Store
deleted file mode 100644
index d992942f..00000000
--- a/wqflask/.DS_Store
+++ /dev/null
Binary files differ
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4cb82665..8906ab69 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -277,7 +277,6 @@ class Markers:
filtered_markers = []
for marker in self.markers:
if marker['name'] in p_values:
- # logger.debug("marker {} IS in p_values".format(i))
marker['p_value'] = p_values[marker['name']]
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
@@ -298,7 +297,6 @@ class HumanMarkers(Markers):
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
- # logger.debug("splat:", splat)
if len(specified_markers) > 0:
if splat[1] in specified_markers:
marker = {}
@@ -398,6 +396,15 @@ class DatasetGroup:
if maternal and paternal:
self.parlist = [maternal, paternal]
+ def get_study_samplelists(self):
+ study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists')
+ try:
+ f = open(study_sample_file)
+ except:
+ return []
+ study_samples = json.load(f)
+ return study_samples
+
def get_genofiles(self):
jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
try:
@@ -737,7 +744,6 @@ class DataSet:
and Strain.SpeciesId=Species.Id
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
- logger.sql(query)
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
@@ -908,7 +914,6 @@ class PhenotypeDataSet(DataSet):
Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, this_trait.locus)
- logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
@@ -938,7 +943,6 @@ class PhenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
- logger.sql(query)
results = g.db.execute(query, (trait, self.id)).fetchall()
return results
@@ -1005,7 +1009,6 @@ class GenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
- logger.sql(query)
results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
@@ -1126,8 +1129,6 @@ class MrnaAssayDataSet(DataSet):
ProbeSet.Name = '%s'
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
-
- logger.sql(query)
result = g.db.execute(query).fetchone()
mean = result[0] if result else 0
@@ -1147,7 +1148,6 @@ class MrnaAssayDataSet(DataSet):
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(species, this_trait.locus)
- logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
@@ -1179,7 +1179,6 @@ class MrnaAssayDataSet(DataSet):
Order BY
Strain.Name
""" % (escape(trait), escape(self.name))
- logger.sql(query)
results = g.db.execute(query).fetchall()
return results
@@ -1190,7 +1189,6 @@ class MrnaAssayDataSet(DataSet):
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
""" % (column_name, escape(str(self.id)))
- logger.sql(query)
results = g.db.execute(query).fetchall()
return dict(results)
@@ -1224,7 +1222,6 @@ def geno_mrna_confidentiality(ob):
query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
- logger.sql(query)
result = g.db.execute(query)
(dataset_id,
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 10851e00..96a09302 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -27,11 +27,13 @@ def create_trait(**kw):
assert bool(kw.get('name')), "Needs trait name"
- if kw.get('dataset_name'):
+ if bool(kw.get('dataset')):
+ dataset = kw.get('dataset')
+ else:
if kw.get('dataset_name') != "Temp":
dataset = create_dataset(kw.get('dataset_name'))
- else:
- dataset = kw.get('dataset')
+ else:
+ dataset = create_dataset("Temp", group_name=kw.get('group_name'))
if dataset.type == 'Publish':
permissions = check_resource_availability(
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index df957bd9..8198b921 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -23,6 +23,9 @@ app_config()
werkzeug_logger = logging.getLogger('werkzeug')
if WEBSERVER_MODE == 'DEBUG':
+ from flask_debugtoolbar import DebugToolbarExtension
+ app.debug = True
+ toolbar = DebugToolbarExtension(app)
app.run(host='0.0.0.0',
port=SERVER_PORT,
debug=True,
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index 4003d68f..58a44b2a 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -81,10 +81,12 @@ class TestGemmaMapping(unittest.TestCase):
def test_gen_pheno_txt_file(self):
"""add tests for generating pheno txt file"""
with mock.patch("builtins.open", mock.mock_open())as mock_open:
- gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[
- "x", "w", "q", "we", "R"], trait_filename="fitr.re")
+ gen_pheno_txt_file(
+ this_dataset=AttributeSetter({"name": "A"}),
+ genofile_name="", vals=[
+ "x", "w", "q", "we", "R"])
mock_open.assert_called_once_with(
- '/home/user/data/gn2/fitr.re.txt', 'w')
+ '/home/user/data/gn2/PHENO_KiAEKlCvM6iGTM9Kh_TAlQ.txt', 'w')
filehandler = mock_open()
values = ["x", "w", "q", "we", "R"]
write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call(
@@ -112,7 +114,7 @@ class TestGemmaMapping(unittest.TestCase):
create_trait.side_effect = create_trait_side_effect
group = MockGroup({"name": "group_X", "samplelist": samplelist})
- this_dataset = AttributeSetter({"group": group})
+ this_dataset = AttributeSetter({"group": group, "name": "A"})
flat_files.return_value = "Home/Genenetwork"
with mock.patch("builtins.open", mock.mock_open())as mock_open:
@@ -132,7 +134,7 @@ class TestGemmaMapping(unittest.TestCase):
flat_files.assert_called_once_with('mapping')
mock_open.assert_called_once_with(
- 'Home/Genenetwork/group_X_covariates.txt', 'w')
+ 'Home/Genenetwork/COVAR_anFZ_LfZYV0Ulywo+7tRCw.txt', 'w')
filehandler = mock_open()
filehandler.write.assert_has_calls([mock.call(
'-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index c220a072..868b0b0b 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -43,11 +43,11 @@ class TestRunMapping(unittest.TestCase):
})
}
self.dataset = AttributeSetter(
- {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"})
+ {"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"})
self.chromosomes = AttributeSetter({"chromosomes": chromosomes})
self.trait = AttributeSetter(
- {"symbol": "IGFI", "chr": "X1", "mb": 123313})
+ {"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"})
def tearDown(self):
self.dataset = AttributeSetter(
@@ -180,34 +180,36 @@ class TestRunMapping(unittest.TestCase):
with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
- results_path="~/results", mapping_scale="physic", score_type="-log(p)",
- transform="qnorm", covariates="Dataset1:Trait1,Dataset2:Trait2", n_samples="100")
+ results_path="~/results", mapping_method="gemma", mapping_scale="physic",
+ score_type="-logP", transform="qnorm",
+ covariates="Dataset1:Trait1,Dataset2:Trait2",
+ n_samples="100", vals_hash="")
write_calls = [
mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
mock.call('Population: Human GP1_\n'), mock.call(
- 'Data Set: dataser_1\n'),
- mock.call('N Samples: 100\n'), mock.call(
- 'Transform - Quantile Normalized\n'),
+ 'Data Set: dataset_1\n'),
+ mock.call('Trait: Test Name\n'),
+ mock.call('Trait Hash: \n'),
+ mock.call('N Samples: 100\n'),
+ mock.call('Mapping Tool: gemma\n'),
+ mock.call('Transform - Quantile Normalized\n'),
mock.call('Gene Symbol: IGFI\n'), mock.call(
'Location: X1 @ 123313 Mb\n'),
mock.call('Cofactors (dataset - trait):\n'),
mock.call('Trait1 - Dataset1\n'),
mock.call('Trait2 - Dataset2\n'),
mock.call('\n'), mock.call('Name,Chr,'),
- mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'),
+ mock.call('Mb,-logP'),
mock.call(',Additive'), mock.call(',Dominance'),
mock.call('\n'), mock.call('MK1,C1,'),
- mock.call('12000,'), mock.call('1,'),
- mock.call('3'), mock.call(',VA'),
- mock.call(',TT'), mock.call('\n'),
- mock.call('MK2,C2,'), mock.call('10000,'),
- mock.call('15,'), mock.call('7'),
+ mock.call('12000,'), mock.call('3'),
+ mock.call(',VA'), mock.call(',TT'),
+ mock.call('\n'), mock.call('MK2,C2,'),
+ mock.call('10000,'), mock.call('7'),
mock.call('\n'), mock.call('MK1,C3,'),
- mock.call('1,'), mock.call('45,'),
- mock.call('7'), mock.call(',VE'),
- mock.call(',Tt')
-
+ mock.call('1,'), mock.call('7'),
+ mock.call(',VE'), mock.call(',Tt')
]
mock_open.assert_called_once_with("~/results", "w+")
filehandler = mock_open()
@@ -232,25 +234,20 @@ class TestRunMapping(unittest.TestCase):
"c1": "c1_value",
"c2": "c2_value",
"w1": "w1_value"
-
},
"S2": {
"w1": "w2_value",
"w2": "w2_value"
-
},
"S3": {
"c1": "c1_value",
"c2": "c2_value"
-
},
-
}})
-
results = get_perm_strata(this_trait={}, sample_list=sample_list,
categorical_vars=categorical_vars, used_samples=used_samples)
- self.assertEqual(results, [2, 1])
+ self.assertEqual(results, [1, 1])
def test_get_chr_length(self):
"""test for getting chromosome length"""
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 9b2c6735..d4256a46 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -139,7 +139,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
max_D = max(data)
min_D = min(data)
# add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
- if max_D == float('inf') or max_D > webqtlConfig.MAXLRS:
+ if (max_D == float('inf') or max_D > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS:
max_D = webqtlConfig.MAXLRS # maximum LRS value
xLow, xTop, stepX = detScale(min_D, max_D)
@@ -156,7 +156,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
j += step
for i, item in enumerate(data):
- if item == float('inf') or item > webqtlConfig.MAXLRS:
+ if (item == float('inf') or item > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS:
item = webqtlConfig.MAXLRS # maximum LRS value
j = int((item - xLow) / step)
Count[j] += 1
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index ff125bd2..de9dde46 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -127,22 +127,20 @@ def check_verification_code(code):
def get_user_groups(user_id):
- # ZS: Get the groups where a user is an admin or a member and
+ # Get the groups where a user is an admin or a member and
# return lists corresponding to those two sets of groups
- admin_group_ids = [] # ZS: Group IDs where user is an admin
- user_group_ids = [] # ZS: Group IDs where user is a regular user
+ admin_group_ids = [] # Group IDs where user is an admin
+ user_group_ids = [] # Group IDs where user is a regular user
groups_list = Redis.hgetall("groups")
- for key in groups_list:
+ for group_id, group_details in groups_list.items():
try:
- group_ob = json.loads(groups_list[key])
- group_admins = set([this_admin.encode(
- 'utf-8') if this_admin else None for this_admin in group_ob['admins']])
- group_members = set([this_member.encode(
- 'utf-8') if this_member else None for this_member in group_ob['members']])
+ _details = json.loads(group_details)
+ group_admins = set([this_admin if this_admin else None for this_admin in _details['admins']])
+ group_members = set([this_member if this_member else None for this_member in _details['members']])
if user_id in group_admins:
- admin_group_ids.append(group_ob['id'])
+ admin_group_ids.append(group_id)
elif user_id in group_members:
- user_group_ids.append(group_ob['id'])
+ user_group_ids.append(group_id)
else:
continue
except:
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 56d0af6f..778fb64d 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -20,8 +20,12 @@ def app_config():
import os
app.config['SECRET_KEY'] = str(os.urandom(24))
mode = WEBSERVER_MODE
- if mode == "DEV" or mode == "DEBUG":
+ if mode in ["DEV", "DEBUG"]:
app.config['TEMPLATES_AUTO_RELOAD'] = True
+ if mode == "DEBUG":
+ from flask_debugtoolbar import DebugToolbarExtension
+ app.debug = True
+ toolbar = DebugToolbarExtension(app)
print("==========================================")
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index f7c06a46..a18bceaf 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -148,14 +148,9 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait):
def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
sample_data = process_samples(
- start_vars, this_dataset.group.samplelist)
+ start_vars, this_dataset.group.all_samples_ordered())
- sample_data = test_process_data(this_trait, this_dataset, start_vars)
-
- if target_dataset.type == "ProbeSet":
- target_dataset.get_probeset_data(list(sample_data.keys()))
- else:
- target_dataset.get_trait_data(list(sample_data.keys()))
+ target_dataset.get_trait_data(list(sample_data.keys()))
this_trait = retrieve_sample_data(this_trait, this_dataset)
this_trait_data = {
"trait_sample_data": sample_data,
diff --git a/wqflask/wqflask/decorators.py b/wqflask/wqflask/decorators.py
index f0978fd3..54aa6795 100644
--- a/wqflask/wqflask/decorators.py
+++ b/wqflask/wqflask/decorators.py
@@ -1,14 +1,36 @@
"""This module contains gn2 decorators"""
from flask import g
+from typing import Dict
from functools import wraps
+from utility.hmac import hmac_creation
+import json
+import requests
-def admin_login_required(f):
+
+def edit_access_required(f):
"""Use this for endpoints where admins are required"""
@wraps(f)
def wrap(*args, **kwargs):
- if g.user_session.record.get(b"user_email_address") not in [
- b"labwilliams@gmail.com"]:
+ resource_id: str = ""
+ if kwargs.get("inbredset_id"): # data type: dataset-publish
+ resource_id = hmac_creation("dataset-publish:"
+ f"{kwargs.get('inbredset_id')}:"
+ f"{kwargs.get('name')}")
+ if kwargs.get("dataset_name"): # data type: dataset-probe
+ resource_id = hmac_creation("dataset-probeset:"
+ f"{kwargs.get('dataset_name')}")
+ response: Dict = {}
+ try:
+ _user_id = g.user_session.record.get(b"user_id",
+ "").decode("utf-8")
+ response = json.loads(
+ requests.get("http://localhost:8080/"
+ "available?resource="
+ f"{resource_id}&user={_user_id}").content)
+ except:
+ response = {}
+ if "edit" not in response.get("data", []):
return "You need to be admin", 401
return f(*args, **kwargs)
return wrap
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index f941267e..6254b9b9 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -24,6 +24,7 @@
#
# Last updated by Zach 12/14/2010
+import datetime
import string
from math import *
from PIL import Image
@@ -271,6 +272,7 @@ class DisplayMappingResults:
# Needing for form submission when doing single chr
# mapping or remapping after changing options
self.sample_vals = start_vars['sample_vals']
+ self.vals_hash= start_vars['vals_hash']
self.sample_vals_dict = json.loads(self.sample_vals)
self.transform = start_vars['transform']
@@ -355,8 +357,7 @@ class DisplayMappingResults:
if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma":
self.use_loco = start_vars['use_loco']
- if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper":
- self.reaper_version = start_vars['reaper_version']
+ if self.mapping_method == "reaper":
if 'output_files' in start_vars:
self.output_files = ",".join(
[(the_file if the_file is not None else "") for the_file in start_vars['output_files']])
@@ -651,7 +652,7 @@ class DisplayMappingResults:
btminfo.append(
'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
- def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""):
+ def plotIntMapping(self, canvas, offset=(80, 120, 110, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""):
im_drawer = ImageDraw.Draw(canvas)
# calculating margins
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -661,7 +662,7 @@ class DisplayMappingResults:
if self.legendChecked:
yTopOffset += 10
if self.covariates != "" and self.controlLocus and self.doControl != "false":
- yTopOffset += 20
+ yTopOffset += 25
if len(self.transform) > 0:
yTopOffset += 5
else:
@@ -1195,43 +1196,47 @@ class DisplayMappingResults:
dataset_label = "%s - %s" % (self.dataset.group.name,
self.dataset.fullname)
- string1 = 'Dataset: %s' % (dataset_label)
+
+ self.current_datetime = datetime.datetime.now().strftime("%b %d %Y %H:%M:%S")
+ string1 = 'UTC Timestamp: %s' % (self.current_datetime)
+ string2 = 'Dataset: %s' % (dataset_label)
+ string3 = 'Trait Hash: %s' % (self.vals_hash)
if self.genofile_string == "":
- string2 = 'Genotype File: %s.geno' % self.dataset.group.name
+ string4 = 'Genotype File: %s.geno' % self.dataset.group.name
else:
- string2 = 'Genotype File: %s' % self.genofile_string
+ string4 = 'Genotype File: %s' % self.genofile_string.split(":")[1]
- string4 = ''
+ string6 = ''
if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
if self.use_loco == "True":
- string3 = 'Using GEMMA mapping method with LOCO and '
+ string5 = 'Using GEMMA mapping method with LOCO and '
else:
- string3 = 'Using GEMMA mapping method with '
+ string5 = 'Using GEMMA mapping method with '
if self.covariates != "":
- string3 += 'the cofactors below:'
+ string5 += 'the cofactors below:'
cofactor_names = ", ".join(
[covar.split(":")[0] for covar in self.covariates.split(",")])
- string4 = cofactor_names
+ string6 = cofactor_names
else:
- string3 += 'no cofactors'
+ string5 += 'no cofactors'
elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
- string3 = 'Using R/qtl mapping method with '
+ string5 = 'Using R/qtl mapping method with '
if self.covariates != "":
- string3 += 'the cofactors below:'
+ string5 += 'the cofactors below:'
cofactor_names = ", ".join(
[covar.split(":")[0] for covar in self.covariates.split(",")])
- string4 = cofactor_names
+ string6 = cofactor_names
elif self.controlLocus and self.doControl != "false":
- string3 += '%s as control' % self.controlLocus
+ string5 += '%s as control' % self.controlLocus
else:
- string3 += 'no cofactors'
+ string5 += 'no cofactors'
else:
- string3 = 'Using Haldane mapping function with '
+ string5 = 'Using Haldane mapping function with '
if self.controlLocus and self.doControl != "false":
- string3 += '%s as control' % self.controlLocus
+ string5 += '%s as control' % self.controlLocus
else:
- string3 += 'no control for other QTLs'
+ string5 += 'no control for other QTLs'
y_constant = 10
if self.this_trait.name:
@@ -1243,24 +1248,26 @@ class DisplayMappingResults:
if self.this_trait.symbol:
identification += "Trait: %s - %s" % (
- self.this_trait.name, self.this_trait.symbol)
+ self.this_trait.display_name, self.this_trait.symbol)
elif self.dataset.type == "Publish":
if self.this_trait.post_publication_abbreviation:
identification += "Trait: %s - %s" % (
- self.this_trait.name, self.this_trait.post_publication_abbreviation)
+ self.this_trait.display_name, self.this_trait.post_publication_abbreviation)
elif self.this_trait.pre_publication_abbreviation:
identification += "Trait: %s - %s" % (
- self.this_trait.name, self.this_trait.pre_publication_abbreviation)
+ self.this_trait.display_name, self.this_trait.pre_publication_abbreviation)
else:
- identification += "Trait: %s" % (self.this_trait.name)
+ identification += "Trait: %s" % (self.this_trait.display_name)
else:
- identification += "Trait: %s" % (self.this_trait.name)
+ identification += "Trait: %s" % (self.this_trait.display_name)
identification += " with %s samples" % (self.n_samples)
d = 4 + max(
im_drawer.textsize(identification, font=labelFont)[0],
im_drawer.textsize(string1, font=labelFont)[0],
- im_drawer.textsize(string2, font=labelFont)[0])
+ im_drawer.textsize(string2, font=labelFont)[0],
+ im_drawer.textsize(string3, font=labelFont)[0],
+ im_drawer.textsize(string4, font=labelFont)[0])
im_drawer.text(
text=identification,
xy=(xLeftOffset, y_constant * fontZoom), font=labelFont,
@@ -1269,7 +1276,9 @@ class DisplayMappingResults:
else:
d = 4 + max(
im_drawer.textsize(string1, font=labelFont)[0],
- im_drawer.textsize(string2, font=labelFont)[0])
+ im_drawer.textsize(string2, font=labelFont)[0],
+ im_drawer.textsize(string3, font=labelFont)[0],
+ im_drawer.textsize(string4, font=labelFont)[0])
if len(self.transform) > 0:
transform_text = "Transform - "
@@ -1296,14 +1305,22 @@ class DisplayMappingResults:
text=string2, xy=(xLeftOffset, y_constant * fontZoom),
font=labelFont, fill=labelColor)
y_constant += 15
- if string3 != '':
+ im_drawer.text(
+ text=string3, xy=(xLeftOffset, y_constant * fontZoom),
+ font=labelFont, fill=labelColor)
+ y_constant += 15
+ im_drawer.text(
+ text=string4, xy=(xLeftOffset, y_constant * fontZoom),
+ font=labelFont, fill=labelColor)
+ y_constant += 15
+ if string4 != '':
im_drawer.text(
- text=string3, xy=(xLeftOffset, y_constant * fontZoom),
+ text=string5, xy=(xLeftOffset, y_constant * fontZoom),
font=labelFont, fill=labelColor)
y_constant += 15
- if string4 != '':
+ if string5 != '':
im_drawer.text(
- text=string4, xy=(xLeftOffset, y_constant * fontZoom),
+ text=string6, xy=(xLeftOffset, y_constant * fontZoom),
font=labelFont, fill=labelColor)
def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
@@ -2113,7 +2130,7 @@ class DisplayMappingResults:
thisChr.append(
[_locus.name, _locus.cM - Locus0CM])
else:
- for j in (0, nLoci / 4, nLoci / 2, nLoci * 3 / 4, -1):
+ for j in (0, round(nLoci / 4), round(nLoci / 2), round(nLoci * 3 / 4), -1):
while _chr[j].name == ' - ':
j += 1
if _chr[j].cM != preLpos:
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 4d6715ba..801674e1 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -178,101 +178,6 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
return marker_obs, permu_vals, bootstrap_vals
-def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
- genotype = dataset.group.read_genotype_file(use_reaper=True)
-
- if manhattan_plot != True:
- genotype = genotype.addinterval()
-
- trimmed_samples = []
- trimmed_values = []
- for i in range(0, len(samples_before)):
- try:
- trimmed_values.append(float(trait_vals[i]))
- trimmed_samples.append(str(samples_before[i]))
- except:
- pass
-
- perm_output = []
- bootstrap_results = []
-
- if num_perm < 100:
- suggestive = 0
- significant = 0
- else:
- perm_output = genotype.permutation(
- strains=trimmed_samples, trait=trimmed_values, nperm=num_perm)
- suggestive = perm_output[int(num_perm * 0.37 - 1)]
- significant = perm_output[int(num_perm * 0.95 - 1)]
- # highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case
-
- json_data['suggestive'] = suggestive
- json_data['significant'] = significant
-
- if control_marker != "" and do_control == "true":
- reaper_results = genotype.regression(strains=trimmed_samples,
- trait=trimmed_values,
- control=str(control_marker))
- if bootCheck:
- control_geno = []
- control_geno2 = []
- _FIND = 0
- for _chr in genotype:
- for _locus in _chr:
- if _locus.name == control_marker:
- control_geno2 = _locus.genotype
- _FIND = 1
- break
- if _FIND:
- break
- if control_geno2:
- _prgy = list(genotype.prgy)
- for _strain in trimmed_samples:
- _idx = _prgy.index(_strain)
- control_geno.append(control_geno2[_idx])
-
- bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
- trait=trimmed_values,
- control=control_geno,
- nboot=num_bootstrap)
- else:
- reaper_results = genotype.regression(strains=trimmed_samples,
- trait=trimmed_values)
-
- if bootCheck:
- bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
- trait=trimmed_values,
- nboot=num_bootstrap)
-
- json_data['chr'] = []
- json_data['pos'] = []
- json_data['lod.hk'] = []
- json_data['markernames'] = []
- # if self.additive:
- # self.json_data['additive'] = []
-
- # Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
- qtl_results = []
- for qtl in reaper_results:
- reaper_locus = qtl.locus
- # ZS: Convert chr to int
- converted_chr = reaper_locus.chr
- if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y":
- converted_chr = int(reaper_locus.chr)
- json_data['chr'].append(converted_chr)
- json_data['pos'].append(reaper_locus.Mb)
- json_data['lod.hk'].append(qtl.lrs)
- json_data['markernames'].append(reaper_locus.name)
- # if self.additive:
- # self.json_data['additive'].append(qtl.additive)
- locus = {"name": reaper_locus.name, "chr": reaper_locus.chr,
- "cM": reaper_locus.cM, "Mb": reaper_locus.Mb}
- qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb,
- "cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance}
- qtl_results.append(qtl)
- return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results
-
-
def natural_sort(marker_list):
"""
Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 09afb8d1..1dca1b1b 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -39,7 +39,7 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n
}
if do_control == "true" and control_marker:
- post_data["control_marker"] = control_marker
+ post_data["control"] = control_marker
if not manhattan_plot:
post_data["interval"] = True
@@ -61,6 +61,7 @@ def get_hash_of_textio(the_file: TextIO) -> str:
the_file.seek(0)
hash_of_file = hashlib.md5(the_file.read().encode()).hexdigest()
+ hash_of_file = hash_of_file.replace("/", "_") # Replace / with _ to prevent issue with filenames being translated to directories
return hash_of_file
@@ -89,7 +90,7 @@ def write_phenotype_file(trait_name: str,
for i, sample in enumerate(samples):
this_row = [sample]
if vals[i] != "x":
- this_row.append(vals[i])
+ this_row.append(str(round(float(vals[i]), 3)))
else:
this_row.append("NA")
for cofactor in cofactor_data:
@@ -126,7 +127,7 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict:
sample_data = trait_ob.data
for index, sample in enumerate(samples):
if sample in sample_data:
- sample_value = sample_data[sample].value
+ sample_value = str(round(float(sample_data[sample].value), 3))
cofactor_dict[cofactor_name].append(sample_value)
else:
cofactor_dict[cofactor_name].append("NA")
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index f601201b..80094057 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -75,6 +75,7 @@ class RunMapping:
self.vals = []
self.samples = []
self.sample_vals = start_vars['sample_vals']
+ self.vals_hash = start_vars['vals_hash']
sample_val_dict = json.loads(self.sample_vals)
samples = sample_val_dict.keys()
if (len(genofile_samplelist) != 0):
@@ -103,9 +104,7 @@ class RunMapping:
if "results_path" in start_vars:
self.mapping_results_path = start_vars['results_path']
else:
- mapping_results_filename = self.dataset.group.name + "_" + \
- ''.join(random.choice(string.ascii_uppercase + string.digits)
- for _ in range(6))
+ mapping_results_filename = "_".join([self.dataset.group.name, self.mapping_method, self.vals_hash]).replace("/", "_")
self.mapping_results_path = "{}{}.csv".format(
webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
@@ -220,7 +219,7 @@ class RunMapping:
elif self.mapping_method == "rqtl_plink":
results = self.run_rqtl_plink()
elif self.mapping_method == "rqtl_geno":
- perm_strata = []
+ self.perm_strata = []
if "perm_strata" in start_vars and "categorical_vars" in start_vars:
self.categorical_vars = start_vars["categorical_vars"].split(
",")
@@ -229,7 +228,7 @@ class RunMapping:
sample_names=self.samples,
this_trait=self.this_trait)
- perm_strata = get_perm_strata(
+ self.perm_strata = get_perm_strata(
self.this_trait, primary_samples, self.categorical_vars, self.samples)
self.score_type = "LOD"
self.control_marker = start_vars['control_marker']
@@ -243,10 +242,10 @@ class RunMapping:
# self.pair_scan = True
if self.permCheck and self.num_perm > 0:
self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl(
- self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
+ self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
else:
results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method,
- self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
+ self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
elif self.mapping_method == "reaper":
if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON
if "additiveCheck" in start_vars:
@@ -272,47 +271,32 @@ class RunMapping:
self.bootCheck = False
self.num_bootstrap = 0
- self.reaper_version = start_vars['reaper_version']
-
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
logger.info("Running qtlreaper")
- if self.reaper_version == "new":
- self.first_run = True
- self.output_files = None
- # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
- if 'first_run' in start_vars:
- self.first_run = False
- if 'output_files' in start_vars:
- self.output_files = start_vars['output_files'].split(
- ",")
-
- results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait,
- self.dataset,
- self.samples,
- self.vals,
- self.json_data,
- self.num_perm,
- self.bootCheck,
- self.num_bootstrap,
- self.do_control,
- self.control_marker,
- self.manhattan_plot,
- self.first_run,
- self.output_files)
- else:
- results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.run_original_reaper(self.this_trait,
- self.dataset,
- self.samples,
- self.vals,
- self.json_data,
- self.num_perm,
- self.bootCheck,
- self.num_bootstrap,
- self.do_control,
- self.control_marker,
- self.manhattan_plot)
+ self.first_run = True
+ self.output_files = None
+ # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
+ if 'first_run' in start_vars:
+ self.first_run = False
+ if 'output_files' in start_vars:
+ self.output_files = start_vars['output_files'].split(
+ ",")
+
+ results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait,
+ self.dataset,
+ self.samples,
+ self.vals,
+ self.json_data,
+ self.num_perm,
+ self.bootCheck,
+ self.num_bootstrap,
+ self.do_control,
+ self.control_marker,
+ self.manhattan_plot,
+ self.first_run,
+ self.output_files)
elif self.mapping_method == "plink":
self.score_type = "-logP"
self.manhattan_plot = True
@@ -422,7 +406,8 @@ class RunMapping:
with Bench("Exporting Results"):
export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
- self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples)
+ self.mapping_method, self.mapping_scale, self.score_type,
+ self.transform, self.covariates, self.n_samples, self.vals_hash)
with Bench("Trimming Markers for Figure"):
if len(self.qtl_results) > 30000:
@@ -540,14 +525,21 @@ class RunMapping:
return trimmed_genotype_data
-def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples):
+def export_mapping_results(dataset, trait, markers, results_path, mapping_method, mapping_scale, score_type, transform, covariates, n_samples, vals_hash):
+ if mapping_scale == "physic":
+ scale_string = "Mb"
+ else:
+ scale_string = "cM"
with open(results_path, "w+") as output_file:
output_file.write(
"Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
output_file.write(
"Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n")
output_file.write("Data Set: " + dataset.fullname + "\n")
+ output_file.write("Trait: " + trait.display_name + "\n")
+ output_file.write("Trait Hash: " + vals_hash + "\n")
output_file.write("N Samples: " + str(n_samples) + "\n")
+ output_file.write("Mapping Tool: " + str(mapping_method) + "\n")
if len(transform) > 0:
transform_text = "Transform - "
if transform == "qnorm":
@@ -577,10 +569,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
output_file.write("Name,Chr,")
if score_type.lower() == "-logP":
score_type = "-logP"
- if 'Mb' in markers[0]:
- output_file.write("Mb," + score_type)
- if 'cM' in markers[0]:
- output_file.write("Cm," + score_type)
+ output_file.write(scale_string + "," + score_type)
if "additive" in list(markers[0].keys()):
output_file.write(",Additive")
if "dominance" in list(markers[0].keys()):
@@ -588,11 +577,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
output_file.write("\n")
for i, marker in enumerate(markers):
output_file.write(marker['name'] + "," + str(marker['chr']) + ",")
- if 'Mb' in marker:
- output_file.write(str(marker['Mb']) + ",")
- if 'cM' in marker:
- output_file.write(str(marker['cM']) + ",")
- if "lod_score" in marker.keys():
+ output_file.write(str(marker[scale_string]) + ",")
+ if score_type == "-logP":
output_file.write(str(marker['lod_score']))
else:
output_file.write(str(marker['lrs_value']))
@@ -765,9 +751,9 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
if sample in list(sample_list.sample_attribute_values.keys()):
combined_string = ""
for var in categorical_vars:
- if var.lower() in sample_list.sample_attribute_values[sample]:
+ if var in sample_list.sample_attribute_values[sample]:
combined_string += str(
- sample_list.sample_attribute_values[sample][var.lower()])
+ sample_list.sample_attribute_values[sample][var])
else:
combined_string += "NA"
else:
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index b28c1b04..c54dd0b3 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -8,8 +8,6 @@ from wqflask import app
from utility.authentication_tools import check_owner_or_admin
from utility.redis_tools import get_resource_info, get_group_info, get_groups_like_unique_column, get_user_id, get_user_by_unique_column, get_users_like_unique_column, add_access_mask, add_resource, change_resource_owner
-from utility.logger import getLogger
-logger = getLogger(__name__)
@app.route("/resources/manage", methods=('GET', 'POST'))
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 92cea550..ae30aa59 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -32,7 +32,7 @@ class SampleList:
for counter, sample_name in enumerate(sample_names, 1):
sample_name = sample_name.replace("_2nd_", "")
- # ZS: self.this_trait will be a list if it is a Temp trait
+ # self.this_trait will be a list if it is a Temp trait
if isinstance(self.this_trait, list):
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
if counter <= len(self.this_trait):
@@ -47,7 +47,7 @@ class SampleList:
name=sample_name,
value=float(self.this_trait[counter - 1]))
else:
- # ZS - If there's no value for the sample/strain,
+ # If there's no value for the sample/strain,
# create the sample object (so samples with no value
# are still displayed in the table)
try:
@@ -63,29 +63,29 @@ class SampleList:
sample.this_id = str(counter)
- # ZS: For extra attribute columns; currently only used by
+ # For extra attribute columns; currently only used by
# several datasets
if self.sample_attribute_values:
sample.extra_attributes = self.sample_attribute_values.get(
sample_name, {})
- # ZS: Add a url so RRID case attributes can be displayed as links
- if 'rrid' in sample.extra_attributes:
+ # Add a url so RRID case attributes can be displayed as links
+ if '36' in sample.extra_attributes:
if self.dataset.group.species == "mouse":
- if len(sample.extra_attributes['rrid'].split(":")) > 1:
- the_rrid = sample.extra_attributes['rrid'].split(":")[
+ if len(sample.extra_attributes['36'].split(":")) > 1:
+ the_rrid = sample.extra_attributes['36'].split(":")[
1]
- sample.extra_attributes['rrid'] = [
- sample.extra_attributes['rrid']]
- sample.extra_attributes['rrid'].append(
+ sample.extra_attributes['36'] = [
+ sample.extra_attributes['36']]
+ sample.extra_attributes['36'].append(
webqtlConfig.RRID_MOUSE_URL % the_rrid)
elif self.dataset.group.species == "rat":
- if len(str(sample.extra_attributes['rrid'])):
- the_rrid = sample.extra_attributes['rrid'].split("_")[
+ if len(str(sample.extra_attributes['36'])):
+ the_rrid = sample.extra_attributes['36'].split("_")[
1]
- sample.extra_attributes['rrid'] = [
- sample.extra_attributes['rrid']]
- sample.extra_attributes['rrid'].append(
+ sample.extra_attributes['36'] = [
+ sample.extra_attributes['36']]
+ sample.extra_attributes['36'].append(
webqtlConfig.RRID_RAT_URL % the_rrid)
self.sample_list.append(sample)
@@ -124,17 +124,19 @@ class SampleList:
# Get attribute names and distinct values for each attribute
results = g.db.execute('''
- SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttributeXRefNew.Value
+ SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttribute.Description, CaseAttributeXRefNew.Value
FROM CaseAttribute, CaseAttributeXRefNew
WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id
AND CaseAttributeXRefNew.InbredSetId = %s
- ORDER BY lower(CaseAttribute.Name)''', (str(self.dataset.group.id),))
+ ORDER BY CaseAttribute.Id''', (str(self.dataset.group.id),))
self.attributes = {}
- for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
- key, name = attr
+ for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name, row.Description)):
+ key, name, description = attr
self.attributes[key] = Bunch()
+ self.attributes[key].id = key
self.attributes[key].name = name
+ self.attributes[key].description = description
self.attributes[key].distinct_values = [
item.Value for item in values]
self.attributes[key].distinct_values = natural_sort(
@@ -168,10 +170,13 @@ class SampleList:
for sample_name, items in itertools.groupby(results.fetchall(), lambda row: row.SampleName):
attribute_values = {}
+ # Make a list of attr IDs without values (that have values for other samples)
+ valueless_attr_ids = [self.attributes[key].id for key in self.attributes.keys()]
for item in items:
+ valueless_attr_ids.remove(item.Id)
attribute_value = item.Value
- # ZS: If it's an int, turn it into one for sorting
+ # If it's an int, turn it into one for sorting
# (for example, 101 would be lower than 80 if
# they're strings instead of ints)
try:
@@ -179,8 +184,10 @@ class SampleList:
except ValueError:
pass
- attribute_values[self.attributes[item.Id].name.lower(
- )] = attribute_value
+ attribute_values[str(item.Id)] = attribute_value
+ for attr_id in valueless_attr_ids:
+ attribute_values[str(attr_id)] = ""
+
self.sample_attribute_values[sample_name] = attribute_values
def get_first_attr_col(self):
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c07430dd..c4d1ae1c 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1,3 +1,5 @@
+from typing import Dict
+
import string
import datetime
import uuid
@@ -176,11 +178,11 @@ class ShowTrait:
self.sample_group_types['samples_primary'] = self.dataset.group.name
sample_lists = [group.sample_list for group in self.sample_groups]
- categorical_var_list = []
+ self.categorical_var_list = []
self.numerical_var_list = []
if not self.temp_trait:
# ZS: Only using first samplelist, since I think mapping only uses those samples
- categorical_var_list = get_categorical_variables(
+ self.categorical_var_list = get_categorical_variables(
self.this_trait, self.sample_groups[0])
self.numerical_var_list = get_numerical_variables(
self.this_trait, self.sample_groups[0])
@@ -192,6 +194,8 @@ class ShowTrait:
[self.dataset.species.chromosomes.chromosomes[this_chr].name, i])
self.genofiles = self.dataset.group.get_genofiles()
+ study_samplelist_json = self.dataset.group.get_study_samplelists()
+ self.study_samplelists = [study["title"] for study in study_samplelist_json]
# ZS: No need to grab scales from .geno file unless it's using
# a mapping method that reads .geno files
@@ -280,10 +284,11 @@ class ShowTrait:
hddn['selected_chr'] = -1
hddn['mapping_display_all'] = True
hddn['suggestive'] = 0
+ hddn['study_samplelists'] = json.dumps(study_samplelist_json)
hddn['num_perm'] = 0
hddn['categorical_vars'] = ""
- if categorical_var_list:
- hddn['categorical_vars'] = ",".join(categorical_var_list)
+ if self.categorical_var_list:
+ hddn['categorical_vars'] = ",".join(self.categorical_var_list)
hddn['manhattan_plot'] = ""
hddn['control_marker'] = ""
if not self.temp_trait:
@@ -295,7 +300,7 @@ class ShowTrait:
hddn['compare_traits'] = []
hddn['export_data'] = ""
hddn['export_format'] = "excel"
- if len(self.scales_in_geno) < 2:
+ if len(self.scales_in_geno) < 2 and bool(self.scales_in_geno):
hddn['mapping_scale'] = self.scales_in_geno[list(
self.scales_in_geno.keys())[0]][0][0]
@@ -318,7 +323,7 @@ class ShowTrait:
has_num_cases=self.has_num_cases,
attributes=self.sample_groups[0].attributes,
categorical_attr_exists=self.categorical_attr_exists,
- categorical_vars=",".join(categorical_var_list),
+ categorical_vars=",".join(self.categorical_var_list),
num_values=self.num_values,
qnorm_values=self.qnorm_vals,
zscore_values=self.z_scores,
@@ -520,6 +525,9 @@ class ShowTrait:
sample_group_type='primary',
header="%s Only" % (self.dataset.group.name))
self.sample_groups = (primary_samples,)
+ print("\nttttttttttttttttttttttttttttttttttttttttttttt\n")
+ print(self.sample_groups)
+ print("\nttttttttttttttttttttttttttttttttttttttttttttt\n")
self.primary_sample_names = primary_sample_names
self.dataset.group.allsamples = all_samples_ordered
@@ -693,7 +701,7 @@ def get_categorical_variables(this_trait, sample_list) -> list:
if len(sample_list.attributes) > 0:
for attribute in sample_list.attributes:
if len(sample_list.attributes[attribute].distinct_values) < 10:
- categorical_var_list.append(sample_list.attributes[attribute].name)
+ categorical_var_list.append(str(sample_list.attributes[attribute].id))
return categorical_var_list
@@ -799,3 +807,41 @@ def get_scales_from_genofile(file_location):
return [["physic", "Mb"], ["morgan", "cM"]]
else:
return [["physic", "Mb"]]
+
+
+
+def get_diff_of_vals(new_vals: Dict, trait_id: str) -> Dict:
+ """ Get the diff between current sample values and the values in the DB
+
+ Given a dict of the changed values and the trait/dataset ID, return a Dict
+ with keys corresponding to each sample with a changed value and a value
+ that is a dict with keys for the old_value and new_value
+
+ """
+
+ trait_name = trait_id.split(":")[0]
+ dataset_name = trait_id.split(":")[1]
+ trait_ob = create_trait(name=trait_name, dataset_name=dataset_name)
+
+ old_vals = {sample : trait_ob.data[sample].value for sample in trait_ob.data}
+
+ shared_samples = set.union(set(new_vals.keys()), set(old_vals.keys()))
+
+ diff_dict = {}
+ for sample in shared_samples:
+ try:
+ new_val = round(float(new_vals[sample]), 3)
+ except:
+ new_val = "x"
+ try:
+ old_val = round(float(old_vals[sample]), 3)
+ except:
+ old_val = "x"
+
+ if new_val != old_val:
+ diff_dict[sample] = {
+ "new_val": new_val,
+ "old_val": old_val
+ }
+
+ return diff_dict
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 782dabc2..b0514e01 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -260,3 +260,33 @@ input.trait-value-input {
div.inline-div {
display: inline;
}
+
+/* div.colorbox_border {
+ border: 1px solid grey;
+} */
+div#cboxContent {
+ /* box-shadow:
+ 0 2.8px 2.2px rgba(0, 0, 0, 0.034),
+ 0 6.7px 5.3px rgba(0, 0, 0, 0.048),
+ 0 12.5px 10px rgba(0, 0, 0, 0.06),
+ 0 22.3px 17.9px rgba(0, 0, 0, 0.072),
+ 0 41.8px 33.4px rgba(0, 0, 0, 0.086),
+ 0 100px 80px rgba(0, 0, 0, 0.12) */
+
+ padding: 10px 10px 5px 10px;
+
+ -moz-box-shadow: 3px 3px 5px #535353;
+ -webkit-box-shadow: 3px 3px 5px #535353;
+ box-shadow: 3px 3px 5px #535353;
+
+ -moz-border-radius: 6px 6px 6px 6px;
+ -webkit-border-radius: 6px;
+ border-radius: 6px 6px 6px 6px;
+
+ /* border: 2px solid grey; */
+}
+
+#cboxClose {
+ margin-right: 5px;
+ margin-bottom: 2px;
+}
diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index 3e414034..00025a32 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -65,10 +65,8 @@ if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) {
collection_click = function() {
var this_collection_url;
- console.log("Clicking on:", $(this));
this_collection_url = $(this).find('.collection_name').prop("href");
this_collection_url += "&json";
- console.log("this_collection_url", this_collection_url);
collection_list = $("#collections_holder").html();
return $.ajax({
dataType: "json",
@@ -79,32 +77,57 @@ collection_click = function() {
submit_click = function() {
var covariates_string = "";
- var covariates_display_string = "";
+ var covariates_as_set = new Set();
+ $(".selected-covariates:first option").each(function() {
+ if ($(this).val() != ""){
+ covariates_as_set.add($(this).val() + "," + $(this).text());
+ }
+ });
$('#collections_holder').find('input[type=checkbox]:checked').each(function() {
var this_dataset, this_trait;
this_trait = $(this).parents('tr').find('.trait').text();
this_trait_display = $(this).parents('tr').find('.trait').data("display_name");
this_description = $(this).parents('tr').find('.description').text();
- console.log("this_trait is:", this_trait_display);
this_dataset = $(this).parents('tr').find('.dataset').data("dataset");
- console.log("this_dataset is:", this_dataset);
- covariates_string += this_trait + ":" + this_dataset + ","
- //this_covariate_display_string = this_trait + ": " + this_description
this_covariate_display_string = this_trait_display
if (this_covariate_display_string.length > 50) {
this_covariate_display_string = this_covariate_display_string.substring(0, 45) + "..."
}
- covariates_display_string += this_covariate_display_string + "\n"
+ covariates_as_set.add(this_trait + ":" + this_dataset + "," + this_covariate_display_string)
+ });
+
+ covariates_as_list = Array.from(covariates_as_set)
+
+ // Removed the starting "No covariates selected" option before adding options for each covariate
+ if (covariates_as_list.length > 0){
+ $(".selected-covariates option[value='']").each(function() {
+ $(this).remove();
+ });
+ }
+
+ $(".selected-covariates option").each(function() {
+ $(this).remove();
});
- // Trim the last newline from display_string
- covariates_display_string = covariates_display_string.replace(/\n$/, "")
- // Trim the last comma
- covariates_string = covariates_string.substring(0, covariates_string.length - 1)
- //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2)
+ covariate_list_for_form = []
+ $.each(covariates_as_list, function (index, value) {
+ option_value = value.split(",")[0]
+ option_text = value.split(",")[1]
+ $(".selected-covariates").append($("<option/>", {
+ value: option_value,
+ text: option_text
+ }))
+ covariate_list_for_form.push(option_value)
+ });
- $("input[name=covariates]").val(covariates_string)
- $(".selected-covariates").val(covariates_display_string)
+ $("input[name=covariates]").val(covariate_list_for_form.join(","));
+
+ cofactor_count = $(".selected-covariates:first option").length;
+ if (cofactor_count > 10){
+ $(".selected-covariates").attr("size", 10);
+ } else {
+ $(".selected-covariates").attr("size", cofactor_count);
+ }
return $.colorbox.close();
};
@@ -186,9 +209,8 @@ color_by_trait = function(trait_sample_data, textStatus, jqXHR) {
process_traits = function(trait_data, textStatus, jqXHR) {
var the_html, trait, _i, _len;
console.log('in process_traits with trait_data:', trait_data);
- the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>";
- the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>";
- the_html += " <button id='submit' class='btn btn-primary btn-small'> Submit </button>";
+ the_html = "<button class='btn btn-success btn-small submit'> Submit </button>";
+ the_html += "<button id='back_to_collections' class='btn btn-inverse btn-small' style='float: right;'>Back</button>";
the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>";
the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>";
the_html += "<tbody>";
@@ -221,6 +243,6 @@ back_to_collections = function() {
};
$(".collection_line").on("click", collection_click);
-$("#submit").on("click", submit_click);
+$(".submit").on("click", submit_click);
$(".trait").on("click", trait_click);
-$("#back_to_collections").on("click", back_to_collections); \ No newline at end of file
+$("#back_to_collections").on("click", back_to_collections);
diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 6ca92fb6..0a060cdc 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -93,15 +93,15 @@ build_columns = function() {
);
}
- attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name.toLowerCase() > js_data.attributes[b].name.toLowerCase()) ? 1 : -1)
+ attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].id > js_data.attributes[b].id) ? 1 : -1)
for (i = 0; i < attr_keys.length; i++){
column_list.push(
{
- 'title': "<div style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>",
+ 'title': "<div title='" + js_data.attributes[attr_keys[i]].description + "' style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>",
'type': "natural",
'data': null,
'render': function(data, type, row, meta) {
- attr_name = Object.keys(data.extra_attributes).sort()[meta.col - data.first_attr_col]
+ attr_name = Object.keys(data.extra_attributes).sort((a, b) => (parseInt(a) > parseInt(b)) ? 1 : -1)[meta.col - data.first_attr_col]
if (attr_name != null && attr_name != undefined){
if (Array.isArray(data.extra_attributes[attr_name])){
@@ -130,6 +130,7 @@ var primary_table = $('#samples_primary').DataTable( {
$(row).addClass("value_se");
if (data.outlier) {
$(row).addClass("outlier");
+ $(row).attr("style", "background-color: orange;");
}
$('td', row).eq(1).addClass("column_name-Index")
$('td', row).eq(2).addClass("column_name-Sample")
@@ -189,6 +190,7 @@ if (js_data.sample_lists.length > 1){
$(row).addClass("value_se");
if (data.outlier) {
$(row).addClass("outlier");
+ $(row).attr("style", "background-color: orange;");
}
$('td', row).eq(1).addClass("column_name-Index")
$('td', row).eq(2).addClass("column_name-Sample")
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 77ef1720..f050d4ae 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -98,11 +98,54 @@ sample_group_types = js_data.sample_group_types;
$(".select_covariates").click(function () {
open_covariate_selection();
});
+
$(".remove_covariates").click(function () {
- $("input[name=covariates]").val("")
- $(".selected-covariates").val("")
+ $(".selected-covariates option:selected").each(function() {
+ this_val = $(this).val();
+ $(".selected-covariates option").each(function(){
+ if ($(this).val() == this_val){
+ $(this).remove();
+ }
+ })
+ cofactor_count = $(".selected-covariates:first option").length
+ if (cofactor_count > 2 && cofactor_count < 11){
+ $(".selected-covariates").each(function() {
+ $(this).attr("size", $(".selected-covariates:first option").length)
+ });
+ } else if (cofactor_count > 10) {
+ $(".selected-covariates").each(function() {
+ $(this).attr("size", 10)
+ });
+ } else {
+ $(".selected-covariates").each(function() {
+ $(this).attr("size", 2)
+ });
+ }
+ if (cofactor_count == 0){
+ $(".selected-covariates").each(function() {
+ $(this).append($("<option/>", {
+ value: "",
+ text: "No covariates selected"
+ }))
+ })
+ }
+ });
+
+ covariates_list = [];
+ $(".selected-covariates:first option").each(function() {
+ covariates_list.push($(this).val());
+ })
+ $("input[name=covariates]").val(covariates_list.join(","))
});
+$(".remove_all_covariates").click(function() {
+ $(".selected-covariates option").each(function() {
+ $(this).remove();
+ });
+ $(".selected-covariates").attr("size", 2)
+ $("input[name=covariates]").val("");
+})
+
open_trait_selection = function() {
return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
return function() {
@@ -608,13 +651,14 @@ $(".corr_compute").on("click", (function(_this) {
create_value_dropdown = function(value) {
return "<option val=" + value + ">" + value + "</option>";
};
+
populate_sample_attributes_values_dropdown = function() {
var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results;
$('#attribute_values').empty();
sample_attributes = [];
var attributes_as_list = Object.keys(js_data.attributes).map(function(key) {
- return [key, js_data.attributes[key].name.toLowerCase()];
+ return [key, js_data.attributes[key].id];
});
attributes_as_list.sort(function(first, second) {
@@ -628,7 +672,7 @@ populate_sample_attributes_values_dropdown = function() {
});
for (i=0; i < attributes_as_list.length; i++) {
- attribute_info = js_data.attributes[attributes_as_list[i][0]]
+ attribute_info = js_data.attributes[attributes_as_list[i][1]]
sample_attributes.push(attribute_info.distinct_values);
}
@@ -667,11 +711,13 @@ block_by_attribute_value = function() {
let exclude_val_nodes = table_api.column(attribute_start_pos + parseInt(exclude_column)).nodes().to$();
for (i = 0; i < exclude_val_nodes.length; i++) {
- let this_col_value = exclude_val_nodes[i].childNodes[0].data;
- let this_val_node = val_nodes[i].childNodes[0];
+ if (exclude_val_nodes[i].hasChildNodes()) {
+ let this_col_value = exclude_val_nodes[i].childNodes[0].data;
+ let this_val_node = val_nodes[i].childNodes[0];
- if (this_col_value == exclude_by_value){
- this_val_node.value = "x";
+ if (this_col_value == exclude_by_value){
+ this_val_node.value = "x";
+ }
}
}
@@ -713,10 +759,34 @@ block_by_index = function() {
for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
index = index_list[_k];
val_nodes[index - 1].childNodes[0].value = "x";
-
}
};
+filter_by_study = function() {
+ let this_study = $('#filter_study').val();
+
+ let study_sample_data = JSON.parse($('input[name=study_samplelists]').val())
+ let filter_samples = study_sample_data[parseInt(this_study)]['samples']
+
+ if ($('#filter_study_group').length){
+ let block_group = $('#filter_study_group').val();
+ if (block_group === "other") {
+ table_api = $('#samples_other').DataTable();
+ } else {
+ table_api = $('#samples_primary').DataTable();
+ }
+ }
+
+ let sample_nodes = table_api.column(2).nodes().to$();
+ let val_nodes = table_api.column(3).nodes().to$();
+ for (i = 0; i < sample_nodes.length; i++) {
+ this_sample = sample_nodes[i].childNodes[0].innerText;
+ if (!filter_samples.includes(this_sample)){
+ val_nodes[i].childNodes[0].value = "x";
+ }
+ }
+}
+
filter_by_value = function() {
let filter_logic = $('#filter_logic').val();
let filter_column = $('#filter_column').val();
@@ -748,7 +818,7 @@ filter_by_value = function() {
var this_col_value = filter_val_nodes[i].childNodes[0].value;
} else {
if (filter_val_nodes[i].childNodes[0] !== undefined){
- var this_col_value = filter_val_nodes[i].childNodes[0].data;
+ var this_col_value = filter_val_nodes[i].innerText;
} else {
continue
}
@@ -1690,6 +1760,11 @@ $('#block_by_index').click(function(){
edit_data_change();
});
+$('#filter_by_study').click(function(){
+ filter_by_study();
+ edit_data_change();
+})
+
$('#filter_by_value').click(function(){
filter_by_value();
edit_data_change();
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 09e9d024..e42fe8c4 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -141,11 +141,11 @@ $('input[name=display_all]').change((function(_this) {
})(this));
//ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
-var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals',
- 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
- 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'do_control', 'genofile',
- 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
- 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
+var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+ 'sample_vals', 'vals_hash', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars',
+ 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker',
+ 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend',
+ 'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'primary_samples']
$(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) {
return function() {
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index c0b99e75..692a7abc 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -81,7 +81,7 @@
<tr>
<td><input type="checkbox" name="read" value="{{ group.id }}"></td>
<td>{{ loop.index }}</td>
- <td>{{ group.name }}</td>
+ <td><a href="/groups/view?id={{ group.id }}">{{ group.name }}</a></td>
<td>{{ group.admins|length + group.members|length }}</td>
<td>{{ group.created_timestamp }}</td>
<td>{{ group.changed_timestamp }}</td>
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 049ebe6d..14e6bc88 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -87,6 +87,7 @@
<li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li>
<li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li>
<li><a href="http://power.genenetwork.org">BXD Power Calculator</a></li>
+ <li><a href="http://notebook.genenetwork.org/">Jupyter Notebook Launcher</a></li>
<li><a href="http://datafiles.genenetwork.org">Interplanetary File System</a></li>
</ul>
</li>
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 0398c6e4..8640fdb8 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -5,7 +5,7 @@
or add to an existing collection.</p>
</div>
<div class="modal-body" style="margin-left: 20px;">
- <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form">
+ <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form" class="form-inline">
{% if traits is defined %}
<input type="hidden" name="traits" value="{{ traits }}" />
{% else %}
@@ -14,10 +14,8 @@
{% if collections|length > 0 %}
<fieldset>
<legend>1. Add to an existing collection</legend>
- <div style="margin-left: 20px;">
- <!--<label>Existing collection name:</label>-->
- <select name="existing_collection" class="form-control">
- <!--<option selected disabled>Select Collection</option>-->
+ <div style="margin-left: 20px;">
+ <select name="existing_collection" class="form-control" style="width: 80%;">
{% for col in collections %}
{% if loop.index == 1 %}
<option value="{{ col.id }}:{{ col.name }}" selected>{{ col.name }}</option>
@@ -26,8 +24,9 @@
{% endif %}
{% endfor %}
</select>
- <br />
- <button type="submit" name="add_to_existing" class="btn btn-primary">Add to existing collection</button>
+ <input type="button" style="display: inline;" id="make_default" value="Make Default">
+ <br><br>
+ <button type="submit" name="add_to_existing" class="btn btn-primary">Add</button>
</div>
</fieldset>
{% endif %}
@@ -35,7 +34,6 @@
<fieldset>
<legend>{% if collections|length > 0 %}2. {% else %}{% endif %}Create a new collection</legend>
<div style="margin-left: 20px;">
- <!--<label>Collection name:</label>-->
<input type="text" name="new_collection" placeholder=" Name of new collection..."
data-trigger="change" data-minlength="5" data-maxlength="50" style="width: 100%">
<button type="submit" name="create_new" class="btn btn-primary" style="margin-top: 20px;">Create collection</button>
@@ -54,6 +52,21 @@
parent.jQuery.colorbox.close();
});
+ make_default = function() {
+ alert("The current collection is now your default collection.")
+ let uc_id = $('[name=existing_collection] option:selected').val().split(":")[0]
+ $.cookie('default_collection', uc_id, {
+ expires: 365,
+ path: '/'
+ });
+
+ let default_collection_id = $.cookie('default_collection');
+ };
+
+ $("#make_default").on("click", function(){
+ make_default();
+ });
+
apply_default = function() {
let default_collection_id = $.cookie('default_collection');
if (default_collection_id) {
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 9ec98ab1..a3090bcf 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -49,7 +49,7 @@
<input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ...">
<button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
<button id="remove" class="btn btn-danger" data-url="/collections/remove" type="button" disabled><i class="icon-minus-sign"></i> Delete Rows</button>
- <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button>
+ <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" type="button" title="Delete this collection" > Delete Collection</button>
</form>
</div>
<div style="margin-top: 10px; margin-bottom: 5px;">
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 6d6136ac..ccf810b0 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -12,6 +12,8 @@
{% if start_vars.tool_used == "Mapping" %}
<h1>Computing the Maps</h1>
<br>
+ <b>Time Elapsed:</b> <span class="timer"></span>
+ <br>
<b>Trait Metadata</b>
<br>
species = <b><i>{{ start_vars.species[0] | upper }}{{ start_vars.species[1:] }}</i></b>
@@ -25,6 +27,8 @@
<br>
transformation = <b><i>{{ start_vars.transform }}</i></b>
{% endif %}
+ <br>
+ hash of sample values = <b><i>{{ start_vars.vals_hash }}</i></b>
<br><br>
<b>Mapping Metadata</b>
<br>
@@ -68,6 +72,29 @@
<div style="text-align: center;">
<img align="center" src="/static/gif/89.gif">
</div>
+ {% if start_vars.vals_diff|length != 0 and start_vars.transform == "" %}
+ <br><br>
+ <button id="show_full_diff">Show Full Diff</button>
+ <br>
+ <div id="diff_table_container" style="display: none; height:200px; overflow:auto;">
+ <table class="table table-hover">
+ <thead>
+ <th>Sample</th>
+ <th>New Value</th>
+ <th>Old Value</th>
+ </thead>
+ <tbody>
+ {% for sample in start_vars.vals_diff %}
+ <tr>
+ <td>{{ sample }}</td>
+ <td>{{ start_vars.vals_diff[sample].new_val }}</td>
+ <td>{{ start_vars.vals_diff[sample].old_val }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ {% endif %}
</div>
</div>
</div>
@@ -76,6 +103,30 @@
<script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
<script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
<script type="text/javascript">
+$('#show_full_diff').click(function() {
+ if ($('#diff_table_container').is(':visible')){
+ $('#diff_table_container').hide();
+ } else {
+ $('#diff_table_container').show();
+ }
+})
+
+var start = new Date;
+
+setInterval(function() {
+ minutes = Math.floor((new Date - start) / 1000 / 60)
+ seconds = Math.round(((new Date - start) / 1000) % 60)
+ if (seconds < 10 && minutes >= 1){
+ seconds_text = "0" + seconds.toString()
+ } else {
+ seconds_text = seconds.toString()
+ }
+ if (minutes < 1) {
+ $('.timer').text(seconds_text + " seconds");
+ } else {
+ $('.timer').text(minutes.toString() + ":" + seconds_text);
+ }
+}, 100);
$("#loading_form").attr("action", "{{ start_vars.form_url }}");
setTimeout(function(){ $("#loading_form").submit()}, 350);
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 35d8a157..f2d11e89 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -34,6 +34,7 @@
<input type="hidden" name="results_path" value="{{ mapping_results_path }}">
<input type="hidden" name="method" value="{{ mapping_method }}">
<input type="hidden" name="sample_vals" value="{{ sample_vals }}">
+ <input type="hidden" name="vals_hash" value="{{ vals_hash }}">
<input type="hidden" name="n_samples" value="{{ n_samples }}">
<input type="hidden" name="maf" value="{{ maf }}">
<input type="hidden" name="use_loco" value="{{ use_loco }}">
@@ -44,7 +45,12 @@
{% endif %}
<input type="hidden" name="num_perm" value="{{ nperm }}">
<input type="hidden" name="perm_info" value="">
- <input type="hidden" name="perm_strata" value="{{ perm_strata }}">
+ {% if categorical_vars is defined %}
+ <input type="hidden" name="categorical_vars" value="{{ categorical_vars|join(',') }}">
+ {% endif %}
+ {% if perm_strata is defined %}
+ <input type="hidden" name="perm_strata" value="True">
+ {% endif %}
<input type="hidden" name="num_bootstrap" value="{{ nboot }}">
<input type="hidden" name="do_control" value="{{ doControl }}">
<input type="hidden" name="control_marker" value="{{ controlLocus }}">
@@ -62,15 +68,16 @@
<h2>Map Viewer: Whole Genome</h2><br>
<b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br>
<b>Database:</b> {{ dataset.fullname }}<br>
- {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.name }}</a><br>
+ {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.display_name }}</a><br>
+ <b>Trait Hash: </b> {{ vals_hash }}<br>
{% if dataset.type == "ProbeSet" %}
<b>Gene Symbol:</b> <i>{{ this_trait.symbol }}</i><br>
<b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb<br>
{% endif %}
- {% if genofile_string is defined %}
- <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}
+ {% if genofile_string != "" %}
+ <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}<br>
{% endif %}
- <br>
+ <b>Current Date/Time:</b> {{ current_datetime }}<br>
<br>
<a class="export_mapping_results" href="#" target="_blank" >Download Full Results</a>
</div>
@@ -524,7 +531,7 @@
});
{% endif %}
- {% if mapping_method != "gemma" and mapping_method != "plink" %}
+ {% if mapping_method != "gemma" and mapping_method != "plink" and nperm > 0 and permChecked == "ON" %}
$('#download_perm').click(function(){
perm_info_dict = {
perm_data: js_data.perm_results,
diff --git a/wqflask/wqflask/templates/new_security/_scripts.html b/wqflask/wqflask/templates/new_security/_scripts.html
deleted file mode 100644
index 5fefe305..00000000
--- a/wqflask/wqflask/templates/new_security/_scripts.html
+++ /dev/null
@@ -1 +0,0 @@
-<!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>-->
diff --git a/wqflask/wqflask/templates/new_security/forgot_password.html b/wqflask/wqflask/templates/new_security/forgot_password.html
index e5c42a45..60a221da 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password.html
+++ b/wqflask/wqflask/templates/new_security/forgot_password.html
@@ -48,6 +48,5 @@
{% endblock %}
{% block js %}
- {% include "new_security/_scripts.html" %}
{% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/forgot_password_step2.html b/wqflask/wqflask/templates/new_security/forgot_password_step2.html
index b4bf41c7..1835fd4c 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password_step2.html
+++ b/wqflask/wqflask/templates/new_security/forgot_password_step2.html
@@ -20,7 +20,6 @@
{% endblock %}
{% block js %}
- {% include "new_security/_scripts.html" %}
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 095036f0..88eab6bc 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -114,31 +114,5 @@ label.error,div.error{
{% endblock %}
{% block js %}
- <!-- Disable plugin, see https://github.com/genenetwork/genenetwork2/issues/310
-
- <script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script>
- <script>
- $(document).ready(function () {
- $("#loginUserForm").validate({
- onkeyup: false,
- onsubmit: true,
- onfocusout: function(element) { $(element).valid(); },
- rules: {
- email_address: {
- required: true,
- email: true
- },
- password: {
- required: true
- }
- }
- });
- });
-
- </script>
-
- -->
-
- {% include "new_security/_scripts.html" %}
{% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/password_reset.html b/wqflask/wqflask/templates/new_security/password_reset.html
index 684c12b1..e21f075c 100644
--- a/wqflask/wqflask/templates/new_security/password_reset.html
+++ b/wqflask/wqflask/templates/new_security/password_reset.html
@@ -73,7 +73,6 @@
{% block js %}
- {% include "new_security/_scripts.html" %}
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/register_user.html b/wqflask/wqflask/templates/new_security/register_user.html
index 3ae4488b..c2895517 100644
--- a/wqflask/wqflask/templates/new_security/register_user.html
+++ b/wqflask/wqflask/templates/new_security/register_user.html
@@ -100,7 +100,6 @@
{% block js %}
- {% include "new_security/_scripts.html" %}
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/registered.html b/wqflask/wqflask/templates/new_security/registered.html
index f2f58ec1..29889a97 100644
--- a/wqflask/wqflask/templates/new_security/registered.html
+++ b/wqflask/wqflask/templates/new_security/registered.html
@@ -19,7 +19,6 @@
{% block js %}
- {% include "new_security/_scripts.html" %}
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/thank_you.html b/wqflask/wqflask/templates/new_security/thank_you.html
index 0ff7ee8d..d4f5e574 100644
--- a/wqflask/wqflask/templates/new_security/thank_you.html
+++ b/wqflask/wqflask/templates/new_security/thank_you.html
@@ -18,7 +18,6 @@
{% endblock %}
{% block js %}
- {% include "new_security/_scripts.html" %}
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/verification_still_needed.html b/wqflask/wqflask/templates/new_security/verification_still_needed.html
index dc0f9e68..1f91fd8d 100644
--- a/wqflask/wqflask/templates/new_security/verification_still_needed.html
+++ b/wqflask/wqflask/templates/new_security/verification_still_needed.html
@@ -21,7 +21,6 @@
{% endblock %}
{% block js %}
- {% include "new_security/_scripts.html" %}
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 7ec335d5..c499aa8f 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -53,6 +53,7 @@
A total of {{ results|count }} records were found.
</p>
+ {% if results|count > 0 %}
{% if go_term is not none %}
<p><b>The associated genes include:</b><br><br>{% for word in search_terms %}{{ word.search_term[0] }}{% endfor %}</p>
{% endif %}
@@ -133,8 +134,11 @@
</div>
</div>
{% endif %}
+ {% else %}
+ <br>
+ <button type="button" onclick="window.location.href='/'">Return To Index Page</button>
+ {% endif %}
</div>
-
<div id="myModal"></div>
<!-- End of body -->
@@ -171,6 +175,7 @@
return params;
};
+ {% if results|count > 0 %}
//ZS: Need to make sort by symbol, also need to make sure blank symbol fields at the bottom and symbols starting with numbers below letters
trait_table = $('#trait_table').DataTable( {
'drawCallback': function( settings ) {
@@ -412,6 +417,7 @@
var table = $('#trait_table').DataTable();
table.colReorder.reset()
});
+ {% endif %}
submit_special = function(url) {
$("#trait_submission_form").attr("action", url);
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 3dbf5f57..f3fa1332 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -254,8 +254,6 @@
} );
{% endif %}
- $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'orange')
-
$('.edit_sample_checkbox:checkbox').change(function() {
if ($(this).is(":checked")) {
if (!$(this).closest('tr').hasClass('selected')) {
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index bb30c54c..2a21dd24 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -236,12 +236,15 @@
<button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
{% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
{% if this_trait.dataset.type == 'Publish' %}
- <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
+ <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/inbredset-id/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
{% endif %}
{% if this_trait.dataset.type == 'ProbeSet' %}
<button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/edit/probeset-name/{{ this_trait.name }}', '_blank')">Edit</button>
{% endif %}
+ {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
+ <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit Privileges</button>
+ {% endif %}
{% endif %}
</div>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 3dd44c85..3af94ed6 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -74,17 +74,20 @@
No collections available. Please add traits to a collection to use them as covariates.
{% else %}
<div class="select-covar-div">
- <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
+ <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button>
<button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
+ <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button>
</div>
- <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
+ <select size="2" name="selected_covariates_gemma" class="form-control selected-covariates" multiple>
+ <option value="">No covariates selected</option>
+ </select>
{% endif %}
</div>
</div>
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div class="col-xs-6">
- <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
+ <button id="gemma_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
</div>
</div>
</div>
@@ -93,15 +96,6 @@
<div class="tab-pane" id="interval_mapping">
<div class="form-horizontal section-form-div">
<div class="mapping_method_fields form-group">
- <label for="reaper_version" class="col-xs-3 control-label">Version<sup><a href="https://github.com/chfi/rust-qtlreaper" target="_blank" title="'New' is the new qtlreaper implementation written in RUST by Christian Fischer. 'Original' corresponds to the original version written in C.">?</a></sup></label>
- <div class="col-xs-3 controls">
- <select name="reaper_version" class="form-control reaper-ver-select">
- <option value="new">New</option>
- <option value="original">Original</option>
- </select>
- </div>
- </div>
- <div class="mapping_method_fields form-group">
<label for="chr_select" class="col-xs-3 control-label">Chromosome</label>
<div class="col-xs-2 controls">
<select id="chr_reaper" class="form-control chr-select">
@@ -187,7 +181,7 @@
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div class="col-xs-6">
- <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button>
+ <button id="interval_mapping_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button>
</div>
</div>
</div>
@@ -226,6 +220,17 @@
</select>
</div>
</div>
+ {% else %}
+ <div class="mapping_method_fields form-group">
+ <label for="scale_select" class="col-xs-3 control-label">Map Scale</label>
+ <div class="col-xs-2 controls">
+ <select id="scale_rqtl_geno" class="form-control scale-select">
+ {% for item in scales_in_geno[dataset.group.name + ".geno"] %}
+ <option value="{{ item[0] }}">{{ item[1] }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
{% endif %}
<div class="mapping_method_fields form-group">
<label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
@@ -249,21 +254,6 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
- <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
- <div class="col-xs-6 controls">
- <input name="control_rqtl_geno" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
- <label class="radio-inline">
- <input type="radio" name="do_control_rqtl" value="true">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="do_control_rqtl" value="false" checked="">
- No
- </label>
- </div>
- </div>
-
- <div class="mapping_method_fields form-group">
<label for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
<div class="col-xs-4 controls">
<select id="mapmodel_rqtl_geno" name="mapmodel_rqtl_geno" class="form-control">
@@ -317,17 +307,20 @@
No collections available. Please add traits to a collection to use them as covariates.
{% else %}
<div class="select-covar-div">
- <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
+ <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button>
<button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
+ <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button>
</div>
- <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
+ <select size="2" name="selected_covariates_rqtl" class="form-control selected-covariates" multiple>
+ <option value="">No covariates selected</option>
+ </select>
{% endif %}
</div>
</div>
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div class="col-xs-6 controls">
- <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
+ <button id="rqtl_geno_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
</div>
</div>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 20f78b48..5e6ed2cf 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -25,7 +25,7 @@
<label for="exclude_column">Block samples by group:</label>
<select id="exclude_column" size=1>
{% for attribute in sample_groups[0].attributes %}
- {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 %}
+ {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 and sample_groups[0].attributes[attribute].distinct_values|length > 1 %}
<option value="{{ loop.index }}">
{{ sample_groups[0].attributes[attribute].name }}
</option>
@@ -45,6 +45,27 @@
<input type="button" id="exclude_by_attr" class="btn btn-danger" value="Block">
</div>
{% endif %}
+ {% if study_samplelists|length > 0 %}
+ <div id="filterMenuSpan" class="input-append block-div-2">
+ <label for="filter_study_select">Filter samples by study: </label>
+ <select id="filter_study">
+ {% for study in study_samplelists %}
+ <option value="{{ loop.index - 1 }}">{{ study }}</option>
+ {% endfor %}
+ </select>
+ {% if sample_groups|length != 1 %}
+ <select id="filter_study_group" size="1">
+ <option value="primary">
+ {{ sample_group_types['samples_primary'] }}
+ </option>
+ <option value="other">
+ {{ sample_group_types['samples_other'] }}
+ </option>
+ </select>
+ {% endif %}
+ <input type="button" id="filter_by_study" class="btn btn-danger" value="Filter">
+ </div>
+ {% endif %}
<div id="filterMenuSpan" class="input-append block-div-2">
<label for="filter_samples_field">Filter samples by {% if (numerical_var_list|length == 0) and (not js_data.se_exists) %}value{% endif %} </label>
{% if (numerical_var_list|length > 0) or js_data.se_exists %}
@@ -53,10 +74,12 @@
{% if js_data.se_exists %}
<option value="stderr">SE</option>
{% endif %}
- {% for attribute in numerical_var_list %}
+ {% for attribute in sample_groups[0].attributes %}
+ {% if sample_groups[0].attributes[attribute].name in numerical_var_list %}
<option value="{{ loop.index }}">
- {{ attribute }}
+ {{ sample_groups[0].attributes[attribute].name }}
</option>
+ {% endif %}
{% endfor %}
</select>
{% endif %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index a462b31a..b0da1f21 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -28,6 +28,7 @@ from zipfile import ZIP_DEFLATED
from wqflask import app
from gn3.commands import run_cmd
+from gn3.computations.gemma import generate_hash_of_string
from gn3.db import diff_from_dict
from gn3.db import fetchall
from gn3.db import fetchone
@@ -63,6 +64,7 @@ from wqflask import server_side
from base.data_set import create_dataset # Used by YAML in marker_regression
from wqflask.show_trait import show_trait
from wqflask.show_trait import export_trait_data
+from wqflask.show_trait.show_trait import get_diff_of_vals
from wqflask.heatmap import heatmap
from wqflask.external_tools import send_to_bnw
from wqflask.external_tools import send_to_webgestalt
@@ -84,7 +86,7 @@ from wqflask.export_traits import export_search_results_csv
from wqflask.gsearch import GSearch
from wqflask.update_search_results import GSearch as UpdateGSearch
from wqflask.docs import Docs, update_text
-from wqflask.decorators import admin_login_required
+from wqflask.decorators import edit_access_required
from wqflask.db_info import InfoPage
from utility import temp_data
@@ -159,28 +161,37 @@ def shutdown_session(exception=None):
@app.errorhandler(Exception)
-def handle_bad_request(e):
+def handle_generic_exceptions(e):
+ import werkzeug
err_msg = str(e)
- logger.error(err_msg)
- logger.error(request.url)
- # get the stack trace and send it to the logger
- exc_type, exc_value, exc_traceback = sys.exc_info()
- logger.error(traceback.format_exc())
now = datetime.datetime.utcnow()
time_str = now.strftime('%l:%M%p UTC %b %d, %Y')
- formatted_lines = [request.url
- + " (" + time_str + ")"] + traceback.format_exc().splitlines()
-
+ # get the stack trace and send it to the logger
+ exc_type, exc_value, exc_traceback = sys.exc_info()
+ formatted_lines = {f"{request.url} ({time_str}) "
+ f" {traceback.format_exc().splitlines()}"}
+
+ _message_templates = {
+ werkzeug.exceptions.NotFound: ("404: Not Found: "
+ f"{time_str}: {request.url}"),
+ werkzeug.exceptions.BadRequest: ("400: Bad Request: "
+ f"{time_str}: {request.url}"),
+ werkzeug.exceptions.RequestTimeout: ("408: Request Timeout: "
+ f"{time_str}: {request.url}")}
+ # Default to the lengthy stack trace!
+ logger.error(_message_templates.get(exc_type,
+ formatted_lines))
# Handle random animations
# Use a cookie to have one animation on refresh
animation = request.cookies.get(err_msg[:32])
if not animation:
- list = [fn for fn in os.listdir(
- "./wqflask/static/gif/error") if fn.endswith(".gif")]
- animation = random.choice(list)
+ animation = random.choice([fn for fn in os.listdir(
+ "./wqflask/static/gif/error") if fn.endswith(".gif")])
resp = make_response(render_template("error.html", message=err_msg,
- stack=formatted_lines, error_image=animation, version=GN_VERSION))
+ stack=formatted_lines,
+ error_image=animation,
+ version=GN_VERSION))
# logger.error("Set cookie %s with %s" % (err_msg, animation))
resp.set_cookie(err_msg[:32], animation)
@@ -372,7 +383,6 @@ def wcgna_results():
results = run_wgcna(dict(request.form))
return render_template("test_wgcna_results.html", **results)
-
@app.route("/ctl_setup", methods=('POST',))
def ctl_setup():
# We are going to get additional user input for the analysis
@@ -382,20 +392,6 @@ def ctl_setup():
return render_template("ctl_setup.html", **request.form)
-# @app.route("/ctl_results", methods=('POST',))
-# def ctl_results():
-# logger.info("In ctl, request.form is:", request.form)
-# logger.info(request.url)
-# # Start R, load the package and pointers and create the analysis
-# ctl = ctl_analysis.CTL()
-# # Start the analysis, a ctlA object should be a separate long running thread
-# ctlA = ctl.run_analysis(request.form)
-# # After the analysis is finished store the result
-# result = ctl.process_results(ctlA)
-# # Display them using the template
-# return render_template("ctl_results.html", **result)
-
-
@app.route("/intro")
def intro():
doc = Docs("intro", request.args)
@@ -430,9 +426,9 @@ def submit_trait_form():
version=GN_VERSION)
-@app.route("/trait/<name>/edit/phenotype-id/<phenotype_id>")
-@admin_login_required
-def edit_phenotype(name, phenotype_id):
+@app.route("/trait/<name>/edit/inbredset-id/<inbredset_id>")
+@edit_access_required
+def edit_phenotype(name, inbredset_id):
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
passwd=current_app.config.get("DB_PASS"),
@@ -441,7 +437,7 @@ def edit_phenotype(name, phenotype_id):
conn=conn,
table="PublishXRef",
where=PublishXRef(id_=name,
- phenotype_id=phenotype_id))
+ inbred_set_id=inbredset_id))
phenotype_ = fetchone(
conn=conn,
table="Phenotype",
@@ -488,7 +484,7 @@ def edit_phenotype(name, phenotype_id):
@app.route("/trait/edit/probeset-name/<dataset_name>")
-# @admin_login_required
+@edit_access_required
def edit_probeset(dataset_name):
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
@@ -531,7 +527,7 @@ def edit_probeset(dataset_name):
@app.route("/trait/update", methods=["POST"])
-@admin_login_required
+@edit_access_required
def update_phenotype():
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
@@ -653,11 +649,11 @@ def update_phenotype():
json_data=json.dumps(diff_data)))
flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success")
return redirect(f"/trait/{data_.get('dataset-name')}"
- f"/edit/phenotype-id/{data_.get('phenotype-id')}")
+ f"/edit/inbredset-id/{data_.get('inbred-set-id')}")
@app.route("/probeset/update", methods=["POST"])
-@admin_login_required
+@edit_access_required
def update_probeset():
conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
user=current_app.config.get("DB_USER"),
@@ -1018,10 +1014,10 @@ def loading_page():
if key in wanted:
start_vars[key] = value
+ sample_vals_dict = json.loads(start_vars['sample_vals'])
if 'n_samples' in start_vars:
n_samples = int(start_vars['n_samples'])
else:
- sample_vals_dict = json.loads(start_vars['sample_vals'])
if 'group' in start_vars:
dataset = create_dataset(
start_vars['dataset'], group_name=start_vars['group'])
@@ -1043,6 +1039,10 @@ def loading_page():
n_samples += 1
start_vars['n_samples'] = n_samples
+ start_vars['vals_hash'] = generate_hash_of_string(str(sample_vals_dict))
+ if start_vars['dataset'] != "Temp": # Currently can't get diff for temp traits
+ start_vars['vals_diff'] = get_diff_of_vals(sample_vals_dict, str(start_vars['trait_id'] + ":" + str(start_vars['dataset'])))
+
start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
start_vars_container['start_vars'] = start_vars
@@ -1067,6 +1067,7 @@ def mapping_results_page():
'samples',
'vals',
'sample_vals',
+ 'vals_hash',
'first_run',
'output_files',
'geno_db_exists',
@@ -1083,7 +1084,6 @@ def mapping_results_page():
'num_perm',
'permCheck',
'perm_strata',
- 'strat_var',
'categorical_vars',
'perm_output',
'num_bootstrap',
@@ -1113,7 +1113,6 @@ def mapping_results_page():
'mapmethod_rqtl_geno',
'mapmodel_rqtl_geno',
'temp_trait',
- 'reaper_version',
'n_samples',
'transform'
)
@@ -1186,7 +1185,7 @@ def export_mapping_results():
results_csv = open(file_path, "r").read()
response = Response(results_csv,
mimetype='text/csv',
- headers={"Content-Disposition": "attachment;filename=mapping_results.csv"})
+ headers={"Content-Disposition": "attachment;filename=" + os.path.basename(file_path)})
return response
@@ -1389,7 +1388,7 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int):
@app.route("/admin/data-sample/diffs/")
-@admin_login_required
+@edit_access_required
def display_diffs_admin():
TMPDIR = current_app.config.get("TMPDIR")
DIFF_DIR = f"{TMPDIR}/sample-data/diffs"