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-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.py14
-rw-r--r--wqflask/utility/redis_tools.py18
-rw-r--r--wqflask/wqflask/decorators.py28
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py3
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py95
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py2
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py59
-rw-r--r--wqflask/wqflask/resource_manager.py2
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js2
-rw-r--r--wqflask/wqflask/templates/admin/group_manager.html2
-rw-r--r--wqflask/wqflask/templates/collections/view.html2
-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_details.html5
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html24
-rw-r--r--wqflask/wqflask/views.py48
25 files changed, 113 insertions, 245 deletions
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..3747aeb8 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -47,7 +47,7 @@ class TestRunMapping(unittest.TestCase):
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(
@@ -181,12 +181,15 @@ 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")
+ 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('Trait: Test Name\n'),
+ mock.call('Trait Hash: \n'),
mock.call('N Samples: 100\n'), mock.call(
'Transform - Quantile Normalized\n'),
mock.call('Gene Symbol: IGFI\n'), mock.call(
@@ -232,25 +235,20 @@ 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/redis_tools.py b/wqflask/utility/redis_tools.py
index 99295c67..de9dde46 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -127,20 +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 if this_admin else None for this_admin in group_ob['admins']])
- group_members = set([this_member 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/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 77d6e2db..6254b9b9 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -357,8 +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']])
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 a148b49c..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
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 1df53fef..290c4a14 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -271,47 +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
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/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index b75d658e..e42fe8c4 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -145,7 +145,7 @@ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form
'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', 'reaper_version', 'primary_samples']
+ '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/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index c5479b17..d347a060 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -71,7 +71,7 @@
<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 id="clustered-heatmap-image-area">
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_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 36d3c15a..2a21dd24 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -233,7 +233,7 @@
<button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button>
{% endif %}
{% endif %}
- <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1-lily.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
+ <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/inbredset-id/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
@@ -242,6 +242,9 @@
{% 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 5365140d..3af94ed6 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -96,15 +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">
@@ -263,21 +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">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 85aa6b17..5067ca0e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -85,7 +85,7 @@ 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
@@ -160,28 +160,37 @@ 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)
@@ -411,7 +420,7 @@ def submit_trait_form():
@app.route("/trait/<name>/edit/inbredset-id/<inbredset_id>")
-@admin_login_required
+@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"),
@@ -468,7 +477,7 @@ def edit_phenotype(name, inbredset_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"),
@@ -511,7 +520,7 @@ 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"),
@@ -637,7 +646,7 @@ def update_phenotype():
@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"),
@@ -1097,7 +1106,6 @@ def mapping_results_page():
'mapmethod_rqtl_geno',
'mapmodel_rqtl_geno',
'temp_trait',
- 'reaper_version',
'n_samples',
'transform'
)
@@ -1373,7 +1381,7 @@ 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"