From e6c21d96f45dc74de43db451383236f28e723847 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 19 Apr 2021 16:46:39 +0000
Subject: Removed unused code
---
wqflask/base/data_set.py | 5 -----
1 file changed, 5 deletions(-)
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 178234fe..44325d5b 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -573,11 +573,6 @@ class DataSet(object):
"""Gets overridden later, at least for Temp...used by trait's get_given_name"""
return None
- # Delete this eventually
- @property
- def riset():
- Weve_Renamed_This_As_Group
-
def get_accession_id(self):
if self.type == "Publish":
results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
--
cgit v1.2.3
From 34b6fbf0044fd950ecb95590b4b772abd2cbcb8e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 19 Apr 2021 16:57:21 +0000
Subject: Fixed NIAAA link because apparently it was changed
---
wqflask/wqflask/templates/base.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ccb2ac5a..1fbaad51 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -191,7 +191,7 @@
Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
- NIAAA
+ NIAAA
Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
--
cgit v1.2.3
From c8f9367bc12340bb8b8a7ce1a5f42789e311555a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 19 Apr 2021 16:57:52 +0000
Subject: Removed commented out js file
---
wqflask/wqflask/templates/base.html | 1 -
1 file changed, 1 deletion(-)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 1fbaad51..e6f22deb 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -257,7 +257,6 @@
-
--
cgit v1.2.3
From 789dd88a0b9a6a8cbe0413c47212c89c1681765c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 19 Apr 2021 17:08:30 +0000
Subject: Removedu nused function from network_graph.py
---
wqflask/wqflask/network_graph/network_graph.py | 12 ------------
1 file changed, 12 deletions(-)
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 1d5316a2..132e1884 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -182,15 +182,3 @@ class NetworkGraph(object):
samples=self.all_sample_list,
sample_data=self.sample_data,
elements=self.elements,)
-
- def get_trait_db_obs(self, trait_db_list):
- self.trait_list = []
- for i, trait_db in enumerate(trait_db_list):
- if i == (len(trait_db_list) - 1):
- break
- trait_name, dataset_name = trait_db.split(":")
- dataset_ob = data_set.create_dataset(dataset_name)
- trait_ob = create_trait(dataset=dataset_ob,
- name=trait_name,
- cellid=None)
- self.trait_list.append((trait_ob, dataset_ob))
--
cgit v1.2.3
From 68ee0a995fceaf6aefdd3c8f780e46a83b51a0e8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 19 Apr 2021 17:11:41 +0000
Subject: Specify only getting the first two items after splitting the
trait/dataset input string
---
wqflask/utility/helper_functions.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 7eb7f013..46eeb35d 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -40,7 +40,7 @@ def get_trait_db_obs(self, trait_db_list):
data, _separator, hmac_string = trait.rpartition(':')
data = data.strip()
assert hmac_string==hmac.hmac_creation(data), "Data tampering?"
- trait_name, dataset_name = data.split(":")
+ trait_name, dataset_name = data.split(":")[:2]
if dataset_name == "Temp":
dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2])
else:
--
cgit v1.2.3
From 315d7f13b254aa62e277805d7d9816b0c7042479 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 22 Apr 2021 18:23:50 +0000
Subject: Added JS that sets the 'add to collection' dropdown to default to the
collection the use set as their default collection
---
wqflask/wqflask/static/new/javascript/search_results.js | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index ecb1220d..48b9b7be 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -326,4 +326,15 @@ $(function() {
} );
}
+ apply_default = function() {
+ let default_collection_id = $.cookie('default_collection');
+ if (default_collection_id) {
+ let the_option = $('[name=existing_collection] option').filter(function() {
+ return ($(this).text().split(":")[0] == default_collection_id);
+ })
+ the_option.prop('selected', true);
+ }
+ }
+ apply_default();
+
});
\ No newline at end of file
--
cgit v1.2.3
From 1a7bb988ee360b3ef48e22e25b419c375dccb9fa Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 22 Apr 2021 18:26:01 +0000
Subject: Account for situations where the trait symbol is null for ProbeSet
traits; previously it could throw an error
---
wqflask/wqflask/search_results.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index f23c0582..cb01a2af 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -119,7 +119,7 @@ class SearchResultPage(object):
trait_dict['dataset'] = this_trait.dataset.name
trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))
if this_trait.dataset.type == "ProbeSet":
- trait_dict['symbol'] = this_trait.symbol
+ trait_dict['symbol'] = this_trait.symbol if this_trait.symbol else "N/A"
trait_dict['description'] = "N/A"
if this_trait.description_display:
trait_dict['description'] = this_trait.description_display
--
cgit v1.2.3
From 6e8afe5a6871a680778bfaed6b79c934b33d0307 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 28 Apr 2021 19:40:58 +0000
Subject: Account for temp traits when adding covariates with GEMMA mapping
---
wqflask/wqflask/marker_regression/gemma_mapping.py | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 83ebcdf9..06c9300a 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -146,7 +146,12 @@ def gen_covariates_file(this_dataset, covariates, samples):
for covariate in covariate_list:
this_covariate_data = []
trait_name = covariate.split(":")[0]
- dataset_ob = create_dataset(covariate.split(":")[1])
+ dataset_name = covariate.split(":")[1]
+ if dataset_name == "Temp":
+ temp_group = trait_name.split("_")[2]
+ dataset_ob = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+ else:
+ dataset_ob = create_dataset(covariate.split(":")[1])
trait_ob = create_trait(dataset=dataset_ob,
name=trait_name,
cellid=None)
--
cgit v1.2.3
From 65a2c8c1f455c5fad48fbac1a3e75310d49ed844 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 28 Apr 2021 19:45:37 +0000
Subject: Added something to jsonable in trait.py to account for temp traits
(this is necessary for them to show up correctly when selecting traits from
collections in pop-up windows, like when selecting cofactors for mapping)
---
wqflask/base/trait.py | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index df96d46e..b4b4452a 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -337,6 +337,10 @@ def jsonable(trait):
dataset_name=dataset.shortname,
location=trait.location_repr
)
+ elif dataset.name == "Temp":
+ return dict(name=trait.name,
+ dataset="Temp",
+ dataset_name="Temp")
else:
return dict()
--
cgit v1.2.3