From 85a384dc779a49f02ccee3088356e4873eacbd9a Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 6 Aug 2020 12:29:13 -0500 Subject: Made a change that should fix the issue with the Y axis ticks extending too high in mapping results * wqflask/wqflask/marker_regression/display_mapping_results.py - When in ful genome view, I changed it to subject the yTopOffset when drawing the Y axis; single chromosome view seems to work okay so it's conditional on that --- .../wqflask/marker_regression/display_mapping_results.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 9ac4946b..75c1a8cd 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1737,9 +1737,17 @@ class DisplayMappingResults(object): LRSLODFont=pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0) yZero = yTopOffset + plotHeight - LRSHeightThresh = drawAreaHeight - AdditiveHeightThresh = drawAreaHeight/2 - DominanceHeightThresh = drawAreaHeight/2 + # LRSHeightThresh = drawAreaHeight + # AdditiveHeightThresh = drawAreaHeight/2 + # DominanceHeightThresh = drawAreaHeight/2 + if self.selectedChr == 1: + LRSHeightThresh = drawAreaHeight - yTopOffset + 30*(zoom - 1) + AdditiveHeightThresh = LRSHeightThresh/2 + DominanceHeightThresh = LRSHeightThresh/2 + else: + LRSHeightThresh = drawAreaHeight + AdditiveHeightThresh = drawAreaHeight/2 + DominanceHeightThresh = drawAreaHeight/2 # LRSHeightThresh = (yZero - yTopOffset + 30*(zoom - 1)) # AdditiveHeightThresh = LRSHeightThresh/2 # DominanceHeightThresh = LRSHeightThresh/2 @@ -1900,7 +1908,7 @@ class DisplayMappingResults(object): startPosX += newStartPosX oldStartPosX = newStartPosX - #ZS: This is beause the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used + #ZS: This is because the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used this_chr = str(self.ChrList[self.selectedChr][0]) if self.plotScale != "physic": this_chr = str(self.ChrList[self.selectedChr][1]+1) -- cgit v1.2.3 From 39f2d8b8599a8daae2c55c3a2bf48366164c6ca2 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 6 Aug 2020 13:54:18 -0500 Subject: Added endpoint for changing some user details * wqflask/wqflask/user_session.py - Added endpoint for /manage/user that lets the user change their full_name or organization. Still need to add something that lets them change their e-mail, since that will require a confirmation --- wqflask/wqflask/user_session.py | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index ba659fe5..3aa2c151 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -13,7 +13,7 @@ from wqflask import app from utility import hmac #from utility.elasticsearch_tools import get_elasticsearch_connection -from utility.redis_tools import get_redis_conn, get_user_id, get_user_collections, save_collections +from utility.redis_tools import get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, get_user_collections, save_collections Redis = get_redis_conn() from utility.logger import getLogger @@ -53,6 +53,18 @@ def create_signed_cookie(): logger.debug("uuid_signed:", uuid_signed) return the_uuid, uuid_signed +@app.route("/user/manage", methods=('GET','POST')) +def manage_user(): + params = request.form if request.form else request.args + if 'new_full_name' in params: + set_user_attribute(g.user_session.user_id, 'full_name', params['new_full_name']) + if 'new_organization' in params: + set_user_attribute(g.user_session.user_id, 'organization', params['new_organization']) + + user_details = get_user_by_unique_column("user_id", g.user_session.user_id) + + return render_template("admin/manage_user.html", user_details = user_details) + class UserSession(object): """Logged in user handling""" -- cgit v1.2.3 From bdbb0fab5b30a9413491c0ad36585d6c5c671d22 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 17 Aug 2020 12:52:22 -0500 Subject: Placed X/Y trait info before the table on the correlation scatterplot page * wqflask/wqflask/templates/corr_scatterplot.html - reordered table and X/Y trait info divs --- wqflask/wqflask/templates/corr_scatterplot.html | 108 ++++++++++++------------ 1 file changed, 54 insertions(+), 54 deletions(-) diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html index 5877e367..6f0511e1 100644 --- a/wqflask/wqflask/templates/corr_scatterplot.html +++ b/wqflask/wqflask/templates/corr_scatterplot.html @@ -132,44 +132,8 @@

-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
StatisticValue
Number{{jsdata.num_overlap}}
Slope{{ jsdata.slope_string }}
Intercept{{'%0.3f' % jsdata.intercept}}
r value{{'%0.3f' % jsdata.r_value}}
P value{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}
- Regression Line -
- y = {{ jsdata.slope_string }} * x {% if jsdata.intercept < 0 %}- {{'%0.3f' % (jsdata.intercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.intercept}}{% endif %} -
-
-
+
+
{% if trait_1.dataset.type == "ProbeSet" %}
X axis: @@ -240,15 +204,7 @@
{% endif %}
-
-
- -
-
-
-
-
-
+
@@ -260,31 +216,39 @@ - + - + - + - + - +
StatisticValue
Slope{{ jsdata.srslope_string }}{{ jsdata.slope_string }}
Intercept{{'%0.3f' % jsdata.srintercept}}{{'%0.3f' % jsdata.intercept}}
r value{{'%0.3f' % jsdata.srr_value}}{{'%0.3f' % jsdata.r_value}}
P value{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}
Regression Line
- y = {{ jsdata.srslope_string }} * x {% if jsdata.srintercept < 0 %}- {{'%0.3f' % (jsdata.srintercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.srintercept}}{% endif %} + y = {{ jsdata.slope_string }} * x {% if jsdata.intercept < 0 %}- {{'%0.3f' % (jsdata.intercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.intercept}}{% endif %}
+
-
+
+ +
+
+
+
+
+
{% if trait_1.dataset.type == "ProbeSet" %}
X axis: @@ -335,6 +299,42 @@
{% endif %}
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
StatisticValue
Number{{jsdata.num_overlap}}
Slope{{ jsdata.srslope_string }}
Intercept{{'%0.3f' % jsdata.srintercept}}
r value{{'%0.3f' % jsdata.srr_value}}
P value{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}
+ Regression Line +
+ y = {{ jsdata.srslope_string }} * x {% if jsdata.srintercept < 0 %}- {{'%0.3f' % (jsdata.srintercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.srintercept}}{% endif %} +
+
-- cgit v1.2.3 From 42ba26dbfd73b48ef463965d5ee22c16e159dc55 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 19 Aug 2020 14:14:16 -0500 Subject: Show short labels by default in Correlation Matrix * wqflask/wqflask/templates/correlation_matrix.html - remove display: none for short label div --- wqflask/wqflask/templates/correlation_matrix.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index cb9fb815..4e17a0b2 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -36,7 +36,7 @@ Trait {{ loop.index }}: {{ trait.dataset.name }}  {{ trait.name }} - +
{% if trait.dataset.type == "ProbeSet" %}Gene Symbol: {{ trait.symbol }}{% elif trait.dataset.type == "Publish" %}Trait Symbol: {{ trait.post_publication_abbreviation }}{% elif trait.dataset.type == "Geno" %}Genotype{% endif %}