From 9bf487c882c6cff773cccf86ea56d54dc6e0d2af Mon Sep 17 00:00:00 2001
From: acenteno
Date: Tue, 21 Apr 2020 21:36:35 -0500
Subject: Update base.html
Fix footer colleagues link to credits---
wqflask/wqflask/templates/base.html | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 487cf3f2..596e671f 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -138,7 +138,8 @@
Design and code by Pjotr Prins, Zach Sloan, Arthur Centeno, Christan Fischer, Danny Arends, Sam Ockman, Lei Yan, Xiaodong Zhou, Christian Fernandez,
Ning Liu, Rudi Alberts, Elissa Chesler, Sujoy Roy, Evan G. Williams, Alexander G. Williams, Kenneth Manly, Jintao Wang, and Robert W. Williams,
- colleagues.
+
+ colleagues.
GeneNetwork support from:
--
cgit v1.2.3
From 443321bd73f93dbbaeedcb3896475112e0268245 Mon Sep 17 00:00:00 2001
From: acenteno
Date: Tue, 21 Apr 2020 21:47:38 -0500
Subject: Create credits.html
Colleagues credit page---
wqflask/wqflask/templates/credits.html | 55 ++++++++++++++++++++++++++++++++++
1 file changed, 55 insertions(+)
create mode 100644 wqflask/wqflask/templates/credits.html
diff --git a/wqflask/wqflask/templates/credits.html b/wqflask/wqflask/templates/credits.html
new file mode 100644
index 00000000..95c424cc
--- /dev/null
+++ b/wqflask/wqflask/templates/credits.html
@@ -0,0 +1,55 @@
+{% extends "base.html" %}
+{% block title %}Credit{% endblock %}
+{% block content %}
+
+
+
+
+ Web site design and coding
+
+- Robert W Williams
+
- Kenneth Manly (design and QTL mapping, 1995-2007)
+
- Jintao Wang (lead programmer, 2001–2006)
+
- Arthur G. Centeno (IT Analyst III, 2001–present)
+
- Zachary Sloan (IT Analyst III, 2009–present)
+
- Lei Yan (systems and web services interface 2008-2018)
+
- Xusheng Wang (data analysis, 2008-2012)
+
- Xiaodong Zhou (lead programmer 2009–2011)
+
- Ning Liu (programmer 2008–2009)
+- Zhaohui Sun (SNP browser, programmer 2007)
+
- Yanhua Qu (data entry, 2005-2008)
+
- Stephen Pitts (programmer)
+
- Hongqiang Li (lead programmer, 2007-2009)
+
- Elissa Chesler (design of QTL Heat Map, Compare Correlations, 2004-2006)
+
- Kevitt Adler (systems, 2006-2008)
+
- Robert Crowell (SNP Browser, 2006-2007)
+
- David Crowell (partial correlations, 2008-2009)
+
- Evan G. Williams (SNP and Variant Browser, data entry, 2004-2006)
+
- Alex G Williams (QTL Maps GUI, 2003-2006)
+
+ Published and Unpublished Phenotype Data
+
+ Genotype / Genomic Data
+
+
+ |
+
+
+{% endblock %}
--
cgit v1.2.3
From 43879769faef11a3646526d1ecd4988bf06722de Mon Sep 17 00:00:00 2001
From: acenteno
Date: Tue, 21 Apr 2020 21:50:25 -0500
Subject: Update views.py
Add credits link---
wqflask/wqflask/views.py | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 76857650..b91d58d7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -305,6 +305,12 @@ def tutorials():
#return render_template("docs.html", **doc.__dict__)
return render_template("tutorials.html")
+@app.route("/credits")
+def credits():
+ #doc = docs.Docs("links", request.args)
+ #return render_template("docs.html", **doc.__dict__)
+ return render_template("credits.html")
+
@app.route("/environments")
def environments():
doc = docs.Docs("environments", request.args)
--
cgit v1.2.3
From f7b87806b658919b5b20c71b0c5ea2578ab82cd8 Mon Sep 17 00:00:00 2001
From: acenteno
Date: Tue, 21 Apr 2020 22:06:43 -0500
Subject: Update base.html
At the end of this text in the footer, it should read
....Jintao Wang, Robert W. Williams, and colleagues.
We need to add Saunak Sen in the list right by Pjotr Prins.
The link at the end to "colleagues" is broken.---
wqflask/wqflask/templates/base.html | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 596e671f..f9d4e859 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -132,12 +132,13 @@
This site is currently operated by
Rob Williams,
Pjotr Prins,
+ Saunak Sen,
Zachary Sloan,
Arthur Centeno,
and Christian Fischer.
Design and code by Pjotr Prins, Zach Sloan, Arthur Centeno, Christan Fischer, Danny Arends, Sam Ockman, Lei Yan, Xiaodong Zhou, Christian Fernandez,
- Ning Liu, Rudi Alberts, Elissa Chesler, Sujoy Roy, Evan G. Williams, Alexander G. Williams, Kenneth Manly, Jintao Wang, and Robert W. Williams,
+ Ning Liu, Rudi Alberts, Elissa Chesler, Sujoy Roy, Evan G. Williams, Alexander G. Williams, Kenneth Manly, Jintao Wang, Robert W. Williams, and
colleagues.
--
cgit v1.2.3
From 2a119affad1830d5a693860279ca2aa2897d84ef Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 24 Apr 2020 12:58:39 -0500
Subject: Made a fix that should prevent the issue where new datasets cause an
error when they're in search results
---
wqflask/base/data_set.py | 62 +++++++++++++++++++++++++++++++++++++++++++++---
1 file changed, 59 insertions(+), 3 deletions(-)
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index ebf3f021..fae62875 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -67,7 +67,6 @@ DS_NAME_MAP = {}
def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None):
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
- logger.debug("dataset_type", dataset_type)
dataset_ob = DS_NAME_MAP[dataset_type]
dataset_class = globals()[dataset_ob]
@@ -96,7 +95,6 @@ Publish or ProbeSet. E.g.
self.datasets = {}
if rebuild: #ZS: May make this the only option
data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content)
- logger.debug("THE DATA:", data)
#data = gen_menu.gen_dropdown_json()
else:
file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
@@ -120,7 +118,65 @@ Publish or ProbeSet. E.g.
logger.debugf(5, "datasets",self.datasets)
def __call__(self, name):
- return self.datasets[name]
+ if name not in self.datasets:
+ mrna_expr_query = """
+ SELECT
+ ProbeSetFreeze.Id
+ FROM
+ ProbeSetFreeze
+ WHERE
+ ProbeSetFreeze.Name = "{0}"
+ """.format(name)
+
+ results = g.db.execute(geno_query).fetchall()
+ if len(results):
+ self.datasets[name] = "ProbeSet"
+ return self.datasets[name]
+
+ group_name = name.replace("Publish", "")
+
+ pheno_query = """SELECT InfoFiles.GN_AccesionId
+ FROM InfoFiles, PublishFreeze, InbredSet
+ WHERE InbredSet.Name = '{0}' AND
+ PublishFreeze.InbredSetId = InbredSet.Id AND
+ InfoFiles.InfoPageName = PublishFreeze.Name""".format(group_name)
+
+ results = g.db.execute(pheno_query).fetchall()
+ if len(results):
+ self.datasets[name] = "Publish"
+ return self.datasets[name]
+
+ #ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary
+ other_pheno_query = """SELECT PublishFreeze.Name
+ FROM PublishFreeze, InbredSet
+ WHERE InbredSet.Name = '{}' AND
+ PublishFreeze.InbredSetId = InbredSet.Id""".format(group_name)
+
+ results = g.db.execute(other_pheno_query).fetchall()
+ if len(results):
+ self.datasets[name] = "Publish"
+ return self.datasets[name]
+
+ geno_query = """
+ SELECT
+ GenoFreezeId
+ FROM
+ GenoFreeze
+ WHERE
+ GenoFreeze.Name = "{0}"
+ {1}
+ """.format(name)
+
+ results = g.db.execute(geno_query).fetchall()
+ if len(results):
+ self.datasets[name] = "Geno"
+ return self.datasets[name]
+
+ #ZS: It shouldn't ever reach this
+ return None
+
+ else:
+ return self.datasets[name]
# Do the intensive work at startup one time only
Dataset_Getter = Dataset_Types()
--
cgit v1.2.3