From 75802ed1f9e5d955987bf5f5eb78a9cb120116ec Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 20 Jun 2020 17:33:22 -0500
Subject: Added some admin functionality and fixed issue with temp traits

---
 wqflask/base/webqtlConfig.py | 4 ++++
 1 file changed, 4 insertions(+)

(limited to 'wqflask/base/webqtlConfig.py')

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 55407123..3d86bc22 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -17,6 +17,10 @@ DEBUG = 1
 #USER privilege
 USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
 
+#Set privileges
+SUPER_PRIVILEGES = {'data': ['no-access', 'view', 'edit'], 'metadata': ['no-access', 'view', 'edit'], 'admin': ['not-admin', 'edit-access', 'edit-admins']}
+DEFAULT_PRIVILEGES = {'data': ['no-access', 'view'], 'metadata': ['no-access', 'view'], 'admin': ['not-admin']}
+
 #minimum number of informative strains
 KMININFORMATIVE = 5
 
-- 
cgit v1.2.3


From 9b1dd2f67d51de2d6cdb687ee332597ba010a0ac Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 25 Jul 2020 11:54:10 +0100
Subject: Removing bimbam check. We'll get rid of bimbam anyway.

---
 wqflask/base/webqtlConfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask/base/webqtlConfig.py')

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 3d86bc22..862ac881 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -85,7 +85,7 @@ assert_writable_dir(GENERATED_TEXT_DIR)
 # Flat file directories
 GENODIR              = flat_files('genotype')+'/'
 assert_dir(GENODIR)
-assert_dir(GENODIR+'bimbam') # for gemma
+# assert_dir(GENODIR+'bimbam') # for gemma
 
 # JSON genotypes are OBSOLETE
 JSON_GENODIR         = flat_files('genotype/json')+'/'
-- 
cgit v1.2.3


From 4dc8f3d24fe82239a8c3d229b7d4ef413a65498f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 18 Feb 2021 16:58:18 +0000
Subject: Fixed SUPER_PRIVILEGES and DEFAULT_PRIVILEGES

---
 wqflask/base/webqtlConfig.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask/base/webqtlConfig.py')

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 862ac881..72d7ac98 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -18,8 +18,8 @@ DEBUG = 1
 USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
 
 #Set privileges
-SUPER_PRIVILEGES = {'data': ['no-access', 'view', 'edit'], 'metadata': ['no-access', 'view', 'edit'], 'admin': ['not-admin', 'edit-access', 'edit-admins']}
-DEFAULT_PRIVILEGES = {'data': ['no-access', 'view'], 'metadata': ['no-access', 'view'], 'admin': ['not-admin']}
+SUPER_PRIVILEGES = {'data': ['edit'], 'metadata': ['edit'], 'admin': ['edit-admins']}
+DEFAULT_PRIVILEGES = {'data': ['view'], 'metadata': ['view'], 'admin': ['not-admin']}
 
 #minimum number of informative strains
 KMININFORMATIVE = 5
-- 
cgit v1.2.3


From b5c07c6a65dc8f342a5c5d65349aa5dfbf83862d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 18 Feb 2021 18:31:11 +0000
Subject: Changed DEFAULT_PERMISSIONS AND SUPER_PERMISSIONS to not have
 permissions be lists (I think the proxy expects them to not be lists, but
 then returns them as lists; need to check about this)

---
 wqflask/base/webqtlConfig.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask/base/webqtlConfig.py')

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 72d7ac98..aee8616a 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -18,8 +18,8 @@ DEBUG = 1
 USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
 
 #Set privileges
-SUPER_PRIVILEGES = {'data': ['edit'], 'metadata': ['edit'], 'admin': ['edit-admins']}
-DEFAULT_PRIVILEGES = {'data': ['view'], 'metadata': ['view'], 'admin': ['not-admin']}
+SUPER_PRIVILEGES = {'data': 'edit', 'metadata': 'edit', 'admin': 'edit-admins'}
+DEFAULT_PRIVILEGES = {'data': 'view', 'metadata': 'view', 'admin': 'not-admin'}
 
 #minimum number of informative strains
 KMININFORMATIVE = 5
-- 
cgit v1.2.3


From 7433bd00b492859e5fc9daeec2c8ba56bfaed495 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Mar 2021 21:34:20 +0000
Subject: Added the RRID urls for mouse and rat to webqtlConfig

---
 wqflask/base/webqtlConfig.py | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'wqflask/base/webqtlConfig.py')

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index aee8616a..bb8704a5 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -63,6 +63,8 @@ OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s"
 UNIPROT_URL = "https://www.uniprot.org/uniprot/%s"
 RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&species=%s"
 PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&genomeVer=rn6&section=geneEQTL"
+RRID_MOUSE_URL = "https://www.jax.org/strain/%s"
+RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%s"
 
 # Temporary storage (note that this TMPDIR can be set as an
 # environment variable - use utility.tools.TEMPDIR when you
-- 
cgit v1.2.3