From dbaea134b1cee2a9cdc4968dac50e50e44c162bb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sun, 15 Mar 2020 15:03:15 -0500
Subject: Fixed digits issue, though still need to figure out how to increase
gap between y axis and title
---
wqflask/wqflask/static/new/javascript/show_trait.js | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 819c4d12..0162f858 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -1017,10 +1017,12 @@ get_bar_range = function(sample_vals, sample_errors = null){
root.chart_range = get_bar_range(get_sample_vals(sample_lists[0]), get_sample_errors(sample_lists[0])[0])
val_range = root.chart_range[1] - root.chart_range[0]
-if (val_range < 5){
- tick_digits = '.1f'
+if (val_range < 0.05){
+ tick_digits = '.3f'
} else if (val_range < 0.5) {
tick_digits = '.2f'
+} else if (val_range < 5){
+ tick_digits = '.1f'
} else {
tick_digits = 'f'
}
@@ -1045,7 +1047,7 @@ if (js_data.num_values < 256) {
},
},
yaxis: {
- title: js_data.unit_type,
+ title: "" + js_data.unit_type + "",
range: root.chart_range,
titlefont: {
size: 16
--
cgit v1.2.3
From 49d1af523c520a80f48f2e8d021877f6fb0f12a3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 19 Mar 2020 11:46:49 -0500
Subject: Made a minor change just to help qtlreaper deal with genotype files
with positions in bases instead of megabases
---
wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 41764c1c..0c560582 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -97,7 +97,10 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
except:
marker['chr'] = line.split("\t")[2]
marker['cM'] = float(line.split("\t")[3])
- marker['Mb'] = float(line.split("\t")[4])
+ if float(line.split("\t")[4]) > 1000:
+ marker['Mb'] = float(line.split("\t")[4])/1000000
+ else:
+ marker['Mb'] = float(line.split("\t")[4])
if float(line.split("\t")[7]) != 1:
marker['p_value'] = float(line.split("\t")[7])
marker['lrs_value'] = float(line.split("\t")[5])
--
cgit v1.2.3
From 3dc5931e6729631affe23cfa736c98836e5e171b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 25 Mar 2020 13:53:20 -0500
Subject: Added fix for issue when creating collections (related to hmac import
change)
---
wqflask/wqflask/collect.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 2a94e63d..74eb869f 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -43,10 +43,10 @@ def process_traits(unprocessed_traits):
unprocessed_traits = unprocessed_traits.split(",")
traits = set()
for trait in unprocessed_traits:
- data, _separator, hmac = trait.rpartition(':')
+ data, _separator, the_hmac = trait.rpartition(':')
data = data.strip()
if g.user_session.logged_in:
- assert hmac == hmac.data_hmac(data), "Data tampering?"
+ assert the_hmac == hmac.hmac_creation(data), "Data tampering?"
traits.add(str(data))
return traits
--
cgit v1.2.3
From 05c172a8330f28c9c81300448d9f2630a6d7ff0f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 4 Apr 2020 20:23:34 -0500
Subject: Changed Y axis on permutation histogram from Frequency to Count
---
wqflask/wqflask/templates/mapping_results.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 86816d17..c046f7fb 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -490,7 +490,7 @@
},
yaxis: {
autorange: true,
- title: "Frequency",
+ title: "Count",
titlefont: {
family: "arial",
size: 20
--
cgit v1.2.3
From dce4f524ae9640553eb8aa319ed593de9d603231 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 6 Apr 2020 17:41:19 -0500
Subject: Added Mean column for phenotype traits in search and global search
result tables
---
wqflask/base/data_set.py | 2 ++
wqflask/base/trait.py | 5 +++--
wqflask/wqflask/do_search.py | 1 +
wqflask/wqflask/gsearch.py | 7 ++++++-
wqflask/wqflask/search_results.py | 3 +++
wqflask/wqflask/templates/gsearch_pheno.html | 6 ++++++
wqflask/wqflask/templates/search_result_page.html | 7 +++++++
7 files changed, 28 insertions(+), 3 deletions(-)
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5b32c5ae..ebf3f021 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -710,6 +710,7 @@ class PhenotypeDataSet(DataSet):
'Phenotype.Pre_publication_description',
'Phenotype.Pre_publication_abbreviation',
'Phenotype.Post_publication_abbreviation',
+ 'PublishXRef.mean',
'Phenotype.Lab_code',
'Publication.PubMed_ID',
'Publication.Abstract',
@@ -725,6 +726,7 @@ class PhenotypeDataSet(DataSet):
'original_description',
'pre_publication_abbreviation',
'post_publication_abbreviation',
+ 'mean',
'lab_code',
'submitter', 'owner',
'authorized_users',
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 8e779a11..5525472e 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -354,7 +354,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
SELECT
PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
- Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+ Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
Publication.Authors, Publication.Title, Publication.Abstract,
Publication.Journal, Publication.Volume, Publication.Pages,
@@ -503,8 +503,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#LRS and its location
trait.LRS_score_repr = "N/A"
trait.LRS_location_repr = "N/A"
- trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = ""
+ trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
if dataset.type == 'ProbeSet' and not trait.cellid:
+ trait.mean = ""
query = """
SELECT
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index b56a858a..05caa100 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -218,6 +218,7 @@ class PhenotypeSearch(DoSearch):
header_fields = ['Index',
'Record',
'Description',
+ 'Mean',
'Authors',
'Year',
'Max LRS',
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 12813e9a..3d9b508a 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -139,7 +139,8 @@ class GSearch(object):
Publication.`PubMed_ID`,
PublishXRef.`LRS`,
PublishXRef.`additive`,
- InbredSet.`InbredSetCode`
+ InbredSet.`InbredSetCode`,
+ PublishXRef.`mean`
FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication
WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
AND PublishFreeze.`InbredSetId`=InbredSet.`Id`
@@ -183,6 +184,10 @@ class GSearch(object):
this_trait['description'] = line[5].decode('utf-8', 'replace')
else:
this_trait['description'] = "N/A"
+ if line[13] != None and line[13] != "":
+ this_trait['mean'] = line[13]
+ else:
+ this_trait['mean'] = "N/A"
this_trait['authors'] = line[7]
this_trait['year'] = line[8]
if this_trait['year'].isdigit():
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 34c647f4..698389ab 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -143,6 +143,9 @@ views.py).
trait_dict['pubmed_id'] = this_trait.pubmed_id
trait_dict['pubmed_link'] = this_trait.pubmed_link
trait_dict['pubmed_text'] = this_trait.pubmed_text
+ trait_dict['mean'] = "N/A"
+ if this_trait.mean != "" and this_trait.mean != None:
+ trait_dict['mean'] = '%.3f' % this_trait.mean
trait_dict['lrs_score'] = this_trait.LRS_score_repr
trait_dict['lrs_location'] = this_trait.LRS_location_repr
trait_dict['additive'] = "N/A"
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 4d5238ef..f6ffff47 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -189,6 +189,12 @@
}
}
},
+ {
+ 'title': "Mean",
+ 'type': "natural",
+ 'width': "10%",
+ 'data': "mean"
+ },
{
'title': "Authors",
'type': "natural",
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 13457030..162bde08 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -349,6 +349,13 @@
}
}
},
+ {
+ 'title': "Mean",
+ 'type': "natural",
+ 'width': "110px",
+ 'data': "mean",
+ 'orderSequence': [ "desc", "asc"]
+ },
{
'title': "Authors",
'type': "natural",
--
cgit v1.2.3
From 3fed8e9bdb24ee0b9276794494df689d7a877421 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 8 Jul 2019 17:14:18 +0000
Subject: Mariadb
---
doc/README.org | 30 ++++++++++++++++--------------
1 file changed, 16 insertions(+), 14 deletions(-)
diff --git a/doc/README.org b/doc/README.org
index 620c946c..b15bc33f 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -7,8 +7,8 @@
- [[#docker][Docker]]
- [[#with-source][With source]]
- [[#running-gn2][Running GN2]]
- - [[#run-mysql-server][Run MySQL server]]
- - [[#install-mysql-with-gnu-guix][Install MySQL with GNU GUIx]]
+ - [[#run-mariadb-server][Run MariaDB server]]
+ - [[#install-mariadb-with-gnu-guix][Install MariaDB with GNU GUIx]]
- [[#load-the-small-database-in-mysql][Load the small database in MySQL]]
- [[#gn2-dependency-graph][GN2 Dependency Graph]]
- [[#working-with-the-gn2-source-code][Working with the GN2 source code]]
@@ -94,8 +94,10 @@ or you can set environment variables to override individual parameters, e.g.
the debug and logging switches can be particularly useful when
developing GN2.
-* Run MySQL server
-** Install MySQL with GNU GUIx
+* Run MariaDB server
+** Install MariaDB with GNU GUIx
+
+/Note we are moving to MariaDB/
These are the steps you can take to install a fresh installation of
mysql (which comes as part of the GNU Guix genenetwork2 install).
@@ -103,30 +105,30 @@ mysql (which comes as part of the GNU Guix genenetwork2 install).
As root configure and run
#+BEGIN_SRC bash
-adduser mysql && addgroup mysql
-mysqld --datadir=/var/mysql --initialize-insecure
-mkdir -p /var/run/mysqld
-chown mysql.mysql ~/mysql /var/run/mysqld
-mysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048"
+adduser mariadb && addgroup mariadb
+mysqld --datadir=/home/mariadb/database --initialize-insecure
+mkdir -p /var/run/mariadbd
+chown mariadb.mariadb /var/run/mariadbd
+mysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048"
#+END_SRC
If you want to run as root you may have to set
: /etc/my.cnf
-: [mysqld]
+: [mariadbd]
: user=root
To check error output in a file on start-up run with something like
-: mysqld -u mysql --console --explicit_defaults_for_timestamp --datadir=/gnu/mysql --log-error=~/test.log
+: mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log
-Other tips are that Guix installs mysqld in your profile, so this may work
+Other tips are that Guix installs mariadbd in your profile, so this may work
-: /home/user/.guix-profile/bin/mysqld -u mysql --explicit_defaults_for_timestamp --datadir=/gnu/mysql
+: /home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb
When you get errors like:
-: qlalchemy.exc.IntegrityError: (_mysql_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')
+: qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')
you may need to set
--
cgit v1.2.3
From 6bdae3220dd52f136f9aeb7fe95bb40e5b0884bc Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 5 Sep 2019 05:22:52 +0000
Subject: Text search comment
---
doc/README.org | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/doc/README.org b/doc/README.org
index b15bc33f..03cba62a 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -118,6 +118,13 @@ If you want to run as root you may have to set
: [mariadbd]
: user=root
+You also need to set
+
+: ft_min_word_len = 3
+
+To make sure word text searches (shh) work and rebuild the tables if
+required.
+
To check error output in a file on start-up run with something like
: mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log
--
cgit v1.2.3
From e72862bdb307b016cb1c2269818edae5c9ddc150 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 20 Apr 2020 09:46:16 -0500
Subject: Remove Elastic
---
doc/README.org | 30 ------------------------------
1 file changed, 30 deletions(-)
diff --git a/doc/README.org b/doc/README.org
index 03cba62a..4057cb79 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -12,8 +12,6 @@
- [[#load-the-small-database-in-mysql][Load the small database in MySQL]]
- [[#gn2-dependency-graph][GN2 Dependency Graph]]
- [[#working-with-the-gn2-source-code][Working with the GN2 source code]]
- - [[#running-elasticsearch][Running ElasticSearch]]
- - [[#systemd][SystemD]]
- [[#read-more][Read more]]
- [[#trouble-shooting][Trouble shooting]]
- [[#importerror-no-module-named-jinja2][ImportError: No module named jinja2]]
@@ -205,34 +203,6 @@ http://biogems.info/contrib/genenetwork/gn2.svg
See [[development.org]].
-* Running ElasticSearch
-
-In order to start up elasticsearch:
-Penguin - change user to "elasticsearch" and use the following command: "env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch"
-
-
-** SystemD
-
-New server - as root run "systemctl restart elasticsearch"
-
-#+BEGIN_SRC
-tux01:/etc/systemd/system# cat elasticsearch.service
-[Unit]
-Description=Run Elasticsearch
-
-[Service]
-ExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch
-Environment=JAVA_HOME=/opt/jdk-9.0.4
-Environment="ES_JAVA_OPTS=-Xms1g -Xmx8g"
-Environment="PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin"
-LimitNOFILE=65536
-StandardOutput=syslog
-StandardError=syslog
-User=elasticsearch
-
-[Install]
-WantedBy=multi-user.target
-#+END_SRC
* Read more
--
cgit v1.2.3
From 960f42184da639a4e352ba7517cf0eece06d58f9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 23 Apr 2020 10:44:46 -0500
Subject: Docs
---
doc/GUIX-Reproducible-from-source.org | 1 -
doc/README.org | 80 ++++++++++++++++-------------------
2 files changed, 36 insertions(+), 45 deletions(-)
diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org
index 83adce99..19e4d14f 100644
--- a/doc/GUIX-Reproducible-from-source.org
+++ b/doc/GUIX-Reproducible-from-source.org
@@ -33,7 +33,6 @@ GNU Guix has to be installed as root. I tested this recipe on a fresh
install of Debian 8.3.0 (in KVM) though it should work on any modern
Linux distribution (including CentOS).
-
Note that GN2 consists of an approx. 5 GB installation including
database. If you use a virtual machine we recommend to use at least
double.
diff --git a/doc/README.org b/doc/README.org
index 4057cb79..828ed2cd 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -3,9 +3,6 @@
* Table of Contents :TOC:
- [[#introduction][Introduction]]
- [[#install][Install]]
- - [[#tarball][Tarball]]
- - [[#docker][Docker]]
- - [[#with-source][With source]]
- [[#running-gn2][Running GN2]]
- [[#run-mariadb-server][Run MariaDB server]]
- [[#install-mariadb-with-gnu-guix][Install MariaDB with GNU GUIx]]
@@ -20,6 +17,8 @@
- [[#rpy2-error-show-now-found][Rpy2 error 'show' now found]]
- [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]]
- [[#irc-session][IRC session]]
+ - [[#notes][NOTES]]
+ - [[#deploying-gn2-official][Deploying GN2 official]]
* Introduction
@@ -38,44 +37,10 @@ an example of the [[#gn2-dependency-graph][GN2 Dependency Graph]].
* Install
-The quickest way to install GN2 is by using a binary installation
-(tarball or Docker image). These installations are bundled by GNU
-Guix and include all dependencies. You can install GeneNetwork on most
-Linux distributions, including Debian, Ubuntu, Fedora and CentOS,
-provided you have administrator privileges (root). The alternative is
-a Docker installation.
-
-** Tarball
-
-Download the ~800Mb tarball from
-[[http://files.genenetwork.org/software/binary_tarball/]]. Validate the checksum and
-unpack to root, for example
-
-: tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz
-: mv /gnu /
-: mv /opt/genenetwork2 /opt/
-
-Now you shoud be able to start the server with
-
-: /opt/genenetwork2/bin/genenetwork2
-
-When the server stops with a MySQL error [[#run-mysql-server][Run MySQL server]]
-and set SQL_URI to point at it. For example:
-
-: export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s
-
-See also [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]].
-
-** Docker
-
-Docker images are also available through
-[[http://files.genenetwork.org/software/]]. Validate the checksum and run
-with [[https://docs.docker.com/engine/reference/commandline/load/][Docker load]].
-
-** With source
-
-For more elaborate installation instructions on deploying GeneNetwork from
-source see [[#source-deployment][Source deployment]].
+Make sure to install GNU Guix using the binary download instructions
+on the main website. Follow the instructions on
+[[GUIX-Reproducible-from-source.org]] to download pre-built binaries. Note
+the download amounts to several GBs of data.
* Running GN2
@@ -95,10 +60,10 @@ developing GN2.
* Run MariaDB server
** Install MariaDB with GNU GUIx
-/Note we are moving to MariaDB/
+/Note: we moved to MariaDB/
These are the steps you can take to install a fresh installation of
-mysql (which comes as part of the GNU Guix genenetwork2 install).
+mariadb (which comes as part of the GNU Guix genenetwork2 install).
As root configure and run
@@ -203,7 +168,6 @@ http://biogems.info/contrib/genenetwork/gn2.svg
See [[development.org]].
-
* Read more
If you want to understand the architecture of GN2 read
@@ -687,3 +651,31 @@ The following derivations would be built:
I am building it on guix.genenetwork.org right now [10:09]
nice [10:10]
#+end_src
+
+* NOTES
+
+** Deploying GN2 official
+
+Let's see how fast we can deploy a second copy of GN2.
+
+- [-] Base install
+ + [X] First install a Debian server with GNU Guix on board
+ + [X] Get Guix build going
+ - [X] Build the correct version of Guix
+ - [X] Check out the correct gn-stable version of guix-bioinformatics http://git.genenetwork.org/pjotrp/guix-bioinformatics
+ - [X] guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable
+ + [X] Create a gn2 user and home with space
+ + [X] Install redis (currently debian)
+ - [X] add to systemd
+ - [X] update redis.cnf
+ - [X] update database
+ + [X] Install mariadb (currently debian mariadb-server)
+ - [X] add to systemd
+ - [X] system stop mysql
+ - [X] update mysql.cnf
+ - [X] update database (see gn-services/services/mariadb.md)
+ - [X] check tables
+ + [ ] run gn2 (rust-qtlreaper not working)
+ + [X] update nginx
+ + [ ] install genenetwork3
+ - [ ] add to systemd
--
cgit v1.2.3
From e5ccb1a586fcd83ec6feddad7e0b767b29a369b2 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 23 Apr 2020 18:09:52 +0200
Subject: Ignore
---
.gitignore | 2 ++
1 file changed, 2 insertions(+)
diff --git a/.gitignore b/.gitignore
index 0006d9a8..70d0273d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,8 @@
*.bak
*.cross
*~
+*.swo
+*.swp
genotype_files/genotype/HSNIH_copy.geno
web/new_genotypes/HSNIH.json
wqflask/secure_server.py
--
cgit v1.2.3
From 92f505e42c6ac6314b29ac152654b393dc581501 Mon Sep 17 00:00:00 2001
From: Arthur Centeno
Date: Sun, 26 Apr 2020 09:59:25 -0500
Subject: URL for finding services
---
etc/default_settings.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 75f84dc4..4a35f42d 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -28,6 +28,8 @@ GN_VERSION = open("../etc/VERSION","r").read()
SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
SQL_ALCHEMY_POOL_RECYCLE = 3600
GN_SERVER_URL = "http://localhost:8880/" # REST API server
+GN2_BASE_URL = "http://genenetwork.org/"
+GN2_BRANCH_URL = GN2_BASE_URL
# ---- Flask configuration (see website)
TRAP_BAD_REQUEST_ERRORS = True
--
cgit v1.2.3