From 537e1d19d33f1000103f3f33b52e87674ca89a31 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 28 Jun 2016 11:03:06 +0000
Subject: Logger: disabled some noisy loggers

---
 wqflask/wqflask/show_trait/SampleList.py | 4 ++--
 wqflask/wqflask/show_trait/show_trait.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 5e3b092e..7e7503d4 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -32,7 +32,7 @@ class SampleList(object):
         self.sample_attribute_values = {}
 
         self.get_attributes()
-        logger.debug("camera: attributes are:", pf(self.attributes))
+        # logger.debug("camera: attributes are:", pf(self.attributes))
 
         if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
             self.get_extra_attribute_values()
@@ -55,7 +55,7 @@ class SampleList(object):
                 sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
                 sample.extra_info['css_class'] = "fs12"
 
-            logger.debug("  type of sample:", type(sample))
+            # logger.debug("  type of sample:", type(sample))
 
             if sample_group_type == 'primary':
                 sample.this_id = "Primary_" + str(counter)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 3eea3f4a..912beabe 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -146,7 +146,7 @@ class ShowTrait(object):
         else:
             self.sample_group_types['samples_primary'] = self.dataset.group.name
         sample_lists = [group.sample_list for group in self.sample_groups]
-        logger.debug("sample_lists is:", pf(sample_lists))
+        # logger.debug("sample_lists is:", pf(sample_lists))
 
         self.get_mapping_methods()
 
-- 
cgit v1.2.3


From 0e975e62810c1b8afac13e1fa039a3998fc58ba9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 16 Jul 2016 12:00:55 +0600
Subject: README: added info

---
 doc/Architecture.org            | 5 +++--
 wqflask/maintenance/README.md   | 4 ++++
 wqflask/maintenance/__init__.py | 0
 3 files changed, 7 insertions(+), 2 deletions(-)
 create mode 100644 wqflask/maintenance/README.md
 delete mode 100644 wqflask/maintenance/__init__.py

(limited to 'wqflask')

diff --git a/doc/Architecture.org b/doc/Architecture.org
index 9a561568..cac40939 100644
--- a/doc/Architecture.org
+++ b/doc/Architecture.org
@@ -56,7 +56,6 @@ from the database. To get the menu data in YAML you can do something like
 see [[https://github.com/genenetwork/gn_server/doc/API.md][GnServer REST API]] documentation.
 
 * Database 
-
 ** Phenotypes
 
 Phenotypes are stored in the SQL database.  For what happens at the
@@ -67,7 +66,7 @@ see the installation [[./README.org][instructions]].
 
 Genotypes are stored in genotype files. These are part of the GNU Guix
 distribution, see the installation [[./README.org][instructions]]. Genotype files are
-currently in GN1 format, and will be aligned with the R/qtl2 format. Now it is
+currently in GN1 format, and will be aligned with the [[http://kbroman.org/qtl2/pages/sampledata.html][R/qtl2 formats]]. Now it is
 for BXD.geno:
 
 #+begin_src js
@@ -93,3 +92,5 @@ B B B B B B D B D B B D B B H H B D B B H H B B D D D D D B B H B B B B D B D B
 D D D D D H B D D B D B B D D B D D B B B B B B U D
 etc
 #+end_src
+
+and, for example, in the method run_rqtl_geno this file gets loaded.
diff --git a/wqflask/maintenance/README.md b/wqflask/maintenance/README.md
new file mode 100644
index 00000000..873eaa32
--- /dev/null
+++ b/wqflask/maintenance/README.md
@@ -0,0 +1,4 @@
+Maintenance files have been moved into a separate repository named
+*gn_extra*. See https://github.com/genenetwork/gn_extra
+
+
diff --git a/wqflask/maintenance/__init__.py b/wqflask/maintenance/__init__.py
deleted file mode 100644
index e69de29b..00000000
-- 
cgit v1.2.3


From 41a8f2381b0d2d2f7d6aa5d50dee93d96af3ff39 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 26 Jul 2016 10:49:46 +0600
Subject: Docs: genotype

---
 doc/Architecture.org                                  | 19 ++++++++++---------
 .../marker_regression/marker_regression_gn1.py        |  2 +-
 2 files changed, 11 insertions(+), 10 deletions(-)

(limited to 'wqflask')

diff --git a/doc/Architecture.org b/doc/Architecture.org
index e3bc8026..a1fcbef2 100644
--- a/doc/Architecture.org
+++ b/doc/Architecture.org
@@ -66,8 +66,9 @@ see the installation [[./README.org][instructions]].
 
 Genotypes are stored in genotype files. These are part of the GNU Guix
 distribution, see the installation [[./README.org][instructions]]. Genotype files are
-currently in GN1 format, and will be aligned with the [[http://kbroman.org/qtl2/pages/sampledata.html][R/qtl2
-formats]]. Currently it is for the stored file BXD.geno:
+currently in GN1 format, and will be aligned with the [[http://kbroman.org/qtl2/pages/sampledata.html][R/qtl2 formats]].
+
+GN1-style (still default GN2) for the stored file BXD.geno:
 
 #+begin_src js
 @name:BXD
@@ -130,21 +131,21 @@ genotype data is tagged as transposed:
 "founder_geno": "recla_foundergeno.csv",
 "founder_geno_transposed": true,
 "genotypes": {
-"1": "1",
-"2": "2",
-"3": "3"
+  "1": "1",
+  "2": "2",
+  "3": "3"
 },
 "pheno": "recla_pheno.csv",
 "pheno_transposed": false,
 "covar": "recla_covar.csv",
 "sex": {
-"covar": "Sex",
-"female": "female",
-"male": "male"
+  "covar": "Sex",
+  "female": "female",
+  "male": "male"
 },
 "x_chr": "X",
 "cross_info": {
-"covar": "ngen"
+  "covar": "ngen"
 },
 "gmap": "recla_gmap.csv",
 "pmap": "recla_pmap.csv",
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 9573a9de..33ebc527 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -382,7 +382,7 @@ class MarkerRegression(object):
             self.GraphInterval = self.MbGraphInterval #Mb
         else:
             self.GraphInterval = self.cMGraphInterval #cM
-			
+
         ################################################################
         # Get Trait Values and Infomation
         ################################################################
-- 
cgit v1.2.3


From ec7d4e1198bc8d2f83ce99b41e2084fbce6a0be7 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 10 Sep 2016 11:43:21 +0200
Subject: Support for running maintenance scripts so they can pick up all
 webserver settings

Run with

   ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
---
 bin/genenetwork2                          | 27 ++++++++++++++++++++++++---
 wqflask/base/data_set.py                  |  2 +-
 wqflask/base/webqtlConfig.py              |  1 -
 wqflask/maintenance/gen_select_dataset.py | 26 +++++++++++++++++---------
 wqflask/utility/tools.py                  |  1 +
 5 files changed, 43 insertions(+), 14 deletions(-)

(limited to 'wqflask')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index d3bf3299..3a8c3ff4 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,6 +1,14 @@
 #! /bin/bash
 #
-# This will run the GN2 server (with default settings if none supplied).
+# This will run the GN2 server (with default settings if none supplied). Pass in
+# your own settings file, e.g.
+#
+#   ./bin/genenetwork2 ~/my_settings.py
+#
+# To run a maintenance script with settings (instead of the webserver) add that with
+# a -c switch, e.g.
+#
+#   ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
 #
 # Environment settings can be used to preconfigure as well as a
 # settings.py file.
@@ -18,7 +26,12 @@ echo $GN2_BASE_PATH
 
 # Handle settings parameter
 settings=$1
-if [ -z $settings ]; then settings=$GN2_BASE_PATH/etc/default_settings.py ; fi
+if [ -z $settings ]; then
+    # get default
+    settings=$GN2_BASE_PATH/etc/default_settings.py
+else
+    shift
+fi
 if [ ! -e $settings ]; then
     echo "ERROR: can not locate settings file - pass it in the command line"
     exit 1
@@ -32,7 +45,15 @@ export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH
 if [ -z $TEMPDIR ]; then
     TEMPDIR="/tmp"
 fi
-                         
+
+# Now handle command parameter -c
+if [ $1 = '-c' ] ; then
+    echo PYTHONPATH=$PYTHONPATH
+    echo RUNNING COMMAND $2
+    /usr/bin/env python $2
+    exit 0
+fi
+
 echo "Starting the redis server:"
 echo -n "dir $TEMPDIR
 dbfilename gn2.rdb
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1b4e1195..6cd3c8e6 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -91,7 +91,7 @@ Publish or ProbeSet. E.g.
         if USE_GN_SERVER:
             data = menu_main()
         else:
-            file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
+            file_name = "wqflask/wqflask/static/new/javascript/dataset_menu_structure.json"
             with open(file_name, 'r') as fh:
                 data = json.load(fh)
 
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index f76d8140..8c67a6fd 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -80,4 +80,3 @@ PORTADDR = "http://50.16.251.170"
 INFOPAGEHREF = '/dbdoc/%s.html'
 CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
 SCRIPTFILE = 'main.py'
-
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index d39bf4a5..5c25c15b 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -1,7 +1,9 @@
 """Script that generates the data for the main dropdown menus on the home page
 
 Writes out data as /static/new/javascript/dataset_menu_structure.json
-It needs to be run manually when database has been changed.
+It needs to be run manually when database has been changed. Run it as
+
+    python gen_select_dataset.py
 
 """
 
@@ -37,9 +39,15 @@ from __future__ import print_function, division
 #print("cdict is:", cdict)
 
 import sys
-# import zach_settings # no hard code paths!
 
-# import MySQLdb
+# NEW: Note we prepend the current path - otherwise a guix instance of GN2 is used instead
+sys.path.insert(0,'./wqflask')
+# NEW: import app to avoid a circular dependency on utility.tools
+from wqflask import app
+
+from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI
+
+import MySQLdb
 
 # import simplejson as json
 import urlparse
@@ -55,14 +63,13 @@ from pprint import pformat as pf
 
 #conn = Engine.connect()
 
-print('ERROR: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!')
-sys.exit()
+print('WARNING: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!')
 
 
 def parse_db_uri(db_uri):
     """Converts a database URI to the db name, host name, user name, and password"""
 
-    parsed_uri = urlparse.urlparse(zach_settings.DB_URI)
+    parsed_uri = urlparse.urlparse(SQL_URI)
 
     db_conn_info = dict(
                         db = parsed_uri.path[1:],
@@ -70,6 +77,7 @@ def parse_db_uri(db_uri):
                         user = parsed_uri.username,
                         passwd = parsed_uri.password)
 
+    print(db_conn_info)
     return db_conn_info
 
 
@@ -258,7 +266,7 @@ def build_datasets(species, group, type_name):
 def main():
     """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
 
-    parse_db_uri(zach_settings.SQL_URI)
+    parse_db_uri(SQL_URI)
 
     species = get_species()
     groups = get_groups(species)
@@ -281,7 +289,7 @@ def main():
 
     #print("data:", data)
 
-    output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json"""
+    output_file = """./wqflask/wqflask/static/new/javascript/dataset_menu_structure.json"""
 
     with open(output_file, 'w') as fh:
         json.dump(data, fh, indent="   ", sort_keys=True)
@@ -297,6 +305,6 @@ def _test_it():
     #print("build_datasets:", pf(datasets))
 
 if __name__ == '__main__':
-    Conn = MySQLdb.Connect(**parse_db_uri(zach_settings.SQL_URI))
+    Conn = MySQLdb.Connect(**parse_db_uri(SQL_URI))
     Cursor = Conn.cursor()
     main()
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index bb8241f5..2c8cc5c5 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -3,6 +3,7 @@
 
 import os
 import sys
+
 from wqflask import app
 
 # Use the standard logger here to avoid a circular dependency
-- 
cgit v1.2.3


From 5e106bad6e59d3a13be0b79715785948a3ff581a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 10 Sep 2016 11:57:55 +0200
Subject: Comment

---
 wqflask/maintenance/gen_select_dataset.py              |  2 +-
 wqflask/wqflask/marker_regression/marker_regression.py | 16 ++++++++--------
 2 files changed, 9 insertions(+), 9 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 5c25c15b..f2f0830f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -3,7 +3,7 @@
 Writes out data as /static/new/javascript/dataset_menu_structure.json
 It needs to be run manually when database has been changed. Run it as
 
-    python gen_select_dataset.py
+  ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
 
 """
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index f3b018b8..a1065adc 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -57,7 +57,7 @@ class MarkerRegression(object):
 
         all_samples_ordered = self.dataset.group.all_samples_ordered()
         primary_sample_names = list(all_samples_ordered)
-        
+
         for sample in self.dataset.group.samplelist:
             in_trait_data = False
             for item in self.this_trait.data:
@@ -241,9 +241,9 @@ class MarkerRegression(object):
                         highest_chr = marker['chr']
                     if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
                         self.qtl_results.append(marker)
-       
+
             self.trimmed_markers = trim_markers_for_table(results)
-			
+
             self.json_data['chr'] = []
             self.json_data['pos'] = []
             self.json_data['lod.hk'] = []
@@ -560,7 +560,7 @@ class MarkerRegression(object):
 
 
     def gen_pheno_txt_file_plink(self, pheno_filename = ''):
-        ped_sample_list = self.get_samples_from_ped_file()	
+        ped_sample_list = self.get_samples_from_ped_file()
         output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb")
         header = 'FID\tIID\t%s\n' % self.this_trait.name
         output_file.write(header)
@@ -595,7 +595,7 @@ class MarkerRegression(object):
         output_file.close()
 
     def gen_pheno_txt_file_rqtl(self, pheno_filename = ''):
-        ped_sample_list = self.get_samples_from_ped_file()	
+        ped_sample_list = self.get_samples_from_ped_file()
         output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb")
         header = 'FID\tIID\t%s\n' % self.this_trait.name
         output_file.write(header)
@@ -653,7 +653,7 @@ class MarkerRegression(object):
             genotype = genotype.addinterval()
 
         samples, values, variances, sample_aliases = self.this_trait.export_informative()
-        
+
         trimmed_samples = []
         trimmed_values = []
         for i in range(0, len(samples)):
@@ -818,7 +818,7 @@ class MarkerRegression(object):
         """Runs permutations and gets significant and suggestive LOD scores"""
 
         top_lod_scores = []
-	
+
         #print("self.num_perm:", self.num_perm)
 
         for permutation in range(self.num_perm):
@@ -1084,7 +1084,7 @@ def create_snp_iterator_file(group):
 
 def trim_markers_for_table(markers):
     num_markers = len(markers)
-	
+
     if 'lod_score' in markers[0].keys():
         sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
     else:
-- 
cgit v1.2.3