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-rw-r--r--wqflask/base/data_set.py2
-rw-r--r--wqflask/base/webqtlConfig.py1
-rw-r--r--wqflask/maintenance/README.md4
-rw-r--r--wqflask/maintenance/__init__.py0
-rw-r--r--wqflask/maintenance/gen_select_dataset.py26
-rw-r--r--wqflask/utility/tools.py1
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py16
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py2
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py4
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py2
10 files changed, 35 insertions, 23 deletions
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/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
--- a/wqflask/maintenance/__init__.py
+++ /dev/null
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index d39bf4a5..f2f0830f 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
+
+ ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/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
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:
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 3db5b0f6..9cef3cec 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -386,7 +386,7 @@ class MarkerRegression(object):
self.GraphInterval = self.MbGraphInterval #Mb
else:
self.GraphInterval = self.cMGraphInterval #cM
-
+
################################################################
# Get Trait Values and Infomation
################################################################
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()
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 17:30:05 +0000