From e63c4014e7bc34b440707be19af3779b72102fdb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 26 Jan 2017 16:26:16 +0000
Subject: GEMMA now works with CFW data (had to update where it looks for the
 input files and how it writes the phenotype file)

Y-axis for GEMMA now says -log(p)

Updated the style of the trait sample data table in the trait page

Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs)

Updated dataset menu json file

Added option to show and hide columns to regular search page using colVis

Changed regular and global search result table styles/column widths

Began work on user trait submission code (not working yet though)

Began work on static loading page for mapping results
---
 wqflask/base/data_set.py | 22 ++++++++++++++++------
 wqflask/base/trait.py    | 12 ++++++------
 2 files changed, 22 insertions(+), 12 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 06e02b02..94b38e13 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -44,7 +44,7 @@ from db import webqtlDatabaseFunction
 from utility import webqtlUtil
 from utility.benchmark import Bench
 from utility import chunks
-from utility.tools import locate, locate_ignore_error
+from utility.tools import locate, locate_ignore_error, flat_files
 
 from maintenance import get_group_samplelists
 
@@ -53,7 +53,7 @@ from pprint import pformat as pf
 from db.gn_server import menu_main
 from db.call import fetchall,fetchone,fetch1
 
-from utility.tools import USE_GN_SERVER, USE_REDIS
+from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists
 from utility.logger import getLogger
 logger = getLogger(__name__ )
 
@@ -226,7 +226,7 @@ class Markers(object):
 class HumanMarkers(Markers):
 
     def __init__(self, name, specified_markers = []):
-        marker_data_fh = open(locate('genotype') + '/' + name + '.bim')
+        marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim')
         self.markers = []
         for line in marker_data_fh:
             splat = line.strip().split()
@@ -299,11 +299,21 @@ class DatasetGroup(object):
         self.markers = HumanMarkers(self.name, markers)
 
     def get_markers(self):
-        #logger.debug("self.species is:", self.species)
-        if self.species == "human":
+        logger.debug("self.species is:", self.species)
+
+        def check_plink_gemma():
+            if flat_file_exists("mapping"):
+                MAPPING_PATH = flat_files("mapping")+"/"
+                if (os.path.isfile(MAPPING_PATH+self.name+".bed") and
+                    (os.path.isfile(MAPPING_PATH+self.name+".map") or
+                     os.path.isfile(MAPPING_PATH+self.name+".bim"))):
+                    return True
+            return False
+
+        if check_plink_gemma():
             marker_class = HumanMarkers
         else:
-            marker_class = Markers
+            marker_class = Markers            
 
         self.markers = marker_class(self.name)
 
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index eb5b91c3..bf87e879 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -207,7 +207,7 @@ class GeneralTrait(object):
                 formatted = self.post_publication_description
         else:
             formatted = "Not available"
-        return formatted.capitalize()
+        return formatted
 
     @property
     def alias_fmt(self):
@@ -379,7 +379,7 @@ def jsonable_table_row(trait, dataset_name, index):
             additive = "N/A"
         else:
             additive = "%.3f" % round(float(trait.additive), 2)
-        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                 index,
                 '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
                 trait.symbol,
@@ -395,7 +395,7 @@ def jsonable_table_row(trait, dataset_name, index):
         else:
             additive = "%.2f" % round(float(trait.additive), 2)
         if trait.pubmed_id:
-            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                     index,
                     '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
                     trait.description_display,
@@ -405,7 +405,7 @@ def jsonable_table_row(trait, dataset_name, index):
                     trait.LRS_location_repr,
                     additive]
         else:
-            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                     index,
                     '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
                     trait.description_display,
@@ -415,7 +415,7 @@ def jsonable_table_row(trait, dataset_name, index):
                     trait.LRS_location_repr,
                     additive]
     elif dataset.type == "Geno":
-        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                 index,
                 '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
                 trait.location_repr]
@@ -499,7 +499,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
         for i, field in enumerate(dataset.display_fields):
             holder = trait_info[i]
             if isinstance(trait_info[i], basestring):
-                holder = unicode(trait_info[i], "utf8", "ignore")
+                holder = unicode(trait_info[i], "utf-8", "ignore")
             setattr(trait, field, holder)
 
         if dataset.type == 'Publish':
-- 
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