Merge branch 'master' of https://github.com/genenetwork/genenetwork2

13 files changed, 42 insertions, 37 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 1e47e183..e5f10edf 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -65,7 +65,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp
 # want to reach this base dir
 assert_writable_dir(TEMPDIR)
 
-TMPDIR               = mk_dir(TEMPDIR+'gn2')
+TMPDIR               = mk_dir(TEMPDIR+'/gn2/')
 assert_writable_dir(TMPDIR)
 
 CACHEDIR             = mk_dir(TMPDIR+'/cache/')
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index e5726656..a5fd86e2 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -57,7 +57,7 @@ import urlparse
 
 from pprint import pformat as pf
 
-#Engine = sa.create_engine(zach_settings.SQLALCHEMY_DATABASE_URI)
+#Engine = sa.create_engine(zach_settings.SQL_URI)
 
 # build MySql database connection
 
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index c28c617a..d46a84ba 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -205,21 +205,24 @@ SQL_URI            = get_setting('SQL_URI')
 LOG_LEVEL          = get_setting('LOG_LEVEL')
 LOG_LEVEL_DEBUG    = get_setting_int('LOG_LEVEL_DEBUG')
 LOG_SQL            = get_setting_bool('LOG_SQL')
-LOG_SQLALCHEMY     = get_setting_bool('LOG_SQLALCHEMY')
+LOG_SQL_ALCHEMY    = get_setting_bool('LOG_SQL_ALCHEMY')
 LOG_BENCH          = get_setting_bool('LOG_BENCH')
 LOG_FORMAT         = "%(message)s"    # not yet in use
 USE_REDIS          = get_setting_bool('USE_REDIS')
 USE_GN_SERVER      = get_setting_bool('USE_GN_SERVER')
 
 GENENETWORK_FILES  = get_setting('GENENETWORK_FILES')
-TEMP_TRAITS        = get_setting('TEMP_TRAITS')
+GUIX_JS_PATH       = get_setting('GUIX_JS_PATH')
+assert_dir(GUIX_JS_PATH)
 
 PYLMM_COMMAND      = pylmm_command()
 GEMMA_COMMAND      = gemma_command()
-GEMMA_RESULTS_PATH = get_setting('GEMMA_RESULTS_PATH')
 PLINK_COMMAND      = plink_command()
 TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
 
+TWITTER_POST_FETCHER_JS_PATH = GUIX_JS_PATH + "/Twitter-Post-Fetcher"
+assert_dir(TWITTER_POST_FETCHER_JS_PATH)
+
 from six import string_types
 
 if os.environ.get('WQFLASK_OVERRIDES'):
@@ -234,5 +237,3 @@ if os.environ.get('WQFLASK_OVERRIDES'):
             else:
                 OVERRIDES[k] = cmd
             logger.debug(OVERRIDES)
-
-assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH"))
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index 4df872ad..96c2c301 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -22,8 +22,8 @@ def init_db():
     # they will be registered properly on the metadata.  Otherwise
     # you will have to import them first before calling init_db()
     #import yourapplication.models
+    logger.info("Initializing database connection")
     import wqflask.model
-    logger.debug("Creating all model metadata")
     Base.metadata.create_all(bind=engine)
     logger.info("Done creating all model metadata")
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 87532445..8882c515 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -37,7 +37,7 @@ from utility import temp_data
 from utility.benchmark import Bench
 from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
 
-from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, GEMMA_RESULTS_PATH, PLINK_COMMAND, TEMPDIR
+from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
 from utility.external import shell
 from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 49959a74..82a44796 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1018,7 +1018,7 @@ class MarkerRegression(object):
         else:
             if self.selectedChr > -1:
                 for i, qtlresult in enumerate(self.qtlresults):
-                    if qtlresult['Chr'] != self.selectedChr:
+                    if qtlresult['chr'] != self.selectedChr:
                         continue
 
                     if i==0 and qtlresult['Mb'] >= Mb:
@@ -1027,7 +1027,7 @@ class MarkerRegression(object):
 
                     #the trait's position is between two traits
                     if i > 0 and self.qtlresults[i-1]['Mb'] < Mb and qtlresult['Mb'] >= Mb:
-                        locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['cM']+(qtlresult['cM']-self.qtlresults[i-1]['cM'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb']))
+                        locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['Mb']+(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb']))
                         break
 
                     #the trait's position is on the right of the last genotype
@@ -1036,11 +1036,12 @@ class MarkerRegression(object):
             else:
                 locPixel = xLeftOffset
                 for i, _chr in enumerate(self.ChrList):
-                    if _chr != Chr:
-                        locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
-                    else:
-                        locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
-                        break
+                    if i < (len(self.ChrList)-1):
+                        if _chr != Chr:
+                            locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+                        else:
+                            locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
+                            break
         if locPixel >= 0 and self.plotScale == 'physic':
             traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12))
             canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ec55ebeb..9ca3d63a 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -144,7 +144,7 @@
         <p>
           Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> and find us on <a href="https://webchat.freenode.net/">IRC</a> (#genenetwork channel).
         {% if version: %}
-        <p><small>GeneNetwork v{{ version }}</small></p>
+        <p><small>GeneNetwork {{ version }}</small></p>
         {% endif %}
 
       </div>
diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html
index c707a4fc..2f1e06fa 100644
--- a/wqflask/wqflask/templates/error.html
+++ b/wqflask/wqflask/templates/error.html
@@ -35,7 +35,7 @@
   </p>
 
   <pre>
-    GeneNetwork v{{ version }} {{ stack[0] }}
+    GeneNetwork {{ version }} {{ stack[0] }}
     {{ message }} (error)
     {{ stack[-3] }}
     {{ stack[-2] }}
@@ -50,7 +50,7 @@
   <a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a>
   <div id="Stack" class="collapse">
     <pre>
-      GeneNetwork v{{ version }} {% for line in stack %} {{ line }}
+      GeneNetwork {{ version }} {% for line in stack %} {{ line }}
       {% endfor %}
     </pre>
   </div>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 4cea51b2..65debd10 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -14,7 +14,7 @@
         <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
         <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
         <input type="hidden" name="dataset" value="{{ dataset.name }}">
-        {% if mapping_method == "reaper" %}
+        {% if mapping_method == "reaper" or mapping_method == "rqtl_geno" %}
         <input type="hidden" name="genofile" value="{{ dataset.group.genofile }}">
         {% endif %}
         <input type="hidden" name="method" value="{{ mapping_method }}">
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 56b6cc62..5a880647 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -129,6 +129,7 @@
     <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
+    <script type="text/javascript" src="/static/new/js_external/saveSvgAsPng.js"></script>
     <script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
 
     <script type="text/javascript" src="/static/new/javascript/stats.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 0a0e9990..ac44b656 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -94,12 +94,15 @@
                 <div class="tab-pane" id="probability_plot">
                     <div style="padding: 20px" class="form-horizontal">
                         {% if sample_groups|length != 1 %}
+                        Select Group:
                         <select class="prob_plot_samples_group">
                             {% for group, pretty_group in sample_group_types.items() %}
                                 <option value="{{ group }}">{{ pretty_group }}</option>
                             {% endfor %}
                         </select>
-                        <br><br>
+                        <button type="button" class="btn btn-default" id="down_prob_plot">Export as PNG</button>
+                        <br>
+                        <br>
                         {% endif %}
 
                         <div id="prob_plot_container">
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 1e831896..f7fcd2d0 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -46,7 +46,7 @@ from wqflask.database import db_session
 from wqflask import model
 
 from utility import Bunch, Struct, after
-from utility.tools import LOG_SQL, LOG_SQLALCHEMY
+from utility.tools import LOG_SQL, LOG_SQL_ALCHEMY
 
 import logging
 from utility.logger import getLogger
@@ -69,7 +69,7 @@ class AnonUser(object):
         if self.cookie:
             logger.debug("already is cookie")
             self.anon_id = verify_cookie(self.cookie)
-            
+
         else:
             logger.debug("creating new cookie")
             self.anon_id, self.cookie = create_signed_cookie()
@@ -78,17 +78,17 @@ class AnonUser(object):
         @after.after_this_request
         def set_cookie(response):
             response.set_cookie(self.cookie_name, self.cookie)
-            
+
     def add_collection(self, new_collection):
         collection_dict = dict(name = new_collection.name,
                                created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
                                changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
                                num_members = new_collection.num_members,
                                members = new_collection.get_members())
-                               
+
         Redis.set(self.key, json.dumps(collection_dict))
         Redis.expire(self.key, 60 * 60 * 24 * 5)
-            
+
     def delete_collection(self, collection_name):
         existing_collections = self.get_collections()
         updated_collections = []
@@ -106,7 +106,7 @@ class AnonUser(object):
                 updated_collections.append(this_collection)
 
         Redis.set(self.key, json.dumps(updated_collections))
-            
+
     def get_collections(self):
         json_collections = Redis.get(self.key)
         if json_collections == None or json_collections == "None":
@@ -117,7 +117,7 @@ class AnonUser(object):
                 collection['created_timestamp'] = datetime.datetime.strptime(collection['created_timestamp'], '%b %d %Y %I:%M%p')
                 collection['changed_timestamp'] = datetime.datetime.strptime(collection['changed_timestamp'], '%b %d %Y %I:%M%p')
             return collections
-            
+
     def import_traits_to_user(self):
         collections_list = json.loads(Redis.get(self.key))
         for collection in collections_list:
@@ -131,7 +131,7 @@ class AnonUser(object):
                 uc.members = json.dumps(collection['members'])
                 db_session.add(uc)
                 db_session.commit()
-            
+
     def display_num_collections(self):
         """
         Returns the number of collections or a blank string if there are zero.
@@ -217,7 +217,7 @@ class UserSession(object):
         """Actual sqlalchemy record"""
         # Only look it up once if needed, then store it
         try:
-            if LOG_SQLALCHEMY:
+            if LOG_SQL_ALCHEMY:
                 logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
 
             # Already did this before
@@ -237,7 +237,7 @@ class UserSession(object):
 def before_request():
     g.user_session = UserSession()
     g.cookie_session = AnonUser()
-    
+
 class UsersManager(object):
     def __init__(self):
         self.users = model.User.query.all()
@@ -541,9 +541,9 @@ class LoginUser(object):
                 import_col = "true"
             else:
                 import_col = "false"
-            
-            #g.cookie_session.import_traits_to_user()           
-                
+
+            #g.cookie_session.import_traits_to_user()
+
             return self.actual_login(user, import_collections=import_col)
 
         else:
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 24a7cbca..44ca8de8 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -53,7 +53,7 @@ from wqflask.ctl import ctl_analysis
 #from wqflask.trait_submission import submit_trait
 
 from utility import temp_data
-from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION
+from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,TWITTER_POST_FETCHER_JS_PATH
 from utility.helper_functions import get_species_groups
 
 from base import webqtlFormData
@@ -152,8 +152,7 @@ def tmp_page(img_path):
 
 @app.route("/twitter/<path:filename>")
 def bd_files(filename):
-    bd_path = app.config['TWITTER_POST_FETCHER_JS_PATH']
-    return send_from_directory(bd_path, filename)
+    return send_from_directory(TWITTER_POST_FETCHER_JS_PATH, filename)
 
 #@app.route("/data_sharing")
 #def data_sharing_page():