- Temporary traits can be created, viewed, and added to collections

- Correct PCA trait data is created but can't be saved yet
- Added inner margins by increasing xDomain and yDomain of probability plot on trait page
- Increased X/Y-axis label font size
- Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading
- Improved appearance of correlation page table
- Added links to github to index page
- Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those
- Removed "Tissue" from trait page for phenotype traits

3 files changed, 33 insertions, 20 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 54dd3c4b..7f08135f 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -61,14 +61,17 @@ logger = getLogger(__name__ )
 # Each subclass will add to this
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
+def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
         logger.debug("dataset_type", dataset_type)
 
     dataset_ob = DS_NAME_MAP[dataset_type]
     dataset_class = globals()[dataset_ob]
-    return dataset_class(dataset_name, get_samplelist)
+    if dataset_type == "Temp":
+        return dataset_class(dataset_name, get_samplelist, group_name)
+    else:
+        return dataset_class(dataset_name, get_samplelist)
 
 class Dataset_Types(object):
 
@@ -261,10 +264,13 @@ class DatasetGroup(object):
     has multiple datasets associated with it.
 
     """
-    def __init__(self, dataset):
+    def __init__(self, dataset, name=None):
         """This sets self.group and self.group_id"""
         #logger.debug("DATASET NAME2:", dataset.name)
-        self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+        if name == None:
+            self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+        else:
+            self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
         if self.name == 'BXD300':
             self.name = "BXD"
 
@@ -304,7 +310,7 @@ class DatasetGroup(object):
         elif mapping_id == "2":
             mapping_names = ["GEMMA"]
         elif mapping_id == "4":
-            mapping_names = ["PLINK"]
+            mapping_names = ["GEMMA", "PLINK"]
         else:
             mapping_names = []
 
@@ -319,9 +325,7 @@ class DatasetGroup(object):
         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"))):
+                if os.path.isfile(MAPPING_PATH+self.name+".bed"):
                     return True
             return False
 
@@ -481,7 +485,7 @@ class DataSet(object):
 
     """
 
-    def __init__(self, name, get_samplelist = True):
+    def __init__(self, name, get_samplelist = True, group_name = None):
 
         assert name, "Need a name"
         self.name = name
@@ -493,11 +497,12 @@ class DataSet(object):
 
         self.setup()
 
-        self.check_confidentiality()
-
-        self.retrieve_other_names()
-
-        self.group = DatasetGroup(self)   # sets self.group and self.group_id and gets genotype
+        if self.type == "Temp": #Need to supply group name as input if temp trait
+            self.group = DatasetGroup(self, group_name)   # sets self.group and self.group_id and gets genotype
+        else:
+            self.check_confidentiality()
+            self.retrieve_other_names()
+            self.group = DatasetGroup(self)   # sets self.group and self.group_id and gets genotype
         if get_samplelist == True:
              self.group.get_samplelist()
         self.species = species.TheSpecies(self)
@@ -1156,6 +1161,8 @@ class MrnaAssayDataSet(DataSet):
 class TempDataSet(DataSet):
     '''Temporary user-generated data set'''
 
+    DS_NAME_MAP['Temp'] = 'TempDataSet'
+
     def setup(self):
         self.search_fields = ['name',
                               'description']
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index bf87e879..e22a51e4 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -62,6 +62,11 @@ class GeneralTrait(object):
         self.strand_probe = None
         self.symbol = None
 
+        self.LRS_score_repr = "N/A"
+        self.LRS_score_value = 0
+        self.LRS_location_repr = "N/A"
+        self.LRS_location_value = 1000000
+
         if kw.get('fullname'):
             name2 = value.split("::")
             if len(name2) == 2:
@@ -72,9 +77,10 @@ class GeneralTrait(object):
 
         # Todo: These two lines are necessary most of the time, but perhaps not all of the time
         # So we could add a simple if statement to short-circuit this if necessary
-        self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
-        if get_sample_info != False:
-            self = retrieve_sample_data(self, self.dataset)
+        if self.dataset.type != "Temp":
+            self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
+            if get_sample_info != False:
+                self = retrieve_sample_data(self, self.dataset)
 
 
     def get_name(self):
@@ -315,12 +321,12 @@ def get_sample_data():
     #
     #return jsonable_sample_data
     
-def jsonable(trait, dataset_name):
+def jsonable(trait):
     """Return a dict suitable for using as json
 
     Actual turning into json doesn't happen here though"""
 
-    dataset = create_dataset(dataset_name)
+    dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
     
     if dataset.type == "ProbeSet":
         return dict(name=trait.name,
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index e5f10edf..1e47e183 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/')