Began writing code that writes some objects used in LMM to redis

and writes/reads eachitem in the plink_input

5 files changed, 136 insertions, 64 deletions

diff --git a/misc/notes.txt b/misc/notes.txt
index 6bdcccf3..5d4bcaeb 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -106,6 +106,14 @@ sudo /etc/init.d/redis_6379 start
 
 ===========================================
 
+Run pylint:
+pylint file_name
+
+For options:
+pylint --help 
+
+===========================================
+
 Start screen session:
 
 If "no option -R":
diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py
index aa40badf..4f2cd8a9 100644
--- a/wqflask/maintenance/quick_search_table.py
+++ b/wqflask/maintenance/quick_search_table.py
@@ -1,17 +1,17 @@
-from __future__ import print_function, division, absolute_import
+"""Creates a table used for the quick search feature.
+
+One column contains the terms to match the user's search against. Another contains the result
+fields in json format
 
-"""
 Results will be returned for each of several trait types: mRNA assays, phenotypes, genotypes, and
 (maybe later) genes
 
-For each trait type, the results for each species should be given; for example, have a "Mouse" tab
-with the mouse traits in a table inside it
-
-This table will then list each trait, its dataset, and several columns determined by its trait type
-(phenotype, genotype, etc)
+For each trait type, the results for each species should be given This table will then list
+each trait, its dataset, and several columns determined by its trait type (phenotype, genotype, etc)
 
 """
 
+from __future__ import print_function, division, absolute_import
 
 import sys
 sys.path.append("../../..")
@@ -19,19 +19,17 @@ sys.path.append("../../..")
 import simplejson as json
 
 import sqlalchemy as sa
-from sqlalchemy.dialects import mysql
-from sqlalchemy.orm import scoped_session, sessionmaker, relationship, backref
-from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.orm import scoped_session, sessionmaker
 from sqlalchemy.ext.declarative import declarative_base
 
-from pprint import pformat as pf
+#from pprint import pformat as pf
 
 import zach_settings as settings
 
 Engine = sa.create_engine(settings.SQLALCHEMY_DATABASE_URI,
                        #encoding='utf-8',
                        #client_encoding='utf-8',
-                       #echo="debug",
+                       #echo="debug",w
                        )
 
 Session = scoped_session(sessionmaker(bind=Engine)) #, extension=VersionedListener()))
@@ -41,6 +39,14 @@ Metadata = sa.MetaData()
 Metadata.bind = Engine
 
 class PublishXRef(Base):
+    """Class that corresponds with the PublishXRef table in the database.
+    
+    The PublishXRef table links phenotype traits and their publications.
+    
+    This class is used to add phenotype traits to the quick search table.
+    
+    """
+    
     __tablename__ = 'PublishXRef'
 
     Id = sa.Column(sa.Integer, primary_key=True)
@@ -56,15 +62,16 @@ class PublishXRef(Base):
 
     @classmethod
     def run(cls):
+        """Connects to database and inserts phenotype trait info into the Quicksearch table."""
         conn = Engine.connect()
         counter = 0
-        for ps in page_query(Session.query(cls)):   #all()
+        for pub_row in page_query(Session.query(cls)):   #all()
             values = {}
             values['table_name'] = cls.__tablename__
-            values['the_key'] = json.dumps([ps.Id, ps.InbredSetId])
-            values['terms'] = cls.get_unique_terms(ps.Id, ps.InbredSetId)
+            values['the_key'] = json.dumps([pub_row.Id, pub_row.InbredSetId])
+            values['terms'] = cls.get_unique_terms(pub_row.Id, pub_row.InbredSetId)
             print("terms is:", values['terms'])
-            values['result_fields'] = cls.get_result_fields(ps.Id, ps.InbredSetId)
+            values['result_fields'] = cls.get_result_fields(pub_row.Id, pub_row.InbredSetId)
             ins = QuickSearch.insert().values(**values)
             conn.execute(ins)
             counter += 1
@@ -72,6 +79,7 @@ class PublishXRef(Base):
 
     @staticmethod
     def get_unique_terms(publishxref_id, inbredset_id):
+        """Finds unique terms for each item in the PublishXRef table to match a query against"""
         results = Session.query(
                 "pre_publication_description",
                 "post_publication_description",
@@ -119,6 +127,7 @@ class PublishXRef(Base):
 
     @staticmethod
     def get_result_fields(publishxref_id, inbredset_id):
+        """Gets the result fields (columns) that appear on the result page as a json string"""
         results = Session.query(
                 "phenotype_id",
                 "species",
@@ -150,17 +159,10 @@ class PublishXRef(Base):
                 "PublishXRef.PublicationId = Publication.Id and "
                 "InbredSet.Id = :inbredset_id and "
                 "Species.Id = InbredSet.SpeciesId ").params(publishxref_id=publishxref_id,
-                                                            inbredset_id=inbredset_id).all()                
-                #"InbredSet.SpeciesId = Species.Id and "
-                #"Geno.SpeciesId = Species.Id and "
-                #"Geno.Name = PublishXRef.Locus ").params(publishxref_id=publishxref_id,
-                #                                            inbredset_id=inbredset_id).all()
-        #for result in results:
-        #    print("****", result)
+                                                            inbredset_id=inbredset_id).all()
 
         assert len(set(result for result in results)) == 1, "Different results or no results"
 
-        #print("results are:", results)
         result = results[0]
         result = row2dict(result)
         try:
@@ -176,7 +178,16 @@ class PublishXRef(Base):
 
         return json_results
 
+
 class GenoXRef(Base):
+    """Class that corresponds with the GenoXRef table in the database.
+    
+    The GenoXRef table links genotype traits and their data.
+    
+    This class is used to add genotype traits to the quick search table.
+    
+    """
+    
     __tablename__ = 'GenoXRef'
     
     GenoFreezeId = sa.Column(sa.Integer, primary_key=True)
@@ -187,6 +198,7 @@ class GenoXRef(Base):
 
     @classmethod
     def run(cls):
+        """Connects to database and inserts genotype trait info into the Quicksearch table."""
         conn = Engine.connect()
         counter = 0
         for item in page_query(Session.query(cls)):   #all()
@@ -201,9 +213,10 @@ class GenoXRef(Base):
                 conn.execute(ins)
             counter += 1
             print("Done:", counter)
-    
+
     @staticmethod
     def get_unique_terms(geno_id):
+        """Finds unique terms for each item in the GenoXRef table to match a query against"""
         print("geno_id: ", geno_id)
         results = Session.query(
                 "name",
@@ -214,8 +227,6 @@ class GenoXRef(Base):
                 "FROM Geno "
                 "WHERE Geno.Id = :geno_id ").params(geno_id=geno_id).all()
         
-        #print("results: ", pf(results))
-        
         unique = set()
         if len(results):
             for item in results[0]:
@@ -234,12 +245,12 @@ class GenoXRef(Base):
                             continue 
                         
                         unique.add(token)
-        #print("\nUnique terms are: {}\n".format(unique))
         return " ".join(unique)
 
 
     @staticmethod
     def get_result_fields(geno_id, dataset_id):
+        """Gets the result fields (columns) that appear on the result page as a json string"""
         results = Session.query(
                 "name",
                 "marker_name",
@@ -271,11 +282,8 @@ class GenoXRef(Base):
                 "InbredSet.Id = GenoFreeze.InbredSetId and "
                 "InbredSet.SpeciesId = Species.Id ").params(geno_id=geno_id,
                                                                     dataset_id=dataset_id).all()
-        #for result in results:
-        #    print(result)
         assert len(set(result for result in results)) == 1, "Different results"
         
-        #print("results are:", results)
         result = results[0]
         result = row2dict(result)
         try:
@@ -292,6 +300,14 @@ class GenoXRef(Base):
         return json_results    
 
 class ProbeSetXRef(Base):
+    """Class that corresponds with the ProbeSetXRef table in the database.
+    
+    The ProbeSetXRef table links mRNA expression traits and their sample data.
+    
+    This class is used to add mRNA expression traits to the quick search table.
+    
+    """
+    
     __tablename__ = 'ProbeSetXRef'
     
     ProbeSetFreezeId = sa.Column(sa.Integer, primary_key=True)
@@ -310,16 +326,17 @@ class ProbeSetXRef(Base):
 
     @classmethod
     def run(cls):
+        """Connects to db and inserts mRNA expression trait info into the Quicksearch table."""
         conn = Engine.connect()
         counter = 0
-        for ps in page_query(Session.query(cls)):   #all()
+        for ps_row in page_query(Session.query(cls)):   #all()
             values = {}
             values['table_name'] = cls.__tablename__
-            values['the_key'] = json.dumps([ps.ProbeSetId, ps.ProbeSetFreezeId])
-            values['terms'] = cls.get_unique_terms(ps.ProbeSetId)
+            values['the_key'] = json.dumps([ps_row.ProbeSetId, ps_row.ProbeSetFreezeId])
+            values['terms'] = cls.get_unique_terms(ps_row.ProbeSetId)
             print("terms is:", values['terms'])
-            #values['species'] = get_species("ProbeSet", ps.Id)
-            values['result_fields'] = cls.get_result_fields(ps.ProbeSetId, ps.ProbeSetFreezeId)
+            values['result_fields'] = cls.get_result_fields(ps_row.ProbeSetId,
+                                                            ps_row.ProbeSetFreezeId)
             if values['result_fields'] == None:
                 continue
             ins = QuickSearch.insert().values(**values)
@@ -329,6 +346,7 @@ class ProbeSetXRef(Base):
     
     @staticmethod
     def get_unique_terms(probeset_id):
+        """Finds unique terms for each item in the ProbeSetXRef table to match a query against"""
         results = Session.query(
                 "name",
                 "symbol",
@@ -345,7 +363,6 @@ class ProbeSetXRef(Base):
         unique = set()
         if len(results):
             for item in results[0]:
-                #print("locals:", locals())
                 if not item:
                     continue
                 for token in item.split():
@@ -366,12 +383,12 @@ class ProbeSetXRef(Base):
                             continue 
                         
                         unique.add(token)
-            #print("\nUnique terms are: {}\n".format(unique))
             return " ".join(unique)
 
 
     @staticmethod
     def get_result_fields(probeset_id, dataset_id):
+        """Gets the result fields (columns) that appear on the result page as a json string"""
         print("probeset_id: ", probeset_id)
         print("dataset_id: ", dataset_id)
         results = Session.query(
@@ -420,14 +437,10 @@ class ProbeSetXRef(Base):
                 "ProbeFreeze.InbredSetId = InbredSet.Id and "
                 "InbredSet.SpeciesId = Species.Id ").params(probeset_id=probeset_id,
                                                                     dataset_id=dataset_id).all()
-        #for result in results:
-        #    print("-", result)
             
         if len(set(result for result in results)) != 1:
             return None
-        #assert len(set(result for result in results)) == 1, "Different results"
-        
-        #print("results are:", results)
+
         result = results[0]
         result = row2dict(result)
         try:
@@ -443,10 +456,10 @@ class ProbeSetXRef(Base):
 
         return json_results    
 
-
 QuickSearch = sa.Table("QuickSearch", Metadata,
+        # table_name is the table that item is inserted from
         sa.Column('table_name', sa.String(15),
-                  primary_key=True, nullable=False, autoincrement=False), # table that item is inserted from
+                  primary_key=True, nullable=False, autoincrement=False), 
         sa.Column('the_key', sa.String(30),
                   primary_key=True, nullable=False, autoincrement=False), # key in database table
         sa.Column('terms', sa.Text), # terms to compare search string with
@@ -459,24 +472,29 @@ QuickSearch = sa.Table("QuickSearch", Metadata,
 
 
 def row2dict(row):
-    """http://stackoverflow.com/a/2848519/1175849"""
+    """From http://stackoverflow.com/a/2848519/1175849"""
     return dict(zip(row.keys(), row))
 
 
-def page_query(q):
-    """http://stackoverflow.com/a/1217947/1175849"""
+def page_query(query):
+    """From http://stackoverflow.com/a/1217947/1175849"""
     offset = 0
     while True:
-        r = False
-        for elem in q.limit(1000).offset(offset):
-           r = True
-           yield elem
+        rrr = False
+        for elem in query.limit(1000).offset(offset):
+            rrr = True
+            yield elem
         offset += 1000
-        if not r:
+        if not rrr:
             break
 
 
 def main():
+    """Populate the QuickSearch table that is used with the quick search features.
+    
+    Add all items from the ProbeSetXRef, GenoXRef, and PublishXRef tables to the QuickSearch tables.
+    
+    """
     #ProbeSetXRef.run()
     #GenoXRef.run()
     PublishXRef.run()
diff --git a/wqflask/other_config/pylintrc b/wqflask/other_config/pylintrc
index 36d2bddf..b23af7a4 100644
--- a/wqflask/other_config/pylintrc
+++ b/wqflask/other_config/pylintrc
@@ -38,7 +38,7 @@ load-plugins=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-#disable=
+disable=no-init, star-args, no-member, import-error
 
 
 [REPORTS]
@@ -115,7 +115,7 @@ bad-functions=map,filter,apply,input
 module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
 
 # Regular expression which should only match correct module level names
-const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
+const-rgx=(([A-Z_][A-Za-z0-9_]*)|(__.*__))$
 
 # Regular expression which should only match correct class names
 class-rgx=[A-Z_][a-zA-Z0-9]+$
@@ -153,7 +153,7 @@ no-docstring-rgx=__.*__
 [FORMAT]
 
 # Maximum number of characters on a single line.
-max-line-length=80
+max-line-length=100
 
 # Maximum number of lines in a module
 max-module-lines=1000
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index a3ba8fdb..10221a2e 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -28,6 +28,7 @@ from scipy import stats
 import pdb
 
 import gzip
+import datetime
 import cPickle as pickle
 import simplejson as json
 
@@ -38,6 +39,9 @@ from utility import temp_data
 
 from wqflask.my_pylmm.pyLMM import chunks
 
+import redis
+Redis = redis.Redis()
+
 #np.seterr('raise')
 
 def run_human(pheno_vector,
@@ -65,6 +69,7 @@ def run_human(pheno_vector,
                 covariate_matrix)
     lmm_ob.fit()
 
+
     # Buffers for pvalues and t-stats
     p_values = []
     t_stats = []
@@ -86,19 +91,36 @@ def run_human(pheno_vector,
 
         with Bench("Create list of inputs"):
             inputs = list(plink_input)
-            
+
         with Bench("Divide into chunks"):
             results = chunks.divide_into_chunks(inputs, 64)
 
         result_store = []
-        identifier = uuid.uuid4()
-        for part, result in enumerate(results):
-            # todo: Don't use TempData here. Instead revert old one and store this stuff as a list
-            data_store = temp_data.TempData(identifier, "plink", part)
-            
-            data_store.store("data", pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
-            result_store.append(data_store)
+        identifier = str(uuid.uuid4())
+        
+        lmm_vars = pickle.dumps(dict(
+            pheno_vector = pheno_vector,
+            covariate_matrix = covariate_matrix,
+            kinship_matrix = kinship_matrix
+        ))
+        Redis.hset(identifier, "lmm_vars", pickle.dumps(lmm_vars))
+
 
+        key = "plink_inputs"
+        timestamp = datetime.datetime.utcnow().isoformat()
+
+        for part, result in enumerate(results):
+            #data = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+            holder = pickle.dumps(dict(
+                identifier = identifier,
+                part = part,
+                timestamp = timestamp,
+                result = result
+            ), pickle.HIGHEST_PROTOCOL)
+            print("Adding:", part)
+            Redis.rpush(key, holder)
+
+        print("***** Added to {} queue *****".format(key))
         for snp, this_id in plink_input:
             with Bench("part before association"):
                 if count > 2000:
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py b/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py
new file mode 100644
index 00000000..5ce7adbc
--- /dev/null
+++ b/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py
@@ -0,0 +1,24 @@
+from __future__ import absolute_import, print_function, division
+
+import cPickle as pickle
+import redis
+Redis = redis.Redis()
+
+from wqflask.my_pylmm.pyLMM import lmm
+
+lmm_vars_pickled = Redis.get("lmm_vars")
+
+
+plink_pickled = Redis.lpop("plink_inputs")
+
+plink_data = pickle.loads(plink_pickled)
+
+
+ps, ts = lmm.human_association(snp,
+                                n,
+                                keep,
+                                lmm_ob,
+                                pheno_vector,
+                                covariate_matrix,
+                                kinship_matrix,
+                                refit)
\ No newline at end of file