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authorLei Yan2013-06-19 21:08:43 +0000
committerLei Yan2013-06-19 21:08:43 +0000
commit0dd5dfb3925b2198487480d6093eed0d92201fc6 (patch)
treecc103e4067d42442b0d86602f104a406d172945d /wqflask
parent71f1a5d52d58d07294ef3f2cfa87026025358e74 (diff)
parentaac1dd2f9c5b216b24c6e35676ba5d50f9d5d3c2 (diff)
downloadgenenetwork2-0dd5dfb3925b2198487480d6093eed0d92201fc6.tar.gz
Merge branch 'flask' of git://github.com/zsloan/genenetwork into flask
Conflicts: wqflask/base/data_set.py
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/base/data_set.py2
-rwxr-xr-xwqflask/base/trait.py2
-rw-r--r--wqflask/maintenance/print_benchmark.py43
-rw-r--r--wqflask/maintenance/quick_search_table.py137
-rw-r--r--wqflask/other_config/pylintrc264
-rw-r--r--wqflask/wqflask/correlation/correlation_plot.py7
-rw-r--r--wqflask/wqflask/do_search.py8
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py5
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py103
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/process_plink.py127
-rw-r--r--wqflask/wqflask/search_results.py51
-rw-r--r--wqflask/wqflask/templates/all_results.html134
-rw-r--r--wqflask/wqflask/templates/index_page.html12
-rw-r--r--wqflask/wqflask/templates/quick_search.html317
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html4
-rw-r--r--wqflask/wqflask/views.py36
16 files changed, 1012 insertions, 240 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 0903bf16..07fe9cd9 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -394,7 +394,7 @@ class PhenotypeDataSet(DataSet):
continue # for now
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users):
description = this_trait.pre_publication_description
- this_trait.description_display = description
+ this_trait.description_display = unicode(description, "utf8")
if not this_trait.year.isdigit():
this_trait.pubmed_text = "N/A"
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 82e013ae..38b3a625 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -319,7 +319,7 @@ class GeneralTrait(object):
#XZ: assign SQL query result to trait attributes.
for i, field in enumerate(self.dataset.display_fields):
- setattr(self, field, traitInfo[i])
+ setattr(self, field, str(traitInfo[i]))
if self.dataset.type == 'Publish':
self.confidential = 0
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
new file mode 100644
index 00000000..540e0904
--- /dev/null
+++ b/wqflask/maintenance/print_benchmark.py
@@ -0,0 +1,43 @@
+#!/usr/bin/python
+
+from __future__ import absolute_import, print_function, division
+
+import time
+
+from pprint import pformat as pf
+
+
+class TheCounter(object):
+ Counters = {}
+
+ def __init__(self):
+ start_time = time.time()
+ for counter in range(170000):
+ self.print_it(counter)
+ self.time_took = time.time() - start_time
+ TheCounter.Counters[self.__class__.__name__] = self.time_took
+
+class PrintAll(TheCounter):
+ def print_it(self, counter):
+ print(counter)
+
+class PrintSome(TheCounter):
+ def print_it(self, counter):
+ if counter % 1000 == 0:
+ print(counter)
+
+class PrintNone(TheCounter):
+ def print_it(self, counter):
+ pass
+
+
+def new_main():
+ print("Running new_main")
+ tests = [PrintAll, PrintSome, PrintNone]
+ for test in tests:
+ test()
+
+ print(pf(TheCounter.Counters))
+
+if __name__ == '__main__':
+ new_main() \ No newline at end of file
diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py
index 046a05c4..b07e7656 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",
@@ -136,7 +145,7 @@ class PublishXRef(Base):
"Phenotype.Original_description as description, "
"PublishXRef.LRS as lrs, "
"PublishXRef.PublicationId as publication_id, "
- "Publication.PubMed_ID"
+ "Publication.PubMed_ID as pubmed_id, "
"Publication.Year as year, "
"Publication.Authors as authors "
"FROM PublishXRef, "
@@ -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:
@@ -443,42 +456,48 @@ 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
- sa.Column('result_fields', sa.Text) # json
+ sa.Column('result_fields', sa.Text), # json
+ mysql_engine = 'MyISAM',
)
-QuickSearch.drop(Engine, checkfirst=True)
-Metadata.create_all(Engine)
+#QuickSearch.drop(Engine, checkfirst=True)
+#Metadata.create_all(Engine)
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()
+ #GenoXRef.run()
+ #PublishXRef.run()
if __name__ == "__main__":
main() \ No newline at end of file
diff --git a/wqflask/other_config/pylintrc b/wqflask/other_config/pylintrc
new file mode 100644
index 00000000..b23af7a4
--- /dev/null
+++ b/wqflask/other_config/pylintrc
@@ -0,0 +1,264 @@
+[MASTER]
+
+# Specify a configuration file.
+#rcfile=
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+#init-hook=
+
+# Profiled execution.
+profile=no
+
+# Add files or directories to the blacklist. They should be base names, not
+# paths.
+ignore=CVS
+
+# Pickle collected data for later comparisons.
+persistent=yes
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+load-plugins=
+
+
+[MESSAGES CONTROL]
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time. See also the "--disable" option for examples.
+#enable=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once).You can also use "--disable=all" to
+# disable everything first and then reenable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --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=no-init, star-args, no-member, import-error
+
+
+[REPORTS]
+
+# Set the output format. Available formats are text, parseable, colorized, msvs
+# (visual studio) and html. You can also give a reporter class, eg
+# mypackage.mymodule.MyReporterClass.
+output-format=text
+
+# Include message's id in output
+include-ids=no
+
+# Include symbolic ids of messages in output
+symbols=no
+
+# Put messages in a separate file for each module / package specified on the
+# command line instead of printing them on stdout. Reports (if any) will be
+# written in a file name "pylint_global.[txt|html]".
+files-output=no
+
+# Tells whether to display a full report or only the messages
+reports=yes
+
+# Python expression which should return a note less than 10 (10 is the highest
+# note). You have access to the variables errors warning, statement which
+# respectively contain the number of errors / warnings messages and the total
+# number of statements analyzed. This is used by the global evaluation report
+# (RP0004).
+evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
+
+# Add a comment according to your evaluation note. This is used by the global
+# evaluation report (RP0004).
+comment=no
+
+
+[SIMILARITIES]
+
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+
+# Ignore comments when computing similarities.
+ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+ignore-docstrings=yes
+
+# Ignore imports when computing similarities.
+ignore-imports=no
+
+
+[VARIABLES]
+
+# Tells whether we should check for unused import in __init__ files.
+init-import=no
+
+# A regular expression matching the beginning of the name of dummy variables
+# (i.e. not used).
+dummy-variables-rgx=_|dummy
+
+# List of additional names supposed to be defined in builtins. Remember that
+# you should avoid to define new builtins when possible.
+additional-builtins=
+
+
+[BASIC]
+
+# Required attributes for module, separated by a comma
+required-attributes=
+
+# List of builtins function names that should not be used, separated by a comma
+bad-functions=map,filter,apply,input
+
+# Regular expression which should only match correct module names
+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-Za-z0-9_]*)|(__.*__))$
+
+# Regular expression which should only match correct class names
+class-rgx=[A-Z_][a-zA-Z0-9]+$
+
+# Regular expression which should only match correct function names
+function-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct method names
+method-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct instance attribute names
+attr-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct argument names
+argument-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct variable names
+variable-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct list comprehension /
+# generator expression variable names
+inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
+
+# Good variable names which should always be accepted, separated by a comma
+good-names=i,j,k,ex,Run,_
+
+# Bad variable names which should always be refused, separated by a comma
+bad-names=foo,bar,baz,toto,tutu,tata
+
+# Regular expression which should only match functions or classes name which do
+# not require a docstring
+no-docstring-rgx=__.*__
+
+
+[FORMAT]
+
+# Maximum number of characters on a single line.
+max-line-length=100
+
+# Maximum number of lines in a module
+max-module-lines=1000
+
+# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1
+# tab).
+indent-string=' '
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,XXX,TODO
+
+
+[TYPECHECK]
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+ignore-mixin-members=yes
+
+# List of classes names for which member attributes should not be checked
+# (useful for classes with attributes dynamically set).
+ignored-classes=SQLObject
+
+# When zope mode is activated, add a predefined set of Zope acquired attributes
+# to generated-members.
+zope=no
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E0201 when accessed. Python regular
+# expressions are accepted.
+generated-members=REQUEST,acl_users,aq_parent
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method
+max-args=5
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore
+ignored-argument-names=_.*
+
+# Maximum number of locals for function / method body
+max-locals=15
+
+# Maximum number of return / yield for function / method body
+max-returns=6
+
+# Maximum number of branch for function / method body
+max-branchs=12
+
+# Maximum number of statements in function / method body
+max-statements=50
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=7
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=2
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=20
+
+
+[IMPORTS]
+
+# Deprecated modules which should not be used, separated by a comma
+deprecated-modules=regsub,string,TERMIOS,Bastion,rexec
+
+# Create a graph of every (i.e. internal and external) dependencies in the
+# given file (report RP0402 must not be disabled)
+import-graph=
+
+# Create a graph of external dependencies in the given file (report RP0402 must
+# not be disabled)
+ext-import-graph=
+
+# Create a graph of internal dependencies in the given file (report RP0402 must
+# not be disabled)
+int-import-graph=
+
+
+[CLASSES]
+
+# List of interface methods to ignore, separated by a comma. This is used for
+# instance to not check methods defines in Zope's Interface base class.
+ignore-iface-methods=isImplementedBy,deferred,extends,names,namesAndDescriptions,queryDescriptionFor,getBases,getDescriptionFor,getDoc,getName,getTaggedValue,getTaggedValueTags,isEqualOrExtendedBy,setTaggedValue,isImplementedByInstancesOf,adaptWith,is_implemented_by
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods=__init__,__new__,setUp
+
+# List of valid names for the first argument in a class method.
+valid-classmethod-first-arg=cls
+
+# List of valid names for the first argument in a metaclass class method.
+valid-metaclass-classmethod-first-arg=mcs
+
+
+[EXCEPTIONS]
+
+# Exceptions that will emit a warning when being caught. Defaults to
+# "Exception"
+overgeneral-exceptions=Exception
diff --git a/wqflask/wqflask/correlation/correlation_plot.py b/wqflask/wqflask/correlation/correlation_plot.py
index 4b043fc3..c2b64d70 100644
--- a/wqflask/wqflask/correlation/correlation_plot.py
+++ b/wqflask/wqflask/correlation/correlation_plot.py
@@ -24,6 +24,10 @@ class CorrelationPlot(object):
self.samples_1 = self.get_samples(self.dataset1, sample_names_1, self.trait1)
self.samples_2 = self.get_samples(self.dataset2, sample_names_2, self.trait2)
+ coords = {}
+ for sample in self.samples_1:
+ coords[sample.name] = (sample.val)
+
def get_sample_names(self, dataset):
if dataset.group.parlist:
@@ -45,4 +49,5 @@ class CorrelationPlot(object):
sample_group_type='primary',
header="%s Only" % (dataset.group.name))
- return samples \ No newline at end of file
+ return samples
+ \ No newline at end of file
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 1b1b56fb..7b3e0869 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -36,7 +36,7 @@ class DoSearch(object):
def execute(self, query):
"""Executes query and returns results"""
query = self.normalize_spaces(query)
- print("in do_search query is:", pf(query))
+ #print("in do_search query is:", pf(query))
results = g.db.execute(query, no_parameters=True).fetchall()
#results = self.cursor.fetchall()
return results
@@ -90,7 +90,7 @@ class QuickMrnaAssaySearch(DoSearch):
AGAINST ('%s' IN BOOLEAN MODE))
""" % (escape(self.search_term[0]))
- print("final query is:", pf(query))
+ #print("final query is:", pf(query))
return self.execute(query)
@@ -134,7 +134,7 @@ class MrnaAssaySearch(DoSearch):
where_clause,
escape(self.dataset.id)))
- print("query is:", pf(query))
+ #print("query is:", pf(query))
return query
@@ -155,7 +155,7 @@ class MrnaAssaySearch(DoSearch):
""" % (escape(self.search_term[0]),
escape(str(self.dataset.id)))
- print("final query is:", pf(query))
+ #print("final query is:", pf(query))
return self.execute(query)
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 6ae1318e..334ce631 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -78,8 +78,9 @@ class MarkerRegression(object):
genotype_matrix = np.array(trimmed_genotype_data).T
- print("pheno_vector is: ", pf(pheno_vector))
- print("genotype_matrix is: ", pf(genotype_matrix))
+ print("pheno_vector: ", pf(pheno_vector))
+ print("genotype_matrix: ", pf(genotype_matrix))
+ print("genotype_matrix.shape: ", pf(genotype_matrix.shape))
t_stats, p_values = lmm.run(
pheno_vector,
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index a3ba8fdb..5bfc3a01 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -28,6 +28,8 @@ from scipy import stats
import pdb
import gzip
+import zlib
+import datetime
import cPickle as pickle
import simplejson as json
@@ -38,6 +40,9 @@ 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,
@@ -51,6 +56,20 @@ def run_human(pheno_vector,
keep = True - v
keep = keep.reshape((len(keep),))
+ identifier = str(uuid.uuid4())
+
+ print("pheno_vector: ", pf(pheno_vector))
+ print("kinship_matrix: ", pf(kinship_matrix))
+ print("kinship_matrix.shape: ", pf(kinship_matrix.shape))
+
+ lmm_vars = pickle.dumps(dict(
+ pheno_vector = pheno_vector,
+ covariate_matrix = covariate_matrix,
+ kinship_matrix = kinship_matrix
+ ))
+ Redis.hset(identifier, "lmm_vars", lmm_vars)
+ Redis.expire(identifier, 60*60)
+
if v.sum():
pheno_vector = pheno_vector[keep]
#print("pheno_vector shape is now: ", pf(pheno_vector.shape))
@@ -60,16 +79,18 @@ def run_human(pheno_vector,
kinship_matrix = kinship_matrix[keep,:][:,keep]
n = kinship_matrix.shape[0]
+ #print("n is:", n)
lmm_ob = LMM(pheno_vector,
kinship_matrix,
covariate_matrix)
lmm_ob.fit()
+
# Buffers for pvalues and t-stats
p_values = []
t_stats = []
- print("input_file: ", plink_input_file)
+ #print("input_file: ", plink_input_file)
with Bench("Opening and loading pickle file"):
with gzip.open(plink_input_file, "rb") as input_file:
@@ -87,45 +108,65 @@ def run_human(pheno_vector,
with Bench("Create list of inputs"):
inputs = list(plink_input)
+ print("len(genotypes): ", len(inputs))
+
with Bench("Divide into chunks"):
results = chunks.divide_into_chunks(inputs, 64)
result_store = []
- identifier = uuid.uuid4()
+
+ key = "plink_inputs"
+
+ # Todo: Delete below line when done testing
+ Redis.delete(key)
+
+ timestamp = datetime.datetime.utcnow().isoformat()
+
+ #print("Starting adding loop")
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 = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+ holder = pickle.dumps(dict(
+ identifier = identifier,
+ part = part,
+ timestamp = timestamp,
+ result = result
+ ), pickle.HIGHEST_PROTOCOL)
- data_store.store("data", pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
- result_store.append(data_store)
-
+ #print("Adding:", part)
+ Redis.rpush(key, zlib.compress(holder))
+ #print("End adding loop")
+ #print("***** Added to {} queue *****".format(key))
for snp, this_id in plink_input:
- with Bench("part before association"):
- if count > 2000:
- break
- count += 1
-
- percent_complete = (float(count) / total_snps) * 100
- #print("percent_complete: ", percent_complete)
- loading_progress.store("percent_complete", percent_complete)
-
- with Bench("actual association"):
- ps, ts = human_association(snp,
- n,
- keep,
- lmm_ob,
- pheno_vector,
- covariate_matrix,
- kinship_matrix,
- refit)
-
- with Bench("after association"):
- p_values.append(ps)
- t_stats.append(ts)
+ #with Bench("part before association"):
+ if count > 2000:
+ break
+ count += 1
+
+ percent_complete = (float(count) / total_snps) * 100
+ #print("percent_complete: ", percent_complete)
+ loading_progress.store("percent_complete", percent_complete)
+
+ #with Bench("actual association"):
+ ps, ts = human_association(snp,
+ n,
+ keep,
+ lmm_ob,
+ pheno_vector,
+ covariate_matrix,
+ kinship_matrix,
+ refit)
+
+ #with Bench("after association"):
+ p_values.append(ps)
+ t_stats.append(ts)
return p_values, t_stats
+#class HumanAssociation(object):
+# def __init__(self):
+#
+
def human_association(snp,
n,
keep,
@@ -202,6 +243,8 @@ def run(pheno_vector,
with Bench("LMM_ob fitting"):
lmm_ob.fit()
+ print("genotype_matrix: ", genotype_matrix.shape)
+
with Bench("Doing GWAS"):
t_stats, p_values = GWAS(pheno_vector,
genotype_matrix,
@@ -304,7 +347,7 @@ def GWAS(pheno_vector,
covariate_matrix - n x q covariate matrix
restricted_max_likelihood - use restricted maximum likelihood
refit - refit the variance component for each SNP
-
+
"""
if kinship_eigen_vals == None:
kinship_eigen_vals = []
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..e47c18e1
--- /dev/null
+++ b/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py
@@ -0,0 +1,127 @@
+from __future__ import absolute_import, print_function, division
+
+import sys
+sys.path.append("../../..")
+
+print("sys.path: ", sys.path)
+
+import numpy as np
+
+import zlib
+import cPickle as pickle
+import redis
+Redis = redis.Redis()
+
+import lmm
+
+class ProcessLmmChunk(object):
+
+ def __init__(self):
+ self.get_snp_data()
+ self.get_lmm_vars()
+
+ keep = self.trim_matrices()
+
+ self.do_association(keep)
+
+ print("p_values is: ", self.p_values)
+
+ def get_snp_data(self):
+ plink_pickled = zlib.decompress(Redis.lpop("plink_inputs"))
+ plink_data = pickle.loads(plink_pickled)
+
+ self.snps = np.array(plink_data['result'])
+ self.identifier = plink_data['identifier']
+
+ def get_lmm_vars(self):
+ lmm_vars_pickled = Redis.hget(self.identifier, "lmm_vars")
+ lmm_vars = pickle.loads(lmm_vars_pickled)
+
+ self.pheno_vector = np.array(lmm_vars['pheno_vector'])
+ self.covariate_matrix = np.array(lmm_vars['covariate_matrix'])
+ self.kinship_matrix = np.array(lmm_vars['kinship_matrix'])
+
+ def trim_matrices(self):
+ v = np.isnan(self.pheno_vector)
+ keep = True - v
+ keep = keep.reshape((len(keep),))
+
+ if v.sum():
+ self.pheno_vector = self.pheno_vector[keep]
+ self.covariate_matrix = self.covariate_matrix[keep,:]
+ self.kinship_matrix = self.kinship_matrix[keep,:][:,keep]
+
+ return keep
+
+ def do_association(self, keep):
+ n = self.kinship_matrix.shape[0]
+ lmm_ob = lmm.LMM(self.pheno_vector,
+ self.kinship_matrix,
+ self.covariate_matrix)
+ lmm_ob.fit()
+
+ self.p_values = []
+
+ for snp in self.snps:
+ snp = snp[0]
+ p_value, t_stat = lmm.human_association(snp,
+ n,
+ keep,
+ lmm_ob,
+ self.pheno_vector,
+ self.covariate_matrix,
+ self.kinship_matrix,
+ False)
+
+ self.p_values.append(p_value)
+
+
+#plink_pickled = zlib.decompress(Redis.lpop("plink_inputs"))
+#
+#plink_data = pickle.loads(plink_pickled)
+#result = np.array(plink_data['result'])
+#print("snp size is: ", result.shape)
+#identifier = plink_data['identifier']
+#
+#lmm_vars_pickled = Redis.hget(identifier, "lmm_vars")
+#lmm_vars = pickle.loads(lmm_vars_pickled)
+#
+#pheno_vector = np.array(lmm_vars['pheno_vector'])
+#covariate_matrix = np.array(lmm_vars['covariate_matrix'])
+#kinship_matrix = np.array(lmm_vars['kinship_matrix'])
+#
+#v = np.isnan(pheno_vector)
+#keep = True - v
+#keep = keep.reshape((len(keep),))
+#print("keep is: ", keep)
+#
+#if v.sum():
+# pheno_vector = pheno_vector[keep]
+# covariate_matrix = covariate_matrix[keep,:]
+# kinship_matrix = kinship_matrix[keep,:][:,keep]
+#
+#n = kinship_matrix.shape[0]
+#print("n is: ", n)
+#lmm_ob = lmm.LMM(pheno_vector,
+# kinship_matrix,
+# covariate_matrix)
+#lmm_ob.fit()
+#
+#p_values = []
+#
+#for snp in result:
+# snp = snp[0]
+# p_value, t_stat = lmm.human_association(snp,
+# n,
+# keep,
+# lmm_ob,
+# pheno_vector,
+# covariate_matrix,
+# kinship_matrix,
+# False)
+#
+# p_values.append(p_value)
+
+
+
+
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 4238aa7f..bb0313b3 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -26,8 +26,7 @@ from MySQLdb import escape_string as escape
from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
-from utility.THCell import THCell
-from utility.TDCell import TDCell
+from utility.benchmark import Bench
from base.data_set import create_dataset
from base.trait import GeneralTrait
from wqflask import parser
@@ -74,6 +73,7 @@ class SearchResultPage(object):
self.quick = True
self.search_terms = kw['q']
print("self.search_terms is: ", self.search_terms)
+ self.trait_type = kw['trait_type']
self.quick_search()
else:
self.results = []
@@ -124,24 +124,53 @@ class SearchResultPage(object):
FROM QuickSearch
WHERE MATCH (terms)
AGAINST ('{}' IN BOOLEAN MODE) """.format(search_terms)
- dbresults = g.db.execute(query, no_parameters=True).fetchall()
+
+ with Bench("Doing QuickSearch Query: "):
+ dbresults = g.db.execute(query, no_parameters=True).fetchall()
#print("results: ", pf(results))
self.results = collections.defaultdict(list)
type_dict = {'PublishXRef': 'phenotype',
- 'ProbesetXRef': 'mrna_assay',
+ 'ProbeSetXRef': 'mrna_assay',
'GenoXRef': 'genotype'}
-
+
+ self.species_groups = {}
+
for dbresult in dbresults:
this_result = {}
this_result['table_name'] = dbresult.table_name
- this_result['key'] = dbresult.the_key
- this_result['result_fields'] = json.loads(dbresult.result_fields)
-
- self.results[type_dict[dbresult.table_name]].append(this_result)
+ if self.trait_type == type_dict[dbresult.table_name] or self.trait_type == 'all':
+ this_result['key'] = dbresult.the_key
+ this_result['result_fields'] = json.loads(dbresult.result_fields)
+ this_species = this_result['result_fields']['species']
+ this_group = this_result['result_fields']['group_name']
+ if this_species not in self.species_groups:
+ self.species_groups[this_species] = {}
+ if type_dict[dbresult.table_name] not in self.species_groups[this_species]:
+ self.species_groups[this_species][type_dict[dbresult.table_name]] = []
+ if this_group not in self.species_groups[this_species][type_dict[dbresult.table_name]]:
+ self.species_groups[this_species][type_dict[dbresult.table_name]].append(this_group)
+ #if type_dict[dbresult.table_name] not in self.species_groups:
+ # self.species_groups[type_dict[dbresult.table_name]] = {}
+ #if this_species not in self.species_groups[type_dict[dbresult.table_name]]:
+ # self.species_groups[type_dict[dbresult.table_name]][this_species] = []
+ #if this_group not in self.species_groups[type_dict[dbresult.table_name]][this_species]:
+ # self.species_groups[type_dict[dbresult.table_name]][this_species].append(this_group)
+ self.results[type_dict[dbresult.table_name]].append(this_result)
- print("results: ", pf(self.results['phenotype']))
+ import redis
+ Redis = redis.Redis()
+
+
+
+ #def get_group_species_tree(self):
+ # self.species_groups = collections.default_dict(list)
+ # for key in self.results:
+ # for item in self.results[key]:
+ # self.species_groups[item['result_fields']['species']].append(
+ # item['result_fields']['group_name'])
+
#def quick_search(self):
# self.search_terms = parser.parse(self.search_terms)
@@ -209,6 +238,6 @@ class SearchResultPage(object):
self.dataset,
)
self.results.extend(the_search.run())
- print("in the search results are:", self.results)
+ #print("in the search results are:", self.results)
self.header_fields = the_search.header_fields
diff --git a/wqflask/wqflask/templates/all_results.html b/wqflask/wqflask/templates/all_results.html
new file mode 100644
index 00000000..a42e42d8
--- /dev/null
+++ b/wqflask/wqflask/templates/all_results.html
@@ -0,0 +1,134 @@
+ <ul class="nav nav-tabs">
+ {% for species in species_groups %}
+ <li> <a href="#tab{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
+ {% endfor %}
+ </ul>
+ <div class="tab-content">
+ {% for species in species_groups %}
+ <div class="tab-pane active" id="tab{{ loop.index }}">
+ <div class="tabbable tabs-left">
+ <ul class="nav nav-tabs">
+ {% if species_groups[species]['phenotype'] %}
+ <li class="active"> <a href="#tab{{ loop.index }}_1" data-toggle="tab">Phenotype</a></li>
+ {% endif %}
+ {% if species_groups[species]['mrna_assay'] %}
+ <li> <a href="#tab{{ loop.index }}_2" data-toggle="tab">mRNA Assay</a></li>
+ {% endif %}
+ {% if species_groups[species]['genotype'] %}
+ <li> <a href="#tab{{ loop.index }}_3" data-toggle="tab">Genotype</a></li>
+ {% endif %}
+ </ul>
+ <div class="tab-content">
+ {% if species_groups[species]['phenotype'] %}
+ <div class="tab-pane active" id="tab{{ loop.index }}_1">
+ <table id="pheno_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <th>Id</th>
+ <th>Species</th>
+ <th>Group</th>
+ <th>Description</th>
+ <th>LRS</th>
+ <th>Year</th>
+ <th>Authors</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for result in results.phenotype %}
+ {% if result.result_fields['species'] == species %}
+ <tr>
+ <td>{{ result.result_fields['phenotype_id'] }}</td>
+ <td>{{ result.result_fields['species'] }}</td>
+ <td>{{ result.result_fields['group_name'] }}</td>
+ <td>{{ result.result_fields['description'] }}</td>
+ <td>{{ result.result_fields['lrs'] }}</td>
+ <td>
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
+ {{ result.result_fields['year'] }}
+ </a>
+ </td>
+ <td>{{ result.result_fields['authors'] }}</td>
+ </tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ {% endif %}
+ {% if species_groups[species]['mrna_assay'] %}
+ <div class="tab-pane" id="tab{{ loop.index }}_2">
+ <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <th>Record ID</th>
+ <th>Species</th>
+ <th>Group</th>
+ <th>Data Set</th>
+ <th>Symbol</th>
+ <th>Description</th>
+ <th>Location</th>
+ <th>Mean Expr</th>
+ <th>Max LRS</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for result in results.mrna_assay %}
+ {% if result.result_fields['species'] == species %}
+ <tr>
+ <td>
+ <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
+ {{ result.result_fields['name'] }}
+ </a>
+ </td>
+ <td>{{ result.result_fields['species'] }}</td>
+ <td>{{ result.result_fields['group_name'] }}</td>
+ <td>{{ result.result_fields['dataset_name'] }}</td>
+ <td>{{ result.result_fields['symbol'] }}</td>
+ <td>{{ result.result_fields['description'] }}</td>
+ <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
+ <td>{{ result.result_fields['mean'] }}</td>
+ <td>{{ result.result_fields['lrs'] }}</td>
+ </tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ {% endif %}
+ {% if species_groups[species]['genotype'] %}
+ <div class="tab-pane" id="tab{{ loop.index }}_3">
+ <table id="geno_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <th>Marker</th>
+ <th>Species</th>
+ <th>Group</th>
+ <th>Data Set</th>
+ <th>Location</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for result in results.genotype %}
+ {% if result.result_fields['species'] == species %}
+ <tr>
+ <td>
+ <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
+ {{ result.result_fields['marker_name'] }}
+ </a>
+ </td>
+ <td>{{ result.result_fields['species'] }}</td>
+ <td>{{ result.result_fields['group_name'] }}</td>
+ <td>{{ result.result_fields['dataset_name'] }}</td>
+ <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
+ </tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ {% endif %}
+ </div>
+ </div>
+ </div>
+ {% endfor %}
+ </div> \ No newline at end of file
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 0cc1c353..a9f2cb24 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -9,7 +9,6 @@
<div class="container">
<h1>GeneNetwork</h1>
<p class="lead">Open source bioinformatics for systems genetics</p>
- <p>- Lei Yan</p>
</div>
</header>
@@ -33,7 +32,14 @@
</div>
<form method="get" action="/search" name="SEARCHFORM">
<fieldset>
- <label for="quick">Search:</label>
+ <div class="input-prepend">
+ <select id="trait_type" name="trait_type" class="span2">
+ <option value="all">All</option>
+ <option value="mrna_assay">Molecular Assays</option>
+ <option value="phenotype">Phenotypes</option>
+ <option value="genotype">Genotypes</option>
+ </select>
+ </div>
<div class="input-append">
<input class="input-xlarge"
id="quick" name="q"
@@ -43,11 +49,9 @@
class="btn btn-primary" value="Search">
</div>
</fieldset>
-
</form>
</section>
<section id="search">
-
<div class="page-header">
<h1>Select and search</h1>
</div>
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index d50b4937..b0e38708 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -21,30 +21,158 @@
<ul>
{% if search_terms %}
<li>
- {% for word in search_terms %}
- <strong>{{word}}</strong> {% if not loop.last %} or {% endif %}
- {% endfor %}
+ <strong>{{search_terms}}</strong>
</li>
{% endif %}
</ul>
-
- <p>To study a record, click on its ID below.<br />
- Check records below and click Add button to add to selection.</p>
+
<div class="tabbable"> <!-- Only required for left/right tabs -->
+ {% if trait_type == 'all' %}
+ {% include 'all_results.html' %}
+ {% else %}
<ul class="nav nav-tabs">
- <li class="active"> <a href="#tab1" data-toggle="tab">Phenotype</a></li>
- <li> <a href="#tab2" data-toggle="tab">mRNA Assay</a></li>
- <li> <a href="#tab3" data-toggle="tab">Genotype</a></li>
+ {% for species in species_groups %}
+ <li> <a href="#tab{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
+ {% endfor %}
</ul>
<div class="tab-content">
- <div class="tab-pane active" id="tab1">
- <table class="table table-hover">
+ {% for species in species_groups %}
+ <div class="tab-pane active" id="tab{{ loop.index }}">
+ <div>
+ {#
+ <ul class="nav nav-tabs">
+ {% if species_groups[species]['phenotype'] %}
+ <li class="active"> <a href="#tab{{ loop.index }}_1" data-toggle="tab">Phenotype</a></li>
+ {% endif %}
+ {% if species_groups[species]['mrna_assay'] %}
+ <li> <a href="#tab{{ loop.index }}_2" data-toggle="tab">mRNA Assay</a></li>
+ {% endif %}
+ {% if species_groups[species]['genotype'] %}
+ <li> <a href="#tab{{ loop.index }}_3" data-toggle="tab">Genotype</a></li>
+ {% endif %}
+ </ul>
+ #}
+ <div>
+ {% if trait_type == 'phenotype' and species_groups[species]['phenotype'] %}
+ <table id="pheno_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <th>Id</th>
+ <th>Species</th>
+ <th>Group</th>
+ <th>Description</th>
+ <th>LRS</th>
+ <th>Year</th>
+ <th>Authors</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for result in results.phenotype %}
+ {% if result.result_fields['species'] == species %}
+ <tr>
+ <td>{{ result.result_fields['phenotype_id'] }}</td>
+ <td>{{ result.result_fields['species'] }}</td>
+ <td>{{ result.result_fields['group_name'] }}</td>
+ <td>{{ result.result_fields['description'] }}</td>
+ <td>{{ result.result_fields['lrs'] }}</td>
+ <td>
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
+ {{ result.result_fields['year'] }}
+ </a>
+ </td>
+ <td>{{ result.result_fields['authors'] }}</td>
+ </tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ {% endif %}
+ {% if trait_type == 'mrna_assay' and species_groups[species]['mrna_assay'] %}
+ <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <th>Record ID</th>
+ <th>Species</th>
+ <th>Group</th>
+ <th>Data Set</th>
+ <th>Symbol</th>
+ <th>Description</th>
+ <th>Location</th>
+ <th>Mean Expr</th>
+ <th>Max LRS</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for result in results.mrna_assay %}
+ {% if result.result_fields['species'] == species %}
+ <tr>
+ <td>
+ <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
+ {{ result.result_fields['name'] }}
+ </a>
+ </td>
+ <td>{{ result.result_fields['species'] }}</td>
+ <td>{{ result.result_fields['group_name'] }}</td>
+ <td>{{ result.result_fields['dataset_name'] }}</td>
+ <td>{{ result.result_fields['symbol'] }}</td>
+ <td>{{ result.result_fields['description'] }}</td>
+ <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
+ <td>{{ result.result_fields['mean'] }}</td>
+ <td>{{ result.result_fields['lrs'] }}</td>
+ </tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ {% endif %}
+ {% if trait_type == 'genotype' and species_groups[species]['genotype'] %}
+ <table id="geno_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <th>Marker</th>
+ <th>Species</th>
+ <th>Group</th>
+ <th>Data Set</th>
+ <th>Location</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for result in results.genotype %}
+ {% if result.result_fields['species'] == species %}
+ <tr>
+ <td>
+ <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
+ {{ result.result_fields['marker_name'] }}
+ </a>
+ </td>
+ <td>{{ result.result_fields['species'] }}</td>
+ <td>{{ result.result_fields['group_name'] }}</td>
+ <td>{{ result.result_fields['dataset_name'] }}</td>
+ <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
+ </tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ {% endif %}
+ </div>
+ </div>
+ </div>
+ {% endfor %}
+ </div>
+ {% endif %}
+ </div>
+ </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+ {#
+ <table id="pheno_results" class="table table-hover table-striped table-bordered">
<thead>
<tr>
- <!-- {% for key, _value in results.phenotype[0].result_fields.items() %}
- <th>{{key}}</th>
- {% endfor %}-->
<th>Id</th>
<th>Species</th>
<th>Group</th>
@@ -57,26 +185,24 @@
<tbody>
{% for result in results.phenotype %}
<tr>
- {% for result in result.result_fields.items() %}
- <td>{{ result['phenotype_id'] }}</td>
- <td>{{ result['species'] }}</td>
- <td>{{ result['group_name'] }}</td>
- <td>{{ result['description'] }}</td>
- <td>{{ result['lrs'] }}</td>
+ <td>{{ result.result_fields['phenotype_id'] }}</td>
+ <td>{{ result.result_fields['species'] }}</td>
+ <td>{{ result.result_fields['group_name'] }}</td>
+ <td>{{ result.result_fields['description'] }}</td>
+ <td>{{ result.result_fields['lrs'] }}</td>
<td>
- <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result['pubmed_id'] }}&dopt=Abstract">
- {{ result['year'] }}
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
+ {{ result.result_fields['year'] }}
</a>
</td>
- <td>{{ result['authors'] }}</td>
- {% endfor %}
+ <td>{{ result.result_fields['authors'] }}</td>
</tr>
{% endfor %}
</tbody>
</table>
</div>
<div class="tab-pane" id="tab2">
- <table class="table table-hover">
+ <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
<thead>
<tr>
<th>Record ID</th>
@@ -93,28 +219,26 @@
<tbody>
{% for result in results.mrna_assay %}
<tr>
- {% for result in result.result_fields.items() %}
<td>
- <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result['name'] }}&dataset={{ result['dataset'] }}"
- {{ result['name'] }}
+ <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
+ {{ result.result_fields['name'] }}
</a>
</td>
- <td>{{ result['species'] }}</td>
- <td>{{ result['group_name'] }}</td>
- <td>{{ result['dataset_name'] }}</td>
- <td>{{ result['symbol'] }}</td>
- <td>{{ result['description'] }}</td>
- <td>{{ result['chr'] }} : {{ result['mb'] }}</td>
- <td>{{ result['mean'] }}</td>
- <td>{{ result['lrs'] }}</td>
- {% endfor %}
+ <td>{{ result.result_fields['species'] }}</td>
+ <td>{{ result.result_fields['group_name'] }}</td>
+ <td>{{ result.result_fields['dataset_name'] }}</td>
+ <td>{{ result.result_fields['symbol'] }}</td>
+ <td>{{ result.result_fields['description'] }}</td>
+ <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
+ <td>{{ result.result_fields['mean'] }}</td>
+ <td>{{ result.result_fields['lrs'] }}</td>
</tr>
{% endfor %}
</tbody>
</table>
</div>
<div class="tab-pane" id="tab3">
- <table class="table table-hover">
+ <table id="geno_results" class="table table-hover table-striped table-bordered">
<thead>
<tr>
<th>Marker</th>
@@ -125,91 +249,58 @@
</tr>
</thead>
<tbody>
- {% for result in results.mrna_assay %}
+ {% for result in results.genotype %}
<tr>
- {% for result in result.result_fields.items() %}
<td>
- <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result['marker_name'] }}&dataset={{ result['dataset'] }}">
- {{ result['marker_name'] }}
+ <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
+ {{ result.result_fields['marker_name'] }}
</a>
</td>
- <td>{{ result['species'] }}</td>
- <td>{{ result['group_name'] }}</td>
- <td>{{ result['dataset_name'] }}</td>
- <td>{{ result['chr'] }} : {{ result['mb'] }}</td>
- {% endfor %}
+ <td>{{ result.result_fields['species'] }}</td>
+ <td>{{ result.result_fields['group_name'] }}</td>
+ <td>{{ result.result_fields['dataset_name'] }}</td>
+ <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
</tr>
{% endfor %}
</tbody>
</table>
</div>
- </div>
- </div>
-
-
-
- <!--<div class="bs-docs-example">
- <table class="table table-hover">
- <thead>
- <tr>
- {% for header in header_fields %}
- <th>{{header}}</th>
- {% endfor %}
- </tr>
- </thead>
-
- <tbody>
- {% for this_trait in trait_list %}
- <TR id="{{ this_trait }}">
- <TD>
- <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox"
- VALUE="{{ this_trait }}">
- </TD>
- <TD>
- <a href="{{ url_for('show_trait_page',
- trait_id = this_trait.name,
- dataset = dataset.name
- )}}">
- {{ this_trait.name }}
- </a>
- </TD>
- {% if dataset.type == 'ProbeSet' %}
- <TD>{{ this_trait.symbol }}</TD>
- <TD>{{ this_trait.description_display }}</TD>
- <TD>{{ this_trait.location_repr }}</TD>
- <TD>{{ this_trait.mean }}</TD>
- <TD>{{ this_trait.LRS_score_repr }}</TD>
- <TD>{{ this_trait.LRS_location_repr }}</TD>
- {% elif dataset.type == 'Publish' %}
- <TD>{{ this_trait.description_display }}</TD>
- <TD>{{ this_trait.authors }}</TD>
- <TD>
- <a href="{{ this_trait.pubmed_link }}">
- {{ this_trait.pubmed_text }}
- </a>
- </TD>
- <TD>{{ this_trait.LRS_score_repr }}</TD>
- <TD>{{ this_trait.LRS_location_repr }}</TD>
- {% elif dataset.type == 'Geno' %}
- <TD>{{ this_trait.location_repr }}</TD>
- {% endif %}
- </TR>
- {% endfor %}
- </tbody>
+ #}
- </table>
- <br />
-
- <button class="btn"><i class="icon-ok"></i> Select</button>
- <button class="btn"><i class="icon-remove"></i> Deselect</button>
- <button class="btn"><i class="icon-resize-vertical"></i> Invert</button>
- <button class="btn"><i class="icon-plus-sign"></i> Add</button>
- <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
- </div>-->
-
- </div>
-
-<!-- End of body -->
+{% block js %}
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+ <script type="text/javascript" charset="utf-8">
+ $(document).ready( function () {
+ console.time("Creating table");
+ $('#pheno_results, #mrna_assay_results, #geno_results').dataTable( {
+ //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+ "sDom": "lTftipr",
+ "oTableTools": {
+ "aButtons": [
+ "copy",
+ "print",
+ {
+ "sExtends": "collection",
+ "sButtonText": 'Save <span class="caret" />',
+ "aButtons": [ "csv", "xls", "pdf" ]
+ }
+ ],
+ "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+ },
+ "iDisplayLength": 50,
+ "bLengthChange": true,
+ "bDeferRender": true,
+ "bSortClasses": false
+ } );
+ console.timeEnd("Creating table");
+ });
+ </script>
{% endblock %}
+
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index c3abfc9f..b57c3c21 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -19,11 +19,11 @@
BLAT Specifity
</a>
</dt>
- <dd>{{ "%.1f" % (this_trait.probe_set_specificity) }}</dd>
+ <dd>{{ "%s" % (this_trait.probe_set_specificity) }}</dd>
{% endif %}
{% if this_trait.probe_set_blat_score %}
<dt>BLAT Score</dt>
- <dd>{{ "%i" % (this_trait.probe_set_blat_score) }}</dd>
+ <dd>{{ "%s" % (this_trait.probe_set_blat_score) }}</dd>
{% endif %}
</dl>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 102863f0..d50a9aa2 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -78,17 +78,28 @@ def search_page():
else:
return render_template("data_sharing.html", **template_vars.__dict__)
else:
- print("calling search_results.SearchResultPage")
- the_search = search_results.SearchResultPage(request.args)
- print("template_vars is:", pf(the_search.__dict__))
- #print("trait_list is:", pf(the_search.__dict__['trait_list'][0].__dict__))
- #for trait in the_search.trait_list:
- # print(" -", trait.description_display)
-
- if the_search.quick:
- return render_template("quick_search.html", **the_search.__dict__)
+ key = "search_results:v2:" + json.dumps(request.args, sort_keys=True)
+ print("key is:", pf(key))
+ with Bench("Loading cache"):
+ result = Redis.get(key)
+
+ if result:
+ print("Cache hit!!!")
+ with Bench("Loading results"):
+ result = pickle.loads(result)
else:
- return render_template("search_result_page.html", **the_search.__dict__)
+ print("calling search_results.SearchResultPage")
+ the_search = search_results.SearchResultPage(request.args)
+ result = the_search.__dict__
+
+ print("result: ", pf(result))
+ Redis.set(key, pickle.dumps(result))
+ Redis.expire(key, 60*60)
+
+ if result['quick']:
+ return render_template("quick_search.html", **result)
+ else:
+ return render_template("search_result_page.html", **result)
@app.route("/whats_new")
@@ -173,9 +184,10 @@ def marker_regression_page():
for key, value in initial_start_vars.iteritems():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
-
+
version = "v14"
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
+ print("key is:", pf(key))
with Bench("Loading cache"):
result = Redis.get(key)
@@ -258,4 +270,4 @@ def json_default_handler(obj):
#@app.after_request
#def after_request(response):
-# gc.collect() \ No newline at end of file
+# gc.collect()