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-rwxr-xr-xwqflask/wqflask/do_search.py188
-rwxr-xr-xwqflask/wqflask/search_results.py69
-rwxr-xr-xwqflask/wqflask/show_trait/SampleList.py114
3 files changed, 176 insertions, 195 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 921a4a47..a3260f34 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -58,7 +58,14 @@ class DoSearch(object):
@classmethod
def get_search(cls, search_type):
print("search_types are:", pf(cls.search_types))
- return cls.search_types[search_type]
+
+ search_type_string = search_type['dataset_type']
+ if 'key' in search_type:
+ search_type_string += '_' + search_type['key']
+
+ print("search_type_string is:", search_type_string)
+
+ return cls.search_types[search_type_string]
class QuickMrnaAssaySearch(DoSearch):
"""A general search for mRNA assays"""
@@ -120,6 +127,22 @@ class MrnaAssaySearch(DoSearch):
'Max LRS Location',
'Additive Effect']
+ def get_where_clause(self):
+ where_clause = """(MATCH (ProbeSet.Name,
+ ProbeSet.description,
+ ProbeSet.symbol,
+ alias,
+ GenbankId,
+ UniGeneId,
+ Probe_Target_Description)
+ AGAINST ('%s' IN BOOLEAN MODE))
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetXRef.ProbeSetFreezeId = %s
+ """ % (escape(self.search_term[0]),
+ escape(str(self.dataset.id)))
+
+ return where_clause
+
def compile_final_query(self, from_clause = '', where_clause = ''):
"""Generates the final query string"""
@@ -138,23 +161,7 @@ class MrnaAssaySearch(DoSearch):
return query
- def get_where_clause(self):
- where_clause = """(MATCH (ProbeSet.Name,
- ProbeSet.description,
- ProbeSet.symbol,
- alias,
- GenbankId,
- UniGeneId,
- Probe_Target_Description)
- AGAINST ('%s' IN BOOLEAN MODE))
- and ProbeSet.Id = ProbeSetXRef.ProbeSetId
- and ProbeSetXRef.ProbeSetFreezeId = %s
- """ % (escape(self.search_term[0]),
- escape(str(self.dataset.id)))
-
- return where_clause
-
- def run_combined(self, from_clause, where_clause):
+ def run_combined(self, from_clause = '', where_clause = ''):
"""Generates and runs a combined search of an mRNA expression dataset"""
print("Running ProbeSetSearch")
@@ -173,7 +180,6 @@ class MrnaAssaySearch(DoSearch):
print("final query is:", pf(query))
-
return self.execute(query)
def run(self):
@@ -219,7 +225,7 @@ class PhenotypeSearch(DoSearch):
'Max LRS Location',
'Additive Effect']
- def get_fields_clause(self):
+ def get_where_clause(self):
"""Generate clause for WHERE portion of query"""
#Todo: Zach will figure out exactly what both these lines mean
@@ -229,10 +235,10 @@ class PhenotypeSearch(DoSearch):
# This adds a clause to the query that matches the search term
# against each field in the search_fields tuple
- fields_clause = []
+ fields_clause_list = []
for field in self.search_fields:
- fields_clause.append('''%s REGEXP "%s"''' % (field, search_term))
- fields_clause = "(%s) and " % ' OR '.join(fields_clause)
+ fields_clause_list.append('''%s REGEXP "%s"''' % (field, search_term))
+ fields_clause = "(%s) " % ' OR '.join(fields_clause_list)
return fields_clause
@@ -244,6 +250,29 @@ class PhenotypeSearch(DoSearch):
query = (self.base_query +
"""%s
WHERE %s
+ and PublishXRef.InbredSetId = %s
+ and PublishXRef.PhenotypeId = Phenotype.Id
+ and PublishXRef.PublicationId = Publication.Id
+ and PublishFreeze.Id = %s""" % (
+ from_clause,
+ where_clause,
+ escape(str(self.dataset.group.id)),
+ escape(str(self.dataset.id))))
+
+ print("query is:", pf(query))
+
+ return query
+
+ def run_combined(self, from_clause, where_clause):
+ """Generates and runs a combined search of an phenotype dataset"""
+
+ print("Running PhenotypeSearch")
+
+ from_clause = self.normalize_spaces(from_clause)
+
+ query = (self.base_query +
+ """%s
+ WHERE %s
PublishXRef.InbredSetId = %s and
PublishXRef.PhenotypeId = Phenotype.Id and
PublishXRef.PublicationId = Publication.Id and
@@ -253,14 +282,15 @@ class PhenotypeSearch(DoSearch):
escape(str(self.dataset.group.id)),
escape(str(self.dataset.id))))
- print("query is:", pf(query))
+ print("final query is:", pf(query))
- return query
+
+ return self.execute(query)
def run(self):
"""Generates and runs a simple search of a phenotype dataset"""
- query = self.compile_final_query(where_clause = self.get_fields_clause())
+ query = self.compile_final_query(where_clause = self.get_where_clause())
return self.execute(query)
@@ -310,7 +340,7 @@ class QuickPhenotypeSearch(PhenotypeSearch):
def run(self):
"""Generates and runs a search across all phenotype datasets"""
- query = self.compile_final_query(where_clause = self.get_fields_clause())
+ query = self.compile_final_query(where_clause = self.get_where_clause())
return self.execute(query)
@@ -333,7 +363,7 @@ class GenotypeSearch(DoSearch):
'Record',
'Location']
- def get_fields_clause(self):
+ def get_where_clause(self):
"""Generate clause for part of the WHERE portion of query"""
# This adds a clause to the query that matches the search term
@@ -348,7 +378,7 @@ class GenotypeSearch(DoSearch):
field),
self.search_term))
print("hello ;where_clause is:", pf(fields_clause))
- fields_clause = "(%s)" % ' OR '.join(fields_clause)
+ fields_clause = "(%s) " % ' OR '.join(fields_clause)
return fields_clause
@@ -358,10 +388,10 @@ class GenotypeSearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
query = (self.base_query +
- """WHERE %s and
- Geno.Id = GenoXRef.GenoId and
- GenoXRef.GenoFreezeId = GenoFreeze.Id and
- GenoFreeze.Id = %s"""% (where_clause,
+ """WHERE %s
+ and Geno.Id = GenoXRef.GenoId
+ and GenoXRef.GenoFreezeId = GenoFreeze.Id
+ and GenoFreeze.Id = %s"""% (where_clause,
escape(str(self.dataset.id))))
print("query is:", pf(query))
@@ -373,14 +403,14 @@ class GenotypeSearch(DoSearch):
#Todo: Zach will figure out exactly what both these lines mean
#and comment here
- self.query = self.compile_final_query(where_clause = self.get_fields_clause())
+ self.query = self.compile_final_query(where_clause = self.get_where_clause())
return self.execute(self.query)
class RifSearch(MrnaAssaySearch):
"""Searches for traits with a Gene RIF entry including the search term."""
- DoSearch.search_types['RIF'] = "RifSearch"
+ DoSearch.search_types['ProbeSet_RIF'] = "RifSearch"
def get_where_clause(self):
where_clause = """( %s.symbol = GeneRIF_BASIC.symbol and
@@ -390,10 +420,6 @@ class RifSearch(MrnaAssaySearch):
return where_clause
def run(self):
- #where_clause = """( %s.symbol = GeneRIF_BASIC.symbol and
- # MATCH (GeneRIF_BASIC.comment)
- # AGAINST ('+%s' IN BOOLEAN MODE)) """ % (self.dataset.type, self.search_term[0])
-
where_clause = self.get_where_clause()
from_clause = ", GeneRIF_BASIC "
@@ -404,7 +430,7 @@ class RifSearch(MrnaAssaySearch):
class WikiSearch(MrnaAssaySearch):
"""Searches GeneWiki for traits other people have annotated"""
- DoSearch.search_types['WIKI'] = "WikiSearch"
+ DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch"
def get_where_clause(self):
where_clause = """%s.symbol = GeneRIF.symbol
@@ -433,7 +459,7 @@ class WikiSearch(MrnaAssaySearch):
class GoSearch(MrnaAssaySearch):
"""Searches for synapse-associated genes listed in the Gene Ontology."""
- DoSearch.search_types['GO'] = "GoSearch"
+ DoSearch.search_types['ProbeSet_GO'] = "GoSearch"
def run(self):
field = 'GOterm.acc'
@@ -525,43 +551,6 @@ class LrsSearch(MrnaAssaySearch):
def run(self):
self.from_clause = self.get_from_clause()
-
- #self.search_term = [float(value) for value in self.search_term]
- #
- #if self.search_operator == "=":
- # assert isinstance(self.search_term, (list, tuple))
- # self.lrs_min, self.lrs_max = self.search_term[:2]
- #
- # self.sub_clause = """ %sXRef.LRS > %s and
- # %sXRef.LRS < %s and """ % self.mescape(self.dataset.type,
- # min(self.lrs_min, self.lrs_max),
- # self.dataset.type,
- # max(self.lrs_min, self.lrs_max))
- #
- # if len(self.search_term) > 2:
- # self.chr_num = self.search_term[2]
- # self.sub_clause += """ Geno.Chr = %s and """ % (escape(self.chr_num))
- # if len(self.search_term) == 5:
- # self.mb_low, self.mb_high = self.search_term[3:]
- # self.sub_clause += """ Geno.Mb > %s and
- # Geno.Mb < %s and
- # """ % self.mescape(min(self.mb_low, self.mb_high),
- # max(self.mb_low, self.mb_high))
- # print("self.sub_clause is:", pf(self.sub_clause))
- #else:
- # # Deal with >, <, >=, and <=
- # print("self.search_term is:", self.search_term)
- # self.sub_clause = """ %sXRef.LRS %s %s and """ % self.mescape(self.dataset.type,
- # self.search_operator,
- # self.search_term[0])
- #
- #self.where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and
- # Geno.SpeciesId = %s and
- # %s.Chr = Geno.Chr
- # """ % self.mescape(self.dataset.type,
- # self.species_id,
- # self.dataset.type)
-
self.where_clause = self.get_where_clause()
self.query = self.compile_final_query(self.from_clause, self.where_clause)
@@ -673,7 +662,7 @@ class TransLrsSearch(CisTransLrsSearch):
class MeanSearch(MrnaAssaySearch):
"""Searches for genes expressed within an interval (log2 units) determined by the user"""
- DoSearch.search_types['MEAN'] = "MeanSearch"
+ DoSearch.search_types['ProbeSet_MEAN'] = "MeanSearch"
def get_where_clause(self):
self.search_term = [float(value) for value in self.search_term]
@@ -732,7 +721,7 @@ class MeanSearch(MrnaAssaySearch):
class RangeSearch(MrnaAssaySearch):
"""Searches for genes with a range of expression varying between two values"""
- DoSearch.search_types['RANGE'] = "RangeSearch"
+ DoSearch.search_types['ProbeSet_RANGE'] = "RangeSearch"
def get_where_clause(self):
if self.search_operator == "=":
@@ -791,10 +780,8 @@ class PositionSearch(DoSearch):
for search_key in ('POSITION', 'POS', 'MB'):
DoSearch.search_types[search_key] = "PositionSearch"
- def setup(self):
- self.search_term = [float(value) for value in self.search_term]
- self.chr, self.mb_min, self.mb_max = self.search_term[:3]
- self.where_clause = """ %s.Chr = '%s' and
+ def get_where_clause(self):
+ where_clause = """ %s.Chr = %s and
%s.Mb > %s and
%s.Mb < %s """ % self.mescape(self.dataset.type,
self.chr,
@@ -803,6 +790,21 @@ class PositionSearch(DoSearch):
self.dataset.type,
max(self.mb_min, self.mb_max))
+
+ return where_clause
+
+ def setup(self):
+ self.search_term = [float(value) if is_number(value) else value for value in self.search_term]
+ self.chr, self.mb_min, self.mb_max = self.search_term[:3]
+ self.get_chr()
+ self.where_clause = self.get_where_clause()
+
+ def get_chr(self):
+ try:
+ self.chr = int(self.chr)
+ except:
+ self.chr = int(self.chr.replace('chr', ''))
+
def run(self):
self.setup()
@@ -810,9 +812,12 @@ class PositionSearch(DoSearch):
return self.execute(self.query)
-class MrnaPositionSearch(MrnaAssaySearch, PositionSearch):
+class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
"""Searches for genes located within a specified range on a specified chromosome"""
+ for search_key in ('POSITION', 'POS', 'MB'):
+ DoSearch.search_types['ProbeSet_'+search_key] = "MrnaPositionSearch"
+
def run(self):
self.setup()
@@ -820,9 +825,12 @@ class MrnaPositionSearch(MrnaAssaySearch, PositionSearch):
return self.execute(self.query)
-class GenotypePositionSearch(GenotypeSearch, PositionSearch):
+class GenotypePositionSearch(PositionSearch, GenotypeSearch):
"""Searches for genes located within a specified range on a specified chromosome"""
+ for search_key in ('POSITION', 'POS', 'MB'):
+ DoSearch.search_types['Geno_'+search_key] = "GenotypePositionSearch"
+
def run(self):
self.setup()
@@ -863,7 +871,7 @@ class PvalueSearch(MrnaAssaySearch):
class AuthorSearch(PhenotypeSearch):
"""Searches for phenotype traits with specified author(s)"""
- DoSearch.search_types["NAME"] = "AuthorSearch"
+ DoSearch.search_types["Publish_NAME"] = "AuthorSearch"
def run(self):
@@ -875,6 +883,12 @@ class AuthorSearch(PhenotypeSearch):
return self.execute(self.query)
+def is_number(s):
+ try:
+ float(s)
+ return True
+ except ValueError:
+ return False
if __name__ == "__main__":
### Usually this will be used as a library, but call it from the command line for testing
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index df1edb13..2a1e8bb3 100755
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -223,26 +223,7 @@ class SearchResultPage(object):
combined_from_clause = ""
combined_where_clause = ""
for i, a_search in enumerate(self.search_terms):
- print("[kodak] item is:", pf(a_search))
- search_term = a_search['search_term']
- search_operator = a_search['separator']
- if a_search['key']:
- search_type = a_search['key'].upper()
- else:
- # We fall back to the dataset type as the key to get the right object
- search_type = self.dataset.type
-
- print("search_type is:", pf(search_type))
-
- search_ob = do_search.DoSearch.get_search(search_type)
- search_class = getattr(do_search, search_ob)
- the_search = search_class(search_term,
- search_operator,
- self.dataset,
- )
-
- #search_query = the_search.get_final_query()
-
+ the_search = self.get_search_ob(a_search)
get_from_clause = getattr(the_search, "get_from_clause", None)
if callable(get_from_clause):
from_clause = the_search.get_from_clause()
@@ -251,31 +232,37 @@ class SearchResultPage(object):
combined_where_clause += "(" + where_clause + ")"
if (i+1) < len(self.search_terms):
combined_where_clause += "AND"
-
- results = the_search.run_combined(combined_from_clause, combined_where_clause)
+ final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause)
+ results = the_search.execute(final_query)
self.results.extend(results)
-
else:
for a_search in self.search_terms:
- print("[kodak] item is:", pf(a_search))
- search_term = a_search['search_term']
- search_operator = a_search['separator']
- if a_search['key']:
- search_type = a_search['key'].upper()
- else:
- # We fall back to the dataset type as the key to get the right object
- search_type = self.dataset.type
-
- print("search_type is:", pf(search_type))
-
- search_ob = do_search.DoSearch.get_search(search_type)
- search_class = getattr(do_search, search_ob)
- print("search_class is: ", pf(search_class))
- the_search = search_class(search_term,
- search_operator,
- self.dataset,
- )
+ the_search = self.get_search_ob(a_search)
self.results.extend(the_search.run())
#print("in the search results are:", self.results)
self.header_fields = the_search.header_fields
+
+ def get_search_ob(self, a_search):
+ print("[kodak] item is:", pf(a_search))
+ search_term = a_search['search_term']
+ search_operator = a_search['separator']
+ search_type = {}
+ search_type['dataset_type'] = self.dataset.type
+ if a_search['key']:
+ search_type['key'] = a_search['key'].upper()
+ #search_type = a_search['key'].upper()
+ #else:
+ # # We fall back to the dataset type as the key to get the right object
+ # search_type = self.dataset.type
+
+ print("search_type is:", pf(search_type))
+
+ search_ob = do_search.DoSearch.get_search(search_type)
+ search_class = getattr(do_search, search_ob)
+ print("search_class is: ", pf(search_class))
+ the_search = search_class(search_term,
+ search_operator,
+ self.dataset,
+ )
+ return the_search
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 060cb519..e98870e3 100755
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -10,6 +10,8 @@ import numpy as np
from scipy import stats
from pprint import pformat as pf
+import itertools
+
class SampleList(object):
def __init__(self,
dataset,
@@ -24,15 +26,14 @@ class SampleList(object):
self.header = header
self.sample_list = [] # The actual list
+ self.sample_attribute_values = {}
- try:
- self.get_attributes()
- except Exception:
- print("failed to get attributes")
- self.attributes = {}
-
+ self.get_attributes()
print("camera: attributes are:", pf(self.attributes))
+ if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
+ self.get_extra_attribute_values()
+
for counter, sample_name in enumerate(sample_names, 1):
sample_name = sample_name.replace("_2nd_", "")
@@ -59,8 +60,8 @@ class SampleList(object):
sample.this_id = "Other_" + str(counter)
#### For extra attribute columns; currently only used by several datasets - Zach
- if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
- sample.extra_attributes = self.get_extra_attribute_values(sample_name)
+ if self.sample_attribute_values:
+ sample.extra_attributes = self.sample_attribute_values.get(sample_name, {})
print("sample.extra_attributes is", pf(sample.extra_attributes))
self.sample_list.append(sample)
@@ -135,75 +136,54 @@ class SampleList(object):
else:
sample.outlier = False
-
def get_attributes(self):
"""Finds which extra attributes apply to this dataset"""
-
- #ZS: Id and name values for this trait's extra attributes
- case_attributes = g.db.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name
- FROM CaseAttribute, CaseAttributeXRef
- WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND
- CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId
- group by CaseAttributeXRef.CaseAttributeId''',
- (str(self.dataset.id),))
+ # Get attribute names and distinct values for each attribute
+ results = g.db.execute('''
+ SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttributeXRef.Value
+ FROM CaseAttribute, CaseAttributeXRef
+ WHERE CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id
+ AND CaseAttributeXRef.ProbeSetFreezeId = %s
+ ORDER BY CaseAttribute.Name''', (str(self.dataset.id),))
self.attributes = {}
- for key, value in case_attributes.fetchall():
- print("radish: %s - %s" % (key, value))
+ for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
+ key, name = attr
+ print("radish: %s - %s" % (key, name))
self.attributes[key] = Bunch()
- self.attributes[key].name = value
-
- attribute_values = g.db.execute('''SELECT DISTINCT CaseAttributeXRef.Value
- FROM CaseAttribute, CaseAttributeXRef
- WHERE CaseAttribute.Name = %s AND
- CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,))
-
- self.attributes[key].distinct_values = [item[0] for item in attribute_values.fetchall()]
+ self.attributes[key].name = name
+ self.attributes[key].distinct_values = [item.Value for item in values]
self.attributes[key].distinct_values.sort(key=natural_sort_key)
-
- def get_extra_attribute_values(self, sample_name):
-
- attribute_values = {}
-
+ def get_extra_attribute_values(self):
if self.attributes:
+ results = g.db.execute('''
+ SELECT Strain.Name AS SampleName, CaseAttributeId AS Id, CaseAttributeXRef.Value
+ FROM Strain, StrainXRef, InbredSet, CaseAttributeXRef
+ WHERE StrainXRef.StrainId = Strain.Id
+ AND InbredSet.Id = StrainXRef.InbredSetId
+ AND CaseAttributeXRef.StrainId = Strain.Id
+ AND InbredSet.Name = %s
+ AND CaseAttributeXRef.ProbeSetFreezeId = %s
+ ORDER BY SampleName''',
+ (self.dataset.group.name, self.this_trait.dataset.id))
+
+ for sample_name, items in itertools.groupby(results.fetchall(), lambda row: row.SampleName):
+ attribute_values = {}
+ for item in items:
+ attribute_value = item.Value
+
+ #ZS: If it's an int, turn it into one for sorting
+ #(for example, 101 would be lower than 80 if they're strings instead of ints)
+ try:
+ attribute_value = int(attribute_value)
+ except ValueError:
+ pass
+
+ attribute_values[self.attributes[item.Id].name] = attribute_value
+ self.sample_attribute_values[sample_name] = attribute_values
- #ZS: Get StrainId value for the next query
- result = g.db.execute("""SELECT Strain.Id
- FROM Strain, StrainXRef, InbredSet
- WHERE Strain.Name = %s and
- StrainXRef.StrainId = Strain.Id and
- InbredSet.Id = StrainXRef.InbredSetId and
- InbredSet.Name = %s""", (sample_name,
- self.dataset.group.name))
-
- sample_id = result.fetchone().Id
-
- for attribute in self.attributes:
-
- #ZS: Add extra case attribute values (if any)
- result = g.db.execute("""SELECT Value
- FROM CaseAttributeXRef
- WHERE ProbeSetFreezeId = %s AND
- StrainId = %s AND
- CaseAttributeId = %s
- group by CaseAttributeXRef.CaseAttributeId""", (
- self.this_trait.dataset.id, sample_id, str(attribute)))
-
- attribute_value = result.fetchone().Value #Trait-specific attributes, if any
-
- #ZS: If it's an int, turn it into one for sorting
- #(for example, 101 would be lower than 80 if they're strings instead of ints)
- try:
- attribute_value = int(attribute_value)
- except ValueError:
- pass
-
- attribute_values[self.attributes[attribute].name] = attribute_value
-
- return attribute_values
-
def se_exists(self):
"""Returns true if SE values exist for any samples, otherwise false"""