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-rw-r--r--wqflask/wqflask/do_search.py156
1 files changed, 78 insertions, 78 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 48527785..761ae326 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -112,7 +112,7 @@ class MrnaAssaySearch(DoSearch):
match_clause = ""
where_clause = (match_clause
- + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
""" % (escape(str(self.dataset.id))))
@@ -135,7 +135,7 @@ class MrnaAssaySearch(DoSearch):
match_clause = ""
where_clause = (match_clause
- + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
""" % (escape(str(self.dataset.id))))
@@ -147,14 +147,14 @@ class MrnaAssaySearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
query = (self.base_query +
- """%s
+ """%s
WHERE %s
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
ORDER BY ProbeSet.symbol ASC
""" % (escape(from_clause),
- where_clause,
- escape(str(self.dataset.id))))
+ where_clause,
+ escape(str(self.dataset.id))))
return query
def run_combined(self, from_clause='', where_clause=''):
@@ -166,14 +166,14 @@ class MrnaAssaySearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
query = (self.base_query +
- """%s
+ """%s
WHERE %s
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
ORDER BY ProbeSet.symbol ASC
""" % (escape(from_clause),
- where_clause,
- escape(str(self.dataset.id))))
+ where_clause,
+ escape(str(self.dataset.id))))
return self.execute(query)
@@ -199,15 +199,15 @@ class PhenotypeSearch(DoSearch):
FROM Phenotype, PublishFreeze, Publication, PublishXRef """
search_fields = ('Phenotype.Post_publication_description',
- 'Phenotype.Pre_publication_description',
- 'Phenotype.Pre_publication_abbreviation',
- 'Phenotype.Post_publication_abbreviation',
- 'Phenotype.Lab_code',
- 'Publication.PubMed_ID',
- 'Publication.Abstract',
- 'Publication.Title',
- 'Publication.Authors',
- 'PublishXRef.Id')
+ 'Phenotype.Pre_publication_description',
+ 'Phenotype.Pre_publication_abbreviation',
+ 'Phenotype.Post_publication_abbreviation',
+ 'Phenotype.Lab_code',
+ 'Publication.PubMed_ID',
+ 'Publication.Abstract',
+ 'Publication.Title',
+ 'Publication.Authors',
+ 'PublishXRef.Id')
header_fields = ['Index',
'Record',
@@ -250,28 +250,28 @@ class PhenotypeSearch(DoSearch):
if self.search_term[0] == "*":
query = (self.base_query +
- """%s
+ """%s
WHERE PublishXRef.InbredSetId = %s
and PublishXRef.PhenotypeId = Phenotype.Id
and PublishXRef.PublicationId = Publication.Id
and PublishFreeze.Id = %s
ORDER BY PublishXRef.Id""" % (
- from_clause,
- escape(str(self.dataset.group.id)),
- escape(str(self.dataset.id))))
+ from_clause,
+ escape(str(self.dataset.group.id)),
+ escape(str(self.dataset.id))))
else:
query = (self.base_query +
- """%s
+ """%s
WHERE %s
and PublishXRef.InbredSetId = %s
and PublishXRef.PhenotypeId = Phenotype.Id
and PublishXRef.PublicationId = Publication.Id
and PublishFreeze.Id = %s
ORDER BY PublishXRef.Id""" % (
- from_clause,
- where_clause,
- escape(str(self.dataset.group.id)),
- escape(str(self.dataset.id))))
+ from_clause,
+ where_clause,
+ escape(str(self.dataset.group.id)),
+ escape(str(self.dataset.id))))
return query
@@ -283,16 +283,16 @@ class PhenotypeSearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
query = (self.base_query +
- """%s
+ """%s
WHERE %s
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))))
+ from_clause,
+ where_clause,
+ escape(str(self.dataset.group.id)),
+ escape(str(self.dataset.id))))
return self.execute(query)
@@ -336,7 +336,7 @@ class GenotypeSearch(DoSearch):
for field in self.search_fields:
where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type,
field),
- self.search_term))
+ self.search_term))
logger.debug("hello ;where_clause is:", pf(where_clause))
where_clause = "(%s) " % ' OR '.join(where_clause)
@@ -349,16 +349,16 @@ class GenotypeSearch(DoSearch):
if self.search_term[0] == "*":
query = (self.base_query
- + """WHERE Geno.Id = GenoXRef.GenoId
+ + """WHERE Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id))))
else:
query = (self.base_query +
- """WHERE %s
+ """WHERE %s
and Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
and GenoFreeze.Id = %s""" % (where_clause,
- escape(str(self.dataset.id))))
+ escape(str(self.dataset.id))))
return query
@@ -526,7 +526,7 @@ class LrsSearch(DoSearch):
where_clause += """ and %sXRef.Locus = Geno.name and
Geno.SpeciesId = %s
""" % self.mescape(self.dataset.type,
- self.species_id)
+ self.species_id)
else:
# Deal with >, <, >=, and <=
logger.debug("self.search_term is:", self.search_term)
@@ -535,8 +535,8 @@ class LrsSearch(DoSearch):
lrs_val = lrs_val * 4.61
where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type,
- self.search_operator,
- self.search_term[0])
+ self.search_operator,
+ self.search_term[0])
return where_clause
@@ -618,18 +618,18 @@ class CisTransLrsSearch(DoSearch):
sub_clause = """ %sXRef.LRS > %s and
%sXRef.LRS < %s and """ % (
- escape(self.dataset.type),
- escape(str(min(lrs_min, lrs_max))),
- escape(self.dataset.type),
- escape(str(max(lrs_min, lrs_max)))
- )
+ escape(self.dataset.type),
+ escape(str(min(lrs_min, lrs_max))),
+ escape(self.dataset.type),
+ escape(str(max(lrs_min, lrs_max)))
+ )
else:
# Deal with >, <, >=, and <=
sub_clause = """ %sXRef.LRS %s %s and """ % (
- escape(self.dataset.type),
- escape(self.search_operator),
- escape(self.search_term[0])
- )
+ escape(self.dataset.type),
+ escape(self.search_operator),
+ escape(self.search_term[0])
+ )
if cis_trans == "cis":
where_clause = sub_clause + """
@@ -637,27 +637,27 @@ class CisTransLrsSearch(DoSearch):
%sXRef.Locus = Geno.name and
Geno.SpeciesId = %s and
%s.Chr = Geno.Chr""" % (
- escape(self.dataset.type),
- the_operator,
- escape(str(self.mb_buffer)),
- escape(self.dataset.type),
- escape(str(self.species_id)),
- escape(self.dataset.type)
- )
+ escape(self.dataset.type),
+ the_operator,
+ escape(str(self.mb_buffer)),
+ escape(self.dataset.type),
+ escape(str(self.species_id)),
+ escape(self.dataset.type)
+ )
else:
if chromosome:
location_clause = "(%s.Chr = '%s' and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) or (%s.Chr != Geno.Chr and Geno.Chr = '%s')" % (escape(self.dataset.type),
- chromosome,
- escape(
+ chromosome,
+ escape(
self.dataset.type),
- escape(
+ escape(
self.dataset.type),
- the_operator,
- escape(
+ the_operator,
+ escape(
str(self.mb_buffer)),
- escape(
+ escape(
self.dataset.type),
- chromosome)
+ chromosome)
else:
location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(
self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type))
@@ -665,10 +665,10 @@ class CisTransLrsSearch(DoSearch):
%sXRef.Locus = Geno.name and
Geno.SpeciesId = %s and
(%s)""" % (
- escape(self.dataset.type),
- escape(str(self.species_id)),
- location_clause
- )
+ escape(self.dataset.type),
+ escape(str(self.species_id)),
+ location_clause
+ )
return where_clause
@@ -752,15 +752,15 @@ class MeanSearch(MrnaAssaySearch):
where_clause = """ %sXRef.mean > %s and
%sXRef.mean < %s """ % self.mescape(self.dataset.type,
- min(self.mean_min,
- self.mean_max),
- self.dataset.type,
- max(self.mean_min, self.mean_max))
+ min(self.mean_min,
+ self.mean_max),
+ self.dataset.type,
+ max(self.mean_min, self.mean_max))
else:
# Deal with >, <, >=, and <=
where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type,
- self.search_operator,
- self.search_term[0])
+ self.search_operator,
+ self.search_term[0])
return where_clause
@@ -893,17 +893,17 @@ class PvalueSearch(MrnaAssaySearch):
self.pvalue_min, self.pvalue_max = self.search_term[:2]
self.where_clause = """ %sXRef.pValue > %s and %sXRef.pValue < %s
""" % self.mescape(
- self.dataset.type,
- min(self.pvalue_min, self.pvalue_max),
- self.dataset.type,
- max(self.pvalue_min, self.pvalue_max))
+ self.dataset.type,
+ min(self.pvalue_min, self.pvalue_max),
+ self.dataset.type,
+ max(self.pvalue_min, self.pvalue_max))
else:
# Deal with >, <, >=, and <=
self.where_clause = """ %sXRef.pValue %s %s
""" % self.mescape(
- self.dataset.type,
- self.search_operator,
- self.search_term[0])
+ self.dataset.type,
+ self.search_operator,
+ self.search_term[0])
logger.debug("where_clause is:", pf(self.where_clause))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 23:50:13 +0000