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-rwxr-xr-xwqflask/wqflask/do_search.py192
1 files changed, 162 insertions, 30 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 29f3de98..31dc11b5 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -38,7 +38,6 @@ class DoSearch(object):
query = self.normalize_spaces(query)
print("in do_search query is:", pf(query))
results = g.db.execute(query, no_parameters=True).fetchall()
- #results = self.cursor.fetchall()
return results
#def escape(self, stringy):
@@ -139,11 +138,8 @@ class MrnaAssaySearch(DoSearch):
return query
- def run(self):
- """Generates and runs a simple search of an mRNA expression dataset"""
-
- print("Running ProbeSetSearch")
- query = self.base_query + """WHERE (MATCH (ProbeSet.Name,
+ def get_where_clause(self):
+ where_clause = """(MATCH (ProbeSet.Name,
ProbeSet.description,
ProbeSet.symbol,
alias,
@@ -156,6 +152,37 @@ class MrnaAssaySearch(DoSearch):
""" % (escape(self.search_term[0]),
escape(str(self.dataset.id)))
+ return where_clause
+
+ def run_combined(self, from_clause, where_clause):
+ """Generates and runs a combined search of an mRNA expression dataset"""
+
+ print("Running ProbeSetSearch")
+ #query = self.base_query + from_clause + " WHERE " + where_clause
+
+ from_clause = self.normalize_spaces(from_clause)
+
+ query = (self.base_query +
+ """%s
+ WHERE %s
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetXRef.ProbeSetFreezeId = %s
+ """ % (escape(from_clause),
+ where_clause,
+ escape(str(self.dataset.id))))
+
+ print("final query is:", pf(query))
+
+
+ return self.execute(query)
+
+ def run(self):
+ """Generates and runs a simple search of an mRNA expression dataset"""
+
+ print("Running ProbeSetSearch")
+ where_clause = self.get_where_clause()
+ query = self.base_query + "WHERE " + where_clause
+
#print("final query is:", pf(query))
return self.execute(query)
@@ -433,12 +460,15 @@ class LrsSearch(MrnaAssaySearch):
DoSearch.search_types['LRS'] = 'LrsSearch'
- def run(self):
+ def get_from_clause(self):
+ if self.search_operator == "=":
+ return ", Geno"
+ else:
+ return ""
+ def get_where_clause(self):
self.search_term = [float(value) for value in self.search_term]
- self.from_clause = ", Geno"
-
if self.search_operator == "=":
assert isinstance(self.search_term, (list, tuple))
self.lrs_min, self.lrs_max = self.search_term[:2]
@@ -451,7 +481,7 @@ class LrsSearch(MrnaAssaySearch):
if len(self.search_term) > 2:
self.chr_num = self.search_term[2]
- self.sub_clause += """ Geno.Chr = %s and """ % (escape(self.chr_num))
+ self.sub_clause += """ Geno.Chr = %s and """ % (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
@@ -459,21 +489,71 @@ class LrsSearch(MrnaAssaySearch):
""" % 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))
+
+ #%s.Chr = Geno.Chr
+ where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and
+ Geno.SpeciesId = %s
+ """ % self.mescape(self.dataset.type,
+ self.species_id)
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.sub_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type,
self.search_operator,
self.search_term[0])
+ where_clause = self.sub_clause
+
- 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)
+ return where_clause
- print("where_clause is:", pf(self.where_clause))
+ def get_final_query(self):
+ self.from_clause = self.get_from_clause()
+ self.where_clause = self.get_where_clause()
+ self.query = self.compile_final_query(self.from_clause, self.where_clause)
+
+ return self.query
+
+ 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)
@@ -586,25 +666,54 @@ class MeanSearch(MrnaAssaySearch):
DoSearch.search_types['MEAN'] = "MeanSearch"
- def run(self):
-
+ def get_where_clause(self):
self.search_term = [float(value) for value in self.search_term]
if self.search_operator == "=":
assert isinstance(self.search_term, (list, tuple))
self.mean_min, self.mean_max = self.search_term[:2]
- self.where_clause = """ %sXRef.mean > %s and
+ 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))
else:
# Deal with >, <, >=, and <=
- self.where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type,
+ where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type,
self.search_operator,
- self.search_term[0])
+ self.search_term[0])
+
+ return where_clause
+ def get_final_query(self):
+ self.where_clause = self.get_where_clause()
+ print("where_clause is:", pf(self.where_clause))
+
+ self.query = self.compile_final_query(where_clause = self.where_clause)
+
+ return self.query
+
+ def run(self):
+
+ #self.search_term = [float(value) for value in self.search_term]
+ #
+ #if self.search_operator == "=":
+ # assert isinstance(self.search_term, (list, tuple))
+ # self.mean_min, self.mean_max = self.search_term[:2]
+ #
+ # self.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))
+ #else:
+ # # Deal with >, <, >=, and <=
+ # self.where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type,
+ # self.search_operator,
+ # self.search_term[0])
+
+ self.where_clause = self.get_where_clause()
print("where_clause is:", pf(self.where_clause))
self.query = self.compile_final_query(where_clause = self.where_clause)
@@ -616,14 +725,11 @@ class RangeSearch(MrnaAssaySearch):
DoSearch.search_types['RANGE'] = "RangeSearch"
- def run(self):
-
- self.search_term = [float(value) for value in self.search_term]
-
+ def get_where_clause(self):
if self.search_operator == "=":
assert isinstance(self.search_term, (list, tuple))
self.range_min, self.range_max = self.search_term[:2]
- self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ where_clause = """ (SELECT Pow(2, max(value) -min(value))
FROM ProbeSetData
WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND
(SELECT Pow(2, max(value) -min(value))
@@ -633,12 +739,38 @@ class RangeSearch(MrnaAssaySearch):
max(self.range_min, self.range_max))
else:
# Deal with >, <, >=, and <=
- self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ where_clause = """ (SELECT Pow(2, max(value) -min(value))
FROM ProbeSetData
WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s
""" % (escape(self.search_term[0]))
- print("where_clause is:", pf(self.where_clause))
+ print("where_clause is:", pf(where_clause))
+
+ return where_clause
+
+ def run(self):
+
+ #self.search_term = [float(value) for value in self.search_term]
+ #
+ #if self.search_operator == "=":
+ # assert isinstance(self.search_term, (list, tuple))
+ # self.range_min, self.range_max = self.search_term[:2]
+ # self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ # FROM ProbeSetData
+ # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND
+ # (SELECT Pow(2, max(value) -min(value))
+ # FROM ProbeSetData
+ # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) < %s
+ # """ % self.mescape(min(self.range_min, self.range_max),
+ # max(self.range_min, self.range_max))
+ #else:
+ # # Deal with >, <, >=, and <=
+ # self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ # FROM ProbeSetData
+ # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s
+ # """ % (escape(self.search_term[0]))
+
+ self.where_clause = self.get_where_clause()
self.query = self.compile_final_query(where_clause = self.where_clause)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 16:06:24 +0000