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-rw-r--r--wqflask/base/data_set.py4
-rw-r--r--wqflask/base/trait.py15
-rw-r--r--wqflask/wqflask/gsearch.py6
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py14
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py4
5 files changed, 20 insertions, 23 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index aac8585e..470aa28b 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1218,8 +1218,8 @@ def geno_mrna_confidentiality(ob):
with database_connection() as conn, conn.cursor() as cursor:
cursor.execute(
"SELECT confidentiality, "
- "AuthorisedUsers FROM %s WHERE Name = %s",
- (f"{ob.type}Freeze", ob.name,)
+ f"AuthorisedUsers FROM {ob.type}Freeze WHERE Name = %s",
+ (ob.name,)
)
result = cursor.fetchall()[0]
if result:
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 21575230..2ca34028 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -426,14 +426,13 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
display_fields_string = f'ProbeSet.{display_fields_string}'
cursor.execute(
- "SELECT %s FROM ProbeSet, ProbeSetFreeze, "
+ f"SELECT {display_fields_string} FROM ProbeSet, ProbeSetFreeze, "
"ProbeSetXRef WHERE "
"ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
"AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
"ProbeSetFreeze.Name = %s AND "
"ProbeSet.Name = %s",
- (display_fields_string, dataset.name,
- str(trait.name),)
+ (dataset.name, str(trait.name),)
)
trait_info = cursor.fetchone()
# XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
@@ -442,20 +441,20 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
display_fields_string = ',Geno.'.join(dataset.display_fields)
display_fields_string = f'Geno.{display_fields_string}'
cursor.execute(
- "SELECT %s FROM Geno, GenoFreeze, "
+ f"SELECT {display_fields_string} FROM Geno, GenoFreeze, "
"GenoXRef WHERE "
"GenoXRef.GenoFreezeId = GenoFreeze.Id "
"AND GenoXRef.GenoId = Geno.Id "
"AND GenoFreeze.Name = %s "
"AND Geno.Name = %s",
- (display_fields_string, dataset.name, trait.name)
+ (dataset.name, trait.name)
)
trait_info = cursor.fetchone()
else: # Temp type
cursor.execute(
- "SELECT %s FROM %s WHERE Name = %s",
- (','.join(dataset.display_fields),
- dataset.type, trait.name,)
+ f"SELECT {','.join(dataset.display_fields)} "
+ f"FROM {dataset.type} WHERE Name = %s",
+ (trait.name,)
)
trait_info = cursor.fetchone()
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index cd3724d9..dac3b917 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -205,9 +205,9 @@ class GSearch:
"Phenotype.Lab_code) AGAINST (%s IN BOOLEAN MODE) ) "
"OR (MATCH (Publication.Abstract, Publication.Title, "
"Publication.Authors) AGAINST (%s IN BOOLEAN MODE) ) "
- ") %s ORDER BY Species.`Name`, InbredSet.`Name`, "
- "PublishXRef.`Id` LIMIT 6000",
- (search_term, search_term, group_clause,)
+ f") {group_clause} ORDER BY Species.`Name`, "
+ "InbredSet.`Name`, PublishXRef.`Id` LIMIT 6000",
+ ((search_term,)*2)
)
_result = cursor.fetchall()
trait_list = []
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 6adf528f..9e56f66b 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -13,7 +13,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
speciesDict = {}
results = []
with database_connection() as conn, conn.cursor() as cursor:
- cursor.execute("SELECT Species.Name, GeneList.SpeciesId"
+ cursor.execute("SELECT Species.Name, GeneList.SpeciesId "
"FROM Species, GeneList WHERE "
"GeneList.SpeciesId = Species.Id "
"GROUP BY GeneList.SpeciesId")
@@ -25,14 +25,13 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
speciesId = speciesDict[species]
otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())]
otherSpecies.remove([species, speciesId])
- cursor.execute("SELECT %s FROM GeneList "
- "WHERE SpeciesId = %d AND "
+ cursor.execute(f"SELECT {', '.join(fetchFields)} FROM GeneList "
+ "WHERE SpeciesId = %s AND "
"Chromosome = %s AND "
"((TxStart > %s and TxStart <= %s) "
"OR (TxEnd > %s and TxEnd <= %s)) "
"ORDER BY txStart",
- (", ".join(fetchFields),
- speciesId, chrName,
+ (speciesId, chrName,
startMb, endMb,
startMb, endMb))
results = cursor.fetchall()
@@ -69,11 +68,10 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
othSpec, othSpecId = item
newdict2 = {}
cursor.execute(
- "SELECT %s FROM GeneList WHERE "
+ f"SELECT {', '.join(fetchFields)} FROM GeneList WHERE "
"SpeciesId = %s AND "
"geneSymbol= '%s' LIMIT 1",
- (", ".join(fetchFields),
- othSpecId,
+ (othSpecId,
newdict["GeneSymbol"]))
resultsOther = cursor.fetchone()
if resultsOther:
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index cd47f293..0dfa3e64 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -249,9 +249,9 @@ class SnpBrowser:
"a.Mb_start, a.Mb_end, a.Strand, a.Type, a.Size, "
"a.InDelSequence, b.Name FROM IndelAll a, "
"SnpSource b WHERE a.Chromosome = %s AND "
- "a.Mb_start >= %2.6f AND a.Mb_start < (%2.6f+.0010) "
+ "a.Mb_start >= %s AND a.Mb_start < %s "
"AND b.Id = a.SourceId ORDER BY a.Mb_start")
- __vars = (self.chr, f"{self.start_mb:2.6f}",
+ __vars = (self.chr, f"{self.start_mb+0.0010:2.6f}",
f"{self.end_mb+0.0010:2.6f}",)
cursor.execute(__query, __vars)
return self.filter_results(cursor.fetchall())
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 16:59:37 +0000