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authorzsloan2021-02-25 20:26:07 +0000
committerzsloan2021-02-25 20:26:07 +0000
commit818897630e0bd2e97de9bbc3fca805eed64fd44f (patch)
tree37fcfe90f7fa145cad7af64b52c88c91a12e429c
parent74a6e3f3d21edb9204b8e6e1188b04424c2f7446 (diff)
downloadgenenetwork2-818897630e0bd2e97de9bbc3fca805eed64fd44f.tar.gz
mRNA Assay searches without trait creation should work now
-rw-r--r--wqflask/wqflask/do_search.py35
-rw-r--r--wqflask/wqflask/search_results.py39
2 files changed, 36 insertions, 38 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 1478d2b6..4448e81e 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -78,16 +78,31 @@ class MrnaAssaySearch(DoSearch):
DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch"
- base_query = """SELECT distinct ProbeSet.Name as TNAME,
- 0 as thistable,
- ProbeSetXRef.Mean as TMEAN,
- ProbeSetXRef.LRS as TLRS,
- ProbeSetXRef.PVALUE as TPVALUE,
- ProbeSet.Chr_num as TCHR_NUM,
- ProbeSet.Mb as TMB,
- ProbeSet.Symbol as TSYMBOL,
- ProbeSet.name_num as TNAME_NUM
- FROM ProbeSetXRef, ProbeSet """
+ base_query = """
+ SELECT
+ ProbeSetFreeze.`Name`,
+ ProbeSetFreeze.`FullName`,
+ ProbeSet.`Name`,
+ ProbeSet.`Symbol`,
+ CAST(ProbeSet.`description` AS BINARY),
+ CAST(ProbeSet.`Probe_Target_Description` AS BINARY),
+ ProbeSet.`Chr`,
+ ProbeSet.`Mb`,
+ ProbeSetXRef.`Mean`,
+ ProbeSetXRef.`LRS`,
+ ProbeSetXRef.`Locus`,
+ ProbeSetXRef.`pValue`,
+ ProbeSetXRef.`additive`,
+ Geno.`Chr` as geno_chr,
+ Geno.`Mb` as geno_mb
+ FROM Species
+ INNER JOIN InbredSet ON InbredSet.`SpeciesId`= Species.`Id`
+ INNER JOIN ProbeFreeze ON ProbeFreeze.`InbredSetId` = InbredSet.`Id`
+ INNER JOIN Tissue ON ProbeFreeze.`TissueId` = Tissue.`Id`
+ INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.`ProbeFreezeId` = ProbeFreeze.`Id`
+ INNER JOIN ProbeSetXRef ON ProbeSetXRef.`ProbeSetFreezeId` = ProbeSetFreeze.`Id`
+ INNER JOIN ProbeSet ON ProbeSet.`Id` = ProbeSetXRef.`ProbeSetId`
+ LEFT JOIN Geno ON ProbeSetXRef.`Locus` = Geno.`Name` AND Geno.`SpeciesId` = Species.`Id` """
header_fields = ['Index',
'Record',
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index b8e9f5de..97cc6581 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -130,38 +130,21 @@ class SearchResultPage(object):
trait_dict['dataset'] = self.dataset.name
trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait_dict['name'], trait_dict['dataset']))
if self.dataset.type == "ProbeSet":
- trait_dict['symbol'] = "N/A"
- if result[10]:
- trait_dict['symbol'] = result[10]
- trait_dict['description'] = "N/A"
- description_string = result[2]
- if str(description_string) != "" and description_string != None:
- description_display = description_string
- else:
- description_display = trait_dict['symbol']
+ trait_dict['symbol'] = "N/A" if result[3] is None else result[3].strip()
+ description_text = "N/A" if result[4] is None or str(result[4]) == "" else trait_dict['symbol']
- target_string = result[3]
- if str(target_string) != "" and target_string != None:
- description_display = description_display + "; " + target_string.strip()
+ target_string = result[5]
+ description_display = description_text if target_string is None or str(target_string) == "" else description_text + "; " + str(target_string).strip()
trait_dict['description'] = description_display
trait_dict['location'] = "N/A"
- if (result[8] != "NULL" and result[8] != "") and (result[9] != 0):
- trait_dict['location'] = f"Chr{result[8]}: {float(result[9]):.6f}"
- trait_dict['mean'] = "N/A"
- trait_dict['additive'] = "N/A"
- if result[4] != "" and result[4] != None:
- trait_dict['mean'] = f"{result[4]:.3f}"
- try:
- trait_dict['lod_score'] = f"{float(result[5]) / 4.61:.1f}"
- except:
- trait_dict['lod_score'] = "N/A"
- try:
- trait_dict['lrs_location'] = f"Chr{result[12]}: {float(result[13]):.6f}"
- except:
- trait_dict['lrs_location'] = "N/A"
- if result[5] != "":
- trait_dict['additive'] = f"{result[7]:.3f}"
+ if (result[6] is not None) and (result[6] != "") and (result[7] is not None) and (result[7] != 0):
+ trait_dict['location'] = f"Chr{result[6]}: {float(result[7]):.6f}"
+
+ trait_dict['mean'] = "N/A" if result[8] is None or result[8] == "" else f"{result[8]:.3f}"
+ trait_dict['additive'] = "N/A" if result[12] is None or result[12] == "" else f"{result[12]:.3f}"
+ trait_dict['lod_score'] = "N/A" if result[9] is None or result[9] == "" else f"{float(result[9]) / 4.61:.1f}"
+ trait_dict['lrs_location'] = "N/A" if result[13] is None or result[13] == "" or result[14] is None else f"Chr{result[13]}: {float(result[14]):.6f}"
elif self.dataset.type == "Geno":
trait_dict['location'] = "N/A"
if (result[4] != "NULL" and result[4] != "") and (result[5] != 0):