diff options
| -rw-r--r-- | wqflask/wqflask/do_search.py | 35 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 39 |
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): |