diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 47 |
1 files changed, 30 insertions, 17 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 262ba3c2..44a8f7f7 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -169,16 +169,23 @@ class GSearch: PublishXRef.`LRS`, PublishXRef.`additive`, InbredSet.`InbredSetCode`, - PublishXRef.`mean` - FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication - WHERE PublishXRef.`InbredSetId`=InbredSet.`Id` - AND PublishFreeze.`InbredSetId`=InbredSet.`Id` - AND InbredSet.`SpeciesId`=Species.`Id` + PublishXRef.`mean`, + PublishFreeze.Id, + Geno.Chr as geno_chr, + Geno.Mb as geno_mb + FROM Species + INNER JOIN InbredSet ON InbredSet.`SpeciesId`=Species.`Id` + INNER JOIN PublishFreeze ON PublishFreeze.`InbredSetId`=InbredSet.`Id` + INNER JOIN PublishXRef ON PublishXRef.`InbredSetId`=InbredSet.`Id` + INNER JOIN Phenotype ON PublishXRef.`PhenotypeId`=Phenotype.`Id` + INNER JOIN Publication ON PublishXRef.`PublicationId`=Publication.`Id` + LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id + WHERE + ( + (MATCH (Phenotype.Post_publication_description, Phenotype.Pre_publication_description, Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code) AGAINST ('{1}' IN BOOLEAN MODE) ) + OR (MATCH (Publication.Abstract, Publication.Title, Publication.Authors) AGAINST ('{1}' IN BOOLEAN MODE) ) + ) {0} - AND PublishXRef.`PhenotypeId`=Phenotype.`Id` - AND PublishXRef.`PublicationId`=Publication.`Id` - AND (MATCH (Phenotype.Post_publication_description, Phenotype.Pre_publication_description, Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code) AGAINST ('{1}' IN BOOLEAN MODE) ) - AND (MATCH (Publication.Abstract, Publication.Title, Publication.Authors) AGAINST ('{1}' IN BOOLEAN MODE) ) ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id` LIMIT 6000 """.format(group_clause, search_term) @@ -213,6 +220,9 @@ class GSearch: this_trait['mean'] = f"{line[13]:.3f}" else: this_trait['mean'] = "N/A" + this_trait['dataset_id'] = line[14] + this_trait['locus_chr'] = line[15] + this_trait['locus_mb'] = line[16] this_trait['authors'] = line[7] this_trait['year'] = line[8] if this_trait['year'].isdigit(): @@ -233,17 +243,20 @@ class GSearch: if line[11] != "" and line[11] != None: this_trait['additive'] = '%.3f' % line[11] + dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="Publish", species=this_trait["species"]) + permissions = check_resource_availability(dataset_ob, this_trait['name']) + if type(permissions['data']) is list: + if "view" not in permissions['data']: + continue + else: + if permissions['data'] == 'no-access': + continue + this_trait['max_lrs_text'] = "N/A" - trait_ob = create_trait( - dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) - if not trait_ob: - continue if this_trait['dataset'] == this_trait['group'] + "Publish": try: - if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": - this_trait['max_lrs_text'] = "Chr" + \ - str(trait_ob.locus_chr) + \ - ": " + str(trait_ob.locus_mb) + if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None: + this_trait['max_lrs_text'] = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb']) except: this_trait['max_lrs_text'] = "N/A" |