diff options
| -rw-r--r-- | wqflask/base/trait.py | 142 |
1 files changed, 69 insertions, 73 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 98a10916..781abf7a 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -395,79 +395,75 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): the_url = GN_PROXY_URL + "run-action?resource={}&user={}&branch=data&action=view&trait={}".format( resource_id, g.user_session.user_id, trait.name) with database_connection() as conn, conn.cursor() as cursor: - try: - response = requests.get(the_url).content - trait_info = json.loads(response) - except: # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait - trait_info = () - if dataset.type == 'Publish': - cursor.execute( - "SELECT PublishXRef.Id, InbredSet.InbredSetCode, " - "Publication.PubMed_ID, " - "CAST(Phenotype.Pre_publication_description AS BINARY), " - "CAST(Phenotype.Post_publication_description AS BINARY), " - "CAST(Phenotype.Original_description AS BINARY), " - "CAST(Phenotype.Pre_publication_abbreviation AS BINARY), " - "CAST(Phenotype.Post_publication_abbreviation AS BINARY), " - "PublishXRef.mean, Phenotype.Lab_code, " - "Phenotype.Submitter, Phenotype.Owner, " - "Phenotype.Authorized_Users, " - "CAST(Publication.Authors AS BINARY), " - "CAST(Publication.Title AS BINARY), " - "CAST(Publication.Abstract AS BINARY), " - "CAST(Publication.Journal AS BINARY), " - "Publication.Volume, Publication.Pages, " - "Publication.Month, Publication.Year, " - "PublishXRef.Sequence, Phenotype.Units, " - "PublishXRef.comments FROM PublishXRef, Publication, " - "Phenotype, PublishFreeze, InbredSet WHERE " - "PublishXRef.Id = %s AND " - "Phenotype.Id = PublishXRef.PhenotypeId " - "AND Publication.Id = PublishXRef.PublicationId " - "AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId " - "AND PublishXRef.InbredSetId = InbredSet.Id AND " - "PublishFreeze.Id = %s", - (trait.name, dataset.id,) - ) - trait_info = cursor.fetchone() - - # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name - # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. - elif dataset.type == 'ProbeSet': - display_fields_string = ', ProbeSet.'.join(dataset.display_fields) - display_fields_string = f'ProbeSet.{display_fields_string}' - cursor.execute( - 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", - (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 - # to avoid the problem of same marker name from different species. - elif dataset.type == 'Geno': - display_fields_string = ',Geno.'.join(dataset.display_fields) - display_fields_string = f'Geno.{display_fields_string}' - cursor.execute( - 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", - (dataset.name, trait.name) - ) - trait_info = cursor.fetchone() - else: # Temp type - cursor.execute( - f"SELECT {','.join(dataset.display_fields)} " - f"FROM {dataset.type} WHERE Name = %s", - (trait.name,) - ) - trait_info = cursor.fetchone() + trait_info = () + if dataset.type == 'Publish': + cursor.execute( + "SELECT PublishXRef.Id, InbredSet.InbredSetCode, " + "Publication.PubMed_ID, " + "CAST(Phenotype.Pre_publication_description AS BINARY), " + "CAST(Phenotype.Post_publication_description AS BINARY), " + "CAST(Phenotype.Original_description AS BINARY), " + "CAST(Phenotype.Pre_publication_abbreviation AS BINARY), " + "CAST(Phenotype.Post_publication_abbreviation AS BINARY), " + "PublishXRef.mean, Phenotype.Lab_code, " + "Phenotype.Submitter, Phenotype.Owner, " + "Phenotype.Authorized_Users, " + "CAST(Publication.Authors AS BINARY), " + "CAST(Publication.Title AS BINARY), " + "CAST(Publication.Abstract AS BINARY), " + "CAST(Publication.Journal AS BINARY), " + "Publication.Volume, Publication.Pages, " + "Publication.Month, Publication.Year, " + "PublishXRef.Sequence, Phenotype.Units, " + "PublishXRef.comments FROM PublishXRef, Publication, " + "Phenotype, PublishFreeze, InbredSet WHERE " + "PublishXRef.Id = %s AND " + "Phenotype.Id = PublishXRef.PhenotypeId " + "AND Publication.Id = PublishXRef.PublicationId " + "AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId " + "AND PublishXRef.InbredSetId = InbredSet.Id AND " + "PublishFreeze.Id = %s", + (trait.name, dataset.id,) + ) + trait_info = cursor.fetchone() + + # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name + # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. + elif dataset.type == 'ProbeSet': + display_fields_string = ', ProbeSet.'.join(dataset.display_fields) + display_fields_string = f'ProbeSet.{display_fields_string}' + cursor.execute( + 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", + (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 + # to avoid the problem of same marker name from different species. + elif dataset.type == 'Geno': + display_fields_string = ',Geno.'.join(dataset.display_fields) + display_fields_string = f'Geno.{display_fields_string}' + cursor.execute( + 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", + (dataset.name, trait.name) + ) + trait_info = cursor.fetchone() + else: # Temp type + cursor.execute( + f"SELECT {','.join(dataset.display_fields)} " + f"FROM {dataset.type} WHERE Name = %s", + (trait.name,) + ) + trait_info = cursor.fetchone() if trait_info: trait.haveinfo = True |