diff options
Diffstat (limited to 'scripts/index-genenetwork')
| -rwxr-xr-x | scripts/index-genenetwork | 47 |
1 files changed, 32 insertions, 15 deletions
diff --git a/scripts/index-genenetwork b/scripts/index-genenetwork index fe2420c..b5684f2 100755 --- a/scripts/index-genenetwork +++ b/scripts/index-genenetwork @@ -38,6 +38,8 @@ DOCUMENTS_PER_CHUNK = 100000 SQLQuery = namedtuple("SQLQuery", ["fields", "tables", "where", "offset", "limit"], defaults=[Nothing, 0, Nothing]) +SQLTableClause = namedtuple("SQLTableClause", + ["join_type", "table", "condition"]) # FIXME: Some Max LRS values in the DB are wrongly listed as 0.000, # but shouldn't be displayed. Make them NULLs in the database. @@ -62,14 +64,20 @@ genes_query = SQLQuery( "Geno.Chr AS geno_chr", "Geno.Mb as geno_mb"], ["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"""], + SQLTableClause("INNER JOIN", "InbredSet", + "InbredSet.SpeciesId = Species.Id"), + SQLTableClause("INNER JOIN", "ProbeFreeze", + "ProbeFreeze.InbredSetId = InbredSet.Id"), + SQLTableClause("INNER JOIN", "Tissue", + "ProbeFreeze.TissueId = Tissue.Id"), + SQLTableClause("INNER JOIN", "ProbeSetFreeze", + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id"), + SQLTableClause("INNER JOIN", "ProbeSetXRef", + "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id"), + SQLTableClause("INNER JOIN", "ProbeSet", + "ProbeSet.Id = ProbeSetXRef.ProbeSetId"), + SQLTableClause("LEFT JOIN", "Geno", + "ProbeSetXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id")], Just("ProbeSetFreeze.confidentiality < 1 AND ProbeSetFreeze.public > 0")) # FIXME: Some years are blank strings or strings that contain text @@ -101,17 +109,26 @@ phenotypes_query = SQLQuery( "Geno.Chr as geno_chr", "Geno.Mb as geno_mb"], ["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"]) + SQLTableClause("INNER JOIN", "InbredSet", + "InbredSet.SpeciesId = Species.Id"), + SQLTableClause("INNER JOIN", "PublishFreeze", + "PublishFreeze.InbredSetId = InbredSet.Id"), + SQLTableClause("INNER JOIN", "PublishXRef", + "PublishXRef.InbredSetId = InbredSet.Id"), + SQLTableClause("INNER JOIN", "Phenotype", + "PublishXRef.PhenotypeId = Phenotype.Id"), + SQLTableClause("INNER JOIN", "Publication", + "PublishXRef.PublicationId = Publication.Id"), + SQLTableClause("LEFT JOIN", "Geno", + "PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id")]) def serialize_sql(query: SQLQuery) -> str: """Serialize SQLQuery object to a string.""" - sql = f"SELECT {', '.join(query.fields)} FROM {' '.join(query.tables)}" + table_clauses = [clause if isinstance(clause, str) + else f"{clause.join_type} {clause.table} ON {clause.condition}" + for clause in query.tables] + sql = f"SELECT {', '.join(query.fields)} FROM {' '.join(table_clauses)}" def append_to_sql(appendee): nonlocal sql sql += appendee |