diff options
| -rw-r--r-- | scripts/migrate_existing_data.py | 37 |
1 files changed, 20 insertions, 17 deletions
diff --git a/scripts/migrate_existing_data.py b/scripts/migrate_existing_data.py index 1261462..198d37d 100644 --- a/scripts/migrate_existing_data.py +++ b/scripts/migrate_existing_data.py @@ -210,11 +210,12 @@ def __unassigned_mrna__(bioconn, assigned): "FROM Species AS s INNER JOIN InbredSet AS iset " "ON s.SpeciesId=iset.SpeciesId INNER JOIN ProbeFreeze AS pf " "ON iset.InbredSetId=pf.InbredSetId INNER JOIN ProbeSetFreeze AS psf " - "ON pf.ProbeFreezeId=psf.ProbeFreezeId ") + "ON pf.ProbeFreezeId=psf.ProbeFreezeId " + "WHERE s.Name != 'human' ") if len(assigned) > 0: paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(assigned)) query = query + ( - "WHERE (s.SpeciesId, iset.InbredSetId, pf.ProbeFreezeId, psf.Id) " + "AND (s.SpeciesId, iset.InbredSetId, pf.ProbeFreezeId, psf.Id) " f"NOT IN ({paramstr}) ") query = query + "LIMIT 100000" @@ -270,11 +271,12 @@ def __unassigned_geno__(bioconn, assigned): "gf.ShortName AS dataset_shortname " "FROM Species AS s INNER JOIN InbredSet AS iset " "ON s.SpeciesId=iset.SpeciesId INNER JOIN GenoFreeze AS gf " - "ON iset.InbredSetId=gf.InbredSetId ") + "ON iset.InbredSetId=gf.InbredSetId " + "WHERE s.Name != 'human' ") if len(assigned) > 0: paramstr = ", ".join(["(%s, %s, %s)"] * len(assigned)) query = query + ( - "WHERE (s.SpeciesId, iset.InbredSetId, gf.Id) " + "AND (s.SpeciesId, iset.InbredSetId, gf.Id) " f"NOT IN ({paramstr}) ") query = query + "LIMIT 100000" @@ -326,22 +328,23 @@ def __assigned_pheno__(authconn): def __unassigned_pheno__(bioconn, assigned): """Retrieve all unassigned Phenotype data.""" query = ( - "SELECT spc.SpeciesId, iset.InbredSetId, " - "pf.Id AS PublishFreezeId, pf.Name AS dataset_name, " - "pf.FullName AS dataset_fullname, " - "pf.ShortName AS dataset_shortname, pxr.Id AS PublishXRefId " - "FROM " - "Species AS spc " - "INNER JOIN InbredSet AS iset " - "ON spc.SpeciesId=iset.SpeciesId " - "INNER JOIN PublishFreeze AS pf " - "ON iset.InbredSetId=pf.InbredSetId " - "INNER JOIN PublishXRef AS pxr " - "ON pf.InbredSetId=pxr.InbredSetId ") + "SELECT spc.SpeciesId, iset.InbredSetId, " + "pf.Id AS PublishFreezeId, pf.Name AS dataset_name, " + "pf.FullName AS dataset_fullname, " + "pf.ShortName AS dataset_shortname, pxr.Id AS PublishXRefId " + "FROM " + "Species AS spc " + "INNER JOIN InbredSet AS iset " + "ON spc.SpeciesId=iset.SpeciesId " + "INNER JOIN PublishFreeze AS pf " + "ON iset.InbredSetId=pf.InbredSetId " + "INNER JOIN PublishXRef AS pxr " + "ON pf.InbredSetId=pxr.InbredSetId " + "WHERE spc.Name != 'human' ") if len(assigned) > 0: paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(assigned)) query = query + ( - "WHERE (spc.SpeciesId, iset.InbredSetId, pf.Id, pxr.Id) " + "AND (spc.SpeciesId, iset.InbredSetId, pf.Id, pxr.Id) " f"NOT IN ({paramstr}) ") query = query + "LIMIT 100000" |