diff options
Diffstat (limited to 'wqflask/maintenance')
| -rw-r--r-- | wqflask/maintenance/quick_search_table.py | 61 |
1 files changed, 44 insertions, 17 deletions
diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py index 63fb7da5..132d1b72 100644 --- a/wqflask/maintenance/quick_search_table.py +++ b/wqflask/maintenance/quick_search_table.py @@ -43,7 +43,7 @@ Metadata.bind = Engine class ProbeSet(Base): - __tablename__ = 'ProbeSet' + __tablename__ = 'ProbeSetXRef' __table_args__ = {'autoload': True} QuickSearch = sa.Table("QuickSearch", Metadata, @@ -52,11 +52,11 @@ QuickSearch = sa.Table("QuickSearch", Metadata, sa.Column('the_key', sa.String(30), primary_key=True, nullable=False, autoincrement=False), # key in database table sa.Column('terms', sa.Text), # terms to compare search string with - sa.Column('species', sa.Text), + #sa.Column('species', sa.Text), sa.Column('result_fields', sa.Text) # json ) -#QuickSearch.drop(Engine, checkfirst=True) +QuickSearch.drop(Engine, checkfirst=True) Metadata.create_all(Engine) #class QuickSearch(Base): @@ -73,11 +73,26 @@ Metadata.create_all(Engine) # self.result_fields = json.dumps(sort_keys=True) -def get_unique_terms(*args): - if not args: - return None +def get_unique_terms(trait_type, trait_id): + #if not args: + # return None + + if trait_type="ProbeSet": + results = Session.query( + "name", + "symbol", + "description", + "alias" + ).from_statement( + "SELECT ProbeSet.Name as name, " + "ProbeSet.Symbol as symbol, " + "ProbeSet.description as description, " + "ProbeSet.alias as alias " + "FROM ProbeSet" + "WHERE ProbeSet.Id = :probeset_id ").params(probeset_id=trait_id).all() + unique = set() - for item in args: + for item in results[0]: #print("locals:", locals()) if not item: continue @@ -107,12 +122,12 @@ def main(): counter = 0 for ps in page_query(Session.query(ProbeSet)): #all() values = {} - values['table_name'] = "ProbeSet" - values['the_key'] = ps.Id - values['terms'] = get_unique_terms(ps.Name, ps.Symbol, ps.description, ps.alias) + values['table_name'] = "ProbeSetXRef" + values['the_key'] = json.dumps([ps.ProbeSetId, ps.ProbeSetFreezeId]) + values['terms'] = get_unique_terms("ProbeSet", ps.ProbeSetId) print("terms is:", values['terms']) - values['species'] = get_species("ProbeSet", ps.Id) - values['result_fields'] = get_result_fields("ProbeSet", ps.Id) + #values['species'] = get_species("ProbeSet", ps.Id) + values['result_fields'] = get_result_fields("ProbeSet", ps.ProbeSetId, ps.ProbeSetFreezeId) ins = QuickSearch.insert().values(**values) conn.execute(ins) counter += 1 @@ -141,19 +156,31 @@ def get_species(trait_type, trait_id): return results[0].Name -def get_result_fields(trait_type, trait_id): +def get_result_fields(trait_type, *args): if trait_type == "ProbeSet": print("qs1") results = Session.query( - "name", "symbol", "description", "chr", "mb" + "name", + "symbol", + "description", + "chr", "mb", + "genbank_id", + "gene_id", + "chip_id", + "chip_name" ).from_statement( "SELECT ProbeSet.Name as name, " "ProbeSet.Symbol as symbol, " "ProbeSet.description as description, " "ProbeSet.Chr as chr, " - "ProbeSet.Mb as mb " - "FROM ProbeSet " - "WHERE ProbeSet.Id = :probeset_id ").params(probeset_id=trait_id).all() + "ProbeSet.Mb as mb, " + "ProbeSet.GenbankId as genbank_id, " + "ProbeSet.GeneId as gene_id, " + "ProbeSet.ChipId as chip_id, " + "GeneChip.Name as chip_name " + "FROM ProbeSet, GeneChip " + "WHERE ProbeSet.ChipId = GeneChip.Id and " + "ProbeSet.Id = :probeset_id ").params(probeset_id=*args[0], dataset_id=*args[1]).all() print("qs2") for result in results: print(result) |