diff options
Diffstat (limited to 'wqflask/maintenance/quick_search_table.py')
| -rw-r--r-- | wqflask/maintenance/quick_search_table.py | 64 |
1 files changed, 35 insertions, 29 deletions
diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py index a6ca6265..75bc7d00 100644 --- a/wqflask/maintenance/quick_search_table.py +++ b/wqflask/maintenance/quick_search_table.py @@ -24,6 +24,8 @@ from sqlalchemy.orm import scoped_session, sessionmaker, relationship, backref from sqlalchemy.orm.exc import NoResultFound from sqlalchemy.ext.declarative import declarative_base +from pprint import pformat as pf + import zach_settings as settings Engine = sa.create_engine(settings.SQLALCHEMY_DATABASE_URI, @@ -124,6 +126,7 @@ class PublishXRef(Base): "description", "lrs", "publication_id", + "pubmed_id", "year", "authors" ).from_statement( @@ -133,6 +136,7 @@ class PublishXRef(Base): "Phenotype.Original_description as description, " "PublishXRef.LRS as lrs, " "PublishXRef.PublicationId as publication_id, " + "Publication.PubMed_ID" "Publication.Year as year, " "Publication.Authors as authors " "FROM PublishXRef, " @@ -173,7 +177,7 @@ class PublishXRef(Base): return json_results class GenoXRef(Base): - __tablename__ = 'ProbeSetXRef' + __tablename__ = 'GenoXRef' GenoFreezeId = sa.Column(sa.Integer, primary_key=True) GenoId = sa.Column(sa.Integer, primary_key=True) @@ -191,14 +195,16 @@ class GenoXRef(Base): values['the_key'] = json.dumps([item.GenoId, item.GenoFreezeId]) values['terms'] = cls.get_unique_terms(item.GenoId) print("terms is:", values['terms']) - values['result_fields'] = cls.get_result_fields(item.GenoId, item.GenoFreezeId) - ins = QuickSearch.insert().values(**values) - conn.execute(ins) + if values['terms']: + values['result_fields'] = cls.get_result_fields(item.GenoId, item.GenoFreezeId) + ins = QuickSearch.insert().values(**values) + conn.execute(ins) counter += 1 print("Done:", counter) @staticmethod def get_unique_terms(geno_id): + print("geno_id: ", geno_id) results = Session.query( "name", "marker_name" @@ -208,23 +214,26 @@ class GenoXRef(Base): "FROM Geno " "WHERE Geno.Id = :geno_id ").params(geno_id=geno_id).all() + print("results: ", pf(results)) + unique = set() - for item in results[0]: - #print("locals:", locals()) - if not item: - continue - for token in item.split(): - if len(token) > 2: - try: - # This hopefully ensures that the token is utf-8 - token = token.encode('utf-8') - print(" ->", token) - except UnicodeDecodeError: - print("\n-- UDE \n") - # Can't get it into utf-8, we won't use it - continue - - unique.add(token) + if len(results): + for item in results[0]: + #print("locals:", locals()) + if not item: + continue + for token in item.split(): + if len(token) > 2: + try: + # This hopefully ensures that the token is utf-8 + token = token.encode('utf-8') + print(" ->", token) + except UnicodeDecodeError: + print("\n-- UDE \n") + # Can't get it into utf-8, we won't use it + continue + + unique.add(token) print("\nUnique terms are: {}\n".format(unique)) return " ".join(unique) @@ -233,18 +242,13 @@ class GenoXRef(Base): def get_result_fields(geno_id, dataset_id): results = Session.query( "name", - "species", + "marker_name", "group_name", + "species", "dataset", "dataset_name", - "symbol", - "description", "chr", "mb", - "lrs", - "genbank_id", - "gene_id", - "chip_id", - "chip_name" + "source" ).from_statement( "SELECT Geno.Name as name, " "Geno.Marker_Name as marker_name, " @@ -374,7 +378,7 @@ class ProbeSetXRef(Base): "symbol", "description", "chr", "mb", - "lrs", + "lrs", "mean", "genbank_id", "gene_id", "chip_id", @@ -390,6 +394,7 @@ class ProbeSetXRef(Base): "ProbeSet.Chr as chr, " "ProbeSet.Mb as mb, " "ProbeSetXRef.LRS as lrs, " + "ProbeSetXRef.mean as mean, " "ProbeSet.GenbankId as genbank_id, " "ProbeSet.GeneId as gene_id, " "ProbeSet.ChipId as chip_id, " @@ -463,6 +468,7 @@ def page_query(q): def main(): + GenoXRef.run() ProbeSetXRef.run() PublishXRef.run() |