diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/traits.py | 87 |
1 files changed, 79 insertions, 8 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 9742fa2..d8d2b62 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,5 +1,6 @@ """This class contains functions relating to trait data manipulation""" from typing import Any, Dict, Union +from gn3.function_helpers import compose def get_trait_csv_sample_data(conn: Any, @@ -135,8 +136,7 @@ def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any): "Phenotype.Id = PublishXRef.PhenotypeId AND " "Publication.Id = PublishXRef.PublicationId AND " "PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND " - "PublishFreeze.Id =%(trait_dataset_id)s").format( - columns = columns) + "PublishFreeze.Id =%(trait_dataset_id)s").format(columns=columns) with conn.cursor() as cursor: cursor.execute( query, @@ -144,7 +144,17 @@ def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any): k:v for k, v in trait_data_source.items() if k in ["trait_name", "trait_dataset_id"] }) - return dict(zip((k.lower() for k in keys), cursor.fetchone())) + return dict(zip([k.lower() for k in keys], cursor.fetchone())) + +def set_confidential_field(trait_info): + """Post processing function for 'Publish' trait types. + + It sets the value for the 'confidential' key.""" + return { + **trait_info, + "confidential": 1 if ( + trait_info.get("pre_publication_description", None) + and not trait_info.get("pubmed_id", None)) else 0} def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any): """Retrieve trait information for type `ProbeSet` traits. @@ -168,7 +178,7 @@ def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any): "ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " "ProbeSetFreeze.Name = %(trait_dataset_name)s AND " "ProbeSet.Name = %(trait_name)s").format( - columns = ", ".join(["ProbeSet.{}".format(x) for x in keys])) + columns=", ".join(["ProbeSet.{}".format(x) for x in keys])) with conn.cursor() as cursor: cursor.execute( query, @@ -192,7 +202,7 @@ def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any): "GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND " "GenoFreeze.Name = %(trait_dataset_name)s AND " "Geno.Name = %(trait_name)s").format( - columns = ", ".join(["Geno.{}".format(x) for x in keys])) + columns=", ".join(["Geno.{}".format(x) for x in keys])) with conn.cursor() as cursor: cursor.execute( query, @@ -209,7 +219,7 @@ def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any): keys = ("name", "description") query = ( "SELECT {columns} FROM Temp " - "WHERE Name = %(trait_name)s").format(columns = ", ".join(keys)) + "WHERE Name = %(trait_name)s").format(columns=", ".join(keys)) with conn.cursor() as cursor: cursor.execute( query, @@ -219,9 +229,53 @@ def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any): }) return dict(zip(keys, cursor.fetchone())) +def set_haveinfo_field(trait_info): + """ + Common postprocessing function for all trait types. + + Sets the value for the 'haveinfo' field.""" + return {**trait_info, "haveinfo": 1 if trait_info else 0} + +def set_homologene_id_field_probeset(trait_info, conn): + """ + Postprocessing function for 'ProbeSet' traits. + + Sets the value for the 'homologene' key. + """ + query = ( + "SELECT HomologeneId FROM Homologene, Species, InbredSet" + " WHERE Homologene.GeneId = %(geneid)s AND InbredSet.Name = %(riset)s" + " AND InbredSet.SpeciesId = Species.Id AND" + " Species.TaxonomyId = Homologene.TaxonomyId") + with conn.cursor() as cursor: + cursor.execute( + query, + { + k:v for k, v in trait_info.items() + if k in ["geneid", "riset"] + }) + res = cursor.fetchone() + if res: + return {**trait_info, "homologeneid": res[0]} + return {**trait_info, "homologeneid": None} + +def set_homologene_id_field(trait_info, conn): + """ + Common postprocessing function for all trait types. + + Sets the value for the 'homologene' key.""" + set_to_null = lambda ti: {**ti, "homologeneid": None} + functions_table = { + "Temp": set_to_null, + "Geno": set_to_null, + "Publish": set_to_null, + "ProbeSet": lambda ti: set_homologene_id_field_probeset(ti, conn) + } + return functions_table[trait_info["type"]](trait_info) + def retrieve_trait_info( trait_type: str, trait_name: str, trait_dataset_id: int, - trait_dataset_name: str, conn: Any, QTL = None): + trait_dataset_name: str, conn: Any, QTL=None): """Retrieves the trait information. https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456 @@ -234,7 +288,24 @@ def retrieve_trait_info( "Geno": retrieve_geno_trait_info, "Temp": retrieve_temp_trait_info } - return trait_info_function_table[trait_type]( + + common_post_processing_fn = compose( + lambda ti: set_homologene_id_field(ti, conn), + lambda ti: {"type": trait_type, **ti}, + set_haveinfo_field) + + trait_post_processing_functions_table = { + "Publish": compose(set_confidential_field, common_post_processing_fn), + "ProbeSet": compose(common_post_processing_fn), + "Geno": common_post_processing_fn, + "Temp": common_post_processing_fn + } + + retrieve_info = compose( + trait_post_processing_functions_table[trait_type], + trait_info_function_table[trait_type]) + + return retrieve_info( { "trait_name": trait_name, "trait_dataset_id": trait_dataset_id, |