diff options
Diffstat (limited to 'gn3/db/traits.py')
| -rw-r--r-- | gn3/db/traits.py | 33 |
1 files changed, 24 insertions, 9 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index a740352..6ea24be 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -326,10 +326,23 @@ def build_trait_name(trait_fullname): """ Initialises the trait's name, and other values from the search data provided """ + def dataset_type(dset_name): + if dset_name.find('Temp') >= 0: + return "Temp" + if dset_name.find('Geno') >= 0: + return "Geno" + if dset_name.find('Publish') >= 0: + return "Publish" + return "ProbeSet" + name_parts = trait_fullname.split("::") assert len(name_parts) >= 2, "Name format error" + dataset_name = name_parts[0] + dataset_type = dataset_type(dataset_name) return { - "db": {"dataset_name": name_parts[0]}, + "db": { + "dataset_name": dataset_name, + "dataset_type": dataset_type}, "trait_fullname": trait_fullname, "trait_name": name_parts[1], "cellid": name_parts[2] if len(name_parts) == 3 else "" @@ -357,7 +370,7 @@ def retrieve_probeset_sequence(trait, conn): return {**trait, "sequence": seq[0] if seq else ""} def retrieve_trait_info( - trait_type: str, threshold: int, trait_full_name: str, conn: Any, + threshold: int, trait_full_name: str, conn: Any, qtl=None): """Retrieves the trait information. @@ -366,6 +379,7 @@ def retrieve_trait_info( This function, or the dependent functions, might be incomplete as they are currently.""" trait = build_trait_name(trait_full_name) + trait_dataset_type = trait["db"]["dataset_type"] trait_info_function_table = { "Publish": retrieve_publish_trait_info, "ProbeSet": retrieve_probeset_trait_info, @@ -374,14 +388,14 @@ def retrieve_trait_info( } common_post_processing_fn = compose( - lambda ti: load_qtl_info(qtl, trait_type, ti, conn), - lambda ti: set_homologene_id_field(trait_type, ti, conn), - lambda ti: {"trait_type": trait_type, **ti}, + lambda ti: load_qtl_info(qtl, trait_dataset_type, ti, conn), + lambda ti: set_homologene_id_field(trait_dataset_type, ti, conn), + lambda ti: {"trait_type": trait_dataset_type, **ti}, lambda ti: {**trait, **ti}) trait_post_processing_functions_table = { "Publish": compose( - lambda ti: set_confidential_field(trait_type, ti), + lambda ti: set_confidential_field(trait_dataset_type, ti), common_post_processing_fn), "ProbeSet": compose( lambda ti: retrieve_probeset_sequence(ti, conn), @@ -391,9 +405,10 @@ def retrieve_trait_info( } retrieve_info = compose( - set_haveinfo_field, trait_info_function_table[trait_type]) + set_haveinfo_field, trait_info_function_table[trait_dataset_type]) - trait_dataset = retrieve_trait_dataset(trait_type, trait, threshold, conn) + trait_dataset = retrieve_trait_dataset( + trait_dataset_type, trait, threshold, conn) trait_info = retrieve_info( { "trait_name": trait["trait_name"], @@ -403,7 +418,7 @@ def retrieve_trait_info( conn) if trait_info["haveinfo"]: return { - **trait_post_processing_functions_table[trait_type](trait_info), + **trait_post_processing_functions_table[trait_dataset_type](trait_info), "db": {**trait["db"], **trait_dataset}, "riset": trait_dataset["riset"] } |