diff options
Diffstat (limited to 'gn3/db/datasets.py')
| -rw-r--r-- | gn3/db/datasets.py | 64 |
1 files changed, 52 insertions, 12 deletions
diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py index 3ad50f6..53d6811 100644 --- a/gn3/db/datasets.py +++ b/gn3/db/datasets.py @@ -1,7 +1,13 @@ -from typing import Any, Dict, Union +""" +This module contains functions relating to specific trait dataset manipulation +""" +from typing import Any def retrieve_probeset_trait_dataset_name( threshold: int, name: str, connection: Any): + """ + Get the ID, DataScale and various name formats for a `ProbeSet` trait. + """ query = ( "SELECT Id, Name, FullName, ShortName, DataScale " "FROM ProbeSetFreeze " @@ -21,7 +27,11 @@ def retrieve_probeset_trait_dataset_name( "dataset_shortname", "dataset_datascale"], cursor.fetchone)) -def retrieve_publish_trait_dataset_name(threshold: int, name: str, connection: Any): +def retrieve_publish_trait_dataset_name( + threshold: int, name: str, connection: Any): + """ + Get the ID, DataScale and various name formats for a `Publish` trait. + """ query = ( "SELECT Id, Name, FullName, ShortName " "FROM PublishFreeze " @@ -41,7 +51,11 @@ def retrieve_publish_trait_dataset_name(threshold: int, name: str, connection: A "dataset_shortname"], cursor.fetchone)) -def retrieve_geno_trait_dataset_name(threshold: int, name: str, connection: Any): +def retrieve_geno_trait_dataset_name( + threshold: int, name: str, connection: Any): + """ + Get the ID, DataScale and various name formats for a `Geno` trait. + """ query = ( "SELECT Id, Name, FullName, ShortName " "FROM GenoFreeze " @@ -61,7 +75,11 @@ def retrieve_geno_trait_dataset_name(threshold: int, name: str, connection: Any) "dataset_shortname"], cursor.fetchone)) -def retrieve_temp_trait_dataset_name(threshold: int, name: str, connection: Any): +def retrieve_temp_trait_dataset_name( + threshold: int, name: str, connection: Any): + """ + Get the ID, DataScale and various name formats for a `Temp` trait. + """ query = ( "SELECT Id, Name, FullName, ShortName " "FROM TempFreeze " @@ -145,6 +163,9 @@ def retrieve_probeset_riset_fields(name, conn): return {} def retrieve_temp_riset_fields(name, conn): + """ + Retrieve the RISet, and RISetID values for `Temp` trait types. + """ query = ( "SELECT InbredSet.Name, InbredSet.Id " "FROM InbredSet, Temp " @@ -179,6 +200,10 @@ def retrieve_riset_fields(trait_type, trait_name, dataset_info, conn): } def retrieve_temp_trait_dataset(): + """ + Retrieve the dataset that relates to `Temp` traits + """ + # pylint: disable=[C0330] return { "searchfield": ["name", "description"], "disfield": ["name", "description"], @@ -189,28 +214,40 @@ def retrieve_temp_trait_dataset(): } def retrieve_geno_trait_dataset(): + """ + Retrieve the dataset that relates to `Geno` traits + """ + # pylint: disable=[C0330] return { - "searchfield": ["name","chr"], - "disfield": ["name","chr","mb", "source2", "sequence"], + "searchfield": ["name", "chr"], + "disfield": ["name", "chr", "mb", "source2", "sequence"], "type": "Geno" } def retrieve_publish_trait_dataset(): + """ + Retrieve the dataset that relates to `Publish` traits + """ + # pylint: disable=[C0330] return { "searchfield": [ "name", "post_publication_description", "abstract", "title", "authors"], "disfield": [ - "name","pubmed_id", "pre_publication_description", - "post_publication_description", "original_description", + "name", "pubmed_id", "pre_publication_description", + "post_publication_description", "original_description", "pre_publication_abbreviation", "post_publication_abbreviation", "lab_code", "submitter", "owner", "authorized_users", - "authors","title","abstract", "journal","volume","pages","month", - "year","sequence", "units", "comments"], + "authors", "title", "abstract", "journal", "volume", "pages", + "month", "year", "sequence", "units", "comments"], "type": "Publish" } def retrieve_probeset_trait_dataset(): + """ + Retrieve the dataset that relates to `ProbeSet` traits + """ + # pylint: disable=[C0330] return { "searchfield": [ "name", "description", "probe_target_description", "symbol", @@ -228,6 +265,9 @@ def retrieve_probeset_trait_dataset(): } def retrieve_trait_dataset(trait_type, trait, threshold, conn): + """ + Retrieve the dataset that relates to a specific trait. + """ dataset_fns = { "Temp": retrieve_temp_trait_dataset, "Geno": retrieve_geno_trait_dataset, @@ -238,8 +278,8 @@ def retrieve_trait_dataset(trait_type, trait, threshold, conn): "dataset_id": None, "dataset_name": trait["db"]["dataset_name"], **retrieve_dataset_name( - trait_type, threshold, trait["trait_name"], trait["db"]["dataset_name"], - conn) + trait_type, threshold, trait["trait_name"], + trait["db"]["dataset_name"], conn) } riset = retrieve_riset_fields( trait_type, trait["trait_name"], dataset_name_info, conn) |