diff options
Diffstat (limited to 'gn3/db/traits.py')
| -rw-r--r-- | gn3/db/traits.py | 78 |
1 files changed, 43 insertions, 35 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 1031e44..f2673c8 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,5 +1,8 @@ """This class contains functions relating to trait data manipulation""" +import os from typing import Any, Dict, Union, Sequence +from gn3.settings import TMPDIR +from gn3.random import random_string from gn3.function_helpers import compose from gn3.db.datasets import retrieve_trait_dataset @@ -43,7 +46,7 @@ def update_sample_data(conn: Any, count: Union[int, str]): """Given the right parameters, update sample-data from the relevant table.""" - # pylint: disable=[R0913, R0914] + # pylint: disable=[R0913, R0914, C0103] STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s" PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s " "WHERE StrainId = %s AND Id = %s") @@ -60,22 +63,22 @@ def update_sample_data(conn: Any, with conn.cursor() as cursor: # Update the Strains table cursor.execute(STRAIN_ID_SQL, (strain_name, strain_id)) - updated_strains: int = cursor.rowcount + updated_strains = cursor.rowcount # Update the PublishData table cursor.execute(PUBLISH_DATA_SQL, (None if value == "x" else value, strain_id, publish_data_id)) - updated_published_data: int = cursor.rowcount + updated_published_data = cursor.rowcount # Update the PublishSE table cursor.execute(PUBLISH_SE_SQL, (None if error == "x" else error, strain_id, publish_data_id)) - updated_se_data: int = cursor.rowcount + updated_se_data = cursor.rowcount # Update the NStrain table cursor.execute(N_STRAIN_SQL, (None if count == "x" else count, strain_id, publish_data_id)) - updated_n_strains: int = cursor.rowcount + updated_n_strains = cursor.rowcount return (updated_strains, updated_published_data, updated_se_data, updated_n_strains) @@ -223,7 +226,7 @@ def set_homologene_id_field_probeset(trait_info, conn): """ query = ( "SELECT HomologeneId FROM Homologene, Species, InbredSet" - " WHERE Homologene.GeneId = %(geneid)s AND InbredSet.Name = %(riset)s" + " WHERE Homologene.GeneId = %(geneid)s AND InbredSet.Name = %(group)s" " AND InbredSet.SpeciesId = Species.Id AND" " Species.TaxonomyId = Homologene.TaxonomyId") with conn.cursor() as cursor: @@ -231,7 +234,7 @@ def set_homologene_id_field_probeset(trait_info, conn): query, { k:v for k, v in trait_info.items() - if k in ["geneid", "riset"] + if k in ["geneid", "group"] }) res = cursor.fetchone() if res: @@ -419,7 +422,7 @@ def retrieve_trait_info( if trait_info["haveinfo"]: return { **trait_post_processing_functions_table[trait_dataset_type]( - {**trait_info, "riset": trait_dataset["riset"]}), + {**trait_info, "group": trait_dataset["group"]}), "db": {**trait["db"], **trait_dataset} } return trait_info @@ -442,18 +445,18 @@ def retrieve_temp_trait_data(trait_info: dict, conn: Any): query, {"trait_name": trait_info["trait_name"]}) return [dict(zip( - ["strain_name", "value", "se_error", "nstrain", "id"], row)) + ["sample_name", "value", "se_error", "nstrain", "id"], row)) for row in cursor.fetchall()] return [] -def retrieve_species_id(riset, conn: Any): +def retrieve_species_id(group, conn: Any): """ - Retrieve a species id given the RISet value + Retrieve a species id given the Group value """ with conn.cursor as cursor: cursor.execute( - "SELECT SpeciesId from InbredSet WHERE Name = %(riset)s", - {"riset": riset}) + "SELECT SpeciesId from InbredSet WHERE Name = %(group)s", + {"group": group}) return cursor.fetchone()[0] return None @@ -479,9 +482,9 @@ def retrieve_geno_trait_data(trait_info: Dict, conn: Any): {"trait_name": trait_info["trait_name"], "dataset_name": trait_info["db"]["dataset_name"], "species_id": retrieve_species_id( - trait_info["db"]["riset"], conn)}) + trait_info["db"]["group"], conn)}) return [dict(zip( - ["strain_name", "value", "se_error", "id"], row)) + ["sample_name", "value", "se_error", "id"], row)) for row in cursor.fetchall()] return [] @@ -512,7 +515,7 @@ def retrieve_publish_trait_data(trait_info: Dict, conn: Any): {"trait_name": trait_info["trait_name"], "dataset_id": trait_info["db"]["dataset_id"]}) return [dict(zip( - ["strain_name", "value", "se_error", "nstrain", "id"], row)) + ["sample_name", "value", "se_error", "nstrain", "id"], row)) for row in cursor.fetchall()] return [] @@ -545,7 +548,7 @@ def retrieve_cellid_trait_data(trait_info: Dict, conn: Any): "trait_name": trait_info["trait_name"], "dataset_id": trait_info["db"]["dataset_id"]}) return [dict(zip( - ["strain_name", "value", "se_error", "id"], row)) + ["sample_name", "value", "se_error", "id"], row)) for row in cursor.fetchall()] return [] @@ -574,29 +577,29 @@ def retrieve_probeset_trait_data(trait_info: Dict, conn: Any): {"trait_name": trait_info["trait_name"], "dataset_name": trait_info["db"]["dataset_name"]}) return [dict(zip( - ["strain_name", "value", "se_error", "id"], row)) + ["sample_name", "value", "se_error", "id"], row)) for row in cursor.fetchall()] return [] -def with_strainlist_data_setup(strainlist: Sequence[str]): +def with_samplelist_data_setup(samplelist: Sequence[str]): """ - Build function that computes the trait data from provided list of strains. + Build function that computes the trait data from provided list of samples. PARAMETERS - strainlist: (list) - A list of strain names + samplelist: (list) + A list of sample names RETURNS: Returns a function that given some data from the database, computes the - strain's value, variance and ndata values, only if the strain is present - in the provided `strainlist` variable. + sample's value, variance and ndata values, only if the sample is present + in the provided `samplelist` variable. """ def setup_fn(tdata): - if tdata["strain_name"] in strainlist: + if tdata["sample_name"] in samplelist: val = tdata["value"] if val is not None: return { - "strain_name": tdata["strain_name"], + "sample_name": tdata["sample_name"], "value": val, "variance": tdata["se_error"], "ndata": tdata.get("nstrain", None) @@ -604,19 +607,19 @@ def with_strainlist_data_setup(strainlist: Sequence[str]): return None return setup_fn -def without_strainlist_data_setup(): +def without_samplelist_data_setup(): """ Build function that computes the trait data. RETURNS: Returns a function that given some data from the database, computes the - strain's value, variance and ndata values. + sample's value, variance and ndata values. """ def setup_fn(tdata): val = tdata["value"] if val is not None: return { - "strain_name": tdata["strain_name"], + "sample_name": tdata["sample_name"], "value": val, "variance": tdata["se_error"], "ndata": tdata.get("nstrain", None) @@ -624,7 +627,7 @@ def without_strainlist_data_setup(): return None return setup_fn -def retrieve_trait_data(trait: dict, conn: Any, strainlist: Sequence[str] = tuple()): +def retrieve_trait_data(trait: dict, conn: Any, samplelist: Sequence[str] = tuple()): """ Retrieve trait data @@ -647,22 +650,27 @@ def retrieve_trait_data(trait: dict, conn: Any, strainlist: Sequence[str] = tupl if results: # do something with mysqlid mysqlid = results[0]["id"] - if strainlist: + if samplelist: data = [ item for item in - map(with_strainlist_data_setup(strainlist), results) + map(with_samplelist_data_setup(samplelist), results) if item is not None] else: data = [ item for item in - map(without_strainlist_data_setup(), results) + map(without_samplelist_data_setup(), results) if item is not None] return { "mysqlid": mysqlid, "data": dict(map( lambda x: ( - x["strain_name"], - {k:v for k, v in x.items() if x != "strain_name"}), + x["sample_name"], + {k:v for k, v in x.items() if x != "sample_name"}), data))} return {} + +def generate_traits_filename(base_path: str = TMPDIR): + """Generate a unique filename for use with generated traits files.""" + return "{}/traits_test_file_{}.txt".format( + os.path.abspath(base_path), random_string(10)) |