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authorMuriithi Frederick Muriuki2021-08-09 14:25:49 +0300
committerMuriithi Frederick Muriuki2021-08-09 14:25:49 +0300
commit243d76bd5cdb989ee7d3311e44aafb7e8f7da712 (patch)
tree0869114d6207343d3c97fca597d7843aa7d8aa5e /gn3
parent8f022ae1a31224d0526443ad9779f30206b4a770 (diff)
downloadgenenetwork3-243d76bd5cdb989ee7d3311e44aafb7e8f7da712.tar.gz
Set up the trait dataset type correctly
* gn3/db/traits.py: setup `trait_dataset_type` * tests/unit/db/test_traits.py: fix tests The type ('Temp', 'Geno', 'Publish', and 'ProbeSet') relate to a trait's dataset, and not the trait itself. This commit updates the code to take this into consideration. The dataset type is also set up from a trait's full name, therefore this commit removes the `trait_type` argument from the `retrieve_trait_info` function.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/db/traits.py33
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"]
}