diff options
| -rw-r--r-- | wqflask/wqflask/wgcna/gn3_wgcna.py | 66 |
1 files changed, 28 insertions, 38 deletions
diff --git a/wqflask/wqflask/wgcna/gn3_wgcna.py b/wqflask/wqflask/wgcna/gn3_wgcna.py index 520f3d04..96510223 100644 --- a/wqflask/wqflask/wgcna/gn3_wgcna.py +++ b/wqflask/wqflask/wgcna/gn3_wgcna.py @@ -1,10 +1,18 @@ """module contains code to consume gn3-wgcna api and process data to be rendered by datatables """ -from typing import SimpleNamespace + +import requests +from types import SimpleNamespace from utility.helper_functions import get_trait_db_obs +def validate_form(requestform): + return { + "" + } + + def fetch_trait_data(requestform): """fetch trait data""" db_obj = SimpleNamespace() @@ -31,30 +39,14 @@ def process_dataset(trait_list): for strain in trait[0].data: strains.append(strain) input_data[trait[0].name][strain] = trait[0].data[strain].value + # "sample_names": list(set(strains)), + # "trait_names": form_traits, + # "trait_sample_data": form_strains, return { - "wgcna_input": input_data - } - - def process_dataset(trait_list): - """process datasets and strains""" - - input_data = {} - traits = [] - strains = [] - - # xtodo unique traits and strains - - for trait in trait_list: - traits.append(trait[0].name) - - input_data[trait[0].name] = {} - for strain in trait[0].data: - strains.append(strain) - input_data[trait[0].name][strain] = trait[0].data[strain].value - - return { - "wgcna_input": input_data + "input": input_data, + "trait_names": traits, + "sample_names": strains } @@ -91,28 +83,26 @@ def process_image(response): def run_wgcna(form_data): """function to run wgcna""" + GN3_URL = "http://127.0.0.1:8081" + wgcna_api = f"{GN3_URL}/api/wgcna/run_wgcna" # parse form data trait_dataset = fetch_trait_data(form_data) + form_data["minModuleSize"] = int(form_data["MinModuleSize"]) - response = requests.post(wgcna_api, { - "socket_id": form_data.get("socket_id"), # streaming disabled - "sample_names": list(set(strains)), - "trait_names": form_traits, - "trait_sample_data": form_strains, - "TOMtype": form_data["TOMtype"], - "minModuleSize": int(form_data["MinModuleSize"]), - "corType": form_data["corType"] + response = requests.post(wgcna_api, json={ + "sample_names": list(set(trait_dataset["sample_names"])), + "trait_names": trait_dataset["trait_names"], + "trait_sample_data": list(trait_dataset["input"].values()), + **form_data } ).json() - if response.status_code == 200: - return { - {"results": response, - "data": process_wgcna_data(response), - "image": process_image(response) - } - } + return { + "results": response, + "data": process_wgcna_data(response["data"]), + "image": process_image(response["data"]) + } |