diff --git a/.gitignore b/.gitignore index d900542..7108fc3 100644 --- a/.gitignore +++ b/.gitignore @@ -183,3 +183,6 @@ $RECYCLE.BIN/ *.lnk # End of https://www.toptal.com/developers/gitignore/api/osx,windows,linux + +# Requests cache directory +requests_cache/ \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index ca2a000..de8dff7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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@@ from __future__ import annotations +import os import re - -import requests -from requests.auth import HTTPBasicAuth import pandas as pd -import os -from missense_kinase_toolkit import requests_wrapper +from bravado.client import SwaggerClient +from bravado.requests_client import RequestsClient CBIOPORTAL_TOKEN_VAR = "CBIOPORTAL_TOKEN" +CBIOPORTAL_INSTANCE_VAR = "CBIOPORTAL_INSTANCE" -def create_setlist( - input_object: requests.models.Response, - attr: str, -) -> tuple[list, set]: - """Create a list and set of unique values from a response object - - Parameters - ---------- - input_object : requests.models.Response - Response object from a request - attr : str - Attribute to extract from the response object +def maybe_get_cbioportal_token_from_env() -> str | None: + """Get the cBioPortal token from the environment Returns ------- - tuple[list, set] - List and set of unique values from the response object + str | None + cBioPortal token as string if exists, otherwise None """ - list_output = [] - set_output = set() + try: + token = os.environ[CBIOPORTAL_TOKEN_VAR] + except KeyError: + token = None - for entry in input_object: - list_output.append(entry[attr]) - set_output.add(entry[attr]) + return token - return list_output, set_output +def maybe_get_cbioportal_instance_from_env( +) -> str | None: + """Get the cBioPortal instance from the environment -def print_counts( - list_input: list, -) -> None: - """Print the counts of unique values in a list + Returns + ------- + str | None + cBioPortal instance as string if exists, otherwise None + """ + try: + instance = os.environ[CBIOPORTAL_INSTANCE_VAR] + except KeyError: + instance = None + + return instance + +def get_all_mutations_by_study( + str_study_id: str +) -> list | None: + """Get mutations cBioPortal data Parameters ---------- - list_input : list - List of values to count + str_studyid : str + Study ID within cBioPortal instance; + e.g. MSKCC clinical sequencing cohort is "msk_impact_2017" and MSKCC clinical sequencing cohort is "mskimpact" Returns ------- - None + requests.models.Response + cBioPortal data """ - for Unique in set(list_input): - n = list_input.count(Unique) - print(f"{Unique:<15} \t {n:>10}") - - -def parse_obj2dict( - input_object: requests.models.Response, -) -> dict: - """Parse a response object into a dictionary + token = maybe_get_cbioportal_token_from_env() + + instance = maybe_get_cbioportal_instance_from_env() + if instance is not None: + url = f"https://{instance}/api/v2/api-docs" + else: + url = "https://cbioportal.org/api/v2/api-docs" + + if all(v is not None for v in (token, instance)): + http_client = RequestsClient() + http_client.set_api_key( + instance, + f"Bearer {token}", + param_name='Authorization', + param_in='header' + ) + cbioportal = SwaggerClient.from_url( + url, + http_client=http_client, + config={ + "validate_requests":False, + "validate_responses":False, + "validate_swagger_spec": False + } + ) + else: + cbioportal = SwaggerClient.from_url( + url, + config={ + "validate_requests":False, + "validate_responses":False, + "validate_swagger_spec": False + } + ) + + studies = cbioportal.Studies.getAllStudiesUsingGET().result() + study_ids = [study.studyId for study in studies] + + if str_study_id in study_ids: + #TODO - add error handling + #TODO - extract multiple studies + muts = cbioportal.Mutations.getMutationsInMolecularProfileBySampleListIdUsingGET( + molecularProfileId=f"{str_study_id}_mutations", + sampleListId=f"{str_study_id}_all", + projection="DETAILED" + ).result() + else: + raise ValueError(f"Study {str_study_id} not found in cBioPortal instance {instance}") + + return muts + + +def parse_muts2dataframe( + list_input: list, +) -> pd.DataFrame: + """Parse a list of abc.Mutation into a dictionary Parameters ---------- - input_object : requests.models.Response - Response object from a request + input_object : list + List of abc.Mutation objects Returns ------- - dict - Dictionary of values from the response object + pd.DataFrame + Dataframe for the input list of abc.Mutation objects """ dict_output = {} - - list_dir = dir(input_object[0]) - + list_dir = dir(list_input[0]) for attr in list_dir: list_attr = [] - for entry in input_object: + for entry in list_input: try: add = int(entry[attr]) except ValueError: add = str(entry[attr]) list_attr.append(add) dict_output[attr] = list_attr - - return dict_output + df = pd.DataFrame.from_dict(dict_output) + return df def parse_series2dict( @@ -152,57 +202,8 @@ def calc_vaf( return vaf -def get_cbioportal_token( - -) -> str: - """Get the cBioPortal token from the environment - - Returns - ------- - str - cBioPortal token - """ - token = os.environ[CBIOPORTAL_TOKEN_VAR] - - return token - - -def get_cbioprotal_data() -> requests.models.Response: - """Get the cBioPortal data - - Returns - ------- - requests.models.Response - cBioPortal data - """ - token = get_cbioportal_token() - url = "https://cbioportal.mskcc.org/api/v2/api-docs" - - headers = {"Content-Type":"application/json", "Authorization": f"Bearer {token}"} - - res = requests_wrapper.get_cached_session().get( - url, headers=headers - ) - - res.json().keys() - res.json()["paths"].keys() - res.json()["paths"]['/cancer-types'] - res.json()["paths"]["/molecular-profiles/{molecularProfileId}/molecular-data/fetch"] - dir(res) - res.Studies - - headers = {"X-Auth-Token": token} - response = requests.get(url, headers=headers) - - - url = 'https://api_url' - headers = {'Accept': 'application/json'} - auth = HTTPBasicAuth('apikey', '1234abcd') - files = {'file': open('filename', 'rb')} - - req = requests.get(url, headers=headers, auth=auth, files=files) - - return response +muts = get_all_mutations_by_study("mskimpact") +df_muts = parse_muts2dataframe(muts) # from bravado.client import SwaggerClient diff --git a/src/missense_kinase_toolkit/data_models.py b/src/missense_kinase_toolkit/data_models.py new file mode 100644 index 0000000..a55e89e --- /dev/null +++ b/src/missense_kinase_toolkit/data_models.py @@ -0,0 +1,5 @@ +# cBioPortal mutations +# Pfam annotations +# UniProt annotations (cannonical sequence) +# Kinase lists +# KLIFs annotations \ No newline at end of file diff --git a/src/missense_kinase_toolkit/pfam.py b/src/missense_kinase_toolkit/pfam.py index dd5949f..f623e7f 100644 --- a/src/missense_kinase_toolkit/pfam.py +++ b/src/missense_kinase_toolkit/pfam.py @@ -7,7 +7,9 @@ from missense_kinase_toolkit import requests_wrapper -def retrieve_pfam(uniprot_id: str) -> pd.DataFrame | str | None: +def retrieve_pfam( + uniprot_id: str, +) -> pd.DataFrame | str | None: """Retrieve Pfam domain information for a given UniProt ID using InterPro REST API Parameters